Query 011629
Match_columns 481
No_of_seqs 351 out of 2857
Neff 10.1
Searched_HMMs 46136
Date Fri Mar 29 03:29:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011629.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011629hhsearch_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 1.3E-52 2.7E-57 392.7 33.1 420 2-469 140-576 (897)
2 KOG4440 NMDA selective glutama 100.0 2.7E-48 5.8E-53 365.5 28.0 389 3-467 159-597 (993)
3 KOG1053 Glutamate-gated NMDA-t 100.0 6.4E-44 1.4E-48 347.9 32.3 404 1-481 161-615 (1258)
4 cd06390 PBP1_iGluR_AMPA_GluR1 100.0 4.7E-35 1E-39 282.7 27.1 256 1-273 105-363 (364)
5 cd06365 PBP1_Pheromone_recepto 100.0 6.5E-35 1.4E-39 292.4 27.7 249 1-270 160-453 (469)
6 KOG1052 Glutamate-gated kainat 100.0 1.2E-33 2.6E-38 295.6 35.7 354 63-468 6-370 (656)
7 cd06364 PBP1_CaSR Ligand-bindi 100.0 3.9E-34 8.5E-39 288.6 28.1 252 1-270 175-494 (510)
8 cd06375 PBP1_mGluR_groupII Lig 100.0 1.4E-33 3.1E-38 281.6 27.5 247 1-269 162-454 (458)
9 cd06387 PBP1_iGluR_AMPA_GluR3 100.0 4.1E-33 8.8E-38 268.5 27.5 257 1-273 112-371 (372)
10 cd06376 PBP1_mGluR_groupIII Li 100.0 1.9E-32 4.1E-37 275.3 27.9 249 1-269 160-452 (463)
11 cd06374 PBP1_mGluR_groupI Liga 100.0 3.5E-32 7.5E-37 273.9 26.9 249 1-269 174-464 (472)
12 cd06379 PBP1_iGluR_NMDA_NR1 N- 100.0 6.5E-32 1.4E-36 264.9 25.2 217 2-270 143-364 (377)
13 KOG1056 Glutamate-gated metabo 100.0 2.4E-32 5.1E-37 275.5 22.3 273 1-313 182-495 (878)
14 cd06392 PBP1_iGluR_delta_1 N-t 100.0 1.4E-31 3E-36 258.7 26.3 253 2-273 127-398 (400)
15 cd06362 PBP1_mGluR Ligand bind 100.0 2.3E-31 4.9E-36 267.5 27.4 251 2-272 161-449 (452)
16 cd06391 PBP1_iGluR_delta_2 N-t 100.0 9.6E-31 2.1E-35 255.4 27.4 255 2-273 127-398 (400)
17 cd06367 PBP1_iGluR_NMDA N-term 100.0 5.5E-31 1.2E-35 257.2 24.1 223 1-269 124-351 (362)
18 cd06389 PBP1_iGluR_AMPA_GluR2 100.0 2.2E-30 4.8E-35 251.9 27.7 258 1-273 106-368 (370)
19 cd06388 PBP1_iGluR_AMPA_GluR4 100.0 2.8E-30 6E-35 250.7 27.3 254 2-273 113-369 (371)
20 cd06361 PBP1_GPC6A_like Ligand 100.0 2.1E-30 4.6E-35 254.6 26.4 227 1-271 160-395 (403)
21 cd06393 PBP1_iGluR_Kainate_Glu 100.0 7.5E-29 1.6E-33 243.5 25.7 249 2-274 128-382 (384)
22 cd06378 PBP1_iGluR_NMDA_NR2 N- 100.0 1.4E-28 3.1E-33 237.2 23.1 225 1-270 123-351 (362)
23 cd06380 PBP1_iGluR_AMPA N-term 100.0 8.3E-28 1.8E-32 236.5 28.0 262 2-273 115-381 (382)
24 cd06386 PBP1_NPR_C_like Ligand 100.0 1.1E-26 2.3E-31 228.2 25.3 237 2-269 126-378 (387)
25 cd06363 PBP1_Taste_receptor Li 100.0 2.6E-26 5.6E-31 227.5 26.0 227 2-270 165-396 (410)
26 PF01094 ANF_receptor: Recepto 99.9 2.5E-26 5.3E-31 223.5 21.8 234 1-257 109-348 (348)
27 cd06385 PBP1_NPR_A Ligand-bind 99.9 3.3E-25 7E-30 219.7 25.2 241 2-270 132-391 (405)
28 cd06370 PBP1_Speract_GC_like L 99.9 3.2E-25 7E-30 219.3 23.4 233 2-261 125-386 (404)
29 cd06372 PBP1_GC_G_like Ligand- 99.9 7.2E-25 1.6E-29 216.3 24.8 239 2-270 126-386 (391)
30 cd06384 PBP1_NPR_B Ligand-bind 99.9 3.5E-24 7.6E-29 211.6 25.1 241 2-270 132-392 (399)
31 cd06373 PBP1_NPR_like Ligand b 99.9 4.1E-24 9E-29 211.2 23.0 242 2-270 131-389 (396)
32 cd06371 PBP1_sensory_GC_DEF_li 99.9 1.2E-23 2.6E-28 206.2 25.2 233 2-264 121-366 (382)
33 cd06352 PBP1_NPR_GC_like Ligan 99.9 1.4E-23 2.9E-28 207.4 25.1 243 2-270 126-382 (389)
34 cd06381 PBP1_iGluR_delta_like 99.9 2.6E-23 5.5E-28 201.0 24.3 220 2-273 127-362 (363)
35 cd06394 PBP1_iGluR_Kainate_KA1 99.9 6.4E-24 1.4E-28 201.7 15.1 208 1-274 122-332 (333)
36 cd06366 PBP1_GABAb_receptor Li 99.9 1.2E-22 2.5E-27 197.7 22.1 221 2-273 124-346 (350)
37 cd06383 PBP1_iGluR_AMPA_Like N 99.9 2.4E-23 5.3E-28 201.5 13.3 232 1-256 121-358 (368)
38 cd06382 PBP1_iGluR_Kainate N-t 99.9 4.5E-21 9.8E-26 184.7 18.8 204 2-272 118-325 (327)
39 cd06377 PBP1_iGluR_NMDA_NR3 N- 99.9 2.4E-20 5.3E-25 177.5 23.1 216 1-271 139-372 (382)
40 cd06368 PBP1_iGluR_non_NMDA_li 99.9 3.2E-20 6.8E-25 178.7 19.2 206 2-272 116-322 (324)
41 cd06350 PBP1_GPCR_family_C_lik 99.8 2.3E-18 4.9E-23 167.5 19.2 188 2-270 149-340 (348)
42 cd06342 PBP1_ABC_LIVBP_like Ty 99.8 1.5E-17 3.2E-22 160.9 21.1 209 2-256 123-334 (334)
43 KOG1055 GABA-B ion channel rec 99.8 9.8E-19 2.1E-23 172.0 10.7 247 3-271 171-431 (865)
44 cd06351 PBP1_iGluR_N_LIVBP_lik 99.8 2.2E-17 4.7E-22 159.2 18.8 201 1-269 120-322 (328)
45 cd06369 PBP1_GC_C_enterotoxin_ 99.7 7.3E-16 1.6E-20 143.3 18.9 218 3-270 137-365 (380)
46 cd06348 PBP1_ABC_ligand_bindin 99.7 1.2E-15 2.5E-20 148.2 21.4 213 3-251 125-341 (344)
47 cd06338 PBP1_ABC_ligand_bindin 99.7 1E-15 2.2E-20 148.8 20.2 209 2-256 128-345 (345)
48 PRK15404 leucine ABC transport 99.7 4.7E-15 1E-19 144.7 22.4 212 3-260 150-363 (369)
49 cd06345 PBP1_ABC_ligand_bindin 99.7 2.3E-15 4.9E-20 146.1 19.8 200 3-247 129-337 (344)
50 cd06346 PBP1_ABC_ligand_bindin 99.6 6.6E-15 1.4E-19 140.7 17.8 185 2-253 126-310 (312)
51 cd06360 PBP1_alkylbenzenes_lik 99.6 3.8E-14 8.2E-19 137.2 20.8 206 2-249 123-330 (336)
52 cd06347 PBP1_ABC_ligand_bindin 99.6 5.5E-14 1.2E-18 135.9 20.4 200 2-247 123-327 (334)
53 PRK11917 bifunctional adhesin/ 99.6 1.4E-14 3.1E-19 134.1 10.9 116 315-440 35-151 (259)
54 cd06340 PBP1_ABC_ligand_bindin 99.6 1.6E-13 3.5E-18 133.2 18.3 203 2-248 127-341 (347)
55 cd06355 PBP1_FmdD_like Peripla 99.6 4E-13 8.6E-18 130.4 20.7 219 3-263 122-344 (348)
56 PRK10797 glutamate and asparta 99.5 2.8E-14 6E-19 134.9 10.5 113 316-439 38-155 (302)
57 PRK15010 ABC transporter lysin 99.5 3.1E-14 6.7E-19 132.3 10.0 111 317-439 25-135 (260)
58 cd06344 PBP1_ABC_ligand_bindin 99.5 4.1E-13 8.9E-18 129.6 17.5 201 2-248 122-326 (332)
59 cd06336 PBP1_ABC_ligand_bindin 99.5 5.8E-13 1.3E-17 129.3 18.0 202 2-247 127-340 (347)
60 cd06343 PBP1_ABC_ligand_bindin 99.5 2.2E-12 4.7E-17 126.2 22.1 217 2-260 132-361 (362)
61 PRK09495 glnH glutamine ABC tr 99.5 3.9E-14 8.4E-19 130.7 9.1 111 317-440 24-134 (247)
62 cd06269 PBP1_glutamate_recepto 99.5 1.8E-13 3.9E-18 129.7 13.9 107 2-111 129-235 (298)
63 cd06331 PBP1_AmiC_like Type I 99.5 8E-13 1.7E-17 127.7 18.6 204 2-247 121-326 (333)
64 PRK15437 histidine ABC transpo 99.5 4.1E-14 8.9E-19 131.4 9.2 112 317-440 25-136 (259)
65 cd06359 PBP1_Nba_like Type I p 99.5 2E-12 4.3E-17 124.9 19.9 207 2-254 123-331 (333)
66 cd06349 PBP1_ABC_ligand_bindin 99.5 2.9E-12 6.3E-17 124.1 21.0 210 2-259 123-338 (340)
67 cd06357 PBP1_AmiC Periplasmic 99.5 5.4E-12 1.2E-16 123.1 22.5 223 3-265 122-347 (360)
68 cd06332 PBP1_aromatic_compound 99.5 2.5E-12 5.4E-17 124.3 19.8 201 2-247 123-325 (333)
69 PF13458 Peripla_BP_6: Peripla 99.5 3.6E-12 7.8E-17 123.7 20.0 213 2-257 123-339 (343)
70 PRK15007 putative ABC transpor 99.5 1.7E-13 3.8E-18 126.0 9.3 109 317-439 20-128 (243)
71 TIGR03407 urea_ABC_UrtA urea A 99.5 6.4E-12 1.4E-16 122.5 20.4 213 3-257 123-338 (359)
72 cd06330 PBP1_Arsenic_SBP_like 99.5 3.7E-12 8E-17 123.8 18.6 201 2-243 125-333 (346)
73 cd06327 PBP1_SBP_like_1 Peripl 99.4 4E-12 8.8E-17 122.8 17.3 201 2-247 124-328 (334)
74 PF00497 SBP_bac_3: Bacterial 99.4 2.5E-13 5.3E-18 123.2 8.1 94 320-425 1-94 (225)
75 cd06329 PBP1_SBP_like_3 Peripl 99.4 7.7E-12 1.7E-16 121.2 19.0 195 2-242 131-330 (342)
76 cd06358 PBP1_NHase Type I peri 99.4 6.5E-12 1.4E-16 121.3 18.3 198 6-246 125-325 (333)
77 TIGR02995 ectoine_ehuB ectoine 99.4 3.4E-13 7.3E-18 126.3 8.9 108 316-436 31-140 (275)
78 TIGR03669 urea_ABC_arch urea A 99.4 1.7E-11 3.6E-16 119.6 20.9 212 3-258 123-338 (374)
79 PRK11260 cystine transporter s 99.4 5.7E-13 1.2E-17 124.2 9.3 114 315-440 38-152 (266)
80 COG0683 LivK ABC-type branched 99.4 2.7E-11 5.8E-16 118.2 20.9 213 3-258 137-354 (366)
81 TIGR01096 3A0103s03R lysine-ar 99.4 9.6E-13 2.1E-17 121.6 8.5 109 318-438 24-132 (250)
82 cd06337 PBP1_ABC_ligand_bindin 99.4 1.8E-11 4E-16 119.2 17.2 197 2-243 133-342 (357)
83 cd06335 PBP1_ABC_ligand_bindin 99.3 7.6E-11 1.7E-15 114.5 19.4 201 2-242 126-334 (347)
84 TIGR03870 ABC_MoxJ methanol ox 99.3 1.6E-12 3.4E-17 119.6 7.1 100 319-438 1-106 (246)
85 cd06328 PBP1_SBP_like_2 Peripl 99.3 1.8E-10 3.8E-15 111.2 19.7 192 4-242 128-321 (333)
86 cd06339 PBP1_YraM_LppC_lipopro 99.3 2.9E-11 6.2E-16 116.7 13.9 195 2-247 113-330 (336)
87 PRK10859 membrane-bound lytic 99.3 6.4E-12 1.4E-16 126.6 7.9 112 315-439 40-151 (482)
88 cd06334 PBP1_ABC_ligand_bindin 99.2 4.3E-10 9.4E-15 109.1 18.5 214 2-242 124-344 (351)
89 cd06356 PBP1_Amide_Urea_BP_lik 99.2 7.4E-10 1.6E-14 107.0 18.5 201 2-244 121-324 (334)
90 TIGR02285 conserved hypothetic 99.2 8.5E-11 1.8E-15 109.7 8.5 96 317-426 17-114 (268)
91 COG0834 HisJ ABC-type amino ac 99.1 1.5E-10 3.2E-15 108.6 9.3 123 316-446 32-155 (275)
92 cd04509 PBP1_ABC_transporter_G 99.1 4.7E-10 1E-14 106.2 12.1 165 2-177 125-290 (299)
93 PRK09959 hybrid sensory histid 99.1 2.2E-10 4.8E-15 129.4 10.5 99 316-426 300-398 (1197)
94 cd06326 PBP1_STKc_like Type I 99.1 3.3E-09 7.2E-14 102.6 17.4 200 2-246 125-329 (336)
95 PRK09959 hybrid sensory histid 99.1 3.1E-10 6.7E-15 128.2 10.1 100 316-426 54-154 (1197)
96 PF13433 Peripla_BP_5: Peripla 99.1 7E-09 1.5E-13 97.4 16.0 214 3-269 124-339 (363)
97 TIGR03871 ABC_peri_MoxJ_2 quin 99.0 4.6E-10 1E-14 102.4 7.7 90 319-426 1-90 (232)
98 PF10613 Lig_chan-Glu_bd: Liga 99.0 2.1E-10 4.6E-15 79.1 3.3 47 339-387 14-65 (65)
99 cd06341 PBP1_ABC_ligand_bindin 99.0 3.3E-08 7.2E-13 95.8 18.5 198 2-241 121-324 (341)
100 cd00134 PBPb Bacterial peripla 99.0 3.1E-09 6.8E-14 95.1 9.6 109 320-441 1-109 (218)
101 smart00062 PBPb Bacterial peri 98.9 6.3E-09 1.4E-13 93.0 9.0 108 319-439 1-108 (219)
102 cd06333 PBP1_ABC-type_HAAT_lik 98.9 5.7E-08 1.2E-12 92.9 15.6 162 2-179 122-293 (312)
103 cd06268 PBP1_ABC_transporter_L 98.8 1.9E-07 4.2E-12 88.2 14.8 161 2-179 123-287 (298)
104 TIGR03863 PQQ_ABC_bind ABC tra 98.6 7.6E-07 1.7E-11 85.9 14.3 184 2-247 117-307 (347)
105 COG4623 Predicted soluble lyti 98.6 3.3E-08 7.1E-13 90.8 4.4 111 316-439 21-131 (473)
106 cd01391 Periplasmic_Binding_Pr 97.7 0.00037 7.9E-09 64.2 11.6 105 2-108 113-219 (269)
107 TIGR01098 3A0109s03R phosphate 97.4 0.0003 6.4E-09 65.0 5.9 103 317-438 31-142 (254)
108 PF04348 LppC: LppC putative l 96.5 0.024 5.1E-07 58.0 11.1 86 2-90 334-419 (536)
109 PRK00489 hisG ATP phosphoribos 96.2 0.0061 1.3E-07 57.2 4.6 66 376-442 51-118 (287)
110 TIGR03431 PhnD phosphonate ABC 94.9 0.049 1.1E-06 51.3 5.8 100 318-439 27-137 (288)
111 TIGR02990 ectoine_eutA ectoine 93.9 0.66 1.4E-05 42.0 10.4 88 2-92 109-203 (239)
112 cd06282 PBP1_GntR_like_2 Ligan 91.1 1.7 3.7E-05 39.8 9.7 100 3-105 106-210 (266)
113 cd01537 PBP1_Repressors_Sugar_ 90.8 1.8 4E-05 39.4 9.6 101 3-105 108-212 (264)
114 cd06267 PBP1_LacI_sugar_bindin 90.7 2.5 5.5E-05 38.5 10.4 101 4-105 107-211 (264)
115 PRK09860 putative alcohol dehy 90.7 1.2 2.6E-05 43.8 8.4 76 4-79 22-97 (383)
116 cd01536 PBP1_ABC_sugar_binding 89.9 3.7 8.1E-05 37.5 10.8 92 3-96 109-206 (267)
117 cd08192 Fe-ADH7 Iron-containin 89.4 1.8 3.9E-05 42.3 8.5 76 4-79 15-90 (370)
118 cd06273 PBP1_GntR_like_1 This 89.4 2.8 6.1E-05 38.5 9.6 101 3-104 106-211 (268)
119 cd08190 HOT Hydroxyacid-oxoaci 89.3 2 4.3E-05 42.7 8.8 77 4-80 14-90 (414)
120 PF00465 Fe-ADH: Iron-containi 89.3 1.4 2.9E-05 43.1 7.6 86 3-90 13-100 (366)
121 PRK15454 ethanol dehydrogenase 88.8 2 4.4E-05 42.3 8.4 77 4-80 40-116 (395)
122 PF13377 Peripla_BP_3: Peripla 88.3 2.6 5.6E-05 35.2 7.9 98 6-105 2-102 (160)
123 PRK10624 L-1,2-propanediol oxi 88.2 2.5 5.5E-05 41.5 8.7 76 4-79 21-96 (382)
124 cd06298 PBP1_CcpA_like Ligand- 88.2 3.9 8.5E-05 37.5 9.7 101 4-105 107-211 (268)
125 cd08193 HVD 5-hydroxyvalerate 88.2 2.4 5.2E-05 41.6 8.4 77 4-80 17-93 (376)
126 cd08551 Fe-ADH iron-containing 87.8 3.1 6.6E-05 40.7 9.0 85 3-87 13-99 (370)
127 PF13685 Fe-ADH_2: Iron-contai 87.4 4.5 9.9E-05 36.9 9.1 97 4-105 10-107 (250)
128 TIGR01729 taurine_ABC_bnd taur 87.4 0.38 8.2E-06 45.5 2.3 82 353-443 20-106 (300)
129 TIGR01481 ccpA catabolite cont 87.4 5.9 0.00013 37.8 10.6 100 4-104 167-269 (329)
130 cd08194 Fe-ADH6 Iron-containin 86.9 3.4 7.3E-05 40.5 8.6 77 4-80 14-90 (375)
131 cd08185 Fe-ADH1 Iron-containin 86.8 3.4 7.4E-05 40.6 8.6 75 4-79 17-92 (380)
132 COG1454 EutG Alcohol dehydroge 86.7 5 0.00011 38.9 9.4 87 3-89 19-107 (377)
133 cd08189 Fe-ADH5 Iron-containin 86.4 3.9 8.4E-05 40.1 8.7 84 4-87 17-102 (374)
134 PF00532 Peripla_BP_1: Peripla 85.8 9 0.0002 35.7 10.6 98 4-101 109-211 (279)
135 TIGR02638 lactal_redase lactal 85.8 3.9 8.5E-05 40.1 8.5 77 4-80 20-96 (379)
136 cd08181 PPD-like 1,3-propanedi 84.9 4.6 0.0001 39.2 8.5 76 4-80 17-93 (357)
137 cd01545 PBP1_SalR Ligand-bindi 84.5 8.5 0.00018 35.3 9.9 97 4-101 109-209 (270)
138 cd06284 PBP1_LacI_like_6 Ligan 83.9 9.7 0.00021 34.8 9.9 101 3-104 105-209 (267)
139 cd06271 PBP1_AglR_RafR_like Li 83.8 9.5 0.00021 34.8 9.9 101 4-105 111-215 (268)
140 cd08188 Fe-ADH4 Iron-containin 83.8 6.1 0.00013 38.7 8.8 77 4-80 19-95 (377)
141 PRK10423 transcriptional repre 83.6 11 0.00023 35.9 10.4 102 4-105 165-269 (327)
142 cd08191 HHD 6-hydroxyhexanoate 83.3 6.3 0.00014 38.8 8.7 76 4-80 14-89 (386)
143 TIGR02122 TRAP_TAXI TRAP trans 83.1 2.8 6.1E-05 39.9 6.1 84 348-439 48-143 (320)
144 PRK10727 DNA-binding transcrip 83.0 9.1 0.0002 36.8 9.7 101 5-105 168-271 (343)
145 cd08170 GlyDH Glycerol dehydro 82.4 5.5 0.00012 38.6 7.8 74 4-80 14-87 (351)
146 PRK10401 DNA-binding transcrip 82.4 13 0.00027 35.9 10.4 101 4-105 167-271 (346)
147 cd06288 PBP1_sucrose_transcrip 82.2 9.5 0.00021 34.9 9.2 101 4-105 107-211 (269)
148 cd06325 PBP1_ABC_uncharacteriz 81.9 12 0.00026 34.5 9.8 87 3-95 119-208 (281)
149 cd06285 PBP1_LacI_like_7 Ligan 81.7 12 0.00026 34.3 9.6 100 3-102 104-206 (265)
150 PRK10014 DNA-binding transcrip 81.5 15 0.00033 35.2 10.6 96 4-99 173-271 (342)
151 COG1609 PurR Transcriptional r 81.4 21 0.00046 34.3 11.4 98 2-101 164-267 (333)
152 cd06286 PBP1_CcpB_like Ligand- 81.2 12 0.00027 34.0 9.5 102 3-105 104-209 (260)
153 cd08182 HEPD Hydroxyethylphosp 81.2 8 0.00017 37.8 8.5 82 4-88 14-97 (367)
154 COG3473 Maleate cis-trans isom 81.0 25 0.00053 30.8 10.0 88 2-92 107-201 (238)
155 cd01575 PBP1_GntR Ligand-bindi 81.0 16 0.00035 33.3 10.3 101 4-105 107-211 (268)
156 cd06297 PBP1_LacI_like_12 Liga 81.0 13 0.00028 34.3 9.6 98 6-105 108-214 (269)
157 cd08176 LPO Lactadehyde:propan 80.6 7.7 0.00017 38.0 8.2 77 4-80 19-95 (377)
158 cd08187 BDH Butanol dehydrogen 80.4 8.4 0.00018 37.9 8.4 77 3-80 19-96 (382)
159 cd06270 PBP1_GalS_like Ligand 79.9 19 0.00041 33.0 10.3 102 3-105 106-211 (268)
160 cd06272 PBP1_hexuronate_repres 79.8 12 0.00026 34.1 8.9 103 3-105 101-206 (261)
161 cd08171 GlyDH-like2 Glycerol d 79.6 8.2 0.00018 37.3 7.9 75 4-80 14-88 (345)
162 PRK11041 DNA-binding transcrip 79.6 14 0.0003 34.8 9.5 101 4-105 143-247 (309)
163 cd06293 PBP1_LacI_like_11 Liga 79.4 21 0.00046 32.6 10.5 101 4-105 107-211 (269)
164 cd06294 PBP1_ycjW_transcriptio 79.1 19 0.00041 32.9 10.1 101 4-104 113-216 (270)
165 PRK10703 DNA-binding transcrip 79.0 15 0.00032 35.3 9.6 100 5-105 170-273 (341)
166 PRK11553 alkanesulfonate trans 78.9 2.9 6.3E-05 39.7 4.6 99 317-439 26-131 (314)
167 cd06292 PBP1_LacI_like_10 Liga 78.8 18 0.00039 33.2 9.8 102 3-105 112-215 (273)
168 cd06310 PBP1_ABC_sugar_binding 78.6 38 0.00083 30.9 12.0 98 4-104 112-215 (273)
169 cd06320 PBP1_allose_binding Pe 78.4 26 0.00056 32.2 10.8 91 4-96 111-207 (275)
170 cd06290 PBP1_LacI_like_9 Ligan 78.1 18 0.00039 33.0 9.5 100 4-104 106-209 (265)
171 cd06295 PBP1_CelR Ligand bindi 77.7 18 0.00038 33.3 9.4 102 3-105 115-220 (275)
172 cd07766 DHQ_Fe-ADH Dehydroquin 77.6 11 0.00025 36.1 8.3 83 4-88 14-98 (332)
173 cd01544 PBP1_GalR Ligand-bindi 77.3 20 0.00044 32.9 9.7 100 4-105 103-213 (270)
174 cd06319 PBP1_ABC_sugar_binding 77.0 23 0.00051 32.5 10.1 84 12-96 124-210 (277)
175 cd08186 Fe-ADH8 Iron-containin 76.9 13 0.00029 36.5 8.6 76 4-79 14-93 (383)
176 cd06296 PBP1_CatR_like Ligand- 76.8 15 0.00033 33.6 8.7 102 4-105 108-212 (270)
177 cd06300 PBP1_ABC_sugar_binding 76.8 13 0.00028 34.1 8.3 92 3-97 113-210 (272)
178 PF12974 Phosphonate-bd: ABC t 76.6 3.6 7.9E-05 37.4 4.4 83 348-439 17-107 (243)
179 cd06291 PBP1_Qymf_like Ligand 76.6 27 0.00058 31.8 10.3 100 4-104 103-206 (265)
180 cd06299 PBP1_LacI_like_13 Liga 76.5 20 0.00042 32.7 9.3 101 4-105 107-209 (265)
181 PRK09423 gldA glycerol dehydro 76.3 13 0.00028 36.3 8.3 74 4-80 21-94 (366)
182 cd06287 PBP1_LacI_like_8 Ligan 76.1 39 0.00083 31.1 11.2 100 4-105 109-212 (269)
183 PF03808 Glyco_tran_WecB: Glyc 75.7 50 0.0011 28.2 11.1 92 6-107 42-135 (172)
184 cd06317 PBP1_ABC_sugar_binding 75.5 39 0.00085 30.9 11.2 96 6-104 117-218 (275)
185 PF13407 Peripla_BP_4: Peripla 75.1 10 0.00022 34.6 6.9 78 16-95 1-81 (257)
186 cd08183 Fe-ADH2 Iron-containin 75.0 15 0.00033 36.0 8.4 72 4-80 14-85 (374)
187 cd06275 PBP1_PurR Ligand-bindi 74.9 23 0.00049 32.4 9.3 103 3-105 107-212 (269)
188 cd08550 GlyDH-like Glycerol_de 74.8 13 0.00029 35.9 7.9 74 4-80 14-87 (349)
189 PRK09526 lacI lac repressor; R 74.4 45 0.00097 31.9 11.6 99 4-105 172-274 (342)
190 cd08442 PBP2_YofA_SoxR_like Th 73.8 20 0.00043 30.3 8.2 70 345-426 13-82 (193)
191 cd08415 PBP2_LysR_opines_like 73.6 26 0.00056 29.6 8.9 70 345-426 13-82 (196)
192 cd01540 PBP1_arabinose_binding 73.1 39 0.00084 31.3 10.5 93 4-96 118-219 (289)
193 COG3107 LppC Putative lipoprot 72.4 38 0.00082 34.1 10.1 46 5-50 375-420 (604)
194 PF03466 LysR_substrate: LysR 72.4 22 0.00048 30.5 8.3 84 317-426 5-88 (209)
195 cd06289 PBP1_MalI_like Ligand- 72.0 25 0.00053 32.1 8.8 100 4-104 108-211 (268)
196 cd06305 PBP1_methylthioribose_ 71.9 24 0.00053 32.3 8.8 77 16-95 2-81 (273)
197 cd06280 PBP1_LacI_like_4 Ligan 71.7 28 0.00061 31.7 9.1 98 4-105 106-206 (263)
198 PRK07377 hypothetical protein; 71.7 12 0.00025 31.9 5.6 63 317-396 74-136 (184)
199 KOG3857 Alcohol dehydrogenase, 71.7 22 0.00048 33.6 7.9 75 5-79 62-136 (465)
200 cd01574 PBP1_LacI Ligand-bindi 71.3 55 0.0012 29.7 11.0 100 3-105 106-208 (264)
201 cd06274 PBP1_FruR Ligand bindi 71.2 50 0.0011 30.0 10.7 101 4-105 107-212 (264)
202 cd06283 PBP1_RegR_EndR_KdgR_li 70.9 48 0.001 30.1 10.5 102 4-105 107-212 (267)
203 cd08412 PBP2_PAO1_like The C-t 70.8 27 0.00058 29.6 8.3 70 345-426 13-82 (198)
204 PF13379 NMT1_2: NMT1-like fam 70.7 7.2 0.00016 35.7 4.8 97 317-435 5-112 (252)
205 PRK10339 DNA-binding transcrip 70.2 35 0.00075 32.5 9.6 100 4-105 165-268 (327)
206 cd01542 PBP1_TreR_like Ligand- 70.0 37 0.0008 30.7 9.5 99 3-105 104-207 (259)
207 cd08178 AAD_C C-terminal alcoh 69.1 22 0.00047 35.2 8.0 79 10-88 18-98 (398)
208 cd05466 PBP2_LTTR_substrate Th 69.0 26 0.00056 29.3 7.8 69 346-426 14-82 (197)
209 cd08468 PBP2_Pa0477 The C-term 68.3 29 0.00063 29.7 8.0 73 345-426 13-85 (202)
210 cd06307 PBP1_uncharacterized_s 68.1 77 0.0017 29.0 11.3 88 7-96 117-210 (275)
211 cd06303 PBP1_LuxPQ_Quorum_Sens 67.7 73 0.0016 29.4 11.1 84 11-96 129-215 (280)
212 cd06323 PBP1_ribose_binding Pe 67.0 61 0.0013 29.4 10.3 90 4-95 110-205 (268)
213 cd08421 PBP2_LTTR_like_1 The C 66.7 28 0.00061 29.5 7.6 68 347-426 15-82 (198)
214 PRK11242 DNA-binding transcrip 66.4 40 0.00087 31.4 9.1 83 318-426 91-173 (296)
215 cd06279 PBP1_LacI_like_3 Ligan 65.8 55 0.0012 30.3 9.8 102 3-104 106-228 (283)
216 PRK11303 DNA-binding transcrip 65.1 92 0.002 29.5 11.4 97 5-104 171-271 (328)
217 cd08448 PBP2_LTTR_aromatics_li 64.5 41 0.00089 28.3 8.2 70 345-426 13-82 (197)
218 PRK14987 gluconate operon tran 64.3 70 0.0015 30.4 10.5 100 4-105 171-273 (331)
219 cd08440 PBP2_LTTR_like_4 TThe 64.3 42 0.00092 28.1 8.3 70 345-426 13-82 (197)
220 CHL00180 rbcR LysR transcripti 63.8 39 0.00085 31.8 8.5 86 318-426 95-180 (305)
221 cd06301 PBP1_rhizopine_binding 63.7 40 0.00087 30.8 8.4 77 15-94 1-81 (272)
222 cd06353 PBP1_BmpA_Med_like Per 63.7 63 0.0014 29.6 9.6 83 15-106 1-88 (258)
223 TIGR02417 fruct_sucro_rep D-fr 63.7 66 0.0014 30.5 10.1 96 6-105 171-271 (327)
224 cd08175 G1PDH Glycerol-1-phosp 63.6 32 0.0007 33.2 7.9 75 4-80 14-90 (348)
225 cd08453 PBP2_IlvR The C-termin 63.2 46 0.001 28.3 8.3 72 346-426 14-85 (200)
226 PF09084 NMT1: NMT1/THI5 like; 62.9 27 0.0006 30.7 6.9 80 356-444 17-100 (216)
227 cd06305 PBP1_methylthioribose_ 62.7 79 0.0017 28.8 10.2 91 6-96 112-208 (273)
228 cd01541 PBP1_AraR Ligand-bindi 62.6 76 0.0016 29.0 10.1 102 3-105 111-217 (273)
229 cd08438 PBP2_CidR The C-termin 62.5 36 0.00079 28.7 7.5 70 345-426 13-82 (197)
230 cd08425 PBP2_CynR The C-termin 62.2 44 0.00095 28.3 8.0 68 347-426 16-83 (197)
231 cd08486 PBP2_CbnR The C-termin 62.1 45 0.00099 28.5 8.1 69 346-426 15-83 (198)
232 cd06281 PBP1_LacI_like_5 Ligan 62.0 44 0.00096 30.5 8.4 99 5-105 108-210 (269)
233 cd06309 PBP1_YtfQ_like Peripla 61.9 1.2E+02 0.0025 27.8 11.2 99 4-105 113-219 (273)
234 cd01537 PBP1_Repressors_Sugar_ 61.7 33 0.00072 30.9 7.4 76 16-94 2-79 (264)
235 cd08437 PBP2_MleR The substrat 61.5 42 0.0009 28.5 7.7 71 346-426 14-84 (198)
236 cd06267 PBP1_LacI_sugar_bindin 61.0 43 0.00092 30.2 8.0 76 16-95 2-79 (264)
237 cd06303 PBP1_LuxPQ_Quorum_Sens 60.7 37 0.00081 31.3 7.7 79 16-94 2-84 (280)
238 cd08466 PBP2_LeuO The C-termin 60.7 41 0.00088 28.6 7.5 69 346-426 14-82 (200)
239 COG3221 PhnD ABC-type phosphat 60.4 11 0.00025 35.3 4.0 60 318-395 35-94 (299)
240 cd08452 PBP2_AlsR The C-termin 60.1 58 0.0013 27.6 8.4 68 347-426 15-82 (197)
241 cd08549 G1PDH_related Glycerol 60.1 42 0.00091 32.2 7.9 82 4-87 14-99 (332)
242 cd08465 PBP2_ToxR The C-termin 59.8 44 0.00096 28.6 7.6 70 345-426 13-82 (200)
243 cd08177 MAR Maleylacetate redu 59.7 26 0.00056 33.7 6.4 74 4-80 14-87 (337)
244 cd06277 PBP1_LacI_like_1 Ligan 58.7 77 0.0017 28.8 9.4 98 5-104 110-210 (268)
245 cd08411 PBP2_OxyR The C-termin 58.7 53 0.0011 27.8 7.9 69 346-426 15-83 (200)
246 cd06324 PBP1_ABC_sugar_binding 58.6 94 0.002 29.1 10.1 86 16-104 145-235 (305)
247 cd08446 PBP2_Chlorocatechol Th 58.4 59 0.0013 27.5 8.1 69 346-426 15-83 (198)
248 cd06289 PBP1_MalI_like Ligand- 58.4 54 0.0012 29.8 8.3 77 16-95 2-80 (268)
249 cd06301 PBP1_rhizopine_binding 58.0 1.3E+02 0.0028 27.4 10.7 88 6-96 115-208 (272)
250 cd06304 PBP1_BmpA_like Peripla 57.8 52 0.0011 29.9 8.0 89 5-94 111-202 (260)
251 TIGR01256 modA molybdenum ABC 57.6 24 0.00052 31.2 5.5 80 348-437 9-94 (216)
252 cd01536 PBP1_ABC_sugar_binding 57.4 60 0.0013 29.3 8.4 77 15-94 1-80 (267)
253 cd08414 PBP2_LTTR_aromatics_li 57.2 61 0.0013 27.2 8.0 68 347-426 15-82 (197)
254 cd06306 PBP1_TorT-like TorT-li 57.0 58 0.0013 29.8 8.2 80 15-95 1-82 (268)
255 cd08434 PBP2_GltC_like The sub 56.9 51 0.0011 27.6 7.5 69 346-426 14-82 (195)
256 cd03364 TOPRIM_DnaG_primases T 56.9 30 0.00065 24.9 5.0 40 5-45 36-75 (79)
257 PF00731 AIRC: AIR carboxylase 56.8 90 0.002 26.0 8.1 71 15-87 2-72 (150)
258 cd01538 PBP1_ABC_xylose_bindin 56.7 78 0.0017 29.4 9.1 76 16-94 2-80 (288)
259 cd06277 PBP1_LacI_like_1 Ligan 56.7 73 0.0016 29.0 8.8 74 16-94 2-80 (268)
260 PRK00002 aroB 3-dehydroquinate 56.6 62 0.0013 31.4 8.5 84 4-88 22-112 (358)
261 cd08463 PBP2_DntR_like_4 The C 56.5 53 0.0012 28.3 7.5 71 345-426 13-83 (203)
262 cd08418 PBP2_TdcA The C-termin 56.4 61 0.0013 27.4 7.9 71 346-426 14-84 (201)
263 cd08413 PBP2_CysB_like The C-t 56.4 64 0.0014 27.4 8.0 70 346-426 14-83 (198)
264 cd06312 PBP1_ABC_sugar_binding 55.7 61 0.0013 29.6 8.1 78 15-94 1-82 (271)
265 cd08436 PBP2_LTTR_like_3 The C 55.1 64 0.0014 27.0 7.8 71 345-426 13-83 (194)
266 cd08456 PBP2_LysR The C-termin 54.9 76 0.0016 26.7 8.2 69 345-425 13-81 (196)
267 cd08435 PBP2_GbpR The C-termin 54.8 69 0.0015 27.0 8.0 70 347-426 15-84 (201)
268 cd08429 PBP2_NhaR The C-termin 54.8 57 0.0012 28.2 7.5 71 346-425 14-84 (204)
269 cd08173 Gro1PDH Sn-glycerol-1- 54.8 58 0.0013 31.3 8.0 72 5-80 16-88 (339)
270 cd08450 PBP2_HcaR The C-termin 54.8 69 0.0015 26.9 7.9 70 345-426 13-82 (196)
271 cd01543 PBP1_XylR Ligand-bindi 54.7 1.2E+02 0.0025 27.6 9.9 100 4-104 100-204 (265)
272 cd06321 PBP1_ABC_sugar_binding 54.7 1.7E+02 0.0036 26.6 11.2 98 4-105 110-213 (271)
273 cd08184 Fe-ADH3 Iron-containin 54.4 64 0.0014 31.2 8.1 73 4-80 14-91 (347)
274 cd08179 NADPH_BDH NADPH-depend 54.4 67 0.0015 31.4 8.4 72 9-80 19-91 (375)
275 COG2984 ABC-type uncharacteriz 54.4 1.2E+02 0.0027 28.6 9.5 78 12-94 158-239 (322)
276 cd06306 PBP1_TorT-like TorT-li 54.0 1.5E+02 0.0031 27.1 10.4 88 4-95 111-207 (268)
277 cd08420 PBP2_CysL_like C-termi 54.0 65 0.0014 27.1 7.6 70 345-426 13-82 (201)
278 PRK12680 transcriptional regul 53.9 70 0.0015 30.6 8.4 85 317-426 92-176 (327)
279 cd08430 PBP2_IlvY The C-termin 53.9 67 0.0015 27.0 7.7 71 345-426 13-83 (199)
280 PF13380 CoA_binding_2: CoA bi 53.7 21 0.00046 28.1 4.0 85 14-106 1-88 (116)
281 PF13531 SBP_bac_11: Bacterial 53.6 22 0.00048 31.8 4.7 82 345-435 11-99 (230)
282 cd06299 PBP1_LacI_like_13 Liga 53.6 76 0.0016 28.7 8.4 75 16-94 2-78 (265)
283 cd08427 PBP2_LTTR_like_2 The C 53.5 57 0.0012 27.4 7.2 71 346-426 14-84 (195)
284 PRK09492 treR trehalose repres 53.1 1E+02 0.0022 28.9 9.4 87 5-95 167-256 (315)
285 cd06322 PBP1_ABC_sugar_binding 52.9 84 0.0018 28.5 8.6 76 16-94 2-80 (267)
286 TIGR02667 moaB_proteo molybden 52.8 80 0.0017 26.7 7.6 67 12-80 3-73 (163)
287 cd06354 PBP1_BmpA_PnrA_like Pe 52.5 99 0.0021 28.3 9.0 89 5-94 112-206 (265)
288 cd06310 PBP1_ABC_sugar_binding 52.4 74 0.0016 29.0 8.2 79 15-94 1-82 (273)
289 TIGR02405 trehalos_R_Ecol treh 52.1 1.8E+02 0.0039 27.3 10.9 87 5-95 164-253 (311)
290 cd08469 PBP2_PnbR The C-termin 52.0 74 0.0016 27.6 7.8 69 346-426 14-82 (221)
291 cd06312 PBP1_ABC_sugar_binding 52.0 1.5E+02 0.0032 27.0 10.1 97 3-104 114-214 (271)
292 cd08426 PBP2_LTTR_like_5 The C 51.9 73 0.0016 26.9 7.6 69 346-426 14-82 (199)
293 cd08459 PBP2_DntR_NahR_LinR_li 51.9 53 0.0011 27.9 6.7 69 346-426 14-82 (201)
294 cd08417 PBP2_Nitroaromatics_li 51.9 47 0.001 28.1 6.4 69 346-426 14-82 (200)
295 cd06282 PBP1_GntR_like_2 Ligan 51.8 74 0.0016 28.8 8.0 77 16-95 2-80 (266)
296 cd08485 PBP2_ClcR The C-termin 51.6 95 0.0021 26.4 8.3 69 346-426 15-83 (198)
297 cd06313 PBP1_ABC_sugar_binding 51.5 1.9E+02 0.0042 26.4 11.4 90 4-95 112-207 (272)
298 cd08467 PBP2_SyrM The C-termin 51.3 59 0.0013 27.7 6.9 70 345-426 13-82 (200)
299 cd08447 PBP2_LTTR_aromatics_li 50.9 89 0.0019 26.3 8.0 69 345-425 13-81 (198)
300 cd01545 PBP1_SalR Ligand-bindi 50.6 78 0.0017 28.7 8.0 77 16-94 2-80 (270)
301 cd08462 PBP2_NodD The C-termin 50.6 63 0.0014 27.5 7.0 67 347-426 15-81 (200)
302 cd01391 Periplasmic_Binding_Pr 50.3 85 0.0018 27.9 8.2 77 15-94 1-82 (269)
303 cd08449 PBP2_XapR The C-termin 50.3 90 0.0019 26.2 7.9 71 346-426 14-84 (197)
304 cd06278 PBP1_LacI_like_2 Ligan 50.3 1.6E+02 0.0034 26.6 10.0 99 4-105 106-209 (266)
305 cd08180 PDD 1,3-propanediol de 50.2 78 0.0017 30.4 8.0 71 8-79 17-87 (332)
306 cd08451 PBP2_BudR The C-termin 49.7 80 0.0017 26.6 7.5 70 346-426 15-84 (199)
307 cd06273 PBP1_GntR_like_1 This 49.7 1E+02 0.0022 28.0 8.6 75 16-94 2-78 (268)
308 PRK15408 autoinducer 2-binding 49.6 1.2E+02 0.0026 29.1 9.2 80 14-95 24-106 (336)
309 cd08423 PBP2_LTTR_like_6 The C 49.2 93 0.002 26.1 7.9 72 346-426 14-87 (200)
310 cd08197 DOIS 2-deoxy-scyllo-in 49.0 95 0.0021 30.1 8.4 83 5-89 15-105 (355)
311 KOG0025 Zn2+-binding dehydroge 48.9 1.1E+02 0.0023 28.7 7.9 83 2-94 175-257 (354)
312 cd08419 PBP2_CbbR_RubisCO_like 48.9 79 0.0017 26.5 7.4 69 346-426 13-81 (197)
313 PF03830 PTSIIB_sorb: PTS syst 48.8 74 0.0016 26.5 6.6 79 3-89 16-94 (151)
314 cd08416 PBP2_MdcR The C-termin 48.4 99 0.0021 26.0 7.9 72 345-426 13-84 (199)
315 cd08445 PBP2_BenM_CatM_CatR Th 48.4 1.1E+02 0.0023 26.1 8.2 70 345-426 14-83 (203)
316 cd06300 PBP1_ABC_sugar_binding 48.3 1E+02 0.0023 28.0 8.5 79 15-94 1-85 (272)
317 PF07302 AroM: AroM protein; 48.3 1.6E+02 0.0035 26.3 8.9 74 14-91 126-201 (221)
318 PRK10653 D-ribose transporter 47.9 1.2E+02 0.0026 28.2 8.9 79 13-94 26-107 (295)
319 PF05393 Hum_adeno_E3A: Human 47.8 27 0.00059 25.5 3.2 23 441-463 34-56 (94)
320 cd08433 PBP2_Nac The C-teminal 47.7 95 0.0021 26.1 7.7 69 346-426 14-82 (198)
321 cd08460 PBP2_DntR_like_1 The C 47.5 79 0.0017 26.8 7.2 69 345-426 13-81 (200)
322 PRK00843 egsA NAD(P)-dependent 46.7 92 0.002 30.1 7.9 80 4-87 24-106 (350)
323 TIGR00640 acid_CoA_mut_C methy 46.2 1.6E+02 0.0034 23.9 8.1 65 24-94 13-81 (132)
324 PF02502 LacAB_rpiB: Ribose/Ga 46.1 1.5E+02 0.0032 24.4 7.8 59 22-80 6-67 (140)
325 cd01540 PBP1_arabinose_binding 46.0 97 0.0021 28.6 7.9 75 16-94 2-79 (289)
326 PF13362 Toprim_3: Toprim doma 46.0 80 0.0017 23.7 6.0 52 11-65 39-92 (96)
327 cd06302 PBP1_LsrB_Quorum_Sensi 45.7 1.3E+02 0.0029 27.9 8.9 78 16-95 2-82 (298)
328 cd06318 PBP1_ABC_sugar_binding 45.2 1.1E+02 0.0023 28.1 8.0 76 16-94 2-80 (282)
329 cd02071 MM_CoA_mut_B12_BD meth 45.2 1.5E+02 0.0033 23.4 9.4 68 22-95 8-79 (122)
330 cd00886 MogA_MoaB MogA_MoaB fa 45.2 1E+02 0.0022 25.6 7.0 64 15-80 2-71 (152)
331 TIGR02424 TF_pcaQ pca operon t 45.1 97 0.0021 28.9 7.8 86 317-426 92-177 (300)
332 PRK10355 xylF D-xylose transpo 45.0 1.5E+02 0.0033 28.3 9.1 78 14-94 26-106 (330)
333 cd06281 PBP1_LacI_like_5 Ligan 44.9 1.3E+02 0.0028 27.4 8.5 76 16-94 2-79 (269)
334 cd06308 PBP1_sensor_kinase_lik 44.9 2.4E+02 0.0052 25.5 11.8 98 4-105 111-215 (270)
335 cd08441 PBP2_MetR The C-termin 44.6 97 0.0021 26.1 7.3 68 347-426 15-82 (198)
336 cd06323 PBP1_ribose_binding Pe 44.2 1.3E+02 0.0028 27.1 8.4 76 16-94 2-80 (268)
337 cd01539 PBP1_GGBP Periplasmic 44.1 1.5E+02 0.0032 27.8 8.9 78 15-95 1-83 (303)
338 TIGR02136 ptsS_2 phosphate bin 44.1 42 0.0009 31.4 5.0 72 346-426 49-127 (287)
339 TIGR01728 SsuA_fam ABC transpo 44.1 43 0.00092 30.9 5.1 79 353-440 20-104 (288)
340 TIGR00854 pts-sorbose PTS syst 44.0 1.7E+02 0.0036 24.4 8.0 77 4-88 17-93 (151)
341 TIGR03427 ABC_peri_uca ABC tra 43.6 34 0.00073 32.8 4.3 104 318-442 2-111 (328)
342 PRK11151 DNA-binding transcrip 43.5 1E+02 0.0022 28.9 7.6 83 318-426 91-173 (305)
343 PRK11074 putative DNA-binding 43.5 97 0.0021 29.0 7.5 86 317-426 91-176 (300)
344 PRK09756 PTS system N-acetylga 43.4 1.9E+02 0.0041 24.3 8.2 77 3-88 20-97 (158)
345 TIGR00249 sixA phosphohistidin 43.4 1.2E+02 0.0027 25.1 7.2 87 2-91 32-120 (152)
346 cd00001 PTS_IIB_man PTS_IIB, P 43.2 1.7E+02 0.0037 24.3 7.9 78 3-88 15-92 (151)
347 PRK10936 TMAO reductase system 43.1 3.1E+02 0.0067 26.3 11.5 88 12-105 171-262 (343)
348 cd01018 ZntC Metal binding pro 43.1 1.4E+02 0.0029 27.6 8.2 41 7-47 183-223 (266)
349 cd06324 PBP1_ABC_sugar_binding 43.0 1.2E+02 0.0025 28.5 8.0 76 16-94 2-82 (305)
350 PF14503 YhfZ_C: YhfZ C-termin 43.0 19 0.0004 32.4 2.3 93 340-441 23-125 (232)
351 TIGR02955 TMAO_TorT TMAO reduc 42.9 2.6E+02 0.0057 25.9 10.4 86 14-105 126-215 (295)
352 PF02608 Bmp: Basic membrane p 42.9 1.2E+02 0.0026 28.6 8.0 87 15-108 3-94 (306)
353 cd08461 PBP2_DntR_like_3 The C 42.8 92 0.002 26.2 6.8 70 345-426 13-82 (198)
354 cd00758 MoCF_BD MoCF_BD: molyb 42.5 99 0.0021 25.0 6.4 62 16-80 2-68 (133)
355 cd06296 PBP1_CatR_like Ligand- 42.4 1.3E+02 0.0029 27.2 8.2 75 16-94 2-78 (270)
356 PRK10014 DNA-binding transcrip 42.3 1.3E+02 0.0029 28.5 8.5 78 14-94 65-144 (342)
357 PRK11062 nhaR transcriptional 42.0 73 0.0016 29.8 6.4 87 317-426 92-178 (296)
358 cd06319 PBP1_ABC_sugar_binding 41.9 1.3E+02 0.0028 27.4 8.1 76 16-94 2-80 (277)
359 cd06317 PBP1_ABC_sugar_binding 41.9 1.4E+02 0.0031 27.0 8.3 76 16-94 2-81 (275)
360 cd08444 PBP2_Cbl The C-termina 41.7 1.1E+02 0.0023 26.0 7.1 71 345-426 13-83 (198)
361 PRK09791 putative DNA-binding 41.7 1.1E+02 0.0025 28.5 7.7 86 317-426 94-179 (302)
362 PRK12679 cbl transcriptional r 41.7 1.2E+02 0.0026 28.6 7.9 85 317-426 92-176 (316)
363 cd06321 PBP1_ABC_sugar_binding 41.6 1.6E+02 0.0034 26.7 8.6 76 16-94 2-82 (271)
364 cd08457 PBP2_OccR The C-termin 41.5 1.3E+02 0.0028 25.3 7.6 69 345-425 13-81 (196)
365 cd06320 PBP1_allose_binding Pe 41.2 1.5E+02 0.0033 26.9 8.4 78 16-94 2-82 (275)
366 TIGR00177 molyb_syn molybdenum 41.2 1.1E+02 0.0023 25.2 6.4 50 28-80 27-76 (144)
367 cd01542 PBP1_TreR_like Ligand- 41.1 1.4E+02 0.003 26.9 8.0 75 16-94 2-78 (259)
368 cd08439 PBP2_LrhA_like The C-t 41.0 1.3E+02 0.0028 25.1 7.4 66 347-426 15-80 (185)
369 PF13955 Fst_toxin: Toxin Fst, 40.9 45 0.00099 17.3 2.5 18 447-464 4-21 (21)
370 cd08464 PBP2_DntR_like_2 The C 40.8 99 0.0021 26.0 6.7 70 345-426 13-82 (200)
371 cd08443 PBP2_CysB The C-termin 40.7 1.5E+02 0.0032 25.2 7.8 71 345-426 13-83 (198)
372 cd06307 PBP1_uncharacterized_s 40.6 1.3E+02 0.0028 27.5 7.8 79 15-94 1-83 (275)
373 PRK09906 DNA-binding transcrip 40.3 1.2E+02 0.0026 28.2 7.6 68 347-426 105-172 (296)
374 PF08357 SEFIR: SEFIR domain; 40.2 76 0.0016 26.1 5.5 65 14-79 1-68 (150)
375 PRK10341 DNA-binding transcrip 40.2 1.3E+02 0.0028 28.3 7.9 70 347-426 112-181 (312)
376 PRK09701 D-allose transporter 40.1 2E+02 0.0044 27.0 9.2 83 11-94 22-107 (311)
377 cd06533 Glyco_transf_WecG_TagA 40.1 2.3E+02 0.005 24.0 9.1 84 14-106 47-132 (171)
378 PRK10837 putative DNA-binding 40.1 1.6E+02 0.0036 27.1 8.5 83 318-426 89-171 (290)
379 PRK03601 transcriptional regul 40.1 98 0.0021 28.5 6.9 83 318-426 89-171 (275)
380 cd06270 PBP1_GalS_like Ligand 40.1 1.6E+02 0.0036 26.6 8.4 75 16-94 2-78 (268)
381 PF09651 Cas_APE2256: CRISPR-a 39.7 1.2E+02 0.0026 24.7 6.4 45 3-47 9-56 (136)
382 PF04392 ABC_sub_bind: ABC tra 39.6 1.3E+02 0.0028 28.1 7.7 71 4-79 120-193 (294)
383 smart00187 INB Integrin beta s 39.5 2.9E+02 0.0064 27.4 9.9 24 2-25 211-241 (423)
384 cd01575 PBP1_GntR Ligand-bindi 39.4 1.5E+02 0.0033 26.7 8.1 75 16-94 2-78 (268)
385 PRK11425 PTS system N-acetylga 39.4 2.2E+02 0.0048 23.9 8.1 76 4-88 19-94 (157)
386 cd06274 PBP1_FruR Ligand bindi 39.3 1.6E+02 0.0034 26.6 8.1 75 16-94 2-78 (264)
387 PF13607 Succ_CoA_lig: Succiny 38.7 2.1E+02 0.0045 23.4 7.6 75 16-95 4-80 (138)
388 PRK15138 aldehyde reductase; P 38.5 1.2E+02 0.0025 29.9 7.3 72 4-79 22-94 (387)
389 cd03770 SR_TndX_transposase Se 38.2 2.2E+02 0.0047 23.2 8.9 49 30-78 24-76 (140)
390 cd01324 cbb3_Oxidase_CcoQ Cyto 38.0 42 0.00092 21.7 2.8 23 441-463 12-34 (48)
391 PRK13805 bifunctional acetalde 37.9 1.5E+02 0.0032 32.9 8.7 69 12-80 479-549 (862)
392 cd00338 Ser_Recombinase Serine 37.8 2.1E+02 0.0045 22.8 9.3 65 30-94 20-95 (137)
393 PF04273 DUF442: Putative phos 37.8 2E+02 0.0042 22.5 9.1 74 7-81 22-96 (110)
394 PRK10936 TMAO reductase system 37.8 2E+02 0.0044 27.6 8.8 79 14-94 47-128 (343)
395 TIGR03339 phn_lysR aminoethylp 37.7 1.6E+02 0.0035 26.9 8.0 69 346-426 98-166 (279)
396 TIGR00035 asp_race aspartate r 37.6 58 0.0013 29.3 4.7 40 3-45 107-146 (229)
397 cd06285 PBP1_LacI_like_7 Ligan 37.5 1.9E+02 0.0042 26.1 8.4 75 16-94 2-78 (265)
398 PRK09508 leuO leucine transcri 37.4 1E+02 0.0022 29.2 6.6 70 345-426 125-194 (314)
399 cd06292 PBP1_LacI_like_10 Liga 37.2 1.9E+02 0.0042 26.2 8.4 76 16-94 2-83 (273)
400 cd08431 PBP2_HupR The C-termin 37.1 1.3E+02 0.0028 25.2 6.9 70 345-425 13-82 (195)
401 PRK01215 competence damage-ind 36.8 2.9E+02 0.0063 25.5 9.1 63 15-80 5-72 (264)
402 cd08172 GlyDH-like1 Glycerol d 36.8 1.1E+02 0.0024 29.5 6.8 72 4-80 15-86 (347)
403 PRK10586 putative oxidoreducta 36.6 1.8E+02 0.0038 28.4 8.1 72 4-80 25-96 (362)
404 cd06271 PBP1_AglR_RafR_like Li 36.5 1.7E+02 0.0038 26.3 7.9 61 16-79 2-68 (268)
405 PRK11303 DNA-binding transcrip 36.4 2.4E+02 0.0052 26.6 9.1 79 13-94 61-141 (328)
406 PF12916 DUF3834: Protein of u 36.1 55 0.0012 28.3 3.9 44 345-396 77-121 (201)
407 cd06314 PBP1_tmGBP Periplasmic 36.1 1.9E+02 0.0041 26.3 8.1 75 16-92 2-78 (271)
408 COG0107 HisF Imidazoleglycerol 35.8 56 0.0012 29.2 4.0 49 340-395 180-228 (256)
409 TIGR01120 rpiB ribose 5-phosph 35.8 2.5E+02 0.0054 23.1 8.7 63 20-82 4-68 (143)
410 cd06316 PBP1_ABC_sugar_binding 35.7 1.8E+02 0.0039 26.9 8.0 80 15-96 1-83 (294)
411 cd08428 PBP2_IciA_ArgP The C-t 35.6 1.5E+02 0.0032 24.9 7.0 65 348-425 16-80 (195)
412 KOG1014 17 beta-hydroxysteroid 35.4 2.3E+02 0.0049 26.8 8.0 67 6-82 43-112 (312)
413 PF13155 Toprim_2: Toprim-like 35.1 69 0.0015 23.9 4.1 39 3-41 37-75 (96)
414 PRK13054 lipid kinase; Reviewe 35.0 3E+02 0.0064 25.9 9.3 75 14-92 4-78 (300)
415 cd06322 PBP1_ABC_sugar_binding 35.0 3.4E+02 0.0073 24.4 11.4 87 12-105 120-210 (267)
416 cd06315 PBP1_ABC_sugar_binding 35.0 3.3E+02 0.0072 24.9 9.6 78 14-94 1-81 (280)
417 PRK12683 transcriptional regul 35.0 1.7E+02 0.0038 27.4 7.8 85 317-426 92-176 (309)
418 cd08458 PBP2_NocR The C-termin 34.7 2.1E+02 0.0045 24.1 7.7 67 347-425 15-81 (196)
419 PRK09986 DNA-binding transcrip 34.7 2E+02 0.0043 26.6 8.1 86 317-426 96-181 (294)
420 cd06278 PBP1_LacI_like_2 Ligan 34.5 2.2E+02 0.0047 25.6 8.2 74 16-94 2-77 (266)
421 cd03522 MoeA_like MoeA_like. T 34.3 1.8E+02 0.0038 27.7 7.4 78 11-90 157-240 (312)
422 TIGR02634 xylF D-xylose ABC tr 34.3 1.9E+02 0.0042 27.0 8.0 70 22-94 9-79 (302)
423 PF02602 HEM4: Uroporphyrinoge 34.2 1.2E+02 0.0025 27.1 6.2 81 3-90 106-187 (231)
424 COG1794 RacX Aspartate racemas 33.9 1.7E+02 0.0037 26.1 6.7 41 2-45 106-146 (230)
425 PRK11917 bifunctional adhesin/ 33.6 98 0.0021 28.3 5.7 70 349-426 161-232 (259)
426 PF02698 DUF218: DUF218 domain 33.5 83 0.0018 26.0 4.8 90 5-95 30-122 (155)
427 PRK03692 putative UDP-N-acetyl 33.4 2.1E+02 0.0046 26.0 7.6 75 9-90 102-177 (243)
428 cd08169 DHQ-like Dehydroquinat 33.4 2.2E+02 0.0047 27.5 8.2 86 4-90 14-105 (344)
429 cd06295 PBP1_CelR Ligand bindi 33.3 2.8E+02 0.006 25.2 8.8 76 13-94 3-87 (275)
430 PRK10094 DNA-binding transcrip 33.1 1.6E+02 0.0035 27.7 7.2 69 348-426 109-177 (308)
431 PF13662 Toprim_4: Toprim doma 33.1 35 0.00077 24.7 2.1 32 14-45 47-78 (81)
432 COG1058 CinA Predicted nucleot 32.9 94 0.002 28.4 5.2 49 28-79 21-69 (255)
433 PRK10653 D-ribose transporter 32.9 4E+02 0.0086 24.6 12.1 88 6-95 140-231 (295)
434 PRK10481 hypothetical protein; 32.8 3.6E+02 0.0078 24.2 8.7 65 14-82 130-194 (224)
435 cd06578 HemD Uroporphyrinogen- 32.4 3.5E+02 0.0076 23.8 9.1 61 30-92 134-194 (239)
436 PF12727 PBP_like: PBP superfa 32.1 43 0.00093 29.2 2.8 74 348-426 106-179 (193)
437 cd00757 ThiF_MoeB_HesA_family 31.8 3.8E+02 0.0081 24.0 9.4 82 3-90 35-131 (228)
438 cd06298 PBP1_CcpA_like Ligand- 31.6 2.4E+02 0.0052 25.4 8.0 75 16-94 2-78 (268)
439 cd06283 PBP1_RegR_EndR_KdgR_li 31.4 2.6E+02 0.0057 25.0 8.3 75 16-94 2-78 (267)
440 PRK09189 uroporphyrinogen-III 31.3 1.4E+02 0.0031 26.8 6.3 60 30-90 130-189 (240)
441 cd06294 PBP1_ycjW_transcriptio 31.2 2.6E+02 0.0056 25.2 8.2 68 23-94 16-83 (270)
442 smart00857 Resolvase Resolvase 31.2 2.9E+02 0.0062 22.4 8.8 66 29-94 20-95 (148)
443 PRK11716 DNA-binding transcrip 31.1 2.1E+02 0.0046 25.8 7.6 69 346-425 81-149 (269)
444 PF01936 NYN: NYN domain; Int 31.1 2.4E+02 0.0053 22.6 7.2 96 4-105 25-126 (146)
445 cd06309 PBP1_YtfQ_like Peripla 30.6 1.6E+02 0.0034 26.9 6.6 71 22-95 10-81 (273)
446 PRK11233 nitrogen assimilation 30.6 2.3E+02 0.005 26.5 7.9 69 346-426 106-174 (305)
447 cd06286 PBP1_CcpB_like Ligand- 30.5 2.7E+02 0.0058 25.0 8.1 61 16-79 2-64 (260)
448 cd01574 PBP1_LacI Ligand-bindi 30.4 3.2E+02 0.007 24.5 8.7 63 16-80 2-66 (264)
449 cd06311 PBP1_ABC_sugar_binding 30.2 4.2E+02 0.009 24.0 11.7 89 5-96 117-210 (274)
450 PRK11914 diacylglycerol kinase 30.0 2.9E+02 0.0062 26.0 8.3 76 10-90 5-84 (306)
451 cd06268 PBP1_ABC_transporter_L 29.9 3.1E+02 0.0066 24.9 8.6 78 16-94 2-90 (298)
452 cd06276 PBP1_FucR_like Ligand- 29.8 2.8E+02 0.0061 24.9 8.0 86 5-104 107-195 (247)
453 TIGR02637 RhaS rhamnose ABC tr 29.6 3.2E+02 0.0069 25.4 8.6 76 17-94 2-81 (302)
454 PHA02650 hypothetical protein; 29.5 1E+02 0.0023 22.1 3.7 25 436-460 45-69 (81)
455 TIGR02417 fruct_sucro_rep D-fr 29.4 4.1E+02 0.0088 25.0 9.4 79 13-94 60-140 (327)
456 PLN02617 imidazole glycerol ph 29.2 1E+02 0.0022 31.9 5.2 51 339-396 462-512 (538)
457 PF03853 YjeF_N: YjeF-related 28.7 2.8E+02 0.006 23.5 7.2 70 3-73 11-84 (169)
458 TIGR00646 MG010 DNA primase-re 28.7 1.9E+02 0.0041 25.8 6.1 47 5-52 146-192 (218)
459 PF00763 THF_DHG_CYH: Tetrahyd 28.7 2.1E+02 0.0045 22.6 6.0 65 15-80 31-97 (117)
460 cd06304 PBP1_BmpA_like Peripla 28.6 1.3E+02 0.0028 27.4 5.6 60 15-78 1-64 (260)
461 PF00070 Pyr_redox: Pyridine n 28.6 1.7E+02 0.0037 20.8 5.2 45 4-49 14-62 (80)
462 PRK12684 transcriptional regul 28.5 2.3E+02 0.0051 26.6 7.5 85 317-426 92-176 (313)
463 cd00885 cinA Competence-damage 28.5 2E+02 0.0043 24.5 6.2 48 29-79 20-67 (170)
464 COG1105 FruK Fructose-1-phosph 28.5 1.3E+02 0.0028 28.4 5.4 70 12-82 85-170 (310)
465 TIGR00147 lipid kinase, YegS/R 28.5 3.9E+02 0.0083 24.9 8.9 74 14-92 2-79 (293)
466 KOG4132 Uroporphyrinogen III s 28.1 4.4E+02 0.0096 23.6 8.3 69 26-94 141-209 (260)
467 TIGR01118 lacA galactose-6-pho 27.9 3.4E+02 0.0075 22.3 7.8 60 20-80 5-66 (141)
468 PRK12682 transcriptional regul 27.8 2.5E+02 0.0054 26.3 7.6 84 318-426 93-176 (309)
469 TIGR00975 3a0107s03 phosphate 27.5 1.4E+02 0.0029 28.5 5.6 71 349-426 11-87 (314)
470 PRK11482 putative DNA-binding 27.4 2.7E+02 0.0059 26.3 7.8 82 317-426 116-197 (317)
471 cd00858 GlyRS_anticodon GlyRS 27.3 2.3E+02 0.0049 22.3 6.1 45 29-80 43-87 (121)
472 PF13396 PLDc_N: Phospholipase 27.3 60 0.0013 20.5 2.2 28 435-462 17-44 (46)
473 TIGR01162 purE phosphoribosyla 27.2 2.6E+02 0.0057 23.4 6.4 54 28-82 12-65 (156)
474 PF02310 B12-binding: B12 bind 27.1 2.9E+02 0.0064 21.3 6.8 70 2-78 18-87 (121)
475 PRK11070 ssDNA exonuclease Rec 27.1 2.9E+02 0.0063 28.9 8.2 81 14-96 70-153 (575)
476 PF10853 DUF2650: Protein of u 26.7 45 0.00097 20.4 1.4 15 438-452 22-36 (38)
477 PRK15395 methyl-galactoside AB 26.7 4.7E+02 0.01 24.8 9.3 78 14-94 25-106 (330)
478 TIGR03405 Phn_Fe-ADH phosphona 26.7 3E+02 0.0065 26.7 7.9 73 6-80 16-90 (355)
479 PF08854 DUF1824: Domain of un 26.6 68 0.0015 25.7 2.8 40 2-44 26-65 (125)
480 cd06313 PBP1_ABC_sugar_binding 26.5 2.9E+02 0.0063 25.2 7.6 76 16-94 2-80 (272)
481 PLN00125 Succinyl-CoA ligase [ 26.4 4.8E+02 0.01 24.7 8.8 72 15-91 152-231 (300)
482 PF00107 ADH_zinc_N: Zinc-bind 26.4 2.6E+02 0.0057 21.8 6.5 66 3-83 5-71 (130)
483 PF04392 ABC_sub_bind: ABC tra 26.3 1.7E+02 0.0037 27.4 6.0 65 15-80 1-69 (294)
484 PF06057 VirJ: Bacterial virul 26.3 1.9E+02 0.0041 25.2 5.6 67 15-81 3-77 (192)
485 cd06290 PBP1_LacI_like_9 Ligan 26.2 2.3E+02 0.0049 25.6 6.8 61 16-79 2-64 (265)
486 TIGR00696 wecB_tagA_cpsF bacte 26.0 4.2E+02 0.0091 22.7 9.3 72 10-89 46-119 (177)
487 PRK12681 cysB transcriptional 25.5 3.1E+02 0.0067 26.0 7.8 85 317-426 92-176 (324)
488 cd08195 DHQS Dehydroquinate sy 25.4 2.8E+02 0.0062 26.7 7.5 82 11-94 22-111 (345)
489 PRK15421 DNA-binding transcrip 25.4 2.7E+02 0.0057 26.4 7.3 68 347-426 104-171 (317)
490 PRK05752 uroporphyrinogen-III 25.4 2.4E+02 0.0052 25.7 6.7 59 29-88 141-199 (255)
491 smart00852 MoCF_biosynth Proba 25.0 3.6E+02 0.0078 21.6 7.0 49 28-79 18-66 (135)
492 TIGR03702 lip_kinase_YegS lipi 24.9 5.4E+02 0.012 24.0 9.1 73 16-92 2-74 (293)
493 PF10717 ODV-E18: Occlusion-de 24.9 1.3E+02 0.0028 21.9 3.6 34 434-467 18-51 (85)
494 PRK03670 competence damage-ind 24.8 3.3E+02 0.0072 24.9 7.3 49 29-79 21-69 (252)
495 COG3439 Uncharacterized conser 24.6 3.9E+02 0.0085 21.8 7.0 71 26-105 21-93 (137)
496 COG1587 HemD Uroporphyrinogen- 24.6 4.4E+02 0.0094 23.9 8.2 86 3-94 111-198 (248)
497 TIGR01357 aroB 3-dehydroquinat 24.5 3.2E+02 0.0069 26.3 7.7 83 6-92 15-105 (344)
498 cd01538 PBP1_ABC_xylose_bindin 24.5 5.5E+02 0.012 23.5 10.7 85 12-97 124-216 (288)
499 PF10661 EssA: WXG100 protein 24.5 80 0.0017 26.1 3.0 28 436-463 115-142 (145)
500 cd02067 B12-binding B12 bindin 24.2 3.4E+02 0.0075 21.0 9.1 67 22-94 8-78 (119)
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=1.3e-52 Score=392.72 Aligned_cols=420 Identities=17% Similarity=0.306 Sum_probs=333.6
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.|+++|+.||+|..+..+| |.+.|...++.+.+.+..+++.|.....- ...+..++..+++.+.....+.|++.|..+
T Consensus 140 ~al~s~i~hy~W~~fv~ly-D~~rg~s~Lqai~~~a~~~nw~VtA~~v~-~~~d~~~yr~~f~~l~~r~e~rv~iDce~~ 217 (897)
T KOG1054|consen 140 GALLSLIDHYKWEKFVYLY-DTDRGLSILQAIMEAAAQNNWQVTAINVG-NINDVKEYRMLFEMLDRRQENRVLIDCESE 217 (897)
T ss_pred HHHHHHHHhcccceEEEEE-cccchHHHHHHHHHHHHhcCceEEEEEcC-CcccHHHHHHHHHHHhccccceEEEEcccH
Confidence 5899999999999999999 77789999999999999999999876433 233444588999999998899999999999
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhcc-CCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRR-NTLNG 160 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~ 160 (481)
....++.++.+.+....+|++|+.+..-...+. ..+.....++.+|+......|..++|.++|+..... .++..
T Consensus 218 ~~~~il~q~i~~~k~~~~YHYvlaNl~f~d~dl-----~~f~~g~aNitgFqivn~~~~~~~k~~~~~~~l~~~~~~g~~ 292 (897)
T KOG1054|consen 218 RRNRILLQVIELGKHVKGYHYVLANLGFTDIDL-----ERFQHGGANITGFQIVNKNNPMVKKFIQRWKELDEREYPGAS 292 (897)
T ss_pred HHHHHHHHHHHHhhhccceEEEEeeCCCchhhH-----HHHhcCCcceeEEEEecCCChHHHHHHHHHhhhcccccCCCC
Confidence 999999999888888899999999743322222 334455667899999999999999999999976542 34444
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCccc--ccccccCccHHHHHHHHhcccCceeeeE
Q 011629 161 PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRF--SSVSIFNGGKMLLDNILQVNMTGVTGPI 238 (481)
Q Consensus 161 ~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~L~~~l~~v~f~g~sG~v 238 (481)
..++...++..||||.++++|++.+.+++.+.... +...+| .+..+|.+|..+-++|+++.++|++|+|
T Consensus 293 ~~~~k~tsAlthDailV~~eaf~~~~~q~~~~~rR---------G~~GD~~an~~~p~~qG~~I~ralk~v~~eGLTGni 363 (897)
T KOG1054|consen 293 NDPIKYTSALTHDAILVMAEAFRSLRRQRIDISRR---------GNAGDCLANPAVPWEQGIDIERALKQVQVEGLTGNI 363 (897)
T ss_pred CCCcchhhhhhhhHHHHHHHHHHHHHHhhhchhcc---------CCCccccCCCCCchhcchhHHHHHHheeecccccce
Confidence 44556678999999999999999988765433221 111123 1355688899999999999999999999
Q ss_pred EEccCCCCCCCcEEEEEeecCceEEEEEeeCCCCCcccCCccccCCCCCCCCCccccceeecCCCCCCCCCCccc-cCCC
Q 011629 239 KFTSDRDLINPAYEVINVIGTGSRRIGYWSNHSGLSVVPPEALYKEPSNRSASSQHLYSAVWPGQTTQKPRGWVF-PNNG 317 (481)
Q Consensus 239 ~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~W~~~~~~~P~s~~~-~~~~ 317 (481)
.||+.|.|.|.+.+|+.+..++..++|.|+...++...... .+.+-.. ..+.
T Consensus 364 qFd~~G~R~Nyt~~i~elk~~~~rk~~~W~e~~~fv~~~t~---------------------------a~~~~d~~~~~n 416 (897)
T KOG1054|consen 364 QFDKYGRRTNYTIDIVELKSNGSRKVGYWNEGEGFVPGSTV---------------------------AQSRNDQASKEN 416 (897)
T ss_pred eecccCccccceEEEEEeccCCcceeeeecccCceeecccc---------------------------cccccccccccc
Confidence 99999999999999999999999999999987765432211 0000000 1123
Q ss_pred ceEEEeecCCCCCcCcEEec------CCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCC-----CCCC-HHHHHHHH
Q 011629 318 RHLRIGVPSQVIYPEFVAQG------KGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGH-----NSPK-RFDLLRLV 385 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~------~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~-----~~~~-~~~~~~~l 385 (481)
+++.|.+.- -.||.+.. +|+++++||||||+.+||++.+.++++ ..++|++ .++. |+||+++|
T Consensus 417 ~tvvvttiL---~spyvm~kkn~~~~egn~ryEGyCvdLa~~iAkhi~~~Y~l--~iv~dgkyGardaD~k~WnGMvGeL 491 (897)
T KOG1054|consen 417 RTVVVTTIL---ESPYVMLKKNHEQLEGNERYEGYCVDLAAEIAKHIGIKYKL--FIVGDGKYGARDADTKIWNGMVGEL 491 (897)
T ss_pred ceEEEEEec---CCchhHHHhhHHHhcCCcccceeHHHHHHHHHHhcCceEEE--EEecCCcccccCCCcccccchhHHH
Confidence 444444442 24554432 368899999999999999999977444 4444443 4455 99999999
Q ss_pred HcccccEEEeeeeeccccccceeeccceeecceEEEEecCC-CCcCccccccCcchhHHHHHHHHHHHHHHHHHhhhccc
Q 011629 386 SEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK-LNSNAWAFLNPFTPKMWCVTGIFFLVVGVVVWILEHRL 464 (481)
Q Consensus 386 ~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~-~~~~~~~~l~pf~~~~W~~~~~~~~~~~~~~~~~~~~~ 464 (481)
..|++|++++++|+|.+|++.+|||+||+++|++||.+||. .+++.|+||+|+..++|+||+.+++.|++++|++.|++
T Consensus 492 v~grAdiavApLTIt~~REeviDFSKPfMslGISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFS 571 (897)
T KOG1054|consen 492 VYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFS 571 (897)
T ss_pred hcCccceEEeeeeeehhhhhhhccccchhhcCeEEEEeCcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccC
Confidence 99999999999999999999999999999999999999988 77899999999999999999999999999999998887
Q ss_pred CCCCC
Q 011629 465 NDDFR 469 (481)
Q Consensus 465 ~~~~~ 469 (481)
+-||+
T Consensus 572 PYEwh 576 (897)
T KOG1054|consen 572 PYEWH 576 (897)
T ss_pred chhee
Confidence 76763
No 2
>KOG4440 consensus NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=2.7e-48 Score=365.52 Aligned_cols=389 Identities=24% Similarity=0.409 Sum_probs=315.6
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~ 82 (481)
...++|++|.|+.|.++.+||..|.....+++..+++....++....+.+.. +++...+-..|...+|||++..+.++
T Consensus 159 VwleMl~~~~y~~vi~l~s~d~~gra~~~r~qt~~e~~~~~~e~v~~f~p~~--~~~t~~l~~~k~~~~rv~~~~as~dD 236 (993)
T KOG4440|consen 159 VWLEMLRVYSYNHVILLVSDDHEGRAAQKRLQTLLEERESKAEKVLQFDPGT--KNVTALLMEAKELEARVIILSASEDD 236 (993)
T ss_pred HHHHHHHHhhcceEEEEEcccccchhHHhHHHHHHHHHhhhhhhheecCccc--chHHHHHhhhhhhhheeEEeecccch
Confidence 4568899999999999999999998887788888877666666655665543 36788888999999999999999999
Q ss_pred HHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCCCCCC
Q 011629 83 GLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTLNGPI 162 (481)
Q Consensus 83 ~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~ 162 (481)
+..+++.|-.++|++.||+||.++.-... ....+|++|.++-....
T Consensus 237 A~~ifr~Ag~lnmTG~G~VWiV~E~a~~~-----------nn~PdG~LGlqL~~~~~----------------------- 282 (993)
T KOG4440|consen 237 AATIFRAAGMLNMTGSGYVWIVGERAISG-----------NNLPDGILGLQLINGKN----------------------- 282 (993)
T ss_pred HHHHHHhhhhhcccCceEEEEEecccccc-----------CCCCCceeeeEeecCcc-----------------------
Confidence 99999999999999999999999643222 13357889987643211
Q ss_pred CCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHh-cccCceeeeEEEc
Q 011629 163 GLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQ-VNMTGVTGPIKFT 241 (481)
Q Consensus 163 ~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~-v~f~g~sG~v~Fd 241 (481)
..+.+-|+|+++|.|+|+++....-.. .+..||++...|..+..|.+++.. -...|.+|+|.||
T Consensus 283 ----~~~hirDsv~vlasAv~e~~~~e~I~~-----------~P~~c~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~Fn 347 (993)
T KOG4440|consen 283 ----ESAHIRDSVGVLASAVHELLEKENITD-----------PPRGCVDNTNIWKTGPLLKRVLMSSKYADGVTGRVEFN 347 (993)
T ss_pred ----ccceehhhHHHHHHHHHHHHhhccCCC-----------CCCcccCccchhcccHHHHHHHhhhcccCCcceeEEEc
Confidence 235678999999999999987643211 123367777778878888888776 4557899999999
Q ss_pred cCCCCCCCcEEEEEee-cCceEEEEEeeCCCCCcccCCccccCCCCCCCCCccccceeecCCCCCCCCCCccccCCCceE
Q 011629 242 SDRDLINPAYEVINVI-GTGSRRIGYWSNHSGLSVVPPEALYKEPSNRSASSQHLYSAVWPGQTTQKPRGWVFPNNGRHL 320 (481)
Q Consensus 242 ~~Gd~~~~~y~I~~~~-~~~~~~VG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~W~~~~~~~P~s~~~~~~~~~l 320 (481)
++|||..+.|||+|+. ....+-+|.|+... ...+.++|.|||+..+.|+.+..| .+|
T Consensus 348 d~gdRi~a~YdiiN~hq~rk~Vg~~~yd~~r-------------------~~~nd~~IiWpGg~~~KP~gi~~p---thL 405 (993)
T KOG4440|consen 348 DDGDRIFANYDIINLHQNRKLVGVGIYDGTR-------------------VIPNDRKIIWPGGETEKPRGIQMP---THL 405 (993)
T ss_pred CCCceeeccceeEehhhhhhhhhhcccccee-------------------eccCCceeecCCCCcCCCcccccc---cee
Confidence 9999999999999994 45566677776431 123567999999999999998877 468
Q ss_pred EEeecCCCCCcCcEEecC-------------------------------C------CCeEEeeeHHHHHHHHHHCCCccc
Q 011629 321 RIGVPSQVIYPEFVAQGK-------------------------------G------TDKFSGYCIDVFTAVLELLPYAVP 363 (481)
Q Consensus 321 ~v~~~~~~~~~p~~~~~~-------------------------------~------~~~~~G~~~dl~~~ia~~l~~~~~ 363 (481)
|+.+.+ .+||+|..+ + ..|+.||||||+-++++.++|+++
T Consensus 406 rivTi~---~~PFVYv~p~~sd~~c~eef~~~~d~~~k~~c~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nftyd 482 (993)
T KOG4440|consen 406 RIVTIH---QEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTYD 482 (993)
T ss_pred EEEEec---cCCeEEEecCCCCcchhhhccccCCcccceeecCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceEE
Confidence 888874 577877531 0 236789999999999999999987
Q ss_pred EEEEeCCC-CC----------CCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCCCCcCcc
Q 011629 364 YKLVPFGD-GH----------NSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAW 432 (481)
Q Consensus 364 ~~~~~~~~-~~----------~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~ 432 (481)
..+.+.+- |+ ...+|+||+++|..+++||+++++++++||+++++||+||..-|+.|+.+++.+.....
T Consensus 483 ~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpERa~yieFskPfkYqGitILeKk~~r~Stl~ 562 (993)
T KOG4440|consen 483 VHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPERAQYIEFSKPFKYQGITILEKKEIRRSTLD 562 (993)
T ss_pred EEEeecccccceeeeecccccccceehhhhhhhhCCccceEeeceeeChhhhhheeccCcccccceEEEeeCCCCCchHH
Confidence 77776331 11 22379999999999999999999999999999999999999999999999988888899
Q ss_pred ccccCcchhHHHHHHHHHHHHHHHHHhhhcccCCC
Q 011629 433 AFLNPFTPKMWCVTGIFFLVVGVVVWILEHRLNDD 467 (481)
Q Consensus 433 ~~l~pf~~~~W~~~~~~~~~~~~~~~~~~~~~~~~ 467 (481)
+||+||+..+|++++++..+|++++|+++|+++.+
T Consensus 563 SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPFg 597 (993)
T KOG4440|consen 563 SFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPFG 597 (993)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCccc
Confidence 99999999999999999999999999999997764
No 3
>KOG1053 consensus Glutamate-gated NMDA-type ion channel receptor subunit GRIN2A and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=6.4e-44 Score=347.93 Aligned_cols=404 Identities=21% Similarity=0.387 Sum_probs=301.8
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhc--CCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEe
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEK--RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~--gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
+++|+++|+.|+|..+++|.+..+....+...+++...+. |+.+.-...+....+. .......++|+-++.||+++|
T Consensus 161 a~Vml~iL~~ydW~~Fs~vtt~~pg~~~f~~~ir~~~d~s~vgwe~i~v~~l~~s~~d-~~a~~q~qLkki~a~VillyC 239 (1258)
T KOG1053|consen 161 AQVMLKILEEYDWYNFSLVTTQFPGNRTFVSLIRQTNDNSHVGWEMINVLTLDPSTDD-LLAKLQAQLKKIQAPVILLYC 239 (1258)
T ss_pred HHHHHHHHHHcCcceeEEEEeecCchHHHHHHHHHhhhhccccceeeeeeecCCCCCc-hHHHHHHHHHhcCCcEEEEEe
Confidence 4689999999999999999988877677777777776653 6555444444333221 122333456666689999999
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCC
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTL 158 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~ 158 (481)
+.+++..|+..|.++||++++|+||.+...... + +.-...-.|.+.++.. .|+.
T Consensus 240 ~~eea~~IF~~A~q~Gl~g~~y~Wi~pqlv~g~-~------~~pa~~P~GLisv~~~------------~w~~------- 293 (1258)
T KOG1053|consen 240 SREEAERIFEEAEQAGLTGPGYVWIVPQLVEGL-E------PRPAEFPLGLISVSYD------------TWRY------- 293 (1258)
T ss_pred cHHHHHHHHHHHHhcCCcCCceEEEeehhccCC-C------CCCccCccceeeeecc------------chhh-------
Confidence 999999999999999999999999997644331 0 1112344566666432 2221
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccc--cccCccHHHHHHHHhcccCceee
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSV--SIFNGGKMLLDNILQVNMTGVTG 236 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~L~~~l~~v~f~g~sG 236 (481)
...+++-|+|-++|.|.+.++...+..+.. ..+|... .....+..|+++|.|+.|+| +
T Consensus 294 -------~l~~rVrdgvaiva~aa~s~~~~~~~lp~~-----------~~~C~~~~~~~~~~~~~l~r~l~NvT~~g--~ 353 (1258)
T KOG1053|consen 294 -------SLEARVRDGVAIVARAASSMLRIHGFLPEP-----------KMDCREQEETRLTSGETLHRFLANVTWDG--R 353 (1258)
T ss_pred -------hHHHHHhhhHHHHHHHHHHHHhhcccCCCc-----------ccccccccCccccchhhhhhhhheeeecc--c
Confidence 245789999999999999998876653322 1234221 12234788999999999998 6
Q ss_pred eEEEccCCCCCCCcEEEEEeec-CceEEEEEeeCCCCCcccCCccccCCCCCCCCCccccceeecCCCCCCCCCCccccC
Q 011629 237 PIKFTSDRDLINPAYEVINVIG-TGSRRIGYWSNHSGLSVVPPEALYKEPSNRSASSQHLYSAVWPGQTTQKPRGWVFPN 315 (481)
Q Consensus 237 ~v~Fd~~Gd~~~~~y~I~~~~~-~~~~~VG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~W~~~~~~~P~s~~~~~ 315 (481)
.++|+++|-.++...-++.+.. ..|..||.|.... | .++--+||... ..+ ++.+
T Consensus 354 ~lsf~~~g~~v~p~lvvI~l~~~r~We~VG~We~~~-L--------------------~M~y~vWPr~~-~~~--q~~~- 408 (1258)
T KOG1053|consen 354 DLSFNEDGYLVHPNLVVIDLNRDRTWERVGSWENGT-L--------------------VMKYPVWPRYH-KFL--QPVP- 408 (1258)
T ss_pred ceeecCCceeeccceEEEecCCCcchheeceecCCe-E--------------------EEecccccccc-Ccc--CCCC-
Confidence 8999999987777777776654 4799999998642 3 34445677321 111 1212
Q ss_pred CCceEEEeecCCCCCcCcEEecC----------------------------C----CCeEEeeeHHHHHHHHHHCCCccc
Q 011629 316 NGRHLRIGVPSQVIYPEFVAQGK----------------------------G----TDKFSGYCIDVFTAVLELLPYAVP 363 (481)
Q Consensus 316 ~~~~l~v~~~~~~~~~p~~~~~~----------------------------~----~~~~~G~~~dl~~~ia~~l~~~~~ 363 (481)
+..+|+|++.. .+||+...+ . +.|++||||||++.||+..||+
T Consensus 409 d~~HL~VvTLe---E~PFVive~vDP~t~~C~~ntvpc~s~~~~t~ss~~~~~~tvKkCCkGfCIDiLkKlA~~v~Ft-- 483 (1258)
T KOG1053|consen 409 DKLHLTVVTLE---ERPFVIVEDVDPLTQTCVRNTVPCRSQLNSTFSSGDEANRTVKKCCKGFCIDILKKLARDVKFT-- 483 (1258)
T ss_pred CcceeEEEEec---cCCeEEEecCCCCcCcCCCCCCcchhhhhhccCCCccCCchHHhhhhhhhHHHHHHHHhhcCcc--
Confidence 34578887774 466665421 0 3478999999999999999988
Q ss_pred EEEEeCCCCC----CCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCCCCcCccccccCcc
Q 011629 364 YKLVPFGDGH----NSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 364 ~~~~~~~~~~----~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
|.++.+++|+ .|+.|+|||++|..+++||+++++++++||.+.||||.||..+|+++||++.+...+.-+||.||+
T Consensus 484 YDLYlVtnGKhGkk~ng~WnGmIGev~~~rA~MAVgSltINeeRSevVDFSvPFveTgIsVmV~rsngtvspsAFLePfs 563 (1258)
T KOG1053|consen 484 YDLYLVTNGKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEERSEVVDFSVPFVETGISVMVARSNGTVSPSAFLEPFS 563 (1258)
T ss_pred eEEEEecCCcccceecCcchhhHHHHHhhhhheeeeeeEechhhhccccccccccccceEEEEEecCCccCchhhcCCcc
Confidence 6666666665 788999999999999999999999999999999999999999999999999888889999999999
Q ss_pred hhHHHHHHHHHHHH-HHHHHhhhcccCCC---------CCCCcccccccccC
Q 011629 440 PKMWCVTGIFFLVV-GVVVWILEHRLNDD---------FRGPPRRQIGTILW 481 (481)
Q Consensus 440 ~~~W~~~~~~~~~~-~~~~~~~~~~~~~~---------~~~~~~~~~~~~~w 481 (481)
+.+|+.|++++++| ++++|+||++++-. -+|.+.++||+++|
T Consensus 564 ~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp~Ftigkaiw 615 (1258)
T KOG1053|consen 564 PSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGPSFTIGKAIW 615 (1258)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCcccccccccCCCCCCCcceehhhHHH
Confidence 99999999998755 66888999887543 24557889999988
No 4
>cd06390 PBP1_iGluR_AMPA_GluR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=4.7e-35 Score=282.67 Aligned_cols=256 Identities=18% Similarity=0.276 Sum_probs=208.9
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
++|+++|+++|||++|++||++ +||...++.|.+.+++.|+||.....++.. .+++..+|++|++.++|+||++|++
T Consensus 105 ~~Ai~diI~~~~W~~v~iIYd~-d~g~~~lq~l~~~~~~~~~~I~~~~~~~~~--~~d~~~~L~~ik~~~~rvIVl~~~~ 181 (364)
T cd06390 105 QDALISVIEHYKWQKFVYIYDA-DRGLSVLQKVLDTAAEKNWQVTAVNILTTT--EEGYRKLFQDLDKKKERLIVVDCES 181 (364)
T ss_pred HHHHHHHHHHcCCcEEEEEEeC-CccHHHHHHHHHhhhccCceeeEEEeecCC--hHHHHHHHHhccccCCeEEEEECCH
Confidence 4799999999999999999954 599999999999999999999987766533 4489999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccC-CCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRN-TLN 159 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~-~~~ 159 (481)
+.+..+|.++.+.+|+..+|+||+++......+. ..+.....|+++|++..+..+.+++|..+|++....+ +..
T Consensus 182 ~~~~~~L~~a~~~~~~~~gy~wI~t~l~~~~~~~-----~~~~~~~~nitg~r~~~~~~~~~~~~~~~w~~~~~~~~~~~ 256 (364)
T cd06390 182 ERLNAILNQIIKLEKNGIGYHYILANLGFMDIDL-----TKFRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRV 256 (364)
T ss_pred HHHHHHHHHHHHhhccCCceEEEecCCCcccccH-----HHHhcCCcCceEEEEecCCCHHHHHHHHHHHhhccccCCCC
Confidence 9999999999888888999999999833222221 3455678899999999999999999999998765432 222
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccc--cccccCccHHHHHHHHhcccCceeee
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFS--SVSIFNGGKMLLDNILQVNMTGVTGP 237 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~L~~~l~~v~f~g~sG~ 237 (481)
....+..+++++|||||++|+|++++.......+... ....|. ...+|+.|..|+++|++++|.|+||+
T Consensus 257 ~~~~~~~~~~l~yDaV~~~A~A~~~l~~~~~~~~~~~---------~~~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~ 327 (364)
T cd06390 257 DWKRPKYTSALTYDGVRVMAEAFQNLRKQRIDISRRG---------NAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGN 327 (364)
T ss_pred CcCCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccCC---------CCCCCCCCCCCCCccHHHHHHHHHhhcccccccc
Confidence 2234567899999999999999999865433221110 111342 23358889999999999999999999
Q ss_pred EEEccCCCCCCCcEEEEEeecCceEEEEEeeCCCCC
Q 011629 238 IKFTSDRDLINPAYEVINVIGTGSRRIGYWSNHSGL 273 (481)
Q Consensus 238 v~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l 273 (481)
|.||++|+|.+..|+|+|+.+.++++||.|++..|+
T Consensus 328 i~F~~~G~r~~~~~~I~~~~~~g~~~vG~W~~~~g~ 363 (364)
T cd06390 328 VQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDEKL 363 (364)
T ss_pred eeeCCCCCcccceEEEEEecCCcceEEEEECCCCCc
Confidence 999999999999999999998899999999987654
No 5
>cd06365 PBP1_Pheromone_receptor Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptor, the GABAb receptor, the calcium-sensing receptor (CaSR), the T1R taste receptor, and a small group of uncharacterized orphan receptors.
Probab=100.00 E-value=6.5e-35 Score=292.41 Aligned_cols=249 Identities=15% Similarity=0.202 Sum_probs=198.4
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCCh--hHHHHHHHHhccCCceEEEEEe
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSR--NQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~--~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
++||+++++||||+||++|++|++||...++.|.+++++.|+||+..+.++..... .++..++++|+++++||||+++
T Consensus 160 ~~ai~~li~~f~W~~Vaiv~~d~~yg~~~~~~~~~~~~~~gi~I~~~~~i~~~~~~~~~~~~~~l~~i~~~~arvIvl~~ 239 (469)
T cd06365 160 PLGMVSLMLHFSWTWVGLVISDDDRGEQFLSDLREEMQRNGICLAFVEKIPVNMQLYLTRAEKYYNQIMTSSAKVIIIYG 239 (469)
T ss_pred HHHHHHHHHhcCCeEEEEEEecChhHHHHHHHHHHHHHHCCeEEEEEEEecCCchhhHHHHHHHHHHhhcCCCeEEEEEc
Confidence 47999999999999999999999999999999999999999999999999865432 3678899999999999999999
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHH-----------
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVT----------- 147 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~----------- 147 (481)
..+.+..++.++.+.+ +.+++||+++.|....... ....+.++|++++.+.....++|++|++
T Consensus 240 ~~~~~~~l~~~~~~~~--~~~~~wi~s~~w~~~~~~~----~~~~~~~~G~lg~~~~~~~~~~f~~fl~~l~~~~~~~np 313 (469)
T cd06365 240 DTDSLLEVSFRLWQYL--LIGKVWITTSQWDVTTSPK----DFTLNSFHGTLIFSHHHSEIPGFKDFLQTVNPSKYPEDI 313 (469)
T ss_pred CcHHHHHHHHHHHHhc--cCceEEEeecccccccccc----ccccceeeEEEEEEeccCcCcchHHHhhccCcccCCCcc
Confidence 9988888877777654 4579999999886543221 2345778999999999988999999875
Q ss_pred ----HHhhhhc------------cCCCCCCCC----------CChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccc
Q 011629 148 ----RWRHLTR------------RNTLNGPIG----------LNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLS 201 (481)
Q Consensus 148 ----~~~~~~~------------~~~~~~~~~----------~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~ 201 (481)
.|+..|+ .|+.++.+. ....++++|||||++|||||+++.|.....
T Consensus 314 w~~efwe~~f~c~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~v~dAVya~AhALh~~l~c~~~~~-------- 385 (469)
T cd06365 314 FLEKLWWIYFNCSLSKSSCKTLKNCLSNASLEWLPLHYFDMAMSEESYNVYNAVYAVAHALHEMLLQQVETQ-------- 385 (469)
T ss_pred HHHhhHhHhcCcccCcCCccccCCCCCCccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHhhccCC--------
Confidence 3555442 143332221 234678999999999999999998854311
Q ss_pred cccCCCcccccccccCccHHHHHHHHhcccCceee-eEEEccCCCCCCCcEEEEEeec--C---ceEEEEEeeCC
Q 011629 202 ELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTG-PIKFTSDRDLINPAYEVINVIG--T---GSRRIGYWSNH 270 (481)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG-~v~Fd~~Gd~~~~~y~I~~~~~--~---~~~~VG~~~~~ 270 (481)
. ..+|. ....+ +++|+++|++++|.|.+| +|.||++||+. +.|+|+|||. + .+++||.|++.
T Consensus 386 ---~-~~~~~-~~~~~-~~~l~~~l~~v~F~~~~g~~v~Fd~nGd~~-~~YdI~n~q~~~~~~~~~~~VG~~~~~ 453 (469)
T cd06365 386 ---S-ENNGK-RLIFL-PWQLHSFLKNIQFKNPAGDEVNLNQKRKLD-TEYDILNYWNFPQGLGLKVKVGEFSPQ 453 (469)
T ss_pred ---C-cCCCC-CCCcc-HHHHHHHHHhccccCCCCCEEEecCCCCcC-ceeeEEEEEECCCCCEEEEEEEEEeCC
Confidence 0 11232 23344 899999999999999999 79999999985 8999999983 2 47999999863
No 6
>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-33 Score=295.61 Aligned_cols=354 Identities=34% Similarity=0.641 Sum_probs=284.9
Q ss_pred HHHhccCCceEEEEEeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhH
Q 011629 63 LLTVSSMMSRILILHTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEK 142 (481)
Q Consensus 63 l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~ 142 (481)
+.+++....+++++.+.+..+..++.+|.++||...+|+||.++......+.... ....+...+.+.+..+.+.....
T Consensus 6 ~~~~~~~~~~~~v~~~~~~~~~~~~~~a~~~~~~~~~~~~i~t~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~s~~~ 83 (656)
T KOG1052|consen 6 LLKLKAMRTRVFVLHMFPILALAIFSQAEELGMMQFGYVWILTNLLTDALDLDEL--YSLIDVMNGVLGLRGHIPRSELL 83 (656)
T ss_pred HHHhhccCceEEEEeCCHHHHHHHHHHHHHhCccccCeEEEEEecchhhhccccc--ccchhheeeEEeeccCCCccHHH
Confidence 4455556788999988888899999999999999999999999876555444221 33456677888888877888888
Q ss_pred HHHHHHHhhhhccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHH
Q 011629 143 RKFVTRWRHLTRRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKML 222 (481)
Q Consensus 143 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L 222 (481)
++|..+|+.. ......++..+||+++++|.|.+.+... ... ..+|.+...+..+..+
T Consensus 84 ~~~~~~~~~~--------~~~~~~~~~~~~D~~~~~a~~~~~~~~~-~~~--------------~~~~~~~~~~~~~~~~ 140 (656)
T KOG1052|consen 84 QNFVTRWQTS--------NVELLVYALWAYDAIQALARAVESLLNI-GNL--------------SLSCGRNNSWLDALGV 140 (656)
T ss_pred HHHHHHHhhc--------cccccchhhHHHHHHHHHHHHHHHhhcC-CCC--------------ceecCCCCcccchhHH
Confidence 8888888754 1123457899999999999999987641 111 1234433345557888
Q ss_pred HHHHHhcccCc---eeeeEEEccCCCCCCCcEEEEEeecCceEEEEEeeCCCCCcccCCccccCCCCCCCCCccccceee
Q 011629 223 LDNILQVNMTG---VTGPIKFTSDRDLINPAYEVINVIGTGSRRIGYWSNHSGLSVVPPEALYKEPSNRSASSQHLYSAV 299 (481)
Q Consensus 223 ~~~l~~v~f~g---~sG~v~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~ 299 (481)
.++++.....+ .++.+.++.++.+....|+|+|....+...||.|.+..+ ..|.
T Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~n~~~~~~~~ig~W~~~~~-----------------------~~i~ 197 (656)
T KOG1052|consen 141 FNFGKKLLVVNLSGVTGQFQFFRGGLLEYFKYEILNLNGSGERRIGYWYPRGG-----------------------ENIS 197 (656)
T ss_pred HHHHHhhhhhccccceeEEEecCCCccccceEEEEEecCcCceeEEEecCCCC-----------------------ceee
Confidence 88888865544 456778877778878999999998887888999997532 3688
Q ss_pred cCCCCCCCCCCccccCCCceEEEeecCCCCCcCcEEecC------CCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCC
Q 011629 300 WPGQTTQKPRGWVFPNNGRHLRIGVPSQVIYPEFVAQGK------GTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGH 373 (481)
Q Consensus 300 W~~~~~~~P~s~~~~~~~~~l~v~~~~~~~~~p~~~~~~------~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~ 373 (481)
|++.....|+.+..+.++++++|++.. .+||....+ +++++.|+|+||++++++++||++++..++.+.|.
T Consensus 198 ~~~~~~~~~~~~~~~~~~~~l~v~~~~---~~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~ 274 (656)
T KOG1052|consen 198 WPGKDYFVPKGWFFPTNGKPLRVGVVT---EPPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGS 274 (656)
T ss_pred ccCCcccCcCCccccCCCceEEEEEec---cCCceeeeecccccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCCCC
Confidence 999888899888877788999999995 455655433 35689999999999999999999888777765544
Q ss_pred --CCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCCCCcCccccccCcchhHHHHHHHHHH
Q 011629 374 --NSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFTPKMWCVTGIFFL 451 (481)
Q Consensus 374 --~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~~~~W~~~~~~~~ 451 (481)
.+++|+|++++|.+|++|++ ++++++++|++++|||.||++.+++++++++......+.|++||+..+|++++++++
T Consensus 275 ~~~~g~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~~~~fl~Pf~~~vW~~i~~~~l 353 (656)
T KOG1052|consen 275 RDPNGNWDGLVGQLVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSKLWNFLAPFSPEVWLLILASLL 353 (656)
T ss_pred CCCCCChhHHHHHHhcCccccc-cceEEeecccccEEeccceEeccEEEEEEecCCcccceEEecCCcHHHHHHHHHHHH
Confidence 34799999999999999999 899999999999999999999999999998884434899999999999999999999
Q ss_pred HHHHHHHhhhcccCCCC
Q 011629 452 VVGVVVWILEHRLNDDF 468 (481)
Q Consensus 452 ~~~~~~~~~~~~~~~~~ 468 (481)
++++++|+++|+.+.+|
T Consensus 354 ~~~~~~~~~~~~~~~~~ 370 (656)
T KOG1052|consen 354 LVGLLLWILERLSPYEL 370 (656)
T ss_pred HHHHHHHHHhccccccC
Confidence 99999999999988898
No 7
>cd06364 PBP1_CaSR Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. CaSR provides feedback control of extracellular calcium homeostasis by responding sensitively to acute fluctuations in extracellular ionized Ca2+ concentration. This ligand-binding domain has homology to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). CaSR is widely expressed in mammalian tissues and is active in tissues that are not directly involved in extracellular calcium homeostasis. Moreover, CaSR responds to aromatic, aliphatic, and polar amino acids, but not to positively charged or branched chain amino acids, which suggests that changes in plasma amino acid levels are likely to modulate whole body calci
Probab=100.00 E-value=3.9e-34 Score=288.60 Aligned_cols=252 Identities=18% Similarity=0.312 Sum_probs=202.1
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
++|+++++++|||+||++|+.|++||...++.|++.+++.|+||++.+.++...+..++..++++|++++++|||+++..
T Consensus 175 ~~Ai~~l~~~f~wk~VaiI~~dd~yG~~~~~~~~~~~~~~Gi~I~~~~~i~~~~~~~d~~~~l~klk~~~a~vVvl~~~~ 254 (510)
T cd06364 175 ATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFREEAEERDICIDFSELISQYSDEEEIQRVVEVIQNSTAKVIVVFSSG 254 (510)
T ss_pred HHHHHHHHHHcCCeEEEEEEecCcchHHHHHHHHHHHHHCCcEEEEEEEeCCCCCHHHHHHHHHHHHhcCCeEEEEEeCc
Confidence 36899999999999999999999999999999999999999999999888764455688999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHH-------------
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVT------------- 147 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~------------- 147 (481)
.++..++++|.++|+. +++||+++.|....... .....+.+.|++++.+.....++|++|+.
T Consensus 255 ~~~~~ll~qa~~~g~~--~~iwI~s~~w~~~~~~~---~~~~~~~~gg~lg~~~~~~~i~~f~~~l~~l~p~~~~~~~~~ 329 (510)
T cd06364 255 PDLEPLIKEIVRRNIT--GKIWLASEAWASSSLIA---MPEYFDVMGGTIGFALKAGQIPGFREFLQKVHPKKSSHNGFA 329 (510)
T ss_pred HHHHHHHHHHHHhCCC--CcEEEEEchhhcccccc---cCCccceeeEEEEEEECCCcCccHHHHHHhCCcccCCCChHH
Confidence 9999999999999875 57999999886543221 13455788999999999888888888875
Q ss_pred --HHhhhhc-----------------------------------cCCCCCCCC----------CChhHHHHHHHHHHHHH
Q 011629 148 --RWRHLTR-----------------------------------RNTLNGPIG----------LNSFGLYAYDTLWLLAH 180 (481)
Q Consensus 148 --~~~~~~~-----------------------------------~~~~~~~~~----------~~~~~~~~ydAV~~~a~ 180 (481)
.|+..++ .|.+.+.+. ...+++++|||||++||
T Consensus 330 ~~~we~~f~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~AVyAvAh 409 (510)
T cd06364 330 KEFWEETFNCYLEDSPKNALPVDTFLGHEESGDDSENGSTAFRPLCTGDENIASVETPYLDYTHLRISYNVYLAVYSIAH 409 (510)
T ss_pred HHHHHHhcCCCCCCCcccccccccccccccccccccccccccCCCCCChhhhcccCCccccccchhhHHHHHHHHHHHHH
Confidence 3554442 122222211 13457889999999999
Q ss_pred HHHhhhhcCCC-ccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceee-eEEEccCCCCCCCcEEEEEeec
Q 011629 181 AIGAFFDQGGN-ISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTG-PIKFTSDRDLINPAYEVINVIG 258 (481)
Q Consensus 181 Al~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG-~v~Fd~~Gd~~~~~y~I~~~~~ 258 (481)
|||+|+.|... .+..+ ..|......+ +++|+++||+++|+|.+| +|.||++||.. +.|||+||+.
T Consensus 410 aLh~~~~c~~~~~~~~~-----------~~c~~~~~~~-~~~l~~~L~~v~F~~~~g~~v~Fd~~Gd~~-~~YdI~n~q~ 476 (510)
T cd06364 410 ALQDIYTCTPGKGLFTN-----------GSCADIKKVE-AWQVLKHLRHLNFTDNMGEQVRFDEGGDLV-GNYSIINWHL 476 (510)
T ss_pred HHHHHhcCCCCCCCccC-----------CCCCCCCCCC-HHHHHHHHHhcEEecCCCCEEEEecCCCCc-cceeEEEeee
Confidence 99999988642 21111 1355444455 899999999999999998 89999999985 8999999993
Q ss_pred ---C---ceEEEEEeeCC
Q 011629 259 ---T---GSRRIGYWSNH 270 (481)
Q Consensus 259 ---~---~~~~VG~~~~~ 270 (481)
+ .+++||.|++.
T Consensus 477 ~~~~~~~~~v~VG~~~~~ 494 (510)
T cd06364 477 SPEDGSVVFKEVGYYNVY 494 (510)
T ss_pred cCCCCcEEEEEEEEEcCC
Confidence 2 37999999863
No 8
>cd06375 PBP1_mGluR_groupII Ligand binding domain of the group II metabotropic glutamate receptor. Ligand binding domain of the group II metabotropic glutamate receptor, a family that contains mGlu2R and mGlu3R, all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes
Probab=100.00 E-value=1.4e-33 Score=281.62 Aligned_cols=247 Identities=19% Similarity=0.326 Sum_probs=199.2
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc-CCceEEEEEeC
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS-MMSRILILHTY 79 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~-s~~~vIvl~~~ 79 (481)
++||+++++||||+||++|+++++||...++.|++++++.|+||+..+.++......++..++++|++ ++++|||+++.
T Consensus 162 a~ai~~ll~~~~W~~Vaii~~~~~yG~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~l~~~~~a~vVvl~~~ 241 (458)
T cd06375 162 AKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATSEKVGRSADRKSYDSVIRKLLQKPNARVVVLFTR 241 (458)
T ss_pred HHHHHHHHHHCCCeEEEEEEeCchHHHHHHHHHHHHHHHCCeeEEEEEEecCCCCHHHHHHHHHHHhccCCCEEEEEecC
Confidence 36899999999999999999999999999999999999999999999988765555689999999875 68999999999
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHH------------
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVT------------ 147 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~------------ 147 (481)
..++..++++|.++|+. ++||+++.|....... ......+.|++++.+.....++|++|++
T Consensus 242 ~~~~~~ll~~a~~~g~~---~~wigs~~~~~~~~~~----~~~~~~~~G~i~~~~~~~~i~~f~~yl~~l~p~~~~~n~w 314 (458)
T cd06375 242 SEDARELLAAAKRLNAS---FTWVASDGWGAQESIV----KGSEDVAEGAITIELASHPIPDFDRYFQSLTPETNTRNPW 314 (458)
T ss_pred hHHHHHHHHHHHHcCCc---EEEEEeccccccchhh----hccchhhceEEEEEeccccchhHHHHHHhCCcCcCCCCcH
Confidence 99999999999999874 8999999886432211 2234568899999999999999999885
Q ss_pred ---HHhhhhc-----------cCCCCCCC------CCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCC
Q 011629 148 ---RWRHLTR-----------RNTLNGPI------GLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGD 207 (481)
Q Consensus 148 ---~~~~~~~-----------~~~~~~~~------~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~ 207 (481)
.|+..|+ .|++.+.+ .....++++|||||++|||||+|+.+..... .
T Consensus 315 ~~e~w~~~f~c~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~v~~AVyA~AhaLh~~l~~~c~~~-------------~ 381 (458)
T cd06375 315 FKDFWEQKFQCSLQNRDCANTTTNDKERLLDKVNYEQESKIMFVVNAVYAMAHALHNMQRDLCPNT-------------T 381 (458)
T ss_pred HHHHHHHHcCCCCCCCCccCCCCCchhcccccCcccccchHHHHHHHHHHHHHHHHHHHHhcCCCC-------------C
Confidence 4665553 13322222 1244689999999999999999997544311 0
Q ss_pred cccccccccCccHHHH-HHHHhcccC-----ceee-eEEEccCCCCCCCcEEEEEeec--C----ceEEEEEeeC
Q 011629 208 MRFSSVSIFNGGKMLL-DNILQVNMT-----GVTG-PIKFTSDRDLINPAYEVINVIG--T----GSRRIGYWSN 269 (481)
Q Consensus 208 ~~~~~~~~~~~~~~L~-~~l~~v~f~-----g~sG-~v~Fd~~Gd~~~~~y~I~~~~~--~----~~~~VG~~~~ 269 (481)
..|.....++ +++|+ ++|++++|. |.+| +|.||++||.. +.|||+||+. + .+++||.|+.
T Consensus 382 ~~c~~~~~~~-~~~l~~~~L~~v~F~~~~~~~~~g~~v~Fd~nGd~~-~~YdI~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 382 KLCDAMKPLD-GKKLYKEYLLNVSFTAPFRPDLADSEVKFDSQGDGL-GRYNIFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred CCCCCCCCCC-HHHHHHHHHHhccccccccCCCCCCeeEECCCCCCC-cceEEEEEEEcCCCCcEEEEEEEEEec
Confidence 1355544466 89999 599999999 9998 89999999985 8999999993 2 2689999963
No 9
>cd06387 PBP1_iGluR_AMPA_GluR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=4.1e-33 Score=268.50 Aligned_cols=257 Identities=16% Similarity=0.235 Sum_probs=206.7
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.+|+++|++||||++|.+|| |+++|...++.|.+.+...++.|......+.. +..++..++++|++.+.|+||+.|++
T Consensus 112 ~~Ai~diI~~~~Wr~~~~iY-d~d~gl~~Lq~L~~~~~~~~~~V~~~~v~~~~-~~~~~~~~l~el~~~~~r~iIld~s~ 189 (372)
T cd06387 112 KGAILSLLAHYKWEKFVYLY-DTERGFSILQAIMEAAVQNNWQVTARSVGNIK-DVQEFRRIIEEMDRRQEKRYLIDCEV 189 (372)
T ss_pred HHHHHHHHHhcCCCEEEEEe-cCchhHHHHHHHHHhhccCCceEEEEEeccCC-chHHHHHHHHHhccccceEEEEECCH
Confidence 36999999999999999999 77889999999999999999998776544433 34478899999999999999999999
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhcc-CCCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRR-NTLN 159 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~ 159 (481)
+.+..+|++|.++||+..+|+||+++......+. .++.....++++|++..+..+..++|.++|++.... .++.
T Consensus 190 ~~~~~il~~a~e~gM~~~~y~~ilt~ld~~~~dl-----~~~~~g~~NItg~rl~~~~~~~~~~f~~~w~~~~~~~~~~~ 264 (372)
T cd06387 190 ERINTILEQVVILGKHSRGYHYMLANLGFTDISL-----ERVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEA 264 (372)
T ss_pred HHHHHHHHHHHHcCccccceEEEEecCCcccccH-----HHhccCCcceeEEEEecCCCchHHHHHHHHHhCCcccCCCC
Confidence 9999999999999999999999999744333332 233333445999999999999999999999876542 2222
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCccccc--ccccCccHHHHHHHHhcccCceeee
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSS--VSIFNGGKMLLDNILQVNMTGVTGP 237 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~L~~~l~~v~f~g~sG~ 237 (481)
....+..+++++||||+++|.|++++.......+.. +....|.. ..+|..|..|+++|++++|+|+||+
T Consensus 265 ~~~~l~~~~al~yDaV~~~A~A~~~l~~~~~~~~~~---------~~~~~C~~~~~~~W~~G~~l~~~ik~v~~~GLTG~ 335 (372)
T cd06387 265 KNSPLKYTSALTHDAILVIAEAFRYLRRQRVDVSRR---------GSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGN 335 (372)
T ss_pred CCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCcccC---------CCCCCcCCCCCCCccchHHHHHHHHhcccCCCccc
Confidence 223456789999999999999999875433221110 01113422 3468889999999999999999999
Q ss_pred EEEccCCCCCCCcEEEEEeecCceEEEEEeeCCCCC
Q 011629 238 IKFTSDRDLINPAYEVINVIGTGSRRIGYWSNHSGL 273 (481)
Q Consensus 238 v~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l 273 (481)
+.||++|.|.+..|+|+|+.+.++++||.|++..|+
T Consensus 336 i~F~~~G~R~~~~ldIinl~~~g~~kIG~W~~~~g~ 371 (372)
T cd06387 336 IQFDTYGRRTNYTIDVYEMKPSGSRKAGYWNEYERF 371 (372)
T ss_pred eeeCCCCCcccceEEEEEecCCCceeEEEECCCCCc
Confidence 999999999999999999998899999999987654
No 10
>cd06376 PBP1_mGluR_groupIII Ligand-binding domain of the group III metabotropic glutamate receptor. Ligand-binding domain of the group III metabotropic glutamate receptor, a family which contains mGlu4R, mGluR6R, mGluR7, and mGluR8; all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes.
Probab=100.00 E-value=1.9e-32 Score=275.30 Aligned_cols=249 Identities=21% Similarity=0.311 Sum_probs=197.4
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhcc-CCceEEEEEe
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSS-MMSRILILHT 78 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~-s~~~vIvl~~ 78 (481)
++|+++++++|||+||++|+++++||...++.|.+.+++. ++||+..+.++......++..++++|++ +++++||+++
T Consensus 160 ~~ai~~~i~~~~w~~Vaii~~~~~yg~~~~~~~~~~~~~~g~~~v~~~~~i~~~~~~~d~~~~l~~ik~~~~~~vIvl~~ 239 (463)
T cd06376 160 AQAMVDIVKALGWNYVSTLASEGNYGESGVEAFTQISREAGGVCIAQSIKIPREPRPGEFDKIIKRLLETPNARAVIIFA 239 (463)
T ss_pred HHHHHHHHHHcCCeEEEEEEeCChHHHHHHHHHHHHHHHcCCceEEEEEecCCCCCHHHHHHHHHHHhccCCCeEEEEec
Confidence 3689999999999999999999999999999999999987 5899887777655556689999999986 7999999999
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHH-----------
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVT----------- 147 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~----------- 147 (481)
...++..++++|.++|+.+ .++||.++.|....... ......+.|++++.+.....++|++|+.
T Consensus 240 ~~~~~~~ll~~a~~~~~~g-~~~wig~d~~~~~~~~~----~~~~~~~~G~~~~~~~~~~~~~F~~~~~~l~~~~~~~~~ 314 (463)
T cd06376 240 NEDDIRRVLEAAKRANQVG-HFLWVGSDSWGAKISPI----LQQEDVAEGAITILPKRASIEGFDAYFTSRTLENNRRNV 314 (463)
T ss_pred ChHHHHHHHHHHHhcCCcC-ceEEEEecccccccccc----ccCcceeeeEEEEEeccccchhHHHHHHhCCcccCCCCc
Confidence 9999999999999999763 59999999886543221 1223568899999998888899988875
Q ss_pred ----HHhhhhc---------------cCCCCCCCC------CChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCccccc
Q 011629 148 ----RWRHLTR---------------RNTLNGPIG------LNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSE 202 (481)
Q Consensus 148 ----~~~~~~~---------------~~~~~~~~~------~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~ 202 (481)
.|+..++ .|.+.+.+. ....++++|||||++|||||+++++....+.
T Consensus 315 ~~~~~w~~~f~c~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~v~dAVyaiA~ALh~l~~~~c~~~~-------- 386 (463)
T cd06376 315 WFAEFWEENFNCKLTISGSKKEDTDRKCTGQERIGRDSTYEQEGKVQFVIDAVYAMAHALHSMHKDLCPGYT-------- 386 (463)
T ss_pred HHHHHHHHhCCCcccCCCCccccccCcCcchhhccccCcccccchhHHHHHHHHHHHHHHHHHHHhhCCCCC--------
Confidence 5665442 122222221 1236889999999999999999865432110
Q ss_pred ccCCCcccccccccCccHHHHHHHHhcccCceee-eEEEccCCCCCCCcEEEEEeec-----CceEEEEEeeC
Q 011629 203 LSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTG-PIKFTSDRDLINPAYEVINVIG-----TGSRRIGYWSN 269 (481)
Q Consensus 203 ~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG-~v~Fd~~Gd~~~~~y~I~~~~~-----~~~~~VG~~~~ 269 (481)
..|......+ |++|+++|++++|+|.+| +|.||++|++. ..|+|.|++. .++++||.|++
T Consensus 387 -----~~C~~~~~~~-~~~l~~~L~~v~F~g~tg~~v~Fd~~G~~~-~~Ydi~n~q~~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 387 -----GVCPEMEPAD-GKKLLKYIRAVNFNGSAGTPVMFNENGDAP-GRYDIFQYQITNTSSPGYRLIGQWTD 452 (463)
T ss_pred -----CCCccCCCCC-HHHHHHHHHhCCccCCCCCeEEeCCCCCCC-CceEEEEEEecCCCceeEEEEEEECC
Confidence 1354433344 899999999999999999 89999999995 7899999993 26899999975
No 11
>cd06374 PBP1_mGluR_groupI Ligand binding domain of the group I metabotropic glutamate receptor. Ligand binding domain of the group I metabotropic glutamate receptor, a family containing mGlu1R and mGlu5R, all of which stimulate phospholipase C (PLC) hydrolysis. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes.
Probab=100.00 E-value=3.5e-32 Score=273.88 Aligned_cols=249 Identities=17% Similarity=0.270 Sum_probs=195.7
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc--CCceEEEEEe
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS--MMSRILILHT 78 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~--s~~~vIvl~~ 78 (481)
++|+++++++|||+||++|+++++||....+.|.+.+++.|+||+..+.++......++..++++|++ .+++||++++
T Consensus 174 ~~al~~l~~~~~W~~Vaii~~~~~yg~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~lk~~~~da~vvv~~~ 253 (472)
T cd06374 174 ARAMLDIVKRYNWTYVSAVHTEGNYGESGMEAFKELAAHEGLCIAHSDKIYSNAGEQSFDRLLRKLRSRLPKARVVVCFC 253 (472)
T ss_pred HHHHHHHHHHCCCcEEEEEEecchHHHHHHHHHHHHHHHCCeeEEEEEEecCCCchHHHHHHHHHHHhcCCCcEEEEEEe
Confidence 36899999999999999999999999999999999999999999999888655455689999999996 4678888888
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHH-----------
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVT----------- 147 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~----------- 147 (481)
....+..++++|.++|+. .+++||.++.|....... ....+...|++++.++....++|++|+.
T Consensus 254 ~~~~~~~~l~~a~~~g~~-~~~~wi~s~~~~~~~~~~----~~~~~~~~G~l~~~~~~~~~~~F~~~l~~l~~~~~~~~~ 328 (472)
T cd06374 254 EGMTVRGLLMAMRRLGVG-GEFQLIGSDGWADRDDVV----EGYEEEAEGGITIKLQSPEVPSFDDYYLKLRPETNTRNP 328 (472)
T ss_pred chHHHHHHHHHHHHhcCC-CceEEEEecccccchHhh----hcchhhhheeEEEEecCCCCccHHHHHHhCCcccCCCCh
Confidence 888899999999999985 568999999886532221 2234667999999998888888888764
Q ss_pred ----HHhhhhc---------------cCCCCCCCC----CChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCccccccc
Q 011629 148 ----RWRHLTR---------------RNTLNGPIG----LNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELS 204 (481)
Q Consensus 148 ----~~~~~~~---------------~~~~~~~~~----~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~ 204 (481)
.|+..+. .|++.+.+. ...+++++|||||++|+|||+++.+....+
T Consensus 329 ~~~~~w~~~f~c~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~vyDAVyaiA~ALh~~~~~~~~~~----------- 397 (472)
T cd06374 329 WFREFWQHRFQCRLPGHPQENPNYIKICTGNESLDEQYVQDSKMGFVINAIYAMAHGLHNMHQDLCPGH----------- 397 (472)
T ss_pred HHHHHHHHhcCCCcCCccCcCCccCCCCCCcccccccccccceeHHHHHHHHHHHHHHHHHHHhhCCCC-----------
Confidence 5655442 122222111 124567999999999999999986543211
Q ss_pred CCCcccccccccCccHHHHHHHHhcccCceee-eEEEccCCCCCCCcEEEEEeec-----CceEEEEEeeC
Q 011629 205 RGDMRFSSVSIFNGGKMLLDNILQVNMTGVTG-PIKFTSDRDLINPAYEVINVIG-----TGSRRIGYWSN 269 (481)
Q Consensus 205 ~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG-~v~Fd~~Gd~~~~~y~I~~~~~-----~~~~~VG~~~~ 269 (481)
...|+.....+ |.+|+++|++++|.|++| +|.||++|++. ..|+|+|++. ..+++||.|++
T Consensus 398 --~~~c~~~~~~~-~~~l~~~l~~v~F~g~tG~~v~Fd~~G~~~-~~ydI~n~~~~~~~~~~~~~VG~w~~ 464 (472)
T cd06374 398 --VGLCDAMKPID-GRKLLEYLLKTSFSGVSGEEVYFDENGDSP-GRYDIMNLQYTEDLRFDYINVGSWHE 464 (472)
T ss_pred --CCCCcCCCCCC-HHHHHHHHHhCcccCCCCCeEEEcCCCCCC-CceEEEEEEECCCCCEEEEEEEEEeC
Confidence 01244333344 899999999999999999 89999999996 7999999994 26899999985
No 12
>cd06379 PBP1_iGluR_NMDA_NR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore
Probab=100.00 E-value=6.5e-32 Score=264.94 Aligned_cols=217 Identities=22% Similarity=0.387 Sum_probs=181.9
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCC----EEEEEEecCCCCChhHHHHHHHHhccCCceEEEEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRC----RLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILH 77 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi----~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~ 77 (481)
+|+++++++|||++|++|+++++||...++.|++.+++.|+ ||+..+.++.. ..++...+++|++.++++||++
T Consensus 143 ~a~~~~l~~~~w~~vaii~~~~~~g~~~~~~~~~~~~~~g~~~~~~v~~~~~~~~~--~~d~~~~l~~ik~~~~~vIvl~ 220 (377)
T cd06379 143 DVWLEMLRSFKWNKVILLVSDDHEGRAAQKRFETLLEEREIEFKIKVEKVVEFEPG--EKNVTSLLQEAKELTSRVILLS 220 (377)
T ss_pred HHHHHHHHHcCCeEEEEEEEcCcchhHHHHHHHHHHHhcCCccceeeeEEEecCCc--hhhHHHHHHHHhhcCCeEEEEE
Confidence 68999999999999999999999999999999999999999 88888777654 3478999999999999999999
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCC
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNT 157 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~ 157 (481)
++..++..++++|.++||.+.+|+||+++.|... .....|++++++...
T Consensus 221 ~~~~~~~~l~~qa~~~g~~~~~~~wi~t~~~~~~-----------~~~~~g~~g~~~~~~-------------------- 269 (377)
T cd06379 221 ASEDDAAVIYRNAGMLNMTGEGYVWIVSEQAGAA-----------RNAPDGVLGLQLING-------------------- 269 (377)
T ss_pred cCHHHHHHHHHHHHHcCCCCCCEEEEEecccccc-----------ccCCCceEEEEECCC--------------------
Confidence 9999999999999999999889999999887322 133468888876432
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccc-cccCccHHHHHHHHhcccCceee
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSV-SIFNGGKMLLDNILQVNMTGVTG 236 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~L~~~l~~v~f~g~sG 236 (481)
..+++++|||||++|+||++++++.... .....|... .+|..|..|+++|++++|.|++|
T Consensus 270 -------~~~~~~~yDAV~~~A~Al~~~~~~~~~~------------~~~~~c~~~~~~~~~g~~l~~~l~~v~f~G~tg 330 (377)
T cd06379 270 -------KNESSHIRDAVAVLASAIQELFEKENIT------------EPPRECVGNTVIWETGPLFKRALMSSKYPGETG 330 (377)
T ss_pred -------CCHHHHHHHHHHHHHHHHHHHHcCCCCC------------CCCccccCCCCCCcchHHHHHHHHhCCcCCccC
Confidence 1256889999999999999987642211 001134332 24667999999999999999999
Q ss_pred eEEEccCCCCCCCcEEEEEeecCceEEEEEeeCC
Q 011629 237 PIKFTSDRDLINPAYEVINVIGTGSRRIGYWSNH 270 (481)
Q Consensus 237 ~v~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~ 270 (481)
+|.||++||+....|+|+|++..++++||.|++.
T Consensus 331 ~i~Fd~~Gd~~~~~~~I~~~~~~~~~~VG~w~~~ 364 (377)
T cd06379 331 RVEFNDDGDRKFANYDIMNIQNRKLVQVGLYNGD 364 (377)
T ss_pred ceEECCCCCccCccEEEEEecCCCceEeeEEcCc
Confidence 9999999999778999999999899999999863
No 13
>KOG1056 consensus Glutamate-gated metabotropic ion channel receptor subunit GRM2 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=2.4e-32 Score=275.51 Aligned_cols=273 Identities=19% Similarity=0.325 Sum_probs=223.4
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc-CCceEEEEEeC
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS-MMSRILILHTY 79 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~-s~~~vIvl~~~ 79 (481)
++||++++++|||+||+.++++++||+.+.++|+++.++.||||++.++++.....+.++.+++++.+ .++||||+++.
T Consensus 182 a~Am~~il~~f~W~yVstv~s~~dYGE~Gieaf~~~a~~~~iCIa~s~ki~~~~~~~~~~~~l~kl~~~~~a~vvV~F~~ 261 (878)
T KOG1056|consen 182 AQAMVDILKKFNWNYVSTVASEGDYGESGIEAFKEEAAERGICIAFSEKIYQLSIEQEFDCVLRKLLETPNARVVVVFCR 261 (878)
T ss_pred HHHHHHHHHHhCeeEeeehhcCccchhhhHHHHHHhHHhcCceEEehhhcccccchhHHHHHHHHHhhcCCCeEEEEecC
Confidence 47999999999999999999999999999999999999999999999888876666778889988877 89999999999
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHH------------
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVT------------ 147 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~------------ 147 (481)
.++++.++.+|.++++.+ .++||.++.|....+.. ........|++++.+..+..++|++|.+
T Consensus 262 ~~~~r~~~~aa~~~n~~g-~~~wiaSd~W~~~~~~~----~~~e~~a~g~i~i~l~~~~v~~F~~y~~s~~p~nn~~n~w 336 (878)
T KOG1056|consen 262 GEDARRLLKAARRANLTG-EFLWIASDGWASQNSPT----EAPEREAEGAITIKLASPQVPGFDRYFQSLHPENNRRNPW 336 (878)
T ss_pred cchHHHHHHHHHHhCCCc-ceEEEecchhhccCChh----hhhhhhhceeEEEEecCCcchhHHHHHHhcCccccccCcc
Confidence 999999999999988754 59999999998754432 2223477899999999999999999885
Q ss_pred ---HHhhhhc---------------cCCCCCCCC------CChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccc
Q 011629 148 ---RWRHLTR---------------RNTLNGPIG------LNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSEL 203 (481)
Q Consensus 148 ---~~~~~~~---------------~~~~~~~~~------~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~ 203 (481)
+|...+. .|++.+... ......+++||||++|+|||+|.++....
T Consensus 337 ~~e~w~~~f~C~l~~~~~~~~~~~~~Ct~~e~~~~~~~~~q~~k~~~Vi~aVya~A~aLh~m~~~lc~~----------- 405 (878)
T KOG1056|consen 337 FAEFWEDKFNCSLPNSAFKNENLIRLCTAVERITLDSAYEQDSKVQFVIDAVYAMAHALHNMHQDLCPG----------- 405 (878)
T ss_pred cchhhhhcccCCCCcccccchhhhhhcccchhhccccchhhhcccccHHHHHHHHHHHHHHHHHhhcCC-----------
Confidence 3444432 133333111 12246889999999999999999864321
Q ss_pred cCCCcccccccccCccHHHHHHHHhcccCceeeeEEEccCCCCCCCcEEEEEeec-C---ceEEEEEeeCCCCCcccCCc
Q 011629 204 SRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKFTSDRDLINPAYEVINVIG-T---GSRRIGYWSNHSGLSVVPPE 279 (481)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~Fd~~Gd~~~~~y~I~~~~~-~---~~~~VG~~~~~~~l~~~~~~ 279 (481)
....|+.....+ |++|++++++++|.+..|.+.||++||.. +.|+|++|+. + ....||+|+....
T Consensus 406 --~~~~C~~m~~~d-g~~L~~~l~~vnF~~~~~~v~Fd~~gD~~-~~y~I~~~~~~~~~~~y~~vg~w~~~~~------- 474 (878)
T KOG1056|consen 406 --TSGLCSAMKAID-GSLLLKYLLNVNFTGPAGSVRFDENGDGP-GRYDILNYQLTNGSYTYKEVGYWSEGLS------- 474 (878)
T ss_pred --ccccCcCccccC-HHHHHhhhheeEEecCCCceeecCCCCCc-cceeEEEeeccCCCccceeeeeeccccc-------
Confidence 112466666666 99999999999999999999999999995 9999999984 2 6899999997532
Q ss_pred cccCCCCCCCCCccccceeecCCCCCCCCCCccc
Q 011629 280 ALYKEPSNRSASSQHLYSAVWPGQTTQKPRGWVF 313 (481)
Q Consensus 280 ~~~~~~~~~~~~~~~~~~i~W~~~~~~~P~s~~~ 313 (481)
++...+.|.++..++|+|+|.
T Consensus 475 -------------l~i~~~~w~~~~~~v~~S~CS 495 (878)
T KOG1056|consen 475 -------------LNIEDLDWTTKPSGVPKSVCS 495 (878)
T ss_pred -------------ccceeeeeccCCCCCcccccc
Confidence 455688999998899999975
No 14
>cd06392 PBP1_iGluR_delta_1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdel
Probab=100.00 E-value=1.4e-31 Score=258.70 Aligned_cols=253 Identities=20% Similarity=0.281 Sum_probs=187.4
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCC-------hhHHHHHHHHhccCCceEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGS-------RNQIIDTLLTVSSMMSRIL 74 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~-------~~~~~~~l~~i~~s~~~vI 74 (481)
+|+++|+.||+|++|++|| |++||...++.|.+.+.+.+..|.... +....+ .+.....|.+++... |+|
T Consensus 127 ~Ai~dlV~~~~W~~v~~iY-D~d~gl~~lq~L~~~~~~~~~~I~~~~-v~~~~~~~~~~~l~~~~~~~L~~~~~~~-r~i 203 (400)
T cd06392 127 DVMLKLVTELRWQKFIVFY-DSEYDIRGLQSFLDQASRLGLDVSLQK-VDRNISRVFTNLFTTMKTEELNRYRDTL-RRA 203 (400)
T ss_pred HHHHHHHHhCCCcEEEEEE-ECcccHHHHHHHHHHHhhcCceEEEEE-cccCcchhhhhHHHHHHHhhhhhccccc-eEE
Confidence 5899999999999999999 889999999999999999999988654 321110 111233344444444 899
Q ss_pred EEEeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccce-eeEEEeeecCCchhHHHHH----HHH
Q 011629 75 ILHTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQ-GVLTLRMYTQSSEEKRKFV----TRW 149 (481)
Q Consensus 75 vl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~-g~l~~~~~~~~~~~~~~f~----~~~ 149 (481)
|+.|+++.+..+|++|.++||+..+|+||++++.....++ .++..... ++.+|+...+......+|. .+|
T Consensus 204 Vv~~s~~~~~~il~qA~~lgM~~~~y~wI~t~~~~~~~dl-----~~~~~g~~~niT~~r~~~~~~~~~~~~~~~~~~r~ 278 (400)
T cd06392 204 ILLLSPRGAQTFINEAVETNLASKDSHWVFVNEEISDTEI-----LELVHSALGRMTVIRQIFPLSKDNNQRCIRNNHRI 278 (400)
T ss_pred EEEcCcHHHHHHHHHHHHhCcccCCeEEEEecCCcccccH-----HHHhcccccceeeEEEecCCcHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999886654333 22223222 4556888766665454443 567
Q ss_pred hhhhccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCccc--ccccccCccHHHHHHHH
Q 011629 150 RHLTRRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRF--SSVSIFNGGKMLLDNIL 227 (481)
Q Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~L~~~l~ 227 (481)
++............+..+++++|||||++|+|+++++....... .....| ....+|+.|..|+++|+
T Consensus 279 ~~~~~~~~~~~~~~l~~~aalayDaV~~~A~Al~~ll~~~~~~~-----------~~~l~C~~~~~~~w~~G~~ll~~ik 347 (400)
T cd06392 279 SSLLCDPQEGYLQMLQVSNLYLYDSVLMLANAFHRKLEDRKWHS-----------MASLNCIRKSTKPWNGGRSMLETIK 347 (400)
T ss_pred HhhhcccccccccccchhHHHHHHHHHHHHHHHHHHhhccccCC-----------CCCCccCCCCCCCCCChHHHHHHHH
Confidence 64442211111113567899999999999999998764222111 112345 34667999999999999
Q ss_pred hcccCceeeeEEEccCCCCCCCcEEEEEee-----cCceEEEEEeeCCCCC
Q 011629 228 QVNMTGVTGPIKFTSDRDLINPAYEVINVI-----GTGSRRIGYWSNHSGL 273 (481)
Q Consensus 228 ~v~f~g~sG~v~Fd~~Gd~~~~~y~I~~~~-----~~~~~~VG~~~~~~~l 273 (481)
+++|+|+||+|.||++|+|.+..|+|+|+. +.+.++||+|++..||
T Consensus 348 ~v~f~GLTG~I~F~~~G~r~~~~ldIi~l~~~~~~g~g~~~iG~W~~~~gl 398 (400)
T cd06392 348 KGHITGLTGVMEFKEDGANPHVQFEILGTSYSETFGKDVRRLATWDSEKGL 398 (400)
T ss_pred hCCCccCccceeECCCCCCcCCceEEEeccccccCCCCceEeEEecCCCCC
Confidence 999999999999999999999999999975 3459999999998765
No 15
>cd06362 PBP1_mGluR Ligand binding domain of the metabotropic glutamate receptors (mGluR). Ligand binding domain of the metabotropic glutamate receptors (mGluR), which are members of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses. mGluRs bind to glutamate and function as an excitatory neurotransmitter; they are involved in learning, memory, anxiety, and the perception of pain. Eight subtypes of mGluRs have been cloned so far, and are classified into three groups according to their sequence similarities, transduction mechanisms, and pharmacological profiles. Group I is composed of mGlu1R and mGlu5R that both stimulate PLC hydrolysis. Group II includes mGlu2R and mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R, mGlu6R, mGlu7R, and mGlu8R, which form group III.
Probab=100.00 E-value=2.3e-31 Score=267.52 Aligned_cols=251 Identities=19% Similarity=0.280 Sum_probs=197.7
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc-CCceEEEEEeCc
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS-MMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~-s~~~vIvl~~~~ 80 (481)
+|+++++++|||+||++|+++++||....+.|.+.+++.|+||+..+.++......++..++++|++ ++++|||+++..
T Consensus 161 ~a~~~~l~~~~w~~vaii~~~~~~G~~~~~~~~~~~~~~gi~i~~~~~~~~~~~~~d~~~~l~~l~~~~~a~viil~~~~ 240 (452)
T cd06362 161 QAMVDIVKAFNWTYVSTVASEGNYGEKGIEAFEKLAAERGICIAGSEKIPSSATEEEFDNIIRKLLSKPNARVVVLFCRE 240 (452)
T ss_pred HHHHHHHHHCCCcEEEEEEeCCHHHHHHHHHHHHHHHHCCeeEEEEEEcCCCCCHHHHHHHHHHHhhcCCCeEEEEEcCh
Confidence 6899999999999999999999999999999999999999999999888765455689999999987 579999999999
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHH-------------
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVT------------- 147 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~------------- 147 (481)
.++..++++|.++|+. .+++||.++.|....... ........|++++.+.....++|++|+.
T Consensus 241 ~~~~~~~~~a~~~g~~-~~~~~i~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~i~~f~~~l~~l~~~~~~~~~~~ 315 (452)
T cd06362 241 DDIRGLLAAAKRLNAE-GHFQWIASDGWGARNSVV----EGLEDVAEGAITIELQSAEVPGFDEYFLSLTPENNSRNPWF 315 (452)
T ss_pred HHHHHHHHHHHHcCCc-CceEEEEeccccccchhh----cccccccceEEEEEecccccccHHHHhhhCCcCcCCCChHH
Confidence 9999999999999986 568999999886542211 2334678899999888777777777652
Q ss_pred --HHhhhhc-------------cCCCCCC----CCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCc
Q 011629 148 --RWRHLTR-------------RNTLNGP----IGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDM 208 (481)
Q Consensus 148 --~~~~~~~-------------~~~~~~~----~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~ 208 (481)
.|+..+. .|+.... .....+++++|||||++|+|||+++.+..... ..
T Consensus 316 ~~~w~~~~~c~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~vyDAV~a~A~AL~~~l~~~~~~~-------------~~ 382 (452)
T cd06362 316 REFWEQKFNCKLTGNGSTKDNTCCTERILLLSNYEQESKVQFVIDAVYAMAHALHNMHRDLCPGT-------------TG 382 (452)
T ss_pred HHHHHHhcCCCcCCCCccccCCCCccccccccccccccchhHHHHHHHHHHHHHHHHHHhhCCCC-------------CC
Confidence 3444332 1211111 12344789999999999999999987543211 01
Q ss_pred ccccccccCccHHHHHHHHhcccCceee-eEEEccCCCCCCCcEEEEEeec----CceEEEEEeeCCCC
Q 011629 209 RFSSVSIFNGGKMLLDNILQVNMTGVTG-PIKFTSDRDLINPAYEVINVIG----TGSRRIGYWSNHSG 272 (481)
Q Consensus 209 ~~~~~~~~~~~~~L~~~l~~v~f~g~sG-~v~Fd~~Gd~~~~~y~I~~~~~----~~~~~VG~~~~~~~ 272 (481)
.|......+ +++|+++|++++|.|++| .|.||++||+. +.|+|+|++. ..+++||.|++..+
T Consensus 383 ~c~~~~~~~-~~~l~~~l~~v~f~g~tg~~v~Fd~~G~~~-~~y~I~~~~~~~~~~~~~~VG~w~~~~~ 449 (452)
T cd06362 383 LCDAMKPID-GRKLLFYLRNVSFSGLAGGPVRFDANGDGP-GRYDIFNYQRTNGKYDYVKVGSWKGELS 449 (452)
T ss_pred CCcCccCCC-HHHHHHHHHhCCcCCCCCceEEECCCCCCC-CceEEEEEEEcCCceEEEEEEEEecccc
Confidence 244333344 999999999999999998 89999999996 8999999984 36899999987644
No 16
>cd06391 PBP1_iGluR_delta_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related to non-NMDA receptors. GluRdelta2 was shown to function as a
Probab=100.00 E-value=9.6e-31 Score=255.41 Aligned_cols=255 Identities=19% Similarity=0.292 Sum_probs=193.6
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCC---hhHHHH-HHHHhcc--CCceEEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGS---RNQIID-TLLTVSS--MMSRILI 75 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~---~~~~~~-~l~~i~~--s~~~vIv 75 (481)
+|+++|++||||++|++++ |+++|...++.|.+.+++.|+||+... +..... ...+.. .+++|++ +++|+||
T Consensus 127 ~ai~~li~~f~W~~v~i~~-d~~~~~~~l~~l~~~~~~~~i~I~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~rviV 204 (400)
T cd06391 127 DVILRVVTEYAWQKFIIFY-DTDYDIRGIQEFLDKVSQQGMDVALQK-VENNINKMITGLFRTMRIEELNRYRDTLRRAI 204 (400)
T ss_pred HHHHHHHHHcCCcEEEEEE-eCCccHHHHHHHHHHHHHcCCeEEEEe-cCcchhhhhHHHHHHHHHHHHHhhcccccEEE
Confidence 6999999999999999865 677889999999999999999999743 222111 011222 3456665 6689999
Q ss_pred EEeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhcc
Q 011629 76 LHTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRR 155 (481)
Q Consensus 76 l~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~ 155 (481)
++++++.+..+|++|.++||++.+|+||++++.....+.. +.....+.|+.+++++.+....+.+|..+|...+..
T Consensus 205 l~~~~~~~~~ll~~a~~~gm~~~~y~wi~t~~~~~~~dl~----~~~~~~~~~v~~~r~~~~~~~~~~~~~~r~~~~~~~ 280 (400)
T cd06391 205 LVMNPATAKSFITEVVETNLVAFDCHWIIINEEISDMDVQ----ELVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISS 280 (400)
T ss_pred EECCcHHHHHHHHHHHHcCCCCCCeEEEEeCccccccccc----hHHhcccceEEEeccCCchHHHHHHHHHHHhhhccc
Confidence 9999999999999999999999999999999877666552 222344567777877766667778888888775531
Q ss_pred --C-CCCC-CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCccccc--ccccCccHHHHHHHHhc
Q 011629 156 --N-TLNG-PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSS--VSIFNGGKMLLDNILQV 229 (481)
Q Consensus 156 --~-~~~~-~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~L~~~l~~v 229 (481)
+ +..+ ...+..+++++||||+++|.|++++........ .....|.. ..+|..|..|+++|+++
T Consensus 281 ~~~~~~~~~~~~~~~~~alayDaV~~~A~A~~~l~~~~~~~~-----------~~~~~c~~~~~~~w~~G~~ll~~i~~~ 349 (400)
T cd06391 281 SLCDPKDPFAQMMEISNLYIYDTVLLLANAFHKKLEDRKWHS-----------MASLSCIRKNSKPWQGGRSMLETIKKG 349 (400)
T ss_pred cccCccccccccccchhhHHHHHHHHHHHHHHHHHhhccccC-----------CCCcccccCCCCCCCChHHHHHHHHhc
Confidence 1 1111 112456899999999999999998753221110 11123432 34688899999999999
Q ss_pred ccCceeeeEEEccCCCCCCCcEEEEEee-----cCceEEEEEeeCCCCC
Q 011629 230 NMTGVTGPIKFTSDRDLINPAYEVINVI-----GTGSRRIGYWSNHSGL 273 (481)
Q Consensus 230 ~f~g~sG~v~Fd~~Gd~~~~~y~I~~~~-----~~~~~~VG~~~~~~~l 273 (481)
+|+|+||++.||++|.|.+..|+|+|+. +.+.++||+|++..||
T Consensus 350 ~f~GlTG~i~f~~~g~r~~~~~dIin~~~~~~~~~g~rkiG~Ws~~~gl 398 (400)
T cd06391 350 GVSGLTGELEFNENGGNPNVHFEILGTNYGEDLGRGVRKLGCWNPITGL 398 (400)
T ss_pred CcccceeceEECCCCCccCCceEEEEeeccccCCCcceEEEEEcCCcCC
Confidence 9999999999999999999999999996 6689999999987664
No 17
>cd06367 PBP1_iGluR_NMDA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits
Probab=99.98 E-value=5.5e-31 Score=257.18 Aligned_cols=223 Identities=20% Similarity=0.296 Sum_probs=182.7
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCE--EEEEEecCCCCChhHHHHHHHHhccCCceEEEEEe
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCR--LSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~--v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
++|+++++++|||++|++||+++++|.+..+.|++.+++.|+| +.....++... ..++...+.++++.++++||++|
T Consensus 124 ~~ai~~ll~~~~w~~vaii~~~~~~g~~~~~~l~~~l~~~g~~~~i~~~~~~~~~~-~~~~~~~l~~l~~~~~~vivl~~ 202 (362)
T cd06367 124 ADVMLEILEEYDWHQFSVVTSRDPGYRDFLDRVETTLEESFVGWEFQLVLTLDLSD-DDGDARLLRQLKKLESRVILLYC 202 (362)
T ss_pred HHHHHHHHHHcCCeEEEEEEEcCcccHHHHHHHHHHHHhcccceeeeeeEEeccCC-CcchHHHHHHHHhcCCcEEEEeC
Confidence 3689999999999999999999999999999999999999999 77666665432 22678888899999999999999
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCC
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTL 158 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~ 158 (481)
+...+..++++|.++||..++|+||+++.|.... ........|++++++...
T Consensus 203 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~-------~~~~~~~~G~~g~~~~~~--------------------- 254 (362)
T cd06367 203 SKEEAERIFEAAASLGLTGPGYVWIVGELALGSG-------LAPEGLPVGLLGVGLDTW--------------------- 254 (362)
T ss_pred CHHHHHHHHHHHHHcCCCCCCcEEEECccccccc-------CCccCCCCeeEEEEeccc---------------------
Confidence 9999999999999999998899999999886421 122355679999976431
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccc--cCccHHHHHHHHhcccCceee
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSI--FNGGKMLLDNILQVNMTGVTG 236 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~L~~~l~~v~f~g~sG 236 (481)
..+++++||||+++|+|+++++++..... .+...|..... +..|..|+++|++++|.|.+|
T Consensus 255 ------~~~~~~~~Dav~~~a~Al~~~~~~~~~~~-----------~~~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg 317 (362)
T cd06367 255 ------YSLEARVRDAVAIVARAAESLLRDKGALP-----------EPPVNCYDTANKRESSGQYLARFLMNVTFDGETG 317 (362)
T ss_pred ------ccHHHHHHHHHHHHHHHHHHHHHhcCCCC-----------CCCCCcCCCCCCCCCchHHHHHHHhcccccCCCC
Confidence 12568899999999999999987532211 11123544322 556899999999999999999
Q ss_pred eEEEccCCCCCCCcEEEEEee-cCceEEEEEeeC
Q 011629 237 PIKFTSDRDLINPAYEVINVI-GTGSRRIGYWSN 269 (481)
Q Consensus 237 ~v~Fd~~Gd~~~~~y~I~~~~-~~~~~~VG~~~~ 269 (481)
+|.||++|++.+..|+|+|++ ..++++||.|++
T Consensus 318 ~v~F~~~G~~~~~~~~I~~l~~~~~~~~VG~W~~ 351 (362)
T cd06367 318 DVSFNEDGYLSNPKLVIINLRRNRKWERVGSWEN 351 (362)
T ss_pred ceeECCCcccccceEEEEEecCCCcceEEEEEcC
Confidence 999999999977899999999 678999999975
No 18
>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=99.98 E-value=2.2e-30 Score=251.94 Aligned_cols=258 Identities=20% Similarity=0.283 Sum_probs=199.0
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEe--cCCCCChhHHHHHHHHhccCCceEEEEEe
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVP--LSPKGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~--~~~~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
.+|+++++++|||++|++||+ +++|...++.|.+.+++.|+.|..... +.......++..+|++|+++++++||+.|
T Consensus 106 ~~ai~d~i~~~~wk~vailYd-sd~gl~~lq~l~~~~~~~g~~V~~~~~~~i~~~~~~~d~~~~L~~ik~~~~~~Iil~~ 184 (370)
T cd06389 106 KGALLSLIEYYQWDKFAYLYD-SDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDRKDEAYRSLFQDLENKKERRVILDC 184 (370)
T ss_pred hhHHHHHHHhcCCcEEEEEec-CchHHHHHHHHHHhhccCCceEEEEEeecCCCccchHHHHHHHHHhccccceEEEEEC
Confidence 368999999999999999996 569999999999999999987764432 22222344899999999999999999999
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhc-cCC
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTR-RNT 157 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~-~~~ 157 (481)
+.+.+..++++|.++||+.++|+||+++.-....++ ......-.++.+++......+..++|.+.|++... ..+
T Consensus 185 ~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l-----~~~~~~~~nitg~~~~~~~~~~v~~f~~~~~~~~~~~~~ 259 (370)
T cd06389 185 ERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDL-----SKIQFGGANVSGFQIVDYDDPLVSKFIQRWSTLEEKEYP 259 (370)
T ss_pred CHHHHHHHHHHHHHhCccccceEEEEccCCccccch-----hhhccCCcceEEEEEecCCCchHHHHHHHHHhcCccccC
Confidence 999999999999999999999999998642222222 11111223567887777778889999999986432 122
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccc--cccccCccHHHHHHHHhcccCcee
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFS--SVSIFNGGKMLLDNILQVNMTGVT 235 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~L~~~l~~v~f~g~s 235 (481)
+.....+...++++||||+++|.|++++.......... ++...|. ...+|..|..|.++|++++|+|+|
T Consensus 260 ~~~~~~~~~~aAl~yDAV~v~a~A~~~l~~~~~~~~~~---------~~~~~C~~~~~~~w~~G~~i~~~l~~~~~~GlT 330 (370)
T cd06389 260 GAHTKTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR---------GNAGDCLANPAVPWGQGVEIERALKQVQVEGLT 330 (370)
T ss_pred CCCCcCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccC---------CCCCCcCCCCCCCCCCcHHHHHHHHhcccCccc
Confidence 22223456689999999999999999875432211000 1111343 244687899999999999999999
Q ss_pred eeEEEccCCCCCCCcEEEEEeecCceEEEEEeeCCCCC
Q 011629 236 GPIKFTSDRDLINPAYEVINVIGTGSRRIGYWSNHSGL 273 (481)
Q Consensus 236 G~v~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l 273 (481)
|++.||++|+|.+..++|++++.+++++||.|++..|+
T Consensus 331 G~i~Fd~~G~r~~~~~~ii~l~~~g~~kvG~W~~~~~~ 368 (370)
T cd06389 331 GNIKFDQNGKRINYTINVMELKSNGPRKIGYWSEVDKM 368 (370)
T ss_pred cceEeCCCCccccceEEEEEecCCcceEEEEEcCCCCc
Confidence 99999999999877999999998899999999987664
No 19
>cd06388 PBP1_iGluR_AMPA_GluR4 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=99.98 E-value=2.8e-30 Score=250.68 Aligned_cols=254 Identities=18% Similarity=0.266 Sum_probs=197.7
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.|+++++++|||++|++||+ +++|...++.|.+.+++.|+.|......+.. ..|++.+|++|+.+++++||+.|+++
T Consensus 113 ~a~~~~i~~~~wk~vaiiYd-~~~~~~~lq~l~~~~~~~g~~v~~~~~~~~~--~~d~~~~L~~ik~~~~~~iil~~~~~ 189 (371)
T cd06388 113 GALLSLLDHYEWNRFVFLYD-TDRGYSILQAIMEKAGQNGWQVSAICVENFN--DASYRRLLEDLDRRQEKKFVIDCEIE 189 (371)
T ss_pred hHHHHHHHhcCceEEEEEec-CCccHHHHHHHHHhhHhcCCeeeeEEeccCC--cHHHHHHHHHhcccccEEEEEECCHH
Confidence 58889999999999999994 4456678999999999999998876544332 34899999999999999999999999
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccC-CCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRN-TLNG 160 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~-~~~~ 160 (481)
.+..++++|.++||+.++|+||+++......++ .++...-.++.++++.....+..++|++.|.+.+... ++..
T Consensus 190 ~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l-----~~~~~g~~nitg~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 264 (371)
T cd06388 190 RLQNILEQIVSVGKHVKGYHYIIANLGFKDISL-----ERFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSE 264 (371)
T ss_pred HHHHHHHHHHhcCccccceEEEEccCccccccH-----HHHhccCCceEEEEeecCCChhHHHHHHHHHhcCccccCCCC
Confidence 999999999999999999999998642212111 1122223347888887777788999999998765432 1211
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccc--cccccCccHHHHHHHHhcccCceeeeE
Q 011629 161 PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFS--SVSIFNGGKMLLDNILQVNMTGVTGPI 238 (481)
Q Consensus 161 ~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~L~~~l~~v~f~g~sG~v 238 (481)
..+...++++||||+++|.|++++.......+.. +....|. ...+|..|..|.++|++++|+|+||++
T Consensus 265 -~~~~~~aAl~YDaV~l~a~A~~~l~~~~~~~~~~---------~~~~~C~~~~~~~w~~G~~i~~~lk~~~~~GlTG~i 334 (371)
T cd06388 265 -SPPKYTSALTYDGVLVMAEAFRNLRRQKIDISRR---------GNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNI 334 (371)
T ss_pred -CCccchHHHHHHHHHHHHHHHHHHHhcCCCcccC---------CCCCCcCCCCCCCCcccHHHHHHHHhcCcCCCccce
Confidence 2355679999999999999999874322211000 1111342 345688899999999999999999999
Q ss_pred EEccCCCCCCCcEEEEEeecCceEEEEEeeCCCCC
Q 011629 239 KFTSDRDLINPAYEVINVIGTGSRRIGYWSNHSGL 273 (481)
Q Consensus 239 ~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l 273 (481)
.||++|+|.+..++|+++...++++||+|++..||
T Consensus 335 ~Fd~~G~r~~~~l~Ii~l~~~g~~kvG~W~~~~g~ 369 (371)
T cd06388 335 QFDHYGRRVNYTMDVFELKSNGPRKIGYWNDMDKL 369 (371)
T ss_pred eECCCCCcccceEEEEEccCCCceEEEEEcCCCCc
Confidence 99999999877999999998899999999998765
No 20
>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=99.98 E-value=2.1e-30 Score=254.55 Aligned_cols=227 Identities=18% Similarity=0.225 Sum_probs=185.2
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCCh-----hHHHHHHHHhccCCceEEE
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSR-----NQIIDTLLTVSSMMSRILI 75 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~-----~~~~~~l~~i~~s~~~vIv 75 (481)
++||++++++|||+||++|+++++||+...+.|++++++.|+||+..+.++...+. .++..+++.+++++++|||
T Consensus 160 a~ai~~li~~~~w~~Vaii~~~d~yG~~~~~~f~~~~~~~GicIa~~e~~~~~~~~~~~~~~~~~~~~~~ik~~~a~vVv 239 (403)
T cd06361 160 TKAMAHLIKKSGWNWVGIIITDDDYGRSALETFIIQAEANGVCIAFKEILPASLSDNTKLNRIIRTTEKIIEENKVNVIV 239 (403)
T ss_pred HHHHHHHHHHcCCcEEEEEEecCchHHHHHHHHHHHHHHCCeEEEEEEEecCccCcchhHHHHHHHHHHHHhcCCCeEEE
Confidence 47899999999999999999999999999999999999999999999999764321 3455666678899999999
Q ss_pred EEeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhcc
Q 011629 76 LHTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRR 155 (481)
Q Consensus 76 l~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~ 155 (481)
+++...++..++++|.++|+ +++||.++.|........ ........|++++.+.....++|.+|++..
T Consensus 240 v~~~~~~~~~l~~~a~~~g~---~~~wigs~~w~~~~~~~~---~~~~~~~~g~ig~~~~~~~~~~F~~~~~~~------ 307 (403)
T cd06361 240 VFARQFHVFLLFNKAIERNI---NKVWIASDNWSTAKKILT---DPNVKKIGKVVGFTFKSGNISSFHQFLKNL------ 307 (403)
T ss_pred EEeChHHHHHHHHHHHHhCC---CeEEEEECcccCcccccc---CCcccccceEEEEEecCCccchHHHHHHHh------
Confidence 99999999999999999987 699999999875432211 223366789999998887777777665432
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCcee
Q 011629 156 NTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVT 235 (481)
Q Consensus 156 ~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~s 235 (481)
+..++|||||++|+|||++..+. .|......+ +++|+++|++++|.|.+
T Consensus 308 -----------~~~~v~~AVyaiA~Al~~~~~~~-------------------~c~~~~~~~-~~~l~~~L~~~~f~g~~ 356 (403)
T cd06361 308 -----------LIHSIQLAVFALAHAIRDLCQER-------------------QCQNPNAFQ-PWELLGQLKNVTFEDGG 356 (403)
T ss_pred -----------hHHHHHHHHHHHHHHHHHhccCC-------------------CCCCCCCcC-HHHHHHHHheeEEecCC
Confidence 23568999999999999864431 243333345 89999999999999997
Q ss_pred eeEEEccCCCCCCCcEEEEEeecC----ceEEEEEeeCCC
Q 011629 236 GPIKFTSDRDLINPAYEVINVIGT----GSRRIGYWSNHS 271 (481)
Q Consensus 236 G~v~Fd~~Gd~~~~~y~I~~~~~~----~~~~VG~~~~~~ 271 (481)
|++.||++||. ...|+|+||+.+ .+++||.|++..
T Consensus 357 ~~v~Fd~~gd~-~~~y~I~~~~~~~~~~~~~~vg~~~~~~ 395 (403)
T cd06361 357 NMYHFDANGDL-NLGYDVVLWKEDNGHMTVTIMAEYDPQN 395 (403)
T ss_pred ceEEECCCCCC-CcceEEEEeEecCCcEEEEEEEEEeCCC
Confidence 79999999998 489999999964 479999998764
No 21
>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=99.97 E-value=7.5e-29 Score=243.49 Aligned_cols=249 Identities=17% Similarity=0.234 Sum_probs=194.0
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.|+++++++|||++|++||+++ .|...++.|.+.+++.|+||... .++.. ..++..++++||+.++++||+.++..
T Consensus 128 ~a~~~~~~~~~wk~vaily~~~-~g~~~l~~~~~~~~~~g~~v~~~-~~~~~--~~d~~~~L~~ik~~~~~~iil~~~~~ 203 (384)
T cd06393 128 HAILDLVQYLKWRSATVVYDDS-TGLIRLQELIMAPSRYNIRLKIR-QLPTD--SDDARPLLKEMKRGREFRIIFDCSHQ 203 (384)
T ss_pred HHHHHHHHHcCCcEEEEEEeCc-hhHHHHHHHHHhhhccCceEEEE-ECCCC--chHHHHHHHHHhhcCceEEEEECCHH
Confidence 5788999999999999999665 47666778888888999999864 45533 34899999999999999999999999
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhh-hccCCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHL-TRRNTLNG 160 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~-~~~~~~~~ 160 (481)
.+..++++|.++||..+.|+|++++......+. ..+......+.+++......+.+++|.+.|++. ++..+..+
T Consensus 204 ~~~~il~qa~~~gm~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~it~~~~~~~~~~~~~~f~~~~~~~~~~~~p~~~ 278 (384)
T cd06393 204 MAAQILKQAMAMGMMTEYYHFIFTTLDLYALDL-----EPYRYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQAAPKPE 278 (384)
T ss_pred HHHHHHHHHHHhccccCceEEEEccCccccccc-----hhhhcCcceEEEEEecCCCcHHHHHHHHHHHhhhhccccccc
Confidence 999999999999999999999988753322221 111112223578877777888999999999854 43211110
Q ss_pred ----CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceee
Q 011629 161 ----PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTG 236 (481)
Q Consensus 161 ----~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG 236 (481)
...+..+++++||||+++|.|+++..... .....|....+|+.|..|.++|++++|.|+||
T Consensus 279 ~~~~~~~~~~~aal~yDav~~~a~A~~~~~~~~---------------~~~~~c~~~~~w~~G~~i~~~l~~~~~~GltG 343 (384)
T cd06393 279 TGLLDGVMMTDAALLYDAVHMVSVCYQRAPQMT---------------VNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTG 343 (384)
T ss_pred cccccccccchhHHhhhhHHHHHHHHhhhhhcC---------------CCCCCCCCCCCCcccHHHHHHHhheeeccccc
Confidence 01134578999999999999999653211 11224666667988999999999999999999
Q ss_pred eEEEcc-CCCCCCCcEEEEEeecCceEEEEEeeCCCCCc
Q 011629 237 PIKFTS-DRDLINPAYEVINVIGTGSRRIGYWSNHSGLS 274 (481)
Q Consensus 237 ~v~Fd~-~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l~ 274 (481)
++.||+ +|.|.+..++|+|+...++++||.|++..||+
T Consensus 344 ~i~Fd~~~g~r~~~~~~i~~~~~~g~~~vg~W~~~~g~~ 382 (384)
T cd06393 344 RIVFNKTSGLRTDFDLDIISLKEDGLEKVGVWNPNTGLN 382 (384)
T ss_pred ceEecCCCCeeeeeEEEEEEecCCcceeeEEEcCCCCcC
Confidence 999996 67888899999999988999999999987763
No 22
>cd06378 PBP1_iGluR_NMDA_NR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=99.96 E-value=1.4e-28 Score=237.19 Aligned_cols=225 Identities=19% Similarity=0.232 Sum_probs=174.3
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCC-hhHHHHHHHHhccCCceEEEEEeC
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGS-RNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~-~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
++||++|++||||++|++|+++++.+..+.+.+++.+...++|+.....++.... ......+++++++.++||||++|+
T Consensus 123 ~~Ai~~Ii~~f~W~~v~iV~~~~~g~~~~~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~lk~~~arViVl~~s 202 (362)
T cd06378 123 AAVMLKIMEEYDWHAFSVVTSRFPGYDDFVSAVRTTVDNSFVGWELQSVLTLDMSDDDGDARTQRQLKKLESQVILLYCS 202 (362)
T ss_pred HHHHHHHHHHCCCeEEEEEEEcCCCHHHHHHHHHHHHhhcccceeEEEEEeeccCCCcchHHHHHHHHhcCCCEEEEECC
Confidence 3699999999999999999999888778888888888888888876655544322 223678888999999999999999
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCCC
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
.+.+..+|++|.++||++.+|+||++++.....+. .......|++++.. +.|+.
T Consensus 203 ~~~a~~if~~A~~~gm~g~~yvWI~t~~~~~~~~~------~~~~~~~G~i~v~~------------~~w~~-------- 256 (362)
T cd06378 203 KEEAEYIFRAARSAGLTGPGYVWIVPSLVLGNTDL------GPSEFPVGLISVSY------------DGWRY-------- 256 (362)
T ss_pred HHHHHHHHHHHHHcCCcCCCeEEEecccccCCCcc------ccccCCcceEeecc------------ccccc--------
Confidence 99999999999999999999999999876544211 11234466666542 23321
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCccccc-cc-ccCccHHHHHHHHhcccCceeee
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSS-VS-IFNGGKMLLDNILQVNMTGVTGP 237 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~L~~~l~~v~f~g~sG~ 237 (481)
...+.+||||+++|+|++.++......+. ...+|.. .. .|..|..|+++|++++|+|. +
T Consensus 257 ------~~~a~~~DaV~vva~Al~~l~~~~~~~~~-----------~~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~--~ 317 (362)
T cd06378 257 ------SLRARVRDGVAIIATGASAMLRQHGFIPE-----------AKGSCYGQAEKRDLPPNTLHRYMMNVTWEGR--D 317 (362)
T ss_pred ------cHHHHHHHHHHHHHHHHHHHHhccCCCCC-----------CCCCcCCCCCCCCCchHHHHHHhhcceECCC--c
Confidence 13568899999999999988754332211 1123432 22 36679999999999999996 9
Q ss_pred EEEccCCCCCCCcEEEEEeec-CceEEEEEeeCC
Q 011629 238 IKFTSDRDLINPAYEVINVIG-TGSRRIGYWSNH 270 (481)
Q Consensus 238 v~Fd~~Gd~~~~~y~I~~~~~-~~~~~VG~~~~~ 270 (481)
|+||++|++.+..|+|+|+.. .++++||.|+..
T Consensus 318 i~F~~~G~r~~~~ldIinl~~~~g~~kVG~W~~~ 351 (362)
T cd06378 318 LSFTEDGYLVNPKLVVISLNKERVWEEVGKWENG 351 (362)
T ss_pred eeECCCCeEccceEEEEEecCCCCceEEEEEcCC
Confidence 999999999999999999996 489999999953
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=99.96 E-value=8.3e-28 Score=236.51 Aligned_cols=262 Identities=20% Similarity=0.337 Sum_probs=192.7
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcC--CEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKR--CRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~g--i~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
.|+++++++|||++|++||++++ |...++.+.+.+++.| +.|... .+.......|+..+|++||+.++++||+.++
T Consensus 115 ~a~~~~~~~~~wk~vaii~~~~~-~~~~~~~~~~~~~~~g~~i~v~~~-~~~~~~~~~d~~~~L~~ik~~~~~~iil~~~ 192 (382)
T cd06380 115 QALVDLIEHYGWRKVVYLYDSDR-GLLRLQQLLDYLREKDNKWQVTAR-RVDNVTDEEEFLRLLEDLDRRKEKRIVLDCE 192 (382)
T ss_pred HHHHHHHHhcCCeEEEEEECCCc-chHHHHHHHHHHhccCCceEEEEE-EecCCCcHHHHHHHHHHhhcccceEEEEECC
Confidence 57889999999999999996665 6677888889999998 555543 2332223458999999999999999999999
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccC-CC
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRN-TL 158 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~-~~ 158 (481)
..++..++++|.++||..++|+||++++.....+. ........++.+++......+.+++|.+.|++.++.. +.
T Consensus 193 ~~~~~~i~~qa~~~gm~~~~y~~i~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~ 267 (382)
T cd06380 193 SERLNKILEQIVDVGKNRKGYHYILANLGFDDIDL-----SKFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPG 267 (382)
T ss_pred HHHHHHHHHHHHHhhhcccceEEEEccCCcccccH-----HHhccCceeeEEEeccCCCCHHHHHHHHHHHhcCccccCc
Confidence 99999999999999999999999998653332221 1111222346667665556788999999999876421 11
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCccccc--ccccCccHHHHHHHHhcccCceee
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSS--VSIFNGGKMLLDNILQVNMTGVTG 236 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~L~~~l~~v~f~g~sG 236 (481)
.....+..+++++||||+++|.|++++........... ..+.. .+...|.. ..+|.+|..|.++|++++|.|++|
T Consensus 268 ~~~~~~~~~aa~aYDav~~~a~Al~~~~~~~~~~~~~~--~~~~~-~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG 344 (382)
T cd06380 268 AGTSPIKYTAALAHDAVLVMAEAFRSLRRQRGSGRHRI--DISRR-GNGGDCLANPAVPWEHGIDIERALKKVQFEGLTG 344 (382)
T ss_pred CCcCCcchHHHHHHHHHHHHHHHHHHHHHhcccccccc--ccccC-CCCCcCCCCCCCCccchHHHHHHHHhcccCCccc
Confidence 11223456889999999999999999864321100000 00000 11223432 334667999999999999999999
Q ss_pred eEEEccCCCCCCCcEEEEEeecCceEEEEEeeCCCCC
Q 011629 237 PIKFTSDRDLINPAYEVINVIGTGSRRIGYWSNHSGL 273 (481)
Q Consensus 237 ~v~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l 273 (481)
+|.||++|++.+..++|++++.++.++||.|++..|+
T Consensus 345 ~i~Fd~~G~~~~~~~~i~~~~~~~~~~vg~w~~~~g~ 381 (382)
T cd06380 345 NVQFDEFGQRTNYTLDVVELKTRGLRKVGYWNEDDGL 381 (382)
T ss_pred ceEECCCCCcccccEEEEEecCCCceEEEEECCCcCc
Confidence 9999999999878999999998889999999987653
No 24
>cd06386 PBP1_NPR_C_like Ligand-binding domain of type C natriuretic peptide receptor. Ligand-binding domain of type C natriuretic peptide receptor (NPR-C). NPR-C is found in atrial, mesentery, placenta, lung, kidney, venous tissue, aortic smooth muscle, and aortic endothelial cells. The affinity of NPR-C for natriuretic peptides is ANPCNPBNP. The extracellular domain of NPR-C is about 30% identical to NPR-A and NPR-B. However, unlike the cyclase-linked receptors, it contains only 37 intracellular amino acids and no guanylyl cyclase activity. Major function of NPR-C is to clear natriuretic peptides from the circulation or extracellular surroundings through constitutive receptor-mediated internalization and degradation.
Probab=99.95 E-value=1.1e-26 Score=228.21 Aligned_cols=237 Identities=16% Similarity=0.216 Sum_probs=182.7
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccch---HHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEe
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNG---IAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~---~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
.|++++++||||++|++||+++++|... ++.|.+.+++.|+||......+.. ..++..+++++++.+ ||||+++
T Consensus 126 ~a~~~ll~~~~W~~vaiiy~~~~~~~~~~~~~~~l~~~~~~~gi~v~~~~~~~~~--~~d~~~~l~~ik~~~-rvii~~~ 202 (387)
T cd06386 126 ETFSALFERFHWRSALLVYEDDKQERNCYFTLEGVHHVFQEEGYHMSIYPFDETK--DLDLDEIIRAIQASE-RVVIMCA 202 (387)
T ss_pred HHHHHHHHhCCCeEEEEEEEcCCCCccceehHHHHHHHHHhcCceEEEEecCCCC--cccHHHHHHHHHhcC-cEEEEec
Confidence 6889999999999999999999998876 899999999999999876554332 247899999999987 9999999
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccC------Ccccc---ccccccceeeEEEeeecCCchhHHHHHHHH
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDT------DSQLH---SEKMDDIQGVLTLRMYTQSSEEKRKFVTRW 149 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~------~~~~~---~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~ 149 (481)
+.+.++.++++|.++||...+|+||.++...+.... .+..+ ....+.+.|+.++++ ..+.+++|.+++
T Consensus 203 ~~~~~~~ll~~A~~~gm~~~~yv~i~~d~~~~~~~~~~~w~~~~~~~~~~~~a~~~~~~v~~~~~---~~~~~~~f~~~~ 279 (387)
T cd06386 203 GADTIRSIMLAAHRRGLTSGDYIFFNIELFNSSSYGDGSWKRGDKHDFEAKQAYSSLNTVTLLRT---VKPEFEKFSMEV 279 (387)
T ss_pred CHHHHHHHHHHHHHcCCCCCCEEEEEEecccccccCCCCCccCCCcCHHHHHHHHhheEEeccCC---CChHHHHHHHHH
Confidence 999999999999999999999999999765311000 00001 112233445555443 357788899888
Q ss_pred hhhhccCCCCC-CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHh
Q 011629 150 RHLTRRNTLNG-PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQ 228 (481)
Q Consensus 150 ~~~~~~~~~~~-~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~ 228 (481)
++.+...+... ...++.+++.+||||+++|+||++++..+.. +.+|..|.++|++
T Consensus 280 ~~~~~~~~~~~~~~~~~~~aa~~yDav~l~A~Al~~~~~~g~~------------------------~~~g~~l~~~l~~ 335 (387)
T cd06386 280 KSSVEKAGDLNDCDYVNMFVEGFHDAILLYALALHEVLKNGYS------------------------KKDGTKITQRMWN 335 (387)
T ss_pred HHHHHhCCCCcccccchHHHHHHHHHHHHHHHHHHHHhhCCCC------------------------CCCHHHHHHHHhC
Confidence 85554321111 1124578999999999999999998653211 2238999999999
Q ss_pred cccCceeeeEEEccCCCCCCCcEEEEEeec---CceEEEEEeeC
Q 011629 229 VNMTGVTGPIKFTSDRDLINPAYEVINVIG---TGSRRIGYWSN 269 (481)
Q Consensus 229 v~f~g~sG~v~Fd~~Gd~~~~~y~I~~~~~---~~~~~VG~~~~ 269 (481)
++|+|++|++.||++|+|. ..|.++.+++ ++++.||.|..
T Consensus 336 ~~f~G~tG~v~~d~~g~r~-~~~~v~~~~~~~~~~~~~~~~~~~ 378 (387)
T cd06386 336 RTFEGIAGQVSIDANGDRY-GDFSVIAMTDVEAGTYEVVGNYFG 378 (387)
T ss_pred CceeeccccEEECCCCCcc-ccEEEEEccCCCCccEEEEeEEcc
Confidence 9999999999999999996 7999999974 47999999974
No 25
>cd06363 PBP1_Taste_receptor Ligand-binding domain of the T1R taste receptor. Ligand-binding domain of the T1R taste receptor. The T1R is a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptors, GABAb receptors, the calcium-sensing receptor (CaSR), the V2R pheromone receptors, and a small group of uncharacterized orphan receptors.
Probab=99.95 E-value=2.6e-26 Score=227.53 Aligned_cols=227 Identities=18% Similarity=0.270 Sum_probs=182.3
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCC-CChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPK-GSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~-~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.|+++++++|+|++|++|+++++||....+.+++.+++.|+||+..+.++.. ....|+..++++|+.+++++||+++..
T Consensus 165 ~al~~~l~~~~~k~vaii~~~~~~g~~~~~~~~~~l~~~gi~i~~~~~~~~~~~~~~d~~~~l~~i~~~~~dvIil~~~~ 244 (410)
T cd06363 165 EAMVQLLQEFGWNWVAFLGSDDEYGRDGLQLFSELIANTGICIAYQGLIPLDTDPETDYQQILKQINQTKVNVIVVFASR 244 (410)
T ss_pred HHHHHHHHHCCCcEEEEEEeCChhHHHHHHHHHHHHHHCCeEEEEEEEecCCCchHHHHHHHHHHHhcCCCeEEEEEcCh
Confidence 5899999999999999999999999999999999999999999998888753 234589999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCCCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTLNG 160 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 160 (481)
..+..++++|.++|+. +..||.++.|........ ........+++++.......+.+++|.+.
T Consensus 245 ~~~~~il~qa~~~g~~--~~~~i~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~f~~~------------ 307 (410)
T cd06363 245 QPAEAFFNSVIQQNLT--GKVWIASEAWSLNDELPS---LPGIRNIGTVLGVAQQTVTIPGFSDFIYS------------ 307 (410)
T ss_pred HHHHHHHHHHHhcCCC--CCEEEEeCcccccccccC---CccceeeccEEEEEeCCCCCccHHHHHHH------------
Confidence 9999999999999974 458999877653321111 11223455677777766667777777765
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEEE
Q 011629 161 PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKF 240 (481)
Q Consensus 161 ~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~F 240 (481)
+++.+|||||++|+|+++++.++.. .|......+ ++.|.++|++++|.|.+|++.|
T Consensus 308 ------~~~~~YDaV~~~a~Al~~a~~~~~~-----------------~~~~~~~~~-~~~l~~~L~~~~~~g~~g~i~f 363 (410)
T cd06363 308 ------FAFSVYAAVYAVAHALHNVLQCGSG-----------------GCPKRVPVY-PWQLLEELKKVNFTLLGQTVRF 363 (410)
T ss_pred ------HHHHHHHHHHHHHHHHHHHhCCCCC-----------------CCCCCCCCC-HHHHHHHHhccEEecCCcEEEe
Confidence 3567999999999999999766332 122112233 7889999999999999999999
Q ss_pred ccCCCCCCCcEEEEEeecC----ceEEEEEeeCC
Q 011629 241 TSDRDLINPAYEVINVIGT----GSRRIGYWSNH 270 (481)
Q Consensus 241 d~~Gd~~~~~y~I~~~~~~----~~~~VG~~~~~ 270 (481)
|++|++. ..|+|++++.. ++++||+|++.
T Consensus 364 d~~G~~~-~~~~i~~~~~~~~~~~~~~vG~~~~~ 396 (410)
T cd06363 364 DENGDPN-FGYDIVVWWWDNSSGTFEEVGSYSFY 396 (410)
T ss_pred CCCCCCc-cceEEEEEEEcCCceeEEEEEEEECC
Confidence 9999974 78999999642 58999999873
No 26
>PF01094 ANF_receptor: Receptor family ligand binding region The Prosite family is a sub-family of the Pfam family; InterPro: IPR001828 This describes a ligand binding domain and includes extracellular ligand binding domains of a wide range of receptors, as well as the bacterial amino acid binding proteins of known structure [].; PDB: 3SAJ_D 3Q41_B 3QEM_C 3QEK_A 3QEL_C 3MQ4_A 3QLV_G 3OM1_A 3QLU_A 3OM0_A ....
Probab=99.95 E-value=2.5e-26 Score=223.52 Aligned_cols=234 Identities=29% Similarity=0.474 Sum_probs=185.9
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhc-CCEEEE-EEecCCCCChhHHHHHHHHhcc--CCceEEEE
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEK-RCRLSH-KVPLSPKGSRNQIIDTLLTVSS--MMSRILIL 76 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~-gi~v~~-~~~~~~~~~~~~~~~~l~~i~~--s~~~vIvl 76 (481)
++|++++|++|+|++|++|++++++|....+.|++.+++. ++|+.. ........ +....++.+++ .++||||+
T Consensus 109 ~~a~~~~l~~~~w~~v~vv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~rvvil 185 (348)
T PF01094_consen 109 ARALVDLLKHFGWTRVSVVYSDDDYGNSLADSFQDLLRERGGICVAFISVVISSDS---DAEELLKKLKEIKSGARVVIL 185 (348)
T ss_dssp HHHHHHHHHHTTSSEEEEEEESSHHHHHHHHHHHHHHHHHTTCEEEEEEEEETTTS---HHHHHHHHHHHHTTTTSEEEE
T ss_pred HHHHHHhhhcCCCceeeeeccccccccccchhhhhhhcccccceeccccccccccc---chhhhhhhhhhccccceeeee
Confidence 3689999999999999999999999999999999999995 677776 33333222 34444444444 89999999
Q ss_pred EeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhcc-
Q 011629 77 HTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRR- 155 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~- 155 (481)
+++...+..++++|.++||...+|+||+++.+...... ..........|++++....+..+.+++|.+.|+.....
T Consensus 186 ~~~~~~~~~~l~~a~~~~~~~~~~~~i~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~ 262 (348)
T PF01094_consen 186 CSSPEDARQFLEAAYELGMTSGDYVWILTDLDNSSFWQ---NNEDFREAFQGVLGFTPPPPSSPEFEDFMKKWKESNNQS 262 (348)
T ss_dssp ESBHHHHHHHHHHHHHTTTSSTTSEEEEETTTTTTHTS---THCHHHCCHTTEEEEEESTTTSHHHHHHHHHHHTTTHTT
T ss_pred ecccccccccccchhhhhccccceeEEeeccccccccc---ccccccccccceeeeeeecccccchhhhhcccChhhccC
Confidence 99999999999999999998899999999987654211 12456678899999999888889999999999875431
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCcee
Q 011629 156 NTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVT 235 (481)
Q Consensus 156 ~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~s 235 (481)
+..........+++++||||+++|+|+++++++.+... .....+.+|..|.++|++++|.|++
T Consensus 263 ~~~~~~~~~~~~~~~~yDAv~~~a~al~~~~~~~~~~~-----------------~~~~~~~~g~~l~~~l~~~~f~G~t 325 (348)
T PF01094_consen 263 STSGSDQEPSPYAAYAYDAVYLLAHALNRALQDGGPVT-----------------NGRNPWQNGSQLLKYLRNVSFEGLT 325 (348)
T ss_dssp TTTTTTSSGCHHHHHHHHHHHHHHHHHHHHHHHHSTTT-----------------SSSGTSTTHHHHHHHHHTEEEEETT
T ss_pred cccccccccceeeeeehhhhHHHHHHHHHHHHhccCCC-----------------CCccccccHHHHHHHHhheeeeCCC
Confidence 12222334677899999999999999999987643211 0012355699999999999999999
Q ss_pred eeEEEcc-CCCCCCCcEEEEEee
Q 011629 236 GPIKFTS-DRDLINPAYEVINVI 257 (481)
Q Consensus 236 G~v~Fd~-~Gd~~~~~y~I~~~~ 257 (481)
|++.||+ +|++.+..|+|+|+|
T Consensus 326 G~v~f~~~~G~~~~~~~~i~~~~ 348 (348)
T PF01094_consen 326 GRVSFDSNDGDRTNYDYDILNMQ 348 (348)
T ss_dssp EEEEEETTTSBEESEEEEEEEE-
T ss_pred CCEEEeCCCCCcCCCEEEEEECC
Confidence 9999999 999988999999986
No 27
>cd06385 PBP1_NPR_A Ligand-binding domain of type A natriuretic peptide receptor. Ligand-binding domain of type A natriuretic peptide receptor (NPR-A). NPR-A is one of three known single membrane-spanning natriuretic peptide receptors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In mammals there are three natriuretic peptides: ANP, BNP, and CNP. NPR-A is highly expressed in kidney, adrenal, terminal ileum, adipose, aortic, and lung tissues. The rank order of NPR-A activation by natriuretic peptides is ANPBNPCNP. Single allele-inactivating mutations in the promoter of human NPR-A are associated with hypertension and heart failure.
Probab=99.94 E-value=3.3e-25 Score=219.67 Aligned_cols=241 Identities=16% Similarity=0.198 Sum_probs=180.3
Q ss_pred hHhHHHHHHcCCcEEEE-EEEeCCc-ccc---hHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEE
Q 011629 2 AAIADIVDYFGWRNVIA-LYVDDDH-GRN---GIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILIL 76 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~i-i~~dd~~-g~~---~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl 76 (481)
+|+++++++|||++|++ ++.++.. +.. ..+.|.+.+++.|+||+..+..+. +..++..++++|++. +|+||+
T Consensus 132 ~a~~~~~~~~~w~~va~ii~~~~~~~~~~~~~~~~~l~~~~~~~gi~v~~~~~~~~--~~~d~~~~l~~ik~~-~~iii~ 208 (405)
T cd06385 132 EFVLHIHQHFGWRSHAMLIYSDNKVDDRPCYFAMEGLYMELKKNNITVVDLVFEED--DLINYTTLLQDIKQK-GRVIYV 208 (405)
T ss_pred HHHHHHHHhCCCeEEEEEEEecCcccccchHHHHHHHHHHHHhCCeEEEEeeccCC--chhhHHHHHHHHhhc-ceEEEE
Confidence 57899999999999995 5554432 233 468899999999999998763322 244799999999886 599999
Q ss_pred EeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccC---------CccccccccccceeeEEEeeecCCchhHHHHHH
Q 011629 77 HTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDT---------DSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVT 147 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~---------~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~ 147 (481)
+++...+..++++|.++||..++|+||+++.+...... .+..+......+++++......+..+.+++|.+
T Consensus 209 ~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~f~~ 288 (405)
T cd06385 209 CCSPDIFRRLMLQFWREGLPSEDYVFFYIDLFGASLQGPDPKRPWYRGDADDAAAREAFQSVKILTYKEPQNPEYKEFLS 288 (405)
T ss_pred eCCHHHHHHHHHHHHHcCCCCCcEEEEEeecchhhccCCCCCCCCCCCCcccHHHHHhhheeEEEeCCCCCChhHHHHHH
Confidence 99999999999999999999999999999765322111 000011223456777777655556678899999
Q ss_pred HHhhhhccCCCCC--CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHH
Q 011629 148 RWRHLTRRNTLNG--PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDN 225 (481)
Q Consensus 148 ~~~~~~~~~~~~~--~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~ 225 (481)
.|++......+.+ .-.++.+++++|||||++|.||+++++..+. +.+|..|.+.
T Consensus 289 ~~~~~~~~~~~~~~~~~~~~~~aa~~YDav~l~a~Al~~~~~~~~~------------------------~~~g~~i~~~ 344 (405)
T cd06385 289 DLKTDAKEMFNFTVEDSLMNIIAGGFYDGVMLYAHALNETMAKGGT------------------------RPPGTAITQR 344 (405)
T ss_pred HHHHHhhccCCCccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCC------------------------CCCHHHHHHH
Confidence 9987532110110 0114568899999999999999997654211 2248999999
Q ss_pred HHhcccCceeeeEEEccCCCCCCCcEEEEEe---ecCceEEEEEeeCC
Q 011629 226 ILQVNMTGVTGPIKFTSDRDLINPAYEVINV---IGTGSRRIGYWSNH 270 (481)
Q Consensus 226 l~~v~f~g~sG~v~Fd~~Gd~~~~~y~I~~~---~~~~~~~VG~~~~~ 270 (481)
|++++|.|++|.|.||++|+|. ..|.++++ +.++++.||+|+..
T Consensus 345 l~~~~f~G~tG~v~fd~~G~r~-~~~~~~~~~~~~~g~~~~v~~~~~~ 391 (405)
T cd06385 345 MWNRTFYGVTGFVKIDDNGDRE-TDFALWDMTDTESGDFQVVSVYNGT 391 (405)
T ss_pred hhCceEeeceeEEEEcCCCCEe-ceeEEEEccCCCCCcEEEEEEEccc
Confidence 9999999999999999999995 88988866 45789999999864
No 28
>cd06370 PBP1_Speract_GC_like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model.
Probab=99.94 E-value=3.2e-25 Score=219.26 Aligned_cols=233 Identities=16% Similarity=0.225 Sum_probs=178.1
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCC-----ChhHHHHHHHHhccCCceEEEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKG-----SRNQIIDTLLTVSSMMSRILIL 76 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~-----~~~~~~~~l~~i~~s~~~vIvl 76 (481)
+|+++++++|||++|++|+++++||....+.|++.+.+.|+||+..+.++... ...++..++++++.. ++++|+
T Consensus 125 ~a~~~~~~~~~w~~vaii~~~~~~g~~~~~~~~~~~~~~g~~iv~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~v~ 203 (404)
T cd06370 125 KSVIALLKHFNWNKFSVVYENDSKYSSVFETLKEEAELRNITISHVEYYADFYPPDPIMDNPFEDIIQRTKET-TRIYVF 203 (404)
T ss_pred HHHHHHHHHCCCcEEEEEEecCcccHHHHHHHHHHHHHcCCEEEEEEEECCCCCchhhhHHHHHHHHHhccCC-CEEEEE
Confidence 57889999999999999999999999999999999999999999998887642 135788888888775 788888
Q ss_pred EeCcHHHHHHHHHHHHcCCc-cCCeEEEEecccccc---------------ccCCccccccccccceeeEEEeeecCCch
Q 011629 77 HTYDIWGLEVLNAAKHLRMM-ESGYVWIVTDWLSSI---------------LDTDSQLHSEKMDDIQGVLTLRMYTQSSE 140 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~-~~~~~wI~~~~~~~~---------------~~~~~~~~~~~~~~~~g~l~~~~~~~~~~ 140 (481)
++...++..++++|.++||. ..+|+||.++..... ............+.++|++.+..... .+
T Consensus 204 ~~~~~~~~~~l~qa~~~g~~~~~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~ 282 (404)
T cd06370 204 IGEANELRQFLMSMLDEGLLESGDYMVLGVDIEYYDRDSQDYYSLHRGFQSREYNRSDDEKALEAMKSVLIIVPTPV-SP 282 (404)
T ss_pred EcCHHHHHHHHHHHHHcCCCCCCcEEEEEEchhhccccchhhhhhhhhhccccccccccHHHHHHhHheEEEecCCC-Cc
Confidence 88878899999999999998 578999986531000 00000000223356778777754443 66
Q ss_pred hHHHHHHHHhhhhccCCCC-------CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccc
Q 011629 141 EKRKFVTRWRHLTRRNTLN-------GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSV 213 (481)
Q Consensus 141 ~~~~f~~~~~~~~~~~~~~-------~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 (481)
.+.+|.+.|++.....+.. ....++.+++++||||+++|+||++++++...
T Consensus 283 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aa~~yDAv~~~a~Al~~~~~~~~~---------------------- 340 (404)
T cd06370 283 DYDSFSIFVRKYNLEPPFNGDLGESELVLEIDIEAAYLYDAVMLYAKALDETLLEGGD---------------------- 340 (404)
T ss_pred hHHHHHHHHHHhccCCCCcccccccccccccceeeehhHHHHHHHHHHHHHHHHhcCC----------------------
Confidence 7789999998765321111 11235567899999999999999998765221
Q ss_pred cccCccHHHHHHHHhcccCceee-eEEEccCCCCCCCcEEEEEeecCce
Q 011629 214 SIFNGGKMLLDNILQVNMTGVTG-PIKFTSDRDLINPAYEVINVIGTGS 261 (481)
Q Consensus 214 ~~~~~~~~L~~~l~~v~f~g~sG-~v~Fd~~Gd~~~~~y~I~~~~~~~~ 261 (481)
.. ++..|.++|++++|+|++| +|.||++|++. ..|.|++++.+.|
T Consensus 341 -~~-~g~~i~~~l~~~~f~GvtG~~v~fd~~G~~~-~~y~v~~~~~~~~ 386 (404)
T cd06370 341 -IY-NGTAIVSHILNRTYRSITGFDMYIDENGDAE-GNYSVLALQPIPP 386 (404)
T ss_pred -CC-CHHHHHHHHhCcccccccCceEEEcCCCCcc-cceEEEEeccccc
Confidence 02 3889999999999999999 99999999995 9999999987644
No 29
>cd06372 PBP1_GC_G_like Ligand-binding domain of membrane guanylyl cyclase G. This group includes the ligand-binding domain of membrane guanylyl cyclase G (GC-G) which is a sperm surface receptor and might function, similar to its sea urchin counterpart, in the early signaling event that regulates the Ca2+ influx/efflux and subsequent motility response in sperm. GC-G appears to be a pseudogene in human. Furthermore, in contrast to the other orphan receptor GCs, GC-G has a broad tissue distribution in rat, including lung, intestine, kidney, and skeletal muscle.
Probab=99.94 E-value=7.2e-25 Score=216.27 Aligned_cols=239 Identities=16% Similarity=0.262 Sum_probs=170.3
Q ss_pred hHhHHHHHHcCCcEEEEEEEeC---Ccc--cchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDD---DHG--RNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILIL 76 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd---~~g--~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl 76 (481)
+|++++++||||++|++|++++ .++ ....+.+.+.++ .++++...+.++... .++...+.+.+.+++|+||+
T Consensus 126 ~a~~~l~~~~~w~~vaii~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~~~~~~~~~--~d~~~~~l~~~~~~~~vii~ 202 (391)
T cd06372 126 EVLQKSLQHFGWKHIGLFGGSSRDSSWDEVDELWKAVENQLK-FHFNITATVRYSSSN--PDLLQEKLRYISSVARVIIL 202 (391)
T ss_pred HHHHHHHHHCCCeEEEEEEeccccchhhhHHHHHHHHHHHHh-hCEEEEEEEecCCCC--hHHHHHHHHhhhccceEEEE
Confidence 5889999999999999998643 233 123444555553 678998888776543 25555454555678999999
Q ss_pred EeCcHHHHHHHHHHHHcCCccCCeEEEEec-----cccccccCCccccccccccceeeEEEeeecCC-chhHHHHHHHHh
Q 011629 77 HTYDIWGLEVLNAAKHLRMMESGYVWIVTD-----WLSSILDTDSQLHSEKMDDIQGVLTLRMYTQS-SEEKRKFVTRWR 150 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~~~~~~wI~~~-----~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~-~~~~~~f~~~~~ 150 (481)
+++...+..++++|.++||..++|+||++. +|...... . ......+...|++++.+.... .+...+|.+.|+
T Consensus 203 ~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~~~~w~~~~~~-~-~~~~~~~~~~~~~~i~~~~~~~~~~~~~f~~~~~ 280 (391)
T cd06372 203 ICSSEDAKAILQAAEKLGLMKGKFVFFLLQQFEDNFWKEVLTD-D-QVQHLPKVYESVFLIAPSSYGGYSGGYEFRKQVY 280 (391)
T ss_pred EcChHHHHHHHHHHHHcCCCCCCEEEEEehhhcCccccccCCC-c-chHHHHHHHhhEEEEecCCCCCCcchhHHHHHHH
Confidence 999999999999999999988789999963 33221110 0 001122456777777655432 244667777777
Q ss_pred hhhccCCC----CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHH
Q 011629 151 HLTRRNTL----NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNI 226 (481)
Q Consensus 151 ~~~~~~~~----~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l 226 (481)
+.+...+. ........+++++|||||++|+||+++++++.. +.+|..|.++|
T Consensus 281 ~~~~~~p~~~~~~~~~~~~~~a~~~yDav~~~A~Al~~~~~~g~~------------------------~~~g~~l~~~l 336 (391)
T cd06372 281 QKLKRPPFQSSLSSEEQVSPYSAYLHDAVLLYALAVKEMLKAGKD------------------------FRNGRQLVSTL 336 (391)
T ss_pred HHHhcCCccccccccccchHHHHHHHHHHHHHHHHHHHHHhcCCC------------------------CCCHHHHHHHH
Confidence 66542221 111234568999999999999999998764211 32488999999
Q ss_pred H---hcccCceeeeEEEccCCCCCCCcEEEEEeec--C--ceEEEEEeeCC
Q 011629 227 L---QVNMTGVTGPIKFTSDRDLINPAYEVINVIG--T--GSRRIGYWSNH 270 (481)
Q Consensus 227 ~---~v~f~g~sG~v~Fd~~Gd~~~~~y~I~~~~~--~--~~~~VG~~~~~ 270 (481)
+ +++|+|++|+|.||++|+|. +.|.|++++. . ..++||+|+..
T Consensus 337 ~~~~~~~f~G~tG~v~fd~~G~r~-~~y~i~~~~~~~~~~~~~~vg~~~~~ 386 (391)
T cd06372 337 RGANQVELQGITGLVLLDEQGKRQ-MDYSVYALQKSGNSSLFLPFLHYDSH 386 (391)
T ss_pred hhccCceEeccceeEEECCCCCcc-eeEEEEeccccCCccceeeEEEecch
Confidence 9 69999999999999999995 9999999985 2 48999999864
No 30
>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=99.93 E-value=3.5e-24 Score=211.64 Aligned_cols=241 Identities=15% Similarity=0.172 Sum_probs=180.5
Q ss_pred hHhHHHHHHcCCc-EEEEEEEeCCccc----chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEE
Q 011629 2 AAIADIVDYFGWR-NVIALYVDDDHGR----NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILIL 76 (481)
Q Consensus 2 ~Ai~~ll~~fgW~-~V~ii~~dd~~g~----~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl 76 (481)
.++..++++|+|+ ++++||.++..+. ...+.+.+.+++.|+||.....+... ..++..++++|+. ++||||+
T Consensus 132 ~~~~~i~~~~~w~~~vaiiy~~~~~~~~~~~~~~~~~~~~~~~~gi~v~~~~~~~~~--~~d~~~~l~~ik~-~~~vIi~ 208 (399)
T cd06384 132 EFVNHLHEHFNWTSRAALLYLDLKTDDRPHYFISEGVFLALQEENANVSAHPYHIEK--NSDIIEIIQFIKQ-NGRIVYI 208 (399)
T ss_pred HHHHHHHHhCCCcEEEEEEEecCCccCCcceEehHHHHHHHHhcCceEEEEEEeccc--hhhHHHHHHHHhh-cccEEEE
Confidence 4677899999999 5889986542221 23667888889999999876554432 3479999999997 7999999
Q ss_pred EeCcHHHHHHHHHHHHcCCccCCeEEEEecccccccc----------CCccccccccccceeeEEEeeecCCchhHHHHH
Q 011629 77 HTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILD----------TDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFV 146 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~----------~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~ 146 (481)
+++...+..++++|.++||..++|+||..+.+..... ...+......+.+.+++.+....+..+.+++|.
T Consensus 209 ~~~~~~~~~i~~qa~~~g~~~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~F~ 288 (399)
T cd06384 209 CGPLETFLEIMLQAQREGLTPGDYVFFYLDVFGESLRVKSPRESYKQMNHSSWTVLKEAFKSVFVITYREPENPEYKEFQ 288 (399)
T ss_pred eCCchHHHHHHHHHHHcCCCCCcEEEEEehhcccccccCCCCccccCCCCcccHHHHHHHhheEEeecCCCCCchHHHHH
Confidence 9999999999999999999999999998875432111 001111333456778888877666677889999
Q ss_pred HHHhhhhccCCCCCCC--CCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHH
Q 011629 147 TRWRHLTRRNTLNGPI--GLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLD 224 (481)
Q Consensus 147 ~~~~~~~~~~~~~~~~--~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~ 224 (481)
+.|++......+.+.. ....+++++||||+++|.||+++++... .+.+|..|.+
T Consensus 289 ~~~~~~~~~~~~~~~~p~~~~~~aa~~YDav~l~a~Al~~~~~~~~------------------------~~~~g~~i~~ 344 (399)
T cd06384 289 RELHARAKEDFGVELEPSLMNFIAGCFYDGVMLYAMALNETLAEGG------------------------SQKDGLNITR 344 (399)
T ss_pred HHHHHHHhhhcCCCcCcchHhhhhhhhHHHHHHHHHHHHHHHhcCC------------------------CCCCcHhHHH
Confidence 9998754221111111 1255789999999999999999765321 1334889999
Q ss_pred HHHhcccCceeeeEEEccCCCCCCCcEEEE---EeecCceEEEEEeeCC
Q 011629 225 NILQVNMTGVTGPIKFTSDRDLINPAYEVI---NVIGTGSRRIGYWSNH 270 (481)
Q Consensus 225 ~l~~v~f~g~sG~v~Fd~~Gd~~~~~y~I~---~~~~~~~~~VG~~~~~ 270 (481)
+|++++|.|++|++.||++|+|. ..|.++ +++.++++.||+|+..
T Consensus 345 ~l~~~~f~GvtG~v~fd~~G~r~-~~~~~~~~~~~~~g~~~~v~~~~~~ 392 (399)
T cd06384 345 KMQDRRFWGVTGLVSIDKNNDRD-IDFDLWAMTDHETGKYEVVAHYNGI 392 (399)
T ss_pred HHhCceeecceeEEEECCCCCcc-cceEEEEeecCCCCeEEEEEEEcCC
Confidence 99999999999999999999995 778883 5567899999999864
No 31
>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=99.93 E-value=4.1e-24 Score=211.24 Aligned_cols=242 Identities=17% Similarity=0.247 Sum_probs=182.2
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcc----cchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHG----RNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILH 77 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g----~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~ 77 (481)
.|+++++++|||++|++|+.+++++ ....+.+.+.+++.|+||+... +.......++..++++|++.. ++||++
T Consensus 131 ~a~~~~~~~~~w~~vaii~~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~-~~~~~~~~d~~~~l~~ik~~~-~vii~~ 208 (396)
T cd06373 131 EFVLALHEHFNWSRAALLYHDDKNDDRPCYFTLEGVYTVLKEENITVSDFP-FDEDKELDDYKELLRDISKKG-RVVIMC 208 (396)
T ss_pred HHHHHHHHHcCCeEEEEEEECCCCCcchHHHHHHHHHHHHhhcCceeeEEe-ecCCccccCHHHHHHHHHhcC-cEEEEe
Confidence 5788999999999999999887764 4568899999999999998553 443321247899999999875 999999
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEecccccccc----C----CccccccccccceeeEEEeeecCCchhHHHHHHHH
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILD----T----DSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRW 149 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~----~----~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~ 149 (481)
++...+..++++|.++||...+|+||..+....... . .........+...+++++.......+.+++|.+.|
T Consensus 209 ~~~~~~~~~~~qa~~~g~~~~~yv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~F~~~~ 288 (396)
T cd06373 209 ASPDTVREIMLAAHRLGLTSGEYVFFNIDLFGSSLYGGGPWWWERGDEDDEKAKEAYQALMTITLREPDNPEYKEFSLEV 288 (396)
T ss_pred cCHHHHHHHHHHHHHcCCCCCcEEEEEEccchhhhccCCCCcCCCCCcccHHHHHHHHHheEEecCCCCChHHHHHHHHH
Confidence 999999999999999999989999999764422110 0 00000122234567888877766778889999998
Q ss_pred hhhhccCC--CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHH
Q 011629 150 RHLTRRNT--LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNIL 227 (481)
Q Consensus 150 ~~~~~~~~--~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~ 227 (481)
++...... ..+...+..+++.+||||+++|+||+++..+... ..++..|.++|+
T Consensus 289 ~~~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~Al~~~~~~~~~------------------------~~~~~~i~~~l~ 344 (396)
T cd06373 289 KERAKKKFNTTSDDSLVNFFAGAFYDAVLLYALALNETLAEGGD------------------------PRDGTNITRRMW 344 (396)
T ss_pred HHHhhhcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCC------------------------CCChHHHHHHhc
Confidence 86532100 0111234568899999999999999998643211 113889999999
Q ss_pred hcccCceeeeEEEccCCCCCCCcEEEEEe---ecCceEEEEEeeCC
Q 011629 228 QVNMTGVTGPIKFTSDRDLINPAYEVINV---IGTGSRRIGYWSNH 270 (481)
Q Consensus 228 ~v~f~g~sG~v~Fd~~Gd~~~~~y~I~~~---~~~~~~~VG~~~~~ 270 (481)
+++|+|++|++.||++|++. ..|.|+++ +.+.++.+|.|++.
T Consensus 345 ~~~f~G~tG~v~fd~~G~~~-~~~~v~~~~~~~~g~~~~~~~~~~~ 389 (396)
T cd06373 345 NRTFEGITGNVSIDENGDRE-SDFSLWDMTDTETGTFEVVANYNGS 389 (396)
T ss_pred CCceecccCceEeecCCccc-ceeeeeeccCCCCceEEEEeecccc
Confidence 99999999999999999995 88999765 45789999999875
No 32
>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=99.93 E-value=1.2e-23 Score=206.16 Aligned_cols=233 Identities=19% Similarity=0.242 Sum_probs=173.4
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCC-ceEEEEEeCc
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMM-SRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~-~~vIvl~~~~ 80 (481)
+++++++++|+|++|++|++++++|....+.+.+.+++.|+||+..+.++.. ..++..+|++||+.+ +||||+++..
T Consensus 121 ~~~~~~~~~~~w~~vaii~~~~~~~~~~~~~l~~~l~~~gi~v~~~~~~~~~--~~d~~~~L~~lk~~~~~~viv~~~~~ 198 (382)
T cd06371 121 RVLFTVLRYFRWAHVAIVSSPQDIWVETAQKLASALRAHGLPVGLVTSMGPD--EKGAREALKKVRSADRVRVVIMCMHS 198 (382)
T ss_pred HHHHHHHHHCCCeEEEEEEecccchHHHHHHHHHHHHHCCCcEEEEEEecCC--HHHHHHHHHHHhcCCCcEEEEEEeec
Confidence 4788999999999999999999999999999999999999999988888654 348999999999987 6999998876
Q ss_pred -----HHHHHHHHHHHHcCCccCCeEEEEeccccccc-----cCCc-cccccccccceeeEEEeeecCCchhHHHHHHHH
Q 011629 81 -----IWGLEVLNAAKHLRMMESGYVWIVTDWLSSIL-----DTDS-QLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRW 149 (481)
Q Consensus 81 -----~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~-----~~~~-~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~ 149 (481)
.....++++|.++||+..+|+||.++...... .... ..+........+++.+.......+.++.|.+.+
T Consensus 199 ~~~~~~~~~~i~~qa~~~Gm~~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~f~~~~ 278 (382)
T cd06371 199 VLIGGEEQRLLLETALEMGMTDGRYVFIPYDTLLYSLPYRNVSYPALRNNSKLRRAYDAVLTITMDSGEQSFYEAFRAAQ 278 (382)
T ss_pred cccCcHHHHHHHHHHHHcCCcCCcEEEEEeccccccCCCCCccccCCCCCHHHHHHhHhhEEEEecCCCCcHHHHHHHHH
Confidence 67789999999999998999999987432111 0000 001223356777777765544333444455443
Q ss_pred hhhhccCCCC-CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHh
Q 011629 150 RHLTRRNTLN-GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQ 228 (481)
Q Consensus 150 ~~~~~~~~~~-~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~ 228 (481)
+.. ..+.+ +....+.+++++|||++++|.|++++.+.+.. .+ +..+.+.|++
T Consensus 279 ~~~--~~~~~~~~~~~~~~~~~~YDav~~~a~Al~~a~~~g~~------------------------~d-~~~l~~~l~~ 331 (382)
T cd06371 279 ERG--EIPSDLEPEQVSPLFGTIYNSIYLLAHAVENARAAGGG------------------------VS-GANLAQHTRN 331 (382)
T ss_pred hcC--CCCCCCCccccchhHHHHHHHHHHHHHHHHHHHHhCCC------------------------cc-HHHHHHHHhC
Confidence 211 01111 11123456678999999999999998653211 23 8899999999
Q ss_pred cccCceeeeEEEccCCCCCCCcEEEEEeecCceEEE
Q 011629 229 VNMTGVTGPIKFTSDRDLINPAYEVINVIGTGSRRI 264 (481)
Q Consensus 229 v~f~g~sG~v~Fd~~Gd~~~~~y~I~~~~~~~~~~V 264 (481)
++|+|++|+|+||++|++. ..|.|+++...+++-+
T Consensus 332 ~~f~GvtG~v~fd~~g~~~-~~~~v~~~~~~~~~~~ 366 (382)
T cd06371 332 LEFQGFNQRLRTDSGGGGQ-APYVVLDTDGKGDQLY 366 (382)
T ss_pred ccccccceEEEecCCCCcc-cceEEEecCCCCCeee
Confidence 9999999999999999985 9999999987554443
No 33
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=99.92 E-value=1.4e-23 Score=207.35 Aligned_cols=243 Identities=22% Similarity=0.399 Sum_probs=193.7
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCC-cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 2 AAIADIVDYFGWRNVIALYVDDD-HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.+++++++++||++++++++++. ||....+.+.+.+++.|+||.....++...+..++..+++++++++ ++||+++..
T Consensus 126 ~a~~~~l~~~~~~~v~ii~~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~d~~~~l~~i~~~~-~vii~~~~~ 204 (389)
T cd06352 126 EAVLALLRWFNWHVAVVVYSDDSENCFFTLEALEAALREFNLTVSHVVFMEDNSGAEDLLEILQDIKRRS-RIIIMCGSS 204 (389)
T ss_pred HHHHHHHHHcCceEEEEEEecCCccHHHHHHHHHHHHHhcCCeEEEEEEecCCccchhHHHHHHHhhhcc-eEEEEECCH
Confidence 57889999999999999998887 8999999999999999999999988876422347899999999887 999999998
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccC--------CccccccccccceeeEEEeeecCCchhHHHHHHHHhhh
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDT--------DSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHL 152 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~--------~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~ 152 (481)
..+..+++++.++|+...+++||.++.+...... .........+...|++++.......+.+++|.+.|++.
T Consensus 205 ~~~~~~l~q~~~~g~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~ 284 (389)
T cd06352 205 EDVRELLLAAHDLGLTSGDYVFILIDLFNYSLPYQNSYPWERGDGDDEKAKEAYDAVLTITLRPPDNPEYEEFSEEVKEA 284 (389)
T ss_pred HHHHHHHHHHHHcCCCCCcEEEEEEehhccccccCCCCCcccCCcccHHHHHHHHhheEEEecCCCCchHHHHHHHHHHH
Confidence 9999999999999998778999998766543210 01111223456778888877666778899999999987
Q ss_pred hccCCCC---CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhc
Q 011629 153 TRRNTLN---GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQV 229 (481)
Q Consensus 153 ~~~~~~~---~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v 229 (481)
+...+.+ ....+..++..+|||||++|+|++++..+... +.++..+.+.|+++
T Consensus 285 ~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~Al~~~~~~~~~------------------------~~~~~~v~~~l~~~ 340 (389)
T cd06352 285 AKRPPFNTDAEPEQVSPYAGYLYDAVLLYAHALNETLAEGGD------------------------YNGGLIITRRMWNR 340 (389)
T ss_pred HhcccCccCCCccccchhhhhHHHHHHHHHHHHHHHHHhCCC------------------------CCchHHHHHHhcCc
Confidence 7532111 12234668899999999999999998654221 12378899999999
Q ss_pred ccCceeeeEEEccCCCCCCCcEEEEEeec--CceEEEEEeeCC
Q 011629 230 NMTGVTGPIKFTSDRDLINPAYEVINVIG--TGSRRIGYWSNH 270 (481)
Q Consensus 230 ~f~g~sG~v~Fd~~Gd~~~~~y~I~~~~~--~~~~~VG~~~~~ 270 (481)
+|.|++|++.||++|++. ..|+|++++. +....++.+.+.
T Consensus 341 ~f~g~~G~v~fd~~G~~~-~~~~v~~~~~~~~~~~~~~~~~~~ 382 (389)
T cd06352 341 TFSGITGPVTIDENGDRE-GDYSLLDLDSTGGQLEVVYLYDTS 382 (389)
T ss_pred EEEeeeeeEEEcCCCCee-eeEEEEEecCCCceEEEEEecccc
Confidence 999999999999999996 8999999996 467888887754
No 34
>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=99.92 E-value=2.6e-23 Score=201.02 Aligned_cols=220 Identities=17% Similarity=0.206 Sum_probs=162.8
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhc-------cCCceEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVS-------SMMSRIL 74 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~-------~s~~~vI 74 (481)
+|+++++++|||++|+++|++++ |...++.+.+.+++.|+.+.... ...+ ....+..+++.++ ..+.++|
T Consensus 127 ~ai~~lv~~~~wkkvavly~~d~-g~~~l~~~~~~~~~~g~~v~~~~-~~~~-~~~~~~~l~~~~~~~~l~~~~~~~~~v 203 (363)
T cd06381 127 DVMLRLVTEWRWQKFVYFYDNDY-DIRGLQEFLDQLSRQGIDVLLQK-VDLN-ISKMATALFTTMRCEELNRYRDTLRRA 203 (363)
T ss_pred HHHHHHHHhCCCeEEEEEEECCc-hHHHHHHHHHHHHhcCceEEEEe-cccc-cchhhhhhhhHHHHHHHHhhcccceEE
Confidence 58999999999999999998765 66677888889999998666432 3211 1112333333332 4567788
Q ss_pred EEEeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHH----HHHHHHh
Q 011629 75 ILHTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKR----KFVTRWR 150 (481)
Q Consensus 75 vl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~----~f~~~~~ 150 (481)
|+.|+++.+..++++|.++||+..+|+||+++.|....... +.......|+++|++..+..+..+ ++.+.|+
T Consensus 204 Il~~~~~~~~~~l~~a~~~gm~~~~~~wi~~~~l~~~~~~l----~~~~~~~~nitgfrl~~~~~~~~~~~~~~~~~~~~ 279 (363)
T cd06381 204 LLLLSPNGAYTFIDASVETNLAIKDSHWFLINEEISDTEID----ELVRYAHGRMTVIRQTFSKEKTNQRCLRNNHRISS 279 (363)
T ss_pred EEEcCcHHHHHHHHHHHHcCCCcCceEEEEeccccccchhh----HHHhhcCccEEEEEEecCCcCchHHHHHHHHHHHH
Confidence 99999999999999999999999999999988776532111 345677889999999876665555 5556675
Q ss_pred hhhccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcc
Q 011629 151 HLTRRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVN 230 (481)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~ 230 (481)
......++ ....+...++++||||+++ +++|+++.
T Consensus 280 ~~~~~~~~-~~~~~~~~~al~yDaV~~~--------------------------------------------~~~~~~~~ 314 (363)
T cd06381 280 LLCDPKDG-YLQMLEISNLYIYDSVLLL--------------------------------------------LETIKKGP 314 (363)
T ss_pred hhcCCCCC-CCCChhHHHHHHHHHHHHH--------------------------------------------HHHHHhcC
Confidence 43322111 1113455789999999988 23467788
Q ss_pred cCceeeeEEEccCCCCCCCcEEEEEeecCc-----eEEEEEeeCCCCC
Q 011629 231 MTGVTGPIKFTSDRDLINPAYEVINVIGTG-----SRRIGYWSNHSGL 273 (481)
Q Consensus 231 f~g~sG~v~Fd~~Gd~~~~~y~I~~~~~~~-----~~~VG~~~~~~~l 273 (481)
|+|+||+|.||++|.|.+..++|+.+...+ .+.+|+|++..|+
T Consensus 315 ~~GLTG~i~F~~~g~r~~~~l~i~~~~~~~~~~~~~~~~~~w~~~~~~ 362 (363)
T cd06381 315 ITGLTGKLEFNEGGDNSNVQFEILGTGYSETLGKDGRWLATWNPSKGL 362 (363)
T ss_pred ccCcceeEEeCCCCCccccEEEEEEeccCCccccceEEeeeccCCCCC
Confidence 999999999999999999999999998544 7889999987654
No 35
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=99.91 E-value=6.4e-24 Score=201.65 Aligned_cols=208 Identities=21% Similarity=0.287 Sum_probs=154.4
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCC--CCChhHHHHHHHHhccCCceEEEEEe
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSP--KGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~--~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
++|+++|++||||++|.+||+++++ +..|++.++...+. ...++. ..+..++..++++|+++++++||+.|
T Consensus 122 ~~Ai~dli~~~~W~~v~~iYe~d~~----l~~L~~~l~~~~~~---~~~i~~~~~~~~~d~~~~L~~ik~~~~~~iVv~~ 194 (333)
T cd06394 122 SVAVAGILNSFNYPTASLICAKAEC----LLRLEELLRQFLIS---KETLSVRMLDDSRDPTPLLKEIRDDKTATIIIDA 194 (333)
T ss_pred HHHHHHHHHhcCCCEEEEEEeCcHH----HHHHHHHHHhhccc---CCceeeEEccCcccHHHHHHHHHhcCCCEEEEEC
Confidence 3799999999999999999988875 56666666654331 111111 11334799999999999999999999
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhcc-CC
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRR-NT 157 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~-~~ 157 (481)
+.+.+..++++|.++||+.++|+||+++......++ .++......+.+|++..+..+..++|.+.|++.+.+ +.
T Consensus 195 ~~~~a~~il~qa~~lGm~~~~y~~i~T~l~~~~~~L-----~~~~~~~~niTgF~l~d~~~~~v~~f~~~~~~~~~~~~~ 269 (333)
T cd06394 195 NASMSHTILLKASELGMTSAFYKYILTTMDFPLLRL-----DSIVDDRSNILGFSMFNQSHAFYQEFIRSLNQSWRENCD 269 (333)
T ss_pred ChHHHHHHHHHHHHcCCCCCceEEEEecCCcccccH-----HHhhcCCcceEEEEeecCCcHHHHHHHHHHHHhhhhhcc
Confidence 999999999999999999999999999865443333 222233456889998888889999999988765421 11
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeee
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGP 237 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~ 237 (481)
..+-......++.+||||+++ |+||+
T Consensus 270 ~~~~~~~~~~~al~~D~v~~~------------------------------------------------------glTg~ 295 (333)
T cd06394 270 HSPYTGPALSSALLFDAVYAV------------------------------------------------------GLTGR 295 (333)
T ss_pred cccCCCcccceeeecceEEEE------------------------------------------------------eeecc
Confidence 000000111344555554221 89999
Q ss_pred EEEccCCCCCCCcEEEEEeecCceEEEEEeeCCCCCc
Q 011629 238 IKFTSDRDLINPAYEVINVIGTGSRRIGYWSNHSGLS 274 (481)
Q Consensus 238 v~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l~ 274 (481)
|.||++|.|.+...+|+++..++.++||+|++..||+
T Consensus 296 i~f~~~g~R~~~~l~v~~l~~~g~~kig~W~~~~gl~ 332 (333)
T cd06394 296 IEFNSKGQRSNYTLKILQKTRSGFRQIGQWHSNETLS 332 (333)
T ss_pred eecCCCCcCcccEEEEEEecCCcceEEEEEeCCCCcC
Confidence 9999999999999999999999999999999987653
No 36
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=99.91 E-value=1.2e-22 Score=197.73 Aligned_cols=221 Identities=37% Similarity=0.709 Sum_probs=179.6
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++++++++++||++|++|+.++++|....+.+++.+++.|+||...+.++...+..++..++++|+++++++|++++...
T Consensus 124 ~a~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~dvvi~~~~~~ 203 (350)
T cd06366 124 PAIAALLKKFGWRRVATIYEDDDYGSGGLPDLVDALQEAGIEISYRAAFPPSANDDDITDALKKLKEKDSRVIVVHFSPD 203 (350)
T ss_pred HHHHHHHHHCCCcEEEEEEEcCcccchhHHHHHHHHHHcCCEEEEEeccCCCCChhHHHHHHHHHhcCCCeEEEEECChH
Confidence 57899999999999999999999999999999999999999999998887653345899999999999999999999999
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccC-CccccccccccceeeEEEeeecCC-chhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDT-DSQLHSEKMDDIQGVLTLRMYTQS-SEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~-~~~~~~~~~~~~~g~l~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~ 159 (481)
++..+++++.++||..++++||.++.+...++. ..+..........|++++....+. .+.+++|.+.|++.+...+..
T Consensus 204 ~~~~~~~~a~~~g~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~ 283 (350)
T cd06366 204 LARRVFCEAYKLGMMGKGYVWILTDWLSSNWWSSSDCTDEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWRKRFGNENPE 283 (350)
T ss_pred HHHHHHHHHHHcCCcCCCEEEEECcchhhhhccCCCCChHHHHHhhceEEEEeecccccCccHHHHHHHHHHHhcccCcC
Confidence 999999999999998788999999765433210 001112334567888988877666 788999999999887421111
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIK 239 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~ 239 (481)
...+..+++..|||+++ +++|.|++|+|+
T Consensus 284 -~~~p~~~a~~~YDav~~--------------------------------------------------~~~~~G~~G~v~ 312 (350)
T cd06366 284 -LTEPSIYALYAYDAVWA--------------------------------------------------STNFNGLSGPVQ 312 (350)
T ss_pred -cCCCCcccchhhhheee--------------------------------------------------eceEEeeeeeEE
Confidence 11355678889999877 125679999999
Q ss_pred EccCCCCCCCcEEEEEeecCceEEEEEeeCCCCC
Q 011629 240 FTSDRDLINPAYEVINVIGTGSRRIGYWSNHSGL 273 (481)
Q Consensus 240 Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~l 273 (481)
||++|++.+..|+++++..+++++||.|++..++
T Consensus 313 fd~~~~~~~~~~~~~~~~~~~~~~vg~~~~~~~~ 346 (350)
T cd06366 313 FDGGRRLASPAFEIINIIGKGYRKIGFWSSESGL 346 (350)
T ss_pred EcCCCccCCcceEEEEecCCceEEEEEEeCCCCc
Confidence 9999998779999999988899999999987665
No 37
>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=99.90 E-value=2.4e-23 Score=201.55 Aligned_cols=232 Identities=13% Similarity=0.051 Sum_probs=152.5
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHH-HHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGD-KLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~-~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
++|+++|++||||+||++||++++.+....+.+.+ .....++|+. +. ...++...+++|+++++++||+.+.
T Consensus 121 ~~Ai~dlI~~f~W~~v~iIYddd~gl~~~l~~~l~~~~~~~~~~v~-----~~--~~~~~~~~Lk~lk~~~~~rIIi~~s 193 (368)
T cd06383 121 VEAIRDIVSYYNITNAAILYDDDFVMDHKYKSLLQNWPTRHVITII-----NS--IIDEVREQIKRLRNLDIKNIFILGS 193 (368)
T ss_pred HHHHHHHHHHCCCcEEEEEEEcCchhhHHHHHHHHhHHhcCCEEEE-----ec--cchhHHHHHHHHHhCCCeEEEEEeC
Confidence 37999999999999999999776643323333333 3444555553 11 1236789999999988866666666
Q ss_pred -cHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCC
Q 011629 80 -DIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTL 158 (481)
Q Consensus 80 -~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~ 158 (481)
++.+..+|++|.++||++.+|+||++++.....+. +.....-.++.+|++........+++++.|.... ..+
T Consensus 194 ~~~~~~~il~qA~~lgm~~~~y~wilt~ld~~~~dl-----~~~~~~~~Nitgfrl~~~~~~~~~~~~~~~~~~~--~~~ 266 (368)
T cd06383 194 TEEIIRYVLDQALAEGFMGRKYAWFLGNPDLGIYDD-----LSCQLRNASIFVTRPMMDYQSSVRGALLRTDEPT--LRP 266 (368)
T ss_pred CHHHHHHHHHHHHHcCCcCCceEEEEcCCCchhhhh-----hhhccccCcEEEeeccccchhhhccceeeccCCc--cCc
Confidence 49999999999999999999999999875444332 2233344578888885444444466766663211 011
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccc---ccc-CccHHHHHHHHhcccCce
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSV---SIF-NGGKMLLDNILQVNMTGV 234 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~~L~~~l~~v~f~g~ 234 (481)
.........++.+||||+++|.|++++....... .+. ......|... .+| ..|..+.++|+.+.|+|+
T Consensus 267 ~~~~~~~~~~aL~~Dav~~~~~a~~~l~~~~~~~-~~~-------~~~~~~~~g~~~~~~w~~~g~~~~~~~k~~~~~gl 338 (368)
T cd06383 267 VFYFEWAFRLFLAYDAVLAVGEWPRRMRKKRVED-GST-------GTSVLPGFGISPESPLMTLQSSPFNGSSEIKFEML 338 (368)
T ss_pred hhHHHHHHHHHHHHHHHHHhccccchhheeeccC-CCc-------CccccCCCCCCcccchhhcccccccCccceeEeee
Confidence 1111233468999999999999999873221110 000 0011123322 134 456699999999999999
Q ss_pred eeeEEEccCCCCCCCcEEEEEe
Q 011629 235 TGPIKFTSDRDLINPAYEVINV 256 (481)
Q Consensus 235 sG~v~Fd~~Gd~~~~~y~I~~~ 256 (481)
||+|.||++|.|. .|.+.-|
T Consensus 339 tG~i~f~~~g~R~--~~~l~~~ 358 (368)
T cd06383 339 AGRVAIDEGSSVS--TKTIGSW 358 (368)
T ss_pred cCeEEEecCceee--eeeeeeE
Confidence 9999999999874 5555433
No 38
>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=99.87 E-value=4.5e-21 Score=184.69 Aligned_cols=204 Identities=22% Similarity=0.326 Sum_probs=155.2
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCC---EEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEe
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRC---RLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi---~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
+|++++++++||++|++++++++++ +.+.+.+++.+. .|.. ..++.. . |+..++++|+++++++||+++
T Consensus 118 ~a~~~~~~~~~w~~vavl~~~~~~~----~~l~~~~~~~~~~g~~v~~-~~~~~~--~-d~~~~l~~i~~~~~d~vv~~~ 189 (327)
T cd06382 118 RAYADIVKSFNWKSFTIIYESAEGL----LRLQELLQAFGISGITITV-RQLDDD--L-DYRPLLKEIKNSGDNRIIIDC 189 (327)
T ss_pred HHHHHHHHhcCCcEEEEEecChHHH----HHHHHHHHhhccCCCeEEE-EEccCC--c-cHHHHHHHHHhcCceEEEEEC
Confidence 5889999999999999999888754 445555655554 4443 345433 2 799999999999999999999
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccC-C
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRN-T 157 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~-~ 157 (481)
....+..++++|.++||..+.++|++++......+. ........++.++.+..+..+.+++|.+.|++.+... +
T Consensus 190 ~~~~~~~~~~qa~~~g~~~~~~~~i~~~~~~~~~~l-----~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~ 264 (327)
T cd06382 190 SADILIELLKQAQQVGMMSEYYHYIITNLDLHTLDL-----EDYRYSGVNITGFRLVDPDSPEVKEVIRSLELSWDEGCR 264 (327)
T ss_pred CHHHHHHHHHHHHHhCccccceEEEEecCCccccch-----hhhccCceeEEEEEEecCCchhHHHHHHHHHhhcccccc
Confidence 999999999999999999888999998765443322 1112223367777777777889999999999887531 1
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeee
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGP 237 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~ 237 (481)
......+..+++.+|||++++ |+||+
T Consensus 265 ~~~~~~p~~~~a~~yDav~~~------------------------------------------------------g~tG~ 290 (327)
T cd06382 265 ILPSTGVTTESALMYDAVYLF------------------------------------------------------GLTGR 290 (327)
T ss_pred cCCCCCcchhhhhhhceEEEe------------------------------------------------------ecccc
Confidence 111112444566777775332 88999
Q ss_pred EEEccCCCCCCCcEEEEEeecCceEEEEEeeCCCC
Q 011629 238 IKFTSDRDLINPAYEVINVIGTGSRRIGYWSNHSG 272 (481)
Q Consensus 238 v~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~ 272 (481)
|.||++|+|.+..++|+|+..+++++||.|++..+
T Consensus 291 v~f~~~g~r~~~~~~~~~~~~~~~~~vg~w~~~~~ 325 (327)
T cd06382 291 IEFDSSGQRSNFTLDVIELTESGLRKVGTWNSSEG 325 (327)
T ss_pred eeeCCCCCEeeeEEEEEeccccCceEEEEECCCCC
Confidence 99999999999999999999889999999998654
No 39
>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=99.87 E-value=2.4e-20 Score=177.45 Aligned_cols=216 Identities=15% Similarity=0.199 Sum_probs=144.3
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCC-----EEEEEEecCC-CCChhHH-HHHHHHhccCC-ce
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRC-----RLSHKVPLSP-KGSRNQI-IDTLLTVSSMM-SR 72 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi-----~v~~~~~~~~-~~~~~~~-~~~l~~i~~s~-~~ 72 (481)
++|+++||+||||++|++||+.+.. . ..|++.++..+. .|... .++. ..+..++ +.+|+.|+++. ++
T Consensus 139 ~~a~~~ll~~~~W~~f~~iy~~~~g-l---~~lq~l~~~~~~~~~~~~i~v~-~~~~~~~d~~~~~~~~L~~i~~~~~~~ 213 (382)
T cd06377 139 LDVLLSVLQRNGWEDVSLVLCRERD-P---TGLLLLWTNHARFHLGSVLNLS-RNDPSTADLLDFLRAQLELLKDPPGPA 213 (382)
T ss_pred HHHHHHHHHHCCCcEEEEEEecCcC-H---HHHHHHHHHhcccccCceEEEE-eccCccCChhHHHHHHHHHhhcccCce
Confidence 3699999999999999999987763 3 334444444332 22222 2221 1133345 89999999999 99
Q ss_pred EEEEEeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhh
Q 011629 73 ILILHTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHL 152 (481)
Q Consensus 73 vIvl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~ 152 (481)
+|+++|+.+.+..+|.++.+ +|+||+++.. +... .....+-.|+++.. +.
T Consensus 214 ~ill~cs~e~~~~il~~~~~------~y~wIv~~~~----~le~---~~~~g~nigLl~~~-----------------~~ 263 (382)
T cd06377 214 VVLFGCDVARARRVLELTPP------GPHWILGDPL----PPEA---LRTEGLPPGLLAHG-----------------ET 263 (382)
T ss_pred EEEEECCHHHHHHHHHhhcc------ceEEEEcCCc----Chhh---ccCCCCCceEEEEe-----------------ec
Confidence 99999999999999987643 4999998721 1110 00112222333211 00
Q ss_pred hccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccc--c-ccCccHHHHHHHHhc
Q 011629 153 TRRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSV--S-IFNGGKMLLDNILQV 229 (481)
Q Consensus 153 ~~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~L~~~l~~v 229 (481)
.....++++||||+++|.|++.+......... .....+|... . .|..|..|.++|+++
T Consensus 264 ----------~~~~l~ali~DAV~lvA~a~~~l~~~~~~~~l---------~~~~~~C~~~~~~~~W~~G~~l~~~Lknv 324 (382)
T cd06377 264 ----------TQPPLEAYVQDALELVARAVGSATLVQPELAL---------IPATVNCMDLPTKGNESSGQYLARFLANT 324 (382)
T ss_pred ----------ccccHHHHHHHHHHHHHHHHHHhhhccccccc---------CCCCCCcccCCCCCCCCchHHHHHHHHhC
Confidence 00023789999999999999986321111000 0112356433 4 788899999999999
Q ss_pred ccCceeeeEEEccCCCC--CCCcEEEEEee--cC---ceEEEEEeeCCC
Q 011629 230 NMTGVTGPIKFTSDRDL--INPAYEVINVI--GT---GSRRIGYWSNHS 271 (481)
Q Consensus 230 ~f~g~sG~v~Fd~~Gd~--~~~~y~I~~~~--~~---~~~~VG~~~~~~ 271 (481)
+|+|.||+|.|+ .|.| .+..++|++++ .. .|++||+|++..
T Consensus 325 ~~eGlTG~I~F~-~g~R~~~~~~l~I~~L~~~~~G~~~W~kVG~W~~~~ 372 (382)
T cd06377 325 SFDGRTGPVWVT-GSSQVHSSRHFKVWSLRRDPVGQPTWTTVGSWQGGR 372 (382)
T ss_pred cccccceeEEEc-cCeeecccceEEEEEeccccCCCccceEEEEecCCC
Confidence 999999999995 5767 67899999998 33 469999999853
No 40
>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=99.85 E-value=3.2e-20 Score=178.70 Aligned_cols=206 Identities=24% Similarity=0.375 Sum_probs=159.3
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.|+++++++|||++|++|+++++ |...++.+.+.+.+.|++|......+ ..+ ++..++.+|++.++++||+.+...
T Consensus 116 ~a~~~~~~~~~w~~vaii~~~~~-~~~~l~~~~~~~~~~g~~v~~~~~~~-~~~--d~~~~l~~i~~~~~d~Vi~~~~~~ 191 (324)
T cd06368 116 DALLDLIKYFGWRKFVYIYDSDE-GLLRLQELLDALSPKGIQVTVRRLDD-DTD--MYRPLLKEIKREKERRIILDCSPE 191 (324)
T ss_pred HHHHHHHHhcCCCEEEEEECCcH-hHHHHHHHHHhhccCCceEEEEEecC-Cch--HHHHHHHHHhhccCceEEEECCHH
Confidence 58899999999999999997665 55566777788888899998765433 222 799999999999999999999999
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhcc-CCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRR-NTLNG 160 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~ 160 (481)
++..++++|.++||..++++||+++......+. ........++.++.......+.+++|.+.|++.++. ++...
T Consensus 192 ~~~~i~~qa~~~g~~~~~~~~i~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~ 266 (324)
T cd06368 192 RLKEFLEQAVEVGMMSEYYHYILTNLDFHTLDL-----ELFRYGGVNITGFRLVDPDNPEVQKFIQRWERSDHRICPGSG 266 (324)
T ss_pred HHHHHHHHHHHhccccCCcEEEEccCCccccch-----hhhhcCCceEEEEEEecCCChHHHHHHHHHHhccccccCCCC
Confidence 999999999999998889999998643322111 111222335667666667788999999999988742 11111
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEEE
Q 011629 161 PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKF 240 (481)
Q Consensus 161 ~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~F 240 (481)
...+..+++.+||||+++ ||++.|
T Consensus 267 ~~~p~~~aa~~yDav~~~--------------------------------------------------------tg~~~f 290 (324)
T cd06368 267 LKPIKTESALTYDAVLLF--------------------------------------------------------TGRIQF 290 (324)
T ss_pred CCCcchhhHhhhcEEEEe--------------------------------------------------------eeeeEe
Confidence 123455778888886433 778999
Q ss_pred ccCCCCCCCcEEEEEeecCceEEEEEeeCCCC
Q 011629 241 TSDRDLINPAYEVINVIGTGSRRIGYWSNHSG 272 (481)
Q Consensus 241 d~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~~ 272 (481)
|++|+|.+..++|+++..+++..||.|++..+
T Consensus 291 ~~~g~~~~~~~~i~~~~~~~~~~~g~W~~~~~ 322 (324)
T cd06368 291 DENGQRSNFTLDILELKEGGLRKVGTWNPEDG 322 (324)
T ss_pred CCCCcCcceEEEEEEEcCCCceEEEEECCCCC
Confidence 99999999999999999899999999998654
No 41
>cd06350 PBP1_GPCR_family_C_like Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). The metabotropic glutamate receptors (mGluR) are key receptors in the modulation of excitatory synaptic transmission in the central nervous system. The mGluRs are coupled to G proteins and are thus distinct from the iGluRs which internally contain ligand-gated ion channels. The mGluR structure is divided into three regions: the extracellular region, the seven-spanning transmembrane region and the cytoplasmic region. The extr
Probab=99.80 E-value=2.3e-18 Score=167.54 Aligned_cols=188 Identities=25% Similarity=0.437 Sum_probs=148.2
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.|++++++++||++|++|+++++||....+.|++.+++.|+||+..+.++...+..++..++++|+++++++||+++...
T Consensus 149 ~a~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vvv~~~~~~ 228 (348)
T cd06350 149 LAIVALLKHFGWTWVGLVYSDDDYGRSGLSDLEEELEKNGICIAFVEAIPPSSTEEDIKRILKKLKSSTARVIVVFGDED 228 (348)
T ss_pred HHHHHHHHHCCCeEEEEEEecchhHHHHHHHHHHHHHHCCCcEEEEEEccCCCcHHHHHHHHHHHHhCCCcEEEEEeCcH
Confidence 68899999999999999999999999999999999999999999999887654345899999999999999999999999
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTLNGP 161 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~ 161 (481)
++..++++|.++|+ .+..|+.++.|....... ....+...|++++....+.......|.+.+++
T Consensus 229 ~~~~~~~~a~~~g~--~~~~~i~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~---------- 292 (348)
T cd06350 229 DALRLFCEAYKLGM--TGKYWIISTDWDTSTCLL----LFTLDAFQGVLGFSGHAPRSGEIPGFKDFLRK---------- 292 (348)
T ss_pred HHHHHHHHHHHhCC--CCeEEEEEccccCccccc----cCCcceeeeEEEEEEEeecCCcCCChHHHHHH----------
Confidence 99999999999998 345666666554431111 22335567777776655433333334444442
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEEEc
Q 011629 162 IGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKFT 241 (481)
Q Consensus 162 ~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~Fd 241 (481)
+++++|||||+ .+.||
T Consensus 293 -----~~~~~YDav~~-----------------------------------------------------------~v~f~ 308 (348)
T cd06350 293 -----YAYNVYDAVYA-----------------------------------------------------------EVKFD 308 (348)
T ss_pred -----HHHHHHhheeE-----------------------------------------------------------EEEec
Confidence 56788999755 47899
Q ss_pred cCCCCCCCcEEEEEeec----CceEEEEEeeCC
Q 011629 242 SDRDLINPAYEVINVIG----TGSRRIGYWSNH 270 (481)
Q Consensus 242 ~~Gd~~~~~y~I~~~~~----~~~~~VG~~~~~ 270 (481)
++||+. ..|+|.+++. ..+++||.|++.
T Consensus 309 ~~gd~~-~~~~i~~~~~~~~~~~~~~vg~~~~~ 340 (348)
T cd06350 309 ENGDRL-ASYDIINWQIFPGGGGFVKVGFWDPQ 340 (348)
T ss_pred CCCCcc-cceeEEEEEEcCCcEEEEEEEEEcCC
Confidence 999996 8999999986 579999999863
No 42
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=99.78 E-value=1.5e-17 Score=160.89 Aligned_cols=209 Identities=17% Similarity=0.169 Sum_probs=165.5
Q ss_pred hHhHHHH-HHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 2 AAIADIV-DYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~ll-~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.++++++ ++++|++|++++.++++|....+.+++.+++.|++|.....++... .++...+++++++++++|++.+..
T Consensus 123 ~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~--~d~~~~l~~i~~~~~~~vi~~~~~ 200 (334)
T cd06342 123 PAAAKYAVETLKAKKVAIIDDKTAYGQGLADEFKKALKAAGGKVVAREGTTDGA--TDFSAILTKIKAANPDAVFFGGYY 200 (334)
T ss_pred HHHHHHHHHhcCCCEEEEEeCCcchhhHHHHHHHHHHHHcCCEEEEEecCCCCC--ccHHHHHHHHHhcCCCEEEEcCcc
Confidence 4677754 6899999999999999999999999999999999999988887643 378999999999999999999988
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecC--CchhHHHHHHHHhhhhccCCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQ--SSEEKRKFVTRWRHLTRRNTL 158 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~f~~~~~~~~~~~~~ 158 (481)
..+..+++++.+.|+. ..||.++.+... ... ........|++......+ ..+..++|.+.|.+.+..
T Consensus 201 ~~~~~~~~~~~~~g~~---~~~~~~~~~~~~-~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--- 269 (334)
T cd06342 201 PEAGPLVRQMRQLGLK---APFMGGDGLCDP-EFI----KIAGDAAEGTYATFPGGPLEKMPAGKAFVARYKAKFGD--- 269 (334)
T ss_pred hhHHHHHHHHHHcCCC---CcEEecCccCCH-HHH----HHhhHhhCCcEEEecCCCCCCChHHHHHHHHHHHHhCC---
Confidence 8999999999998873 467766544321 110 111234566666654433 467788999999876642
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeE
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPI 238 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v 238 (481)
.++.++...||++++++.|++++- ..+ +..+.+.|++++|.|++|++
T Consensus 270 ----~~~~~~~~~yda~~~~~~al~~~~----------------------------~~~-~~~v~~~l~~~~~~g~~g~i 316 (334)
T cd06342 270 ----PPGAYAPYAYDAANVLAEAIKKAG----------------------------STD-PAKVADALRKVDFDGVTGKI 316 (334)
T ss_pred ----CCchhHHHHHHHHHHHHHHHHHhC----------------------------CCC-HHHHHHHHHhCCCCCcceee
Confidence 134578999999999999998741 022 78899999999999999999
Q ss_pred EEccCCCCCCCcEEEEEe
Q 011629 239 KFTSDRDLINPAYEVINV 256 (481)
Q Consensus 239 ~Fd~~Gd~~~~~y~I~~~ 256 (481)
.|+++|++.+..|+|+||
T Consensus 317 ~f~~~g~~~~~~~~~~~~ 334 (334)
T cd06342 317 SFDAKGDLKGAAVTVYQV 334 (334)
T ss_pred EECCCCCcccCcEEEEeC
Confidence 999999998899999886
No 43
>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=99.77 E-value=9.8e-19 Score=172.02 Aligned_cols=247 Identities=17% Similarity=0.309 Sum_probs=179.8
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~ 82 (481)
.+++++++|+|++|+.++++......-.+.|...+.+.++++.++..+.. |....+++++..++|+|+-..+...
T Consensus 171 ~rl~l~~~~~w~rvgt~~q~e~~f~~~~~dl~~~~~~~~ieiv~~qsf~~-----dp~~~vk~l~~~D~RiI~g~f~~~~ 245 (865)
T KOG1055|consen 171 TRIKLLKKFGWKRVATLQQTEEVFSSTLNDLEARLKEAGIEIVFRQSFSS-----DPADSVKNLKRQDARIIVGLFYETE 245 (865)
T ss_pred ceeeechhcCcceeeeeeeehhhhcchHHHHHHhhhccccEEEEeecccc-----CHHHHHhhccccchhheeccchHhh
Confidence 35688999999999999999988888999999999999999998877654 3446678899999999999999999
Q ss_pred HHHHHHHHHHcCCccCCeEEEEeccccccc-----cCCccccccccccceeeEEEeeecC------C--chhHHHHHHHH
Q 011629 83 GLEVLNAAKHLRMMESGYVWIVTDWLSSIL-----DTDSQLHSEKMDDIQGVLTLRMYTQ------S--SEEKRKFVTRW 149 (481)
Q Consensus 83 ~~~il~~a~~~g~~~~~~~wI~~~~~~~~~-----~~~~~~~~~~~~~~~g~l~~~~~~~------~--~~~~~~f~~~~ 149 (481)
++.++|++++.+|.+..|+|++..+...++ +..+|.-.++..++.|.+++..... . .-...+|+..+
T Consensus 246 Arkv~C~~Y~~~myg~ky~w~~~g~y~d~w~ev~~~~~~ctveem~~A~eg~~s~e~~pl~~~~~~tisg~T~~~~l~~~ 325 (865)
T KOG1055|consen 246 ARKVFCEAYKERLYGRKYVWFLIGWYADNWWEITHPSENCTVEEMTEAAEGHITTEFVMLSPANITTISGMTAQEFLEEL 325 (865)
T ss_pred hhHHHHhhchhhcccceeEEEEEEeeccchhhccCchhhhhHHHHHHHHhhheeeeeeccccccceeeccchhHHHHHHH
Confidence 999999999999999999999986443322 2223444566677777777743211 1 11223444444
Q ss_pred hhhhcc-CCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHh
Q 011629 150 RHLTRR-NTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQ 228 (481)
Q Consensus 150 ~~~~~~-~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~ 228 (481)
...... | +........+++|||||++|+|++++.......... .. ... ...-.-...++++|++
T Consensus 326 ~~~r~~~~---~~~~~~~~~~~ayd~Iwa~ala~n~t~e~l~~~~~~---------l~--~f~-y~~k~i~d~i~eamn~ 390 (865)
T KOG1055|consen 326 TKYRKRHP---EETGGFQEAPLAYDAIWALALALNKTMEGLGRSHVR---------LE--DFN-YNNKTIADQIYEAMNS 390 (865)
T ss_pred Hhhhcccc---ccccCcccCchHHHHHHHHHHHHHHHHhcCCcccee---------cc--ccc-hhhhHHHHHHHHHhhc
Confidence 332221 1 111234467899999999999999887643210000 00 000 0001114679999999
Q ss_pred cccCceeeeEEEccCCCCCCCcEEEEEeecCceEEEEEeeCCC
Q 011629 229 VNMTGVTGPIKFTSDRDLINPAYEVINVIGTGSRRIGYWSNHS 271 (481)
Q Consensus 229 v~f~g~sG~v~Fd~~Gd~~~~~y~I~~~~~~~~~~VG~~~~~~ 271 (481)
++|.|++|.|.|.. |+|. +...|.+++++..+++|.|+...
T Consensus 391 tsF~GvsG~V~F~~-geR~-a~t~ieQ~qdg~y~k~g~Yds~~ 431 (865)
T KOG1055|consen 391 TSFEGVSGHVVFSN-GERM-ALTLIEQFQDGKYKKIGYYDSTK 431 (865)
T ss_pred ccccccccceEecc-hhhH-HHHHHHHHhCCceEeeccccccc
Confidence 99999999999987 9997 99999999999999999998653
No 44
>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=99.77 E-value=2.2e-17 Score=159.24 Aligned_cols=201 Identities=22% Similarity=0.347 Sum_probs=145.4
Q ss_pred ChHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCc-eEEEEEeC
Q 011629 1 MAAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMS-RILILHTY 79 (481)
Q Consensus 1 ~~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~-~vIvl~~~ 79 (481)
++|+++++.+|+|++|++||++++++ ..++.+.+.....+.++... .+....+ ++...++++++.++ +||++++.
T Consensus 120 ~~a~~~~l~~~~w~~v~iiy~~~~~~-~~l~~~~~~~~~~~~~v~~~-~~~~~~~--~~~~~l~~l~~~~~~~vil~~~~ 195 (328)
T cd06351 120 ADALLDLLEYYNWTKFAIIYDSDEGL-SRLQELLDESGIKGIQVTVR-RLDLDDD--NYRQLLKELKRSESRRIILDCSS 195 (328)
T ss_pred HHHHHHHHHHcCCcEEEEEEeCchHH-HHHHHHHHhhcccCceEEEE-EecCCch--hHHHHHHHHhhcccceEEEECCc
Confidence 36899999999999999999888743 33444444444445566654 3443322 68899999999888 66666555
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCCC
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
...+..++++|.++||..++|+||+++......+. ........|++++++.....+.+.+|...|.... +..
T Consensus 196 ~~~~~~~l~~a~~~gm~~~~~~~i~~~~~~~~~d~-----~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~~~---~~~ 267 (328)
T cd06351 196 EEEAKEILEQAVELGMMGYGYHWILTNLDLSDIDL-----EPFQYGPANITGFRLVDPDSPDVSQFLQRWLEES---PGV 267 (328)
T ss_pred HHHHHHHHHHHHHhccccCCcEEEEecCCccccch-----hhhccCCcceEEEEEeCCCchHHHHHHHhhhhcc---CCC
Confidence 58999999999999999999999999865543322 2344566899999999988888999999883211 111
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIK 239 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~ 239 (481)
........++.+||++++ . +|.+.
T Consensus 268 ~~~~~~~~~~~~~d~~~~--------------------------------------~------------------tg~i~ 291 (328)
T cd06351 268 NLRAPIYDAALLYDAVLL--------------------------------------L------------------TGTVS 291 (328)
T ss_pred CcCccchhhHhhhcEEEE--------------------------------------E------------------EeeEE
Confidence 111122233444444210 0 88999
Q ss_pred EccCCCCCCCcEEEEEee-cCceEEEEEeeC
Q 011629 240 FTSDRDLINPAYEVINVI-GTGSRRIGYWSN 269 (481)
Q Consensus 240 Fd~~Gd~~~~~y~I~~~~-~~~~~~VG~~~~ 269 (481)
||++|.|.+..++|+++. ..++.+||.|++
T Consensus 292 f~~~g~r~~~~l~i~~l~~~~~~~~vg~W~~ 322 (328)
T cd06351 292 FDEDGVRSNFTLDIIELNRSRGWRKVGTWNG 322 (328)
T ss_pred ECCCCcccceEEEEEEecCCCCceEEEEecC
Confidence 999999999999999998 789999999984
No 45
>cd06369 PBP1_GC_C_enterotoxin_receptor Ligand-binding domain of the membrane guanylyl cyclase C. Ligand-binding domain of the membrane guanylyl cyclase C (GC-C or StaR). StaR is a key receptor for the STa (Escherichia coli Heat Stable enterotoxin), a potent stimulant of intestinal chloride and bicarbonate secretion that cause acute secretory diarrhea. The catalytic domain of the STa/guanylin receptor type membrane GC is highly similar to those of the natriuretic peptide receptor (NPR) type and sensory organ-specific type membrane GCs (GC-D, GC-E and GC-F). The GC-C receptor is mainly expressed in the intestine of most vertebrates, but is also found in the kidney and other organs. Moreover, GC-C is activated by guanylin and uroguanylin, endogenous peptide ligands synthesized in the intestine and kidney. Consequently, the receptor activation results in increased cGMP levels and phosphorylation of the CFTR chloride channel and secretion.
Probab=99.71 E-value=7.3e-16 Score=143.28 Aligned_cols=218 Identities=14% Similarity=0.195 Sum_probs=156.3
Q ss_pred HhHHHH------HHcCCcEEEEEEEeCCccc---chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceE
Q 011629 3 AIADIV------DYFGWRNVIALYVDDDHGR---NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI 73 (481)
Q Consensus 3 Ai~~ll------~~fgW~~V~ii~~dd~~g~---~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v 73 (481)
.++++. +||+|+..- ||.+++.-+ --+.++....+..+..+.+.+... ..+++.++++.+++ ++||
T Consensus 137 ~~~~f~~~~~~~~~~~W~~ay-vyk~~~~~edCf~~i~al~a~~~~f~~~~~~~~~l~---~~~~~~~il~~~~~-~sRI 211 (380)
T cd06369 137 FFVDFWKEKNFPKKPKWETAY-VYKKQENTEDCFWYINALEAGVAYFSSALKFKELLR---TEEELQKLLTDKNR-KSNV 211 (380)
T ss_pred HHHHHHhcccccCCCCCceeE-EEcCCCCccceeeEhHhhhhhhhhhhhcccceeeec---CchhHHHHHHHhcc-CccE
Confidence 355666 589998555 997764322 236666666666666666555432 23468888888775 4999
Q ss_pred EEEEeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhh
Q 011629 74 LILHTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLT 153 (481)
Q Consensus 74 Ivl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~ 153 (481)
||+|++++.++.++..+ +...+|+.|..+........ +....+++++++.+++..+..+.+.+.
T Consensus 212 iImCG~p~~ir~lm~~~----~~~gDYVf~~IDlF~~sy~~----d~~a~~amqsVLvIT~~~p~~~~~~~~-------- 275 (380)
T cd06369 212 IIMCGTPEDIVNLKGDR----AVAEDIVIILIDLFNDVYYE----NTTSPPYMRNVLVLTLPPRNSTNNSSF-------- 275 (380)
T ss_pred EEEeCCHHHHHHHHhcC----ccCCCEEEEEEecccchhcc----CcchHHHHhceEEEecCCCCCcccccC--------
Confidence 99999999999999863 33468999998866433211 123456788899998776655443321
Q ss_pred ccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCc
Q 011629 154 RRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTG 233 (481)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g 233 (481)
.+.+..+. ..+++..||||.++|+||++++..+++ .+ +..+.+.|+|.+|.|
T Consensus 276 --~~fn~~l~-~~~aa~fyDaVLLYa~AL~EtL~~G~~------------------------~~-~~~I~~~m~NrTF~G 327 (380)
T cd06369 276 --TTDNSLLK-DDYVAAYHDGVLLFGHVLKKFLESQEG------------------------VQ-TFSFINEFRNISFEG 327 (380)
T ss_pred --CCCCcchH-HHHHHHHHHHHHHHHHHHHHHHHhCCC------------------------CC-cHHHHHHHhCcceec
Confidence 01111111 168999999999999999999876432 22 478899999999999
Q ss_pred eeeeEEEccCCCCCCCcEEEEEeec--CceEEEEEeeCC
Q 011629 234 VTGPIKFTSDRDLINPAYEVINVIG--TGSRRIGYWSNH 270 (481)
Q Consensus 234 ~sG~v~Fd~~Gd~~~~~y~I~~~~~--~~~~~VG~~~~~ 270 (481)
++|.|.+|++|||. ..|.++.+.. +++..||.|+..
T Consensus 328 itG~V~IDeNGDRd-~dfsLl~ms~~tg~y~vV~~y~t~ 365 (380)
T cd06369 328 AGGPYTLDEYGDRD-VNFTLLYTSTDTSKYKVLFEFDTS 365 (380)
T ss_pred CCCceEeCCCCCcc-CceEEEEeeCCCCCeEEEEEEECC
Confidence 99999999999995 9999998764 689999999864
No 46
>cd06348 PBP1_ABC_ligand_binding_like_13 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.71 E-value=1.2e-15 Score=148.17 Aligned_cols=213 Identities=15% Similarity=0.224 Sum_probs=157.7
Q ss_pred HhHHHHHHc-CCcEEEEEEEeCC-cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 3 AIADIVDYF-GWRNVIALYVDDD-HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 3 Ai~~ll~~f-gW~~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
++..+++++ ||+++++||.+++ ||....+.+++.+++.|++|.....++... .|+..++.+|+++++++|++.+..
T Consensus 125 ~~~~~~~~~~~~~~v~~l~~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~--~d~~~~v~~i~~~~~d~vi~~~~~ 202 (344)
T cd06348 125 AIAAALKLNPGIKRVAVFYAQDDAFSVSETEIFQKALRDQGLNLVTVQTFQTGD--TDFQAQITAVLNSKPDLIVISALA 202 (344)
T ss_pred HHHHHHHHhcCCeEEEEEEeCCchHHHHHHHHHHHHHHHcCCEEEEEEeeCCCC--CCHHHHHHHHHhcCCCEEEECCcc
Confidence 355677888 9999999997655 999999999999999999999888887643 389999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec--CCchhHHHHHHHHhhhhccCCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT--QSSEEKRKFVTRWRHLTRRNTL 158 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~--~~~~~~~~f~~~~~~~~~~~~~ 158 (481)
..+..+++++.+.|+.. .++.++++... ... ....+..+|++...... ...+..++|.+.|++.+..
T Consensus 203 ~~~~~~~~~~~~~g~~~---~~~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~--- 271 (344)
T cd06348 203 ADGGNLVRQLRELGYNG---LIVGGNGFNTP-NVF----PVCQAACDGVLVAQAYSPENDTPVNRDFVEAYKKKYGK--- 271 (344)
T ss_pred hhHHHHHHHHHHcCCCC---ceeccccccCH-HHH----HhhhHhhcCeEEEeeccCCCCCHHHHHHHHHHHHHHCC---
Confidence 99999999999998753 34554433211 110 11224456666554333 2346788999999877642
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeE
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPI 238 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v 238 (481)
.++.++...|||+++++.|++++..+.... .|.. -..+..|.++|++++|.|++|++
T Consensus 272 ----~p~~~~~~~yda~~~~~~A~~~a~~~~~~~----------------~~~~---~~~~~~l~~~l~~~~~~g~~G~v 328 (344)
T cd06348 272 ----APPQFSAQAFDAVQVVAEALKRLNQKQKLA----------------ELPL---PELRTALNAALLSGQYDTPLGEI 328 (344)
T ss_pred ----CccHHHHHHHHHHHHHHHHHHHhcCCCccc----------------cchh---hhHHHHHHHHHhccCCccceeee
Confidence 234577889999999999999875432110 0100 01256888999999999999999
Q ss_pred EEccCCCCCCCcE
Q 011629 239 KFTSDRDLINPAY 251 (481)
Q Consensus 239 ~Fd~~Gd~~~~~y 251 (481)
.||++|++.+..|
T Consensus 329 ~f~~~g~~~~~~~ 341 (344)
T cd06348 329 SFTPDGEVLQKAF 341 (344)
T ss_pred EECCCCCcccCce
Confidence 9999999865544
No 47
>cd06338 PBP1_ABC_ligand_binding_like_5 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however their ligand specificity has not been determined experimentally.
Probab=99.70 E-value=1e-15 Score=148.77 Aligned_cols=209 Identities=12% Similarity=0.113 Sum_probs=157.8
Q ss_pred hHhHHHHHHcC--CcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 2 AAIADIVDYFG--WRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 2 ~Ai~~ll~~fg--W~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
.++++++++++ |+++++|+.++++|....+.+++.+++.|++|.....++...+ |+..++++|++.++++|++++.
T Consensus 128 ~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~--d~~~~v~~l~~~~~d~i~~~~~ 205 (345)
T cd06338 128 KSLLEMLVALDPRPKKVAILYADDPFSQDVAEGAREKAEAAGLEVVYDETYPPGTA--DLSPLISKAKAAGPDAVVVAGH 205 (345)
T ss_pred HHHHHHHHhcCCCCceEEEEecCCcccHHHHHHHHHHHHHcCCEEEEEeccCCCcc--chHHHHHHHHhcCCCEEEECCc
Confidence 46788999998 9999999999999999999999999999999998877765433 7999999999999999999999
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCC-------chhHHHHHHHHhhh
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQS-------SEEKRKFVTRWRHL 152 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~-------~~~~~~f~~~~~~~ 152 (481)
..++..+++++.+.|+..+ ..+ .+.+.... ... ........|+++.....+. .+..++|.+.|++.
T Consensus 206 ~~~~~~~~~~~~~~g~~~~-~~~-~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~ 278 (345)
T cd06338 206 FPDAVLLVRQMKELGYNPK-ALY-MTVGPAFP-AFV----KALGADAEGVFGPTQWTPALDYKDDLFPSAAEFAAAYKEK 278 (345)
T ss_pred chhHHHHHHHHHHcCCCCC-EEE-EecCCCcH-HHH----HHHhhhhCceeecceeccCcccccccCccHHHHHHHHHHH
Confidence 9999999999999987532 222 22222111 000 1112234566665433222 36789999999887
Q ss_pred hccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccC
Q 011629 153 TRRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMT 232 (481)
Q Consensus 153 ~~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~ 232 (481)
+... +..++...||+++++++|+++.-. .+ +..+.+.|+++.|.
T Consensus 279 ~~~~-------p~~~~~~~y~a~~~~~~a~~~ag~----------------------------~~-~~~v~~al~~~~~~ 322 (345)
T cd06338 279 YGKA-------PDYHAAGAYAAGQVLQEAVERAGS----------------------------LD-PAAVRDALASNDFD 322 (345)
T ss_pred hCCC-------CCcccHHHHHHHHHHHHHHHHhCC----------------------------CC-HHHHHHHHHhCCCc
Confidence 7421 334678899999999999987410 12 67899999999999
Q ss_pred ceeeeEEEccCCCCCCCcEEEEEe
Q 011629 233 GVTGPIKFTSDRDLINPAYEVINV 256 (481)
Q Consensus 233 g~sG~v~Fd~~Gd~~~~~y~I~~~ 256 (481)
|++|++.|+++|++. ..+-+++|
T Consensus 323 ~~~G~~~f~~~~~~~-~~~~~~~~ 345 (345)
T cd06338 323 TFYGPIKFDETGQNN-HPMTVVQW 345 (345)
T ss_pred ccccCeeECCCCCcC-CCceeeeC
Confidence 999999999999985 45555543
No 48
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=99.69 E-value=4.7e-15 Score=144.74 Aligned_cols=212 Identities=11% Similarity=0.105 Sum_probs=162.6
Q ss_pred HhHH-HHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 3 AIAD-IVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 3 Ai~~-ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++++ +.++++|++|++|+.|+.||....+.+++.+++.|.++.....++.... |+..++.+++++++++|++.+...
T Consensus 150 ~~~~~~~~~~~~k~va~i~~d~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~g~~--D~~~~v~~l~~~~~d~v~~~~~~~ 227 (369)
T PRK15404 150 TAAKYILEKVKPKRIAVLHDKQQYGEGLARSVKDGLKKAGANVVFFEGITAGDK--DFSALIAKLKKENVDFVYYGGYHP 227 (369)
T ss_pred HHHHHHHHhcCCCEEEEEeCCCchhHHHHHHHHHHHHHcCCEEEEEEeeCCCCC--chHHHHHHHHhcCCCEEEECCCch
Confidence 5566 4566799999999999999999999999999999999998888876544 799999999999999998877777
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeee-cCCchhHHHHHHHHhhhhccCCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMY-TQSSEEKRKFVTRWRHLTRRNTLNG 160 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~-~~~~~~~~~f~~~~~~~~~~~~~~~ 160 (481)
++..+++++.++|+. ..|+.+.++... .+. ....+...|+++..+. ....+..++|.+.|++.+..
T Consensus 228 ~~~~~~k~~~~~G~~---~~~i~~~~~~~~-~~~----~~~~~~~~Gv~~~~~~~~~~~~~~~~f~~~~~~~~~~----- 294 (369)
T PRK15404 228 EMGQILRQAREAGLK---TQFMGPEGVGNK-SLS----NIAGPASEGMLVTLPKRYDQDPANKAIVDAFKAKKQD----- 294 (369)
T ss_pred HHHHHHHHHHHCCCC---CeEEecCcCCCH-HHH----HhhhhhhcCcEEEccCCCccChhHHHHHHHHHHhcCC-----
Confidence 888999999999864 256766543221 110 1122345666654332 22356788899999876521
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEEE
Q 011629 161 PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKF 240 (481)
Q Consensus 161 ~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~F 240 (481)
.+..++...||++++++.|+++.-. .+ +..|.+.|++.+|.|+.|++.|
T Consensus 295 --~~~~~~~~~Y~~~~~l~~Al~~aG~----------------------------~~-~~~l~~al~~~~~~~~~G~~~~ 343 (369)
T PRK15404 295 --PSGPFVWTTYAAVQSLAAGINRAGS----------------------------DD-PAKVAKYLKANTFDTVIGPLSW 343 (369)
T ss_pred --CCccchHHHHHHHHHHHHHHHhhCC----------------------------CC-HHHHHHHHHhCCCCcceEeeEE
Confidence 2234567899999999999986310 12 6789999999999999999999
Q ss_pred ccCCCCCCCcEEEEEeecCc
Q 011629 241 TSDRDLINPAYEVINVIGTG 260 (481)
Q Consensus 241 d~~Gd~~~~~y~I~~~~~~~ 260 (481)
+.+|+.....|.|++|+.++
T Consensus 344 ~~~g~~~~~~~~i~~~~~~~ 363 (369)
T PRK15404 344 DEKGDLKGFEFGVFEWHADG 363 (369)
T ss_pred CCCCCcccCCEEEEEEEcCC
Confidence 99999877899999988653
No 49
>cd06345 PBP1_ABC_ligand_binding_like_10 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.68 E-value=2.3e-15 Score=146.12 Aligned_cols=200 Identities=16% Similarity=0.163 Sum_probs=150.7
Q ss_pred HhHHHHHH-----cCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEE
Q 011629 3 AIADIVDY-----FGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILH 77 (481)
Q Consensus 3 Ai~~ll~~-----fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~ 77 (481)
++++++.+ +||++|++++.++++|....+.+++.+++.|++|.....++.... ++..++.+|+.+++++|++.
T Consensus 129 ~~~~~~~~~~~~~~~~~~va~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~--d~~~~v~~l~~~~~d~v~~~ 206 (344)
T cd06345 129 SVADALKETLVDKHGFKTAAIVAEDAAWGKGIDAGIKALLPEAGLEVVSVERFSPDTT--DFTPILQQIKAADPDVIIAG 206 (344)
T ss_pred HHHHHHHHhhcccCCCceEEEEecCchhhhHHHHHHHHHHHHcCCeEEEEEecCCCCC--chHHHHHHHHhcCCCEEEEe
Confidence 56677765 899999999999999999999999999999999998887876533 78999999999999999999
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec----CCchhHHHHHHHHhhhh
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT----QSSEEKRKFVTRWRHLT 153 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~----~~~~~~~~f~~~~~~~~ 153 (481)
+...+...+++++.+.|+.. .++..+.+....... ........+........ ...+..++|.++|++.+
T Consensus 207 ~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~ 279 (344)
T cd06345 207 FSGNVGVLFTQQWAEQKVPI---PTIGISVEGNSPAFW----KATNGAGNYVITAESGAPGVEAITDKTVPFTEAYEAKF 279 (344)
T ss_pred ecCchHHHHHHHHHHcCCCC---ceEEecCCcCCHHHH----HhhchhcceEEeecccccCccCCCHHHHHHHHHHHHHh
Confidence 99888899999999998742 233332221111110 11122334444332221 24667889999998877
Q ss_pred ccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCc
Q 011629 154 RRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTG 233 (481)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g 233 (481)
.. .++.++...||+++++++|+.+.-. . .+..+.+.|+.+.|.|
T Consensus 280 g~-------~p~~~~~~~yda~~~l~~A~~~ag~----------------------------~-~~~~i~~al~~~~~~g 323 (344)
T cd06345 280 GG-------PPNYMGASTYDSIYILAEAIERAGS----------------------------T-DGDALVEALEKTDFVG 323 (344)
T ss_pred CC-------CCcccchHHHHHHHHHHHHHHHhcC----------------------------C-CHHHHHHHHHhCCCcC
Confidence 42 2455778899999999999987410 1 2678999999999999
Q ss_pred eeeeEEEccCCCCC
Q 011629 234 VTGPIKFTSDRDLI 247 (481)
Q Consensus 234 ~sG~v~Fd~~Gd~~ 247 (481)
++|+|+||++||+.
T Consensus 324 ~~G~i~f~~~g~~~ 337 (344)
T cd06345 324 TAGRIQFYGDDSAF 337 (344)
T ss_pred CceeEEECCCCCcC
Confidence 99999999999985
No 50
>cd06346 PBP1_ABC_ligand_binding_like_11 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.65 E-value=6.6e-15 Score=140.74 Aligned_cols=185 Identities=17% Similarity=0.216 Sum_probs=144.2
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.++++++.++||++|++|+.+++||....+.+++.+++.|++|.....++.... |+...+++|+++++++|++.+...
T Consensus 126 ~~l~~~~~~~~~~~vail~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~--d~~~~v~~l~~~~pd~v~~~~~~~ 203 (312)
T cd06346 126 QALAQLAAERGYKSVATTYINNDYGVGLADAFTKAFEALGGTVTNVVAHEEGKS--SYSSEVAAAAAGGPDALVVIGYPE 203 (312)
T ss_pred HHHHHHHHHcCCCeEEEEEccCchhhHHHHHHHHHHHHcCCEEEEEEeeCCCCC--CHHHHHHHHHhcCCCEEEEecccc
Confidence 578899999999999999999999999999999999999999998888876544 799999999999999999999888
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTLNGP 161 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~ 161 (481)
++..+++++.++|+. ..|+.++.+... ... .........|+++..+... .+..++|.+.|++.+..
T Consensus 204 ~~~~~~~~~~~~G~~---~~~~~~~~~~~~-~~~---~~~~~~~~~g~~~~~~~~~-~~~~~~f~~~~~~~~g~------ 269 (312)
T cd06346 204 TGSGILRSAYEQGLF---DKFLLTDGMKSD-SFL---PADGGYILAGSYGTSPGAG-GPGLEAFTSAYKAAYGE------ 269 (312)
T ss_pred hHHHHHHHHHHcCCC---CceEeeccccCh-HHH---HhhhHHHhCCcEEccCCCC-chhHHHHHHHHHHHhCC------
Confidence 999999999999873 346666543321 100 0111234567766554333 37788999999988743
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEEEc
Q 011629 162 IGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKFT 241 (481)
Q Consensus 162 ~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~Fd 241 (481)
.+..++...||++++++.| |.|++|++.||
T Consensus 270 -~p~~~~~~~Yd~~~~l~~A-------------------------------------------------~~g~~g~~~f~ 299 (312)
T cd06346 270 -SPSAFADQSYDAAALLALA-------------------------------------------------YQGASGVVDFD 299 (312)
T ss_pred -CCCccchhhHHHHHHHHHH-------------------------------------------------hCCCccceeeC
Confidence 2345678899999999755 45788999999
Q ss_pred cCCCCCCCcEEE
Q 011629 242 SDRDLINPAYEV 253 (481)
Q Consensus 242 ~~Gd~~~~~y~I 253 (481)
++|++. ..|+-
T Consensus 300 ~~g~~~-~~~~~ 310 (312)
T cd06346 300 ENGDVA-GSYDE 310 (312)
T ss_pred CCCCcc-cceee
Confidence 999985 56654
No 51
>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
Probab=99.62 E-value=3.8e-14 Score=137.15 Aligned_cols=206 Identities=14% Similarity=0.194 Sum_probs=158.3
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
+++++.+...||++|++++.++.+|....+.+++.+++.|+++.....++.... |+..+++++++.++++|++.+...
T Consensus 123 ~~~~~~l~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~~--d~~~~v~~~~~~~pd~v~~~~~~~ 200 (336)
T cd06360 123 APMGKYAADDGYKKVVTVAWDYAFGYEVVEGFKEAFTEAGGKIVKELWVPFGTS--DFASYLAQIPDDVPDAVFVFFAGG 200 (336)
T ss_pred HHHHHHHHHcCCCeEEEEeccchhhHHHHHHHHHHHHHcCCEEEEEEecCCCCc--chHHHHHHHHhcCCCEEEEecccc
Confidence 467788888899999999999999999999999999999999988777765433 899999999999999999988888
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecC--CchhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQ--SSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
.+..+++++.+.|+.. +..++.++++.... .. ....+...|++...+... ..+..+.|.+.|++.+..
T Consensus 201 ~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~-~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~~~---- 270 (336)
T cd06360 201 DAIKFVKQYDAAGLKA-KIPLIGSGFLTDGT-TL----GAAGEAAEGVITALHYADTLDNPANQAFVKAYRAAYPD---- 270 (336)
T ss_pred cHHHHHHHHHHcCCcc-CCeEEecccccCHH-HH----HhhHhhhcCceeccccCCCCCCHHHHHHHHHHHHHhCC----
Confidence 8999999999988742 34566555443221 10 112244566665544332 457789999999887742
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIK 239 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~ 239 (481)
.++.++...||++++++.|+++.-.. ..++..+.+.|+++.|.|..|+++
T Consensus 271 ---~~~~~~~~~yda~~~~~~A~~~a~~~---------------------------~~~~~~v~~al~~~~~~~~~g~~~ 320 (336)
T cd06360 271 ---TPSVYAVQGYDAGQALILALEAVGGD---------------------------LSDGQALIAAMAAAKIDSPRGPFT 320 (336)
T ss_pred ---CccHHHHHHHHHHHHHHHHHHHhCCC---------------------------CCCHHHHHHHHhcCCccCCCcceE
Confidence 34568899999999999999874210 112667999999999999999999
Q ss_pred EccCCCCCCC
Q 011629 240 FTSDRDLINP 249 (481)
Q Consensus 240 Fd~~Gd~~~~ 249 (481)
|+++|++...
T Consensus 321 f~~~~~~~~~ 330 (336)
T cd06360 321 LDKAHNPIQD 330 (336)
T ss_pred ECCCCCcccc
Confidence 9999987643
No 52
>cd06347 PBP1_ABC_ligand_binding_like_12 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.61 E-value=5.5e-14 Score=135.89 Aligned_cols=200 Identities=16% Similarity=0.212 Sum_probs=151.0
Q ss_pred hHhHHHH-HHcCCcEEEEEEEeC-CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 2 AAIADIV-DYFGWRNVIALYVDD-DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 2 ~Ai~~ll-~~fgW~~V~ii~~dd-~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
.++++.+ ++++|++|++|+.++ +|+....+.+++.+++.|+|+.....++... .++...++++++.++++|++.+.
T Consensus 123 ~~~~~~~~~~~~~~~v~ii~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~~~~~~--~d~~~~~~~~~~~~~d~i~~~~~ 200 (334)
T cd06347 123 TVMAKFATENLKAKKAAVLYDNSSDYSKGLAKAFKEAFKKLGGEIVAEETFNAGD--TDFSAQLTKIKAKNPDVIFLPGY 200 (334)
T ss_pred HHHHHHHHHhcCCcEEEEEEeCCCchhHHHHHHHHHHHHHcCCEEEEEEEecCCC--CcHHHHHHHHHhcCCCEEEEcCc
Confidence 3566664 778999999999876 8999889999999999999999888776543 37889999999999999999999
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecC--CchhHHHHHHHHhhhhccCC
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQ--SSEEKRKFVTRWRHLTRRNT 157 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~f~~~~~~~~~~~~ 157 (481)
......+++++.+.|+. ..|+.++.|...... ........|......... ..+..++|.+.|++.+..
T Consensus 201 ~~~~~~~~~~~~~~g~~---~~i~~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-- 270 (334)
T cd06347 201 YTEVGLIAKQARELGIK---VPILGGDGWDSPKLE-----EAGGAAAEGVYFTTHFSADDPTPKAKKFVKAYKAKYGK-- 270 (334)
T ss_pred hhhHHHHHHHHHHcCCC---CcEEecccccCHHHH-----HHHHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHCC--
Confidence 88999999999988863 467776666432110 112244566655544333 356788899888876631
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHh-cccCceee
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQ-VNMTGVTG 236 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~-v~f~g~sG 236 (481)
.+..++...||++++++.|+++.-. . ++..+.+.|.+ .+|+|++|
T Consensus 271 -----~~~~~~~~~yda~~~~~~Al~~ag~----------------------------~-~~~~v~~~l~~~~~~~g~~G 316 (334)
T cd06347 271 -----EPDAFAALGYDAYYLLADAIERAGS----------------------------T-DPEAIRDALAKTKDFDGVTG 316 (334)
T ss_pred -----CcchhHHHHHHHHHHHHHHHHHhCC----------------------------C-CHHHHHHHHHhCCCccccee
Confidence 3455778899999999999986310 1 26778888776 47999999
Q ss_pred eEEEccCCCCC
Q 011629 237 PIKFTSDRDLI 247 (481)
Q Consensus 237 ~v~Fd~~Gd~~ 247 (481)
++.|+.+|+..
T Consensus 317 ~v~f~~~g~~~ 327 (334)
T cd06347 317 KITIDENGNPV 327 (334)
T ss_pred eeEECCCCCcC
Confidence 99999999875
No 53
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.57 E-value=1.4e-14 Score=134.06 Aligned_cols=116 Identities=22% Similarity=0.324 Sum_probs=98.1
Q ss_pred CCCceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHC-CCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEE
Q 011629 315 NNGRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELL-PYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAA 393 (481)
Q Consensus 315 ~~~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~ 393 (481)
.+.++|+||+.. ++|||.+.+..+|++.||++||+++||+++ |..+++++.+ .+|.....+|.+|++|++
T Consensus 35 ~~~g~l~vg~~~--~~pP~~~~~~~~g~~~G~~vdl~~~ia~~llg~~~~~~~~~-------~~~~~~~~~l~~g~~D~~ 105 (259)
T PRK11917 35 KSKGQLIVGVKN--DVPHYALLDQATGEIKGFEIDVAKLLAKSILGDDKKIKLVA-------VNAKTRGPLLDNGSVDAV 105 (259)
T ss_pred HhCCEEEEEECC--CCCCceeeeCCCCceeEeeHHHHHHHHHHhcCCCccEEEEE-------cChhhHHHHHHCCCccEE
Confidence 346899999987 899999975437899999999999999995 8655666665 347788899999999999
Q ss_pred EeeeeeccccccceeeccceeecceEEEEecCCCCcCccccccCcch
Q 011629 394 VGDFAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFTP 440 (481)
Q Consensus 394 ~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~~ 440 (481)
++++++|++|++.++||.||+.++.++++++++ ....+++|+..+.
T Consensus 106 ~~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~-~~~s~~dL~g~~V 151 (259)
T PRK11917 106 IATFTITPERKRIYNFSEPYYQDAIGLLVLKEK-NYKSLADMKGANI 151 (259)
T ss_pred EecccCChhhhheeeeccCceeeceEEEEECCC-CCCCHHHhCCCeE
Confidence 999999999999999999999999999999876 4566777766544
No 54
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.56 E-value=1.6e-13 Score=133.24 Aligned_cols=203 Identities=14% Similarity=0.177 Sum_probs=150.8
Q ss_pred hHhHHHHHHcC------CcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEE
Q 011629 2 AAIADIVDYFG------WRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILI 75 (481)
Q Consensus 2 ~Ai~~ll~~fg------W~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIv 75 (481)
.++++++.+++ |++|++|+.|+.||....+.+++.+++.|++|...+.++... .++..++++|+++++++|+
T Consensus 127 ~~~~~~l~~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~i~~l~~~~~d~v~ 204 (347)
T cd06340 127 RDMFDFLKDLNEKTGKPLKTVALVHEDTEFGTSVAEAIKKFAKERGFEIVEDISYPANA--RDLTSEVLKLKAANPDAIL 204 (347)
T ss_pred HHHHHHHHHhhHhcCCCCceEEEEecCchHhHHHHHHHHHHHHHcCCEEEEeeccCCCC--cchHHHHHHHHhcCCCEEE
Confidence 46788888774 599999999999999999999999999999999888887653 3799999999999999999
Q ss_pred EEeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecC-CchhHHHHHHHHhhhhc
Q 011629 76 LHTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQ-SSEEKRKFVTRWRHLTR 154 (481)
Q Consensus 76 l~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~-~~~~~~~f~~~~~~~~~ 154 (481)
+.+...++..+++++.+.|+.. ..++......... ... ....+...|++....... ..+..++|.+.|++.++
T Consensus 205 ~~~~~~~~~~~~~~~~~~G~~~-~~~~~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~f~~~y~~~~~ 278 (347)
T cd06340 205 PASYTNDAILLVRTMKEQRVEP-KAVYSVGGGAEDP-SFV----KALGKDAEGILTRNEWSDPKDPMAKDLNKRFKARFG 278 (347)
T ss_pred EcccchhHHHHHHHHHHcCCCC-cEEEecCCCcCcH-HHH----HHhhHhhheEEeccccCCCCChHHHHHHHHHHHHhC
Confidence 9999999999999999998753 2222222211111 110 112234567776654433 35778899999998774
Q ss_pred cCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHH--HHHHhcccC
Q 011629 155 RNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLL--DNILQVNMT 232 (481)
Q Consensus 155 ~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~--~~l~~v~f~ 232 (481)
. .++.++...||++++++.|++++-. .+ +..+. ..|+...+.
T Consensus 279 ~-------~~~~~~~~~Y~a~~~l~~A~~~ag~----------------------------~~-~~~v~~~~~~~~~~~~ 322 (347)
T cd06340 279 V-------DLSGNSARAYTAVLVIADALERAGS----------------------------AD-PEKIRDLAALASTSGE 322 (347)
T ss_pred C-------CCChHHHHHHHHHHHHHHHHHHhcC----------------------------CC-HHHHHHHHHhccCCcc
Confidence 2 2456788999999999999997421 12 55666 477777665
Q ss_pred ---ceeeeEEEccCCCCCC
Q 011629 233 ---GVTGPIKFTSDRDLIN 248 (481)
Q Consensus 233 ---g~sG~v~Fd~~Gd~~~ 248 (481)
+..|+++||++|+..+
T Consensus 323 ~~~~~~g~~~f~~~g~~~~ 341 (347)
T cd06340 323 DLIMPYGPIKFDAKGQNTN 341 (347)
T ss_pred ccccCCCCeeECCCCCccc
Confidence 4578999999999763
No 55
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=99.56 E-value=4e-13 Score=130.45 Aligned_cols=219 Identities=11% Similarity=0.047 Sum_probs=156.5
Q ss_pred HhHHHHH-HcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 3 AIADIVD-YFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 3 Ai~~ll~-~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++++.+. +.|+++|++|+.|++||....+.+++.+++.|+.|+....++... .|+..++.+|+++++++|++.....
T Consensus 122 ~~~~~~~~~~g~k~vaii~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~D~~~~v~~l~~~~pd~v~~~~~~~ 199 (348)
T cd06355 122 PAVDWLMSNKGGKRFYLVGSDYVYPRTANKILKAQLESLGGEVVGEEYLPLGH--TDFQSIINKIKAAKPDVVVSTVNGD 199 (348)
T ss_pred HHHHHHHhccCCCeEEEECCcchHHHHHHHHHHHHHHHcCCeEEeeEEecCCh--hhHHHHHHHHHHhCCCEEEEeccCC
Confidence 3445444 568999999999999999999999999999999999888887543 4899999999999999999988888
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEee--ecCCchhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRM--YTQSSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~--~~~~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
.+..+++++.+.|+......++.......... ........|++.... .....+..+.|.+.+++.+...+
T Consensus 200 ~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~------~~g~~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~g~~~-- 271 (348)
T cd06355 200 SNVAFFKQLKAAGITASKVPVLSFSVAEEELR------GIGPENLAGHYAAWNYFQSVDTPENKKFVAAFKARYGQDR-- 271 (348)
T ss_pred chHHHHHHHHHcCCCccCCeeEEccccHHHHh------hcChHhhcCCEEeccchhhcCCHHHHHHHHHHHHHcCCCC--
Confidence 89999999999997643345554332111100 111123455554322 22345778899999888764211
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIK 239 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~ 239 (481)
.+..++...||++++++.|+++.-. .+ +..+.+.|++++|.+..|+++
T Consensus 272 ---~~~~~a~~~Y~a~~~~~~Al~~ag~----------------------------~~-~~~i~~aL~~~~~~~~~g~~~ 319 (348)
T cd06355 272 ---VTNDPMEAAYIGVYLWKQAVEKAGS----------------------------FD-VDKVRAALPGQSFDAPEGPVT 319 (348)
T ss_pred ---CCCcHHHHHHHHHHHHHHHHHHhCC----------------------------CC-HHHHHHHhccCcccCCCcceE
Confidence 1233567889999999999987410 22 778999999999999999999
Q ss_pred EccCCCCCCCcEEEEEee-cCceEE
Q 011629 240 FTSDRDLINPAYEVINVI-GTGSRR 263 (481)
Q Consensus 240 Fd~~Gd~~~~~y~I~~~~-~~~~~~ 263 (481)
|++.+......+.|.+++ .+.++.
T Consensus 320 f~~~~~~~~~~~~i~~~~~~g~~~~ 344 (348)
T cd06355 320 VDPANHHLWKPVRIGRIQADGQFEI 344 (348)
T ss_pred eecCCCeeeeeeEEEEEcCCCcEEE
Confidence 998443323455566665 344444
No 56
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.54 E-value=2.8e-14 Score=134.92 Aligned_cols=113 Identities=19% Similarity=0.246 Sum_probs=95.4
Q ss_pred CCceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHH----HCCC-cccEEEEeCCCCCCCCCHHHHHHHHHcccc
Q 011629 316 NGRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLE----LLPY-AVPYKLVPFGDGHNSPKRFDLLRLVSEEVY 390 (481)
Q Consensus 316 ~~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~----~l~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~ 390 (481)
+.++|+||+.. +++||.+.++ +|++.||++||+++||+ ++|. .+++++++ .+|..++.+|.+|++
T Consensus 38 ~~g~L~Vg~~~--~~pP~~f~~~-~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~-------~~~~~~i~~L~~G~~ 107 (302)
T PRK10797 38 KNGVIVVGHRE--SSVPFSYYDN-QQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIP-------ITSQNRIPLLQNGTF 107 (302)
T ss_pred hCCeEEEEEcC--CCCCcceECC-CCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEE-------cChHhHHHHHHCCCc
Confidence 45789999987 8999999875 78999999998887766 5653 35577887 358889999999999
Q ss_pred cEEEeeeeeccccccceeeccceeecceEEEEecCCCCcCccccccCcc
Q 011629 391 DAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 391 d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
|++++++++|++|.+.++||.||+.++.++++++++ .+..+++|...+
T Consensus 108 Di~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~-~i~sl~dL~Gk~ 155 (302)
T PRK10797 108 DFECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG-DIKDFADLKGKA 155 (302)
T ss_pred cEEecCCccCcchhhcceecccEeeccEEEEEECCC-CCCChHHcCCCE
Confidence 999989999999999999999999999999999876 466677776653
No 57
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.53 E-value=3.1e-14 Score=132.30 Aligned_cols=111 Identities=16% Similarity=0.238 Sum_probs=94.0
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.++|+|++.. +++||.+.++ +|++.|+++||++++|+++|.++++... .|+.++.++..|++|+++++
T Consensus 25 ~~~l~v~~~~--~~pPf~~~~~-~g~~~G~~vdl~~~ia~~lg~~~~~~~~---------~~~~~~~~l~~g~~Di~~~~ 92 (260)
T PRK15010 25 PETVRIGTDT--TYAPFSSKDA-KGDFVGFDIDLGNEMCKRMQVKCTWVAS---------DFDALIPSLKAKKIDAIISS 92 (260)
T ss_pred CCeEEEEecC--CcCCceeECC-CCCEEeeeHHHHHHHHHHhCCceEEEeC---------CHHHHHHHHHCCCCCEEEec
Confidence 4689999985 7999999875 7899999999999999999977555443 49999999999999999888
Q ss_pred eeeccccccceeeccceeecceEEEEecCCCCcCccccccCcc
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
++.|++|++.++||.||+..+.+++++++......+.+|...+
T Consensus 93 ~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dl~g~~ 135 (260)
T PRK15010 93 LSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLDSLKGKH 135 (260)
T ss_pred CcCCHHHHhhcccccceEeccEEEEEECCCCCCCChhHcCCCE
Confidence 9999999999999999999999999988763332355665543
No 58
>cd06344 PBP1_ABC_ligand_binding_like_9 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine/isoleucine/valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.52 E-value=4.1e-13 Score=129.62 Aligned_cols=201 Identities=17% Similarity=0.095 Sum_probs=145.8
Q ss_pred hHhHHHHHHcC-CcEEEEEEEeCC-cccchHHHHHHHHHh-cCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEe
Q 011629 2 AAIADIVDYFG-WRNVIALYVDDD-HGRNGIAALGDKLAE-KRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 2 ~Ai~~ll~~fg-W~~V~ii~~dd~-~g~~~~~~l~~~l~~-~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
+++++.+.+.+ |++|++|+.+++ ||+...+.+++.+++ .|+++.....++. ...++...+.++++.++++|++.+
T Consensus 122 ~~~~~~~~~~~~~~~v~~i~~~~~~~g~~~~~~~~~~~~~~~g~~v~~~~~~~~--~~~~~~~~v~~i~~~~~d~v~~~~ 199 (332)
T cd06344 122 RALAKYLKKKNKIKKVAIFYNSTSPYSQSLKQEFTSALLERGGGIVVTPCDLSS--PDFNANTAVSQAINNGATVLVLFP 199 (332)
T ss_pred HHHHHHHHhhcCCCeEEEEeCCCchHhHHHHHHHHHHHHHhcCCeeeeeccCCC--CCCCHHHHHHHHHhcCCCEEEEeC
Confidence 57889888886 999999998876 999999999999999 5999876554443 223677889999999999999988
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhHHHHHHHHhhhhccCCC
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEKRKFVTRWRHLTRRNTL 158 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~ 158 (481)
.......+++++.+.+. ...++.++.+... ... ........|+.+..+..+..+..++|.+.|++.+..
T Consensus 200 ~~~~~~~~~~~~~~~~~---~~~i~~~~~~~~~-~~~----~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~--- 268 (332)
T cd06344 200 DTDTLDKALEVAKANKG---RLTLLGGDSLYTP-DTL----LDGGKDLEGLVLAVPWHPLASPNSPFAKLAQQLWGG--- 268 (332)
T ss_pred ChhHHHHHHHHHHhcCC---CceEEecccccCH-HHH----HhchhhhcCeEEEEecccccccchHHHHHHHHHhcC---
Confidence 88788888888777542 3344554443221 110 112234567776665555556678899888887742
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHH-HHHHhcccCceeee
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLL-DNILQVNMTGVTGP 237 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~-~~l~~v~f~g~sG~ 237 (481)
.++.++...||++++++.|+++.-. .+ +..+. ..++...|.|..|+
T Consensus 269 ----~~~~~a~~~Yda~~~l~~A~~~ag~----------------------------~~-~~~~~~~~~~~~~~~g~~g~ 315 (332)
T cd06344 269 ----DVSWRTATAYDATKALIAALSQGPT----------------------------RE-GVQQVELSLRNFSVQGATGK 315 (332)
T ss_pred ----CchHHHHhHHHHHHHHHHHHHhCCC----------------------------hh-hhhhhhhhcccccccCCCce
Confidence 2456789999999999999986411 11 23333 56777789999999
Q ss_pred EEEccCCCCCC
Q 011629 238 IKFTSDRDLIN 248 (481)
Q Consensus 238 v~Fd~~Gd~~~ 248 (481)
++||++||+..
T Consensus 316 i~f~~~g~~~~ 326 (332)
T cd06344 316 IKFLPSGDRNG 326 (332)
T ss_pred eEeCCCCcccC
Confidence 99999999853
No 59
>cd06336 PBP1_ABC_ligand_binding_like_3 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.52 E-value=5.8e-13 Score=129.31 Aligned_cols=202 Identities=15% Similarity=0.136 Sum_probs=148.2
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.++++++++.+|++|++|+.|+.+|....+.+++.+++.|++|.....++... .|+..++.+|+++++++|++++...
T Consensus 127 ~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~~~l~~~G~~vv~~~~~~~~~--~D~s~~i~~i~~~~~d~v~~~~~~~ 204 (347)
T cd06336 127 VPFLAYAKKPGGKKVALLGPNDAYGQPWVAAYKAAWEAAGGKVVSEEPYDPGT--TDFSPIVTKLLAEKPDVIFLGGPSP 204 (347)
T ss_pred HHHHHHHhhcCCceEEEEccCCchhHHHHHHHHHHHHHcCCEEeeecccCCCC--cchHHHHHHHHhcCCCEEEEcCCCc
Confidence 46677887789999999999999999999999999999999999888887653 3899999999999999999998888
Q ss_pred -HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecC----CchhHHHHHHHHhhhhccC
Q 011629 82 -WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQ----SSEEKRKFVTRWRHLTRRN 156 (481)
Q Consensus 82 -~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~----~~~~~~~f~~~~~~~~~~~ 156 (481)
++..+++++.+.|+.. ...++........ .. ....+...|++...+... ..+..++|.+.|++.+..
T Consensus 205 ~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~--~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~- 276 (347)
T cd06336 205 APAALVIKQARELGFKG-GFLSCTGDKYDEL--LV----ATGADFMEGVYFQFPDVDDPALAFPRAKAFVEEYKKRYGE- 276 (347)
T ss_pred hHHHHHHHHHHHcCCCc-cEEeccCCCchHH--HH----HhcHHhhCceEEEeecccccccCCHHHHHHHHHHHHHHCC-
Confidence 9999999999998753 2222221111110 00 111234567766655433 466788899999887742
Q ss_pred CCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHH-------hc
Q 011629 157 TLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNIL-------QV 229 (481)
Q Consensus 157 ~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~-------~v 229 (481)
.+..++...||++.+++.|+++.-. .+....+...|+ ..
T Consensus 277 ------~p~~~~~~~y~~~~~~~~Al~~ag~----------------------------~~~~~~~~~~~~~~~~~~~~~ 322 (347)
T cd06336 277 ------PPNSEAAVSYDAVYILKAAMEAAGS----------------------------VDDTAAVAALAAMLGVGKPAF 322 (347)
T ss_pred ------CCcHHHHHHHHHHHHHHHHHHhcCC----------------------------CCcHHHHHHHhhccCCCcCcc
Confidence 2455788999999999999987411 110222233333 36
Q ss_pred ccCceeeeEEEccCCCCC
Q 011629 230 NMTGVTGPIKFTSDRDLI 247 (481)
Q Consensus 230 ~f~g~sG~v~Fd~~Gd~~ 247 (481)
.|.+..|.+.||++||..
T Consensus 323 ~~~~~~g~~~~~~~~~~~ 340 (347)
T cd06336 323 GYARWWGKELFGVNGALV 340 (347)
T ss_pred ccccccccccccCCCccc
Confidence 788889999999999986
No 60
>cd06343 PBP1_ABC_ligand_binding_like_8 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.52 E-value=2.2e-12 Score=126.21 Aligned_cols=217 Identities=12% Similarity=0.199 Sum_probs=155.8
Q ss_pred hHhHH-HHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 2 AAIAD-IVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~-ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.++++ +++++||++|++|+.++.||....+.+++.+++.|+++.....++...+ ++..++++|++.++++|++.+..
T Consensus 132 ~~~~~~~~~~~g~~~v~ii~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~--d~~~~v~~i~~~~~d~v~~~~~~ 209 (362)
T cd06343 132 RIYAKYLVEEKPNAKIAVLYQNDDFGKDYLKGLKDGLGDAGLEIVAETSYEVTEP--DFDSQVAKLKAAGADVVVLATTP 209 (362)
T ss_pred HHHHHHHHHhCCCceEEEEEeccHHHHHHHHHHHHHHHHcCCeEEEEeeecCCCc--cHHHHHHHHHhcCCCEEEEEcCc
Confidence 45677 5678899999999999999999999999999999999998888876543 79999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEecccccccc-CCccccccccccceeeEEEeeec-------CCchhHHHHHHHHhhh
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILD-TDSQLHSEKMDDIQGVLTLRMYT-------QSSEEKRKFVTRWRHL 152 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~-~~~~~~~~~~~~~~g~l~~~~~~-------~~~~~~~~f~~~~~~~ 152 (481)
.....+++++.+.|+.. .++.++.+..... .. ........|++...... ...+..++|.+.+++.
T Consensus 210 ~~~~~~~~~~~~~g~~~---~~~~~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~p~~~~~~~~~~f~~~~~~~ 282 (362)
T cd06343 210 KFAAQAIRKAAELGWKP---TFLLSSVSASVASVLK----PAGLEAAEGVIAAAYLKDPTDPAWADDPGVKEFIAFYKKY 282 (362)
T ss_pred HHHHHHHHHHHHcCCCc---eEEEEecccccHHHHH----HhhhHhhCceEEEEEecCCCccccccCHHHHHHHHHHHHh
Confidence 89999999999998753 3555554332210 10 11123345655543321 2356778888888876
Q ss_pred hccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhccc-
Q 011629 153 TRRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNM- 231 (481)
Q Consensus 153 ~~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f- 231 (481)
+... ..++.++...||++.+++.|+++.-. ..+ +..+.+.|+++.+
T Consensus 283 ~~~~-----~~~~~~~~~~y~a~~~~~~a~~~ag~---------------------------~~~-~~~v~~aL~~~~~~ 329 (362)
T cd06343 283 FPEG-----DPPDTYAVYGYAAAETLVKVLKQAGD---------------------------DLT-RENIMKQAESLKDV 329 (362)
T ss_pred cCCC-----CCCchhhhHHHHHHHHHHHHHHHhCC---------------------------CCC-HHHHHHHHHhCCCC
Confidence 6321 12455778899999999999987410 022 6789999999987
Q ss_pred --Ccee-eeEEEccCCCCCCCcEEEEEeecCc
Q 011629 232 --TGVT-GPIKFTSDRDLINPAYEVINVIGTG 260 (481)
Q Consensus 232 --~g~s-G~v~Fd~~Gd~~~~~y~I~~~~~~~ 260 (481)
.+.. +++.|+.+..+....+.|.++..++
T Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~ 361 (362)
T cd06343 330 LPDLLPGIRINTSPDDHLPIEQMQLMRFEGGR 361 (362)
T ss_pred CccccCccceecCccccccceeEEEEEEecCc
Confidence 3333 4899986543333556666665443
No 61
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.51 E-value=3.9e-14 Score=130.65 Aligned_cols=111 Identities=23% Similarity=0.355 Sum_probs=95.2
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.++|+|++.. +++||.+.+ +|++.|+++||++++++++|.++++ ++ .+|.+++.+|.+|++|+++++
T Consensus 24 ~~~l~v~~~~--~~~P~~~~~--~g~~~G~~vdl~~~ia~~lg~~~~~--~~-------~~~~~~~~~l~~G~vDi~~~~ 90 (247)
T PRK09495 24 DKKLVVATDT--AFVPFEFKQ--GDKYVGFDIDLWAAIAKELKLDYTL--KP-------MDFSGIIPALQTKNVDLALAG 90 (247)
T ss_pred CCeEEEEeCC--CCCCeeecC--CCceEEEeHHHHHHHHHHhCCceEE--Ee-------CCHHHHHHHHhCCCcCEEEec
Confidence 4689999876 799999865 6889999999999999999977554 44 359999999999999998888
Q ss_pred eeeccccccceeeccceeecceEEEEecCCCCcCccccccCcch
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFTP 440 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~~ 440 (481)
++.|++|++.++||.||+.++.++++++++..+..+.+|+..+.
T Consensus 91 ~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~I 134 (247)
T PRK09495 91 ITITDERKKAIDFSDGYYKSGLLVMVKANNNDIKSVKDLDGKVV 134 (247)
T ss_pred CccCHHHHhhccccchheecceEEEEECCCCCCCChHHhCCCEE
Confidence 99999999999999999999999999887655667777765543
No 62
>cd06269 PBP1_glutamate_receptors_like Family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domain of the ionotropic glutamate receptors. This CD represents the ligand-binding domain of the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domain of the ionotropic glutamate receptors, all of which are structurally similar and related to the periplasmic-binding fold type I family. The family C GPCRs consist of metabotropic glutamate receptor (mGluR) receptors, a calcium-sensing receptor (CaSR), gamma-aminobutyric receptors (GABAb), the promiscuous L-alpha-amino acid receptor GPR6A, families of taste and pheromone receptors, and orphan receptors. Truncated splicing va
Probab=99.51 E-value=1.8e-13 Score=129.72 Aligned_cols=107 Identities=29% Similarity=0.483 Sum_probs=97.8
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
+|+++++++|||++|+++++++++|....+.+++.+.+.|+|+.....++... .++...++++++++++|||+++...
T Consensus 129 ~a~~~~l~~~~w~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~--~~~~~~l~~l~~~~~~viv~~~~~~ 206 (298)
T cd06269 129 QAIVDLLKHFGWTWVGLVYSDDDYGRRLLELLEEELEKNGICVAFVESIPDGS--EDIRRLLKELKSSTARVIVVFSSEE 206 (298)
T ss_pred HHHHHHHHHCCCeEEEEEEecchhhHHHHHHHHHHHHHCCeeEEEEEEcCCCH--HHHHHHHHHHHhcCCcEEEEEechH
Confidence 68999999999999999999999999999999999999999999988887543 4788999999999999999999989
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEecccccc
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSI 111 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~ 111 (481)
.+..++++|.++||. .+++||+++.|...
T Consensus 207 ~~~~~l~~a~~~g~~-~~~~~i~~~~~~~~ 235 (298)
T cd06269 207 DALRLLEEAVELGMM-TGYHWIITDLWLTS 235 (298)
T ss_pred HHHHHHHHHHHcCCC-CCeEEEEEChhhcc
Confidence 999999999999998 89999999877643
No 63
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=99.51 E-value=8e-13 Score=127.66 Aligned_cols=204 Identities=13% Similarity=0.078 Sum_probs=152.9
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.++++.+..-+|++|++|+.|+.||....+.+++.+++.|.+|.....++... .|+..++.++++.++++|++.+...
T Consensus 121 ~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~~~~~~~d~v~~~~~~~ 198 (333)
T cd06331 121 LPLIPYLMEKYGKRFYLIGSDYVWPRESNRIARALLEELGGEVVGEEYLPLGT--SDFGSVIEKIKAAGPDVVLSTLVGD 198 (333)
T ss_pred HHHHHHHHHhcCCeEEEECCCchhHHHHHHHHHHHHHHcCCEEEEEEEecCCc--ccHHHHHHHHHHcCCCEEEEecCCC
Confidence 35677665545999999999999999999999999999999999888887653 4899999999999999999999988
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec--CCchhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT--QSSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~--~~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
+...+++++.+.|+.... ..+.+...... ... ........|++...+.. ...+..+.|.+.|++.+...
T Consensus 199 ~~~~~~~~~~~~g~~~~~-~~~~~~~~~~~-~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~--- 269 (333)
T cd06331 199 SNVAFYRQFAAAGLDADR-IPILSLTLDEN-ELA----AIGAEAAEGHYSAASYFQSLDTPENKAFVARYRARYGDD--- 269 (333)
T ss_pred ChHHHHHHHHHcCCCcCC-CeeEEcccchh-hhh----ccChhhhCCcEeechhhhhcCChhHHHHHHHHHHHcCCC---
Confidence 889999999999975323 34443322111 110 11123356666654332 24567888999998776321
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIK 239 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~ 239 (481)
..++.++...|||+++++.|+++.- + . ++..|.+.|+++.|.|++|.+.
T Consensus 270 --~~~~~~~~~~yda~~~~~~A~~~ag-------------------------~---~-~~~~l~~al~~~~~~~~~G~i~ 318 (333)
T cd06331 270 --AVINSPAEAAYEAVYLWAAAVEKAG-------------------------S---T-DPEAVRAALEGVSFDAPQGPVR 318 (333)
T ss_pred --cCCCchhHHHHHHHHHHHHHHHHcC-------------------------C---C-CHHHHHHHhhcCcccCCCCceE
Confidence 1345678999999999999998631 0 1 2788999999999999999999
Q ss_pred EccCCCCC
Q 011629 240 FTSDRDLI 247 (481)
Q Consensus 240 Fd~~Gd~~ 247 (481)
|++++.+.
T Consensus 319 f~~~~~~~ 326 (333)
T cd06331 319 IDPDNHHT 326 (333)
T ss_pred ecCCCCcc
Confidence 99887664
No 64
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.51 E-value=4.1e-14 Score=131.38 Aligned_cols=112 Identities=17% Similarity=0.236 Sum_probs=95.1
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.++|+|++.. +++||.+.++ +|++.|+++|+++++++++|.++++...+ |+.++.++.+|++|+++++
T Consensus 25 ~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~vdi~~~ia~~lg~~i~~~~~p---------w~~~~~~l~~g~~D~~~~~ 92 (259)
T PRK15437 25 PQNIRIGTDP--TYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVENP---------LDALIPSLKAKKIDAIMSS 92 (259)
T ss_pred CCeEEEEeCC--CCCCcceeCC-CCCEEeeeHHHHHHHHHHcCCceEEEeCC---------HHHHHHHHHCCCCCEEEec
Confidence 4689999875 6999999876 78999999999999999999876655544 9999999999999999888
Q ss_pred eeeccccccceeeccceeecceEEEEecCCCCcCccccccCcch
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFTP 440 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~~ 440 (481)
++.|++|++.++||.||+..+..+++++++......++|++.+.
T Consensus 93 ~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dl~g~~I 136 (259)
T PRK15437 93 LSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESLKGKRV 136 (259)
T ss_pred CCCCHHHhhhccccchhhcCceEEEEECCCCCCCChHHhCCCEE
Confidence 99999999999999999999999999987633323566666543
No 65
>cd06359 PBP1_Nba_like Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway. This group includes the type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; their substrate specificities are not well characterized.
Probab=99.50 E-value=2e-12 Score=124.90 Aligned_cols=207 Identities=13% Similarity=0.178 Sum_probs=148.9
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.+++++++..||++|++++.|+++|....+.+++.+. ..+.....++... .|+..++.+++++++++|++.....
T Consensus 123 ~~~~~~~~~~g~~~vail~~~~~~g~~~~~~~~~~~~---~~v~~~~~~~~~~--~d~~~~i~~l~~~~pd~v~~~~~~~ 197 (333)
T cd06359 123 EAMGKYAQDKGYKRVFLIAPNYQAGKDALAGFKRTFK---GEVVGEVYTKLGQ--LDFSAELAQIRAAKPDAVFVFLPGG 197 (333)
T ss_pred HHHHHHHHHhCCCeEEEEecCchhhHHHHHHHHHHhC---ceeeeeecCCCCC--cchHHHHHHHHhCCCCEEEEEccCc
Confidence 4677888888999999999999999988888888774 3455444444333 3799999999999999999988877
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecC--CchhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQ--SSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
.+..+++++.+.|+.. ...++.+...... +.. ....+...|++......+ ..+..++|.+.|++.+..
T Consensus 198 ~~~~~~~~~~~~G~~~-~~~~~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~---- 267 (333)
T cd06359 198 MGVNFVKQYRQAGLKK-DIPLYSPGFSDEE-DTL----PAVGDAALGLYNTAQWAPDLDNPANKKFVADFEKKYGR---- 267 (333)
T ss_pred cHHHHHHHHHHcCccc-CCeeeccCcccCH-HHH----HhcchhhcCeeeccccCCCCCCHHHHHHHHHHHHHhCC----
Confidence 8889999999998742 3345554433211 110 112234566666544333 457788999999887732
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIK 239 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~ 239 (481)
.+..++...||++++++.|+++.-.. ..+ +..+.+.|+++.|.|++|++.
T Consensus 268 ---~~~~~~~~~yda~~~~~~A~~~ag~~--------------------------~~~-~~~v~~al~~~~~~~~~G~~~ 317 (333)
T cd06359 268 ---LPTLYAAQAYDAAQLLDSAVRKVGGN--------------------------LSD-KDALRAALRAADFKSVRGAFR 317 (333)
T ss_pred ---CCcHHHHHHHHHHHHHHHHHHHhcCC--------------------------CCC-HHHHHHHHhcCccccCccceE
Confidence 34567889999999999999874110 012 678999999999999999999
Q ss_pred EccCCCCCCCcEEEE
Q 011629 240 FTSDRDLINPAYEVI 254 (481)
Q Consensus 240 Fd~~Gd~~~~~y~I~ 254 (481)
|+.+|+.. ..+-|+
T Consensus 318 ~~~~~~~~-~~~~~~ 331 (333)
T cd06359 318 FGTNHFPI-QDFYLR 331 (333)
T ss_pred ECCCCCcc-eeEEEE
Confidence 99888754 444443
No 66
>cd06349 PBP1_ABC_ligand_binding_like_14 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.50 E-value=2.9e-12 Score=124.14 Aligned_cols=210 Identities=20% Similarity=0.230 Sum_probs=150.6
Q ss_pred hHhHHH-HHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 2 AAIADI-VDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~l-l~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.++++. ++++||++|++++.|+++|....+.+++.+++.|+||+....++.... |+...+.+++.+++++|++.+..
T Consensus 123 ~~~~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~--d~~~~v~~l~~~~~d~v~~~~~~ 200 (340)
T cd06349 123 PLLADYAVKDLGFKKVAILSVNTDWGRTSADIFVKAAEKLGGQVVAHEEYVPGEK--DFRPTITRLRDANPDAIILISYY 200 (340)
T ss_pred HHHHHHHHHHcCCcEEEEEecCChHhHHHHHHHHHHHHHcCCEEEEEEEeCCCCC--cHHHHHHHHHhcCCCEEEEcccc
Confidence 356776 477899999999999999999999999999999999998777765533 78999999999999999999998
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec--CCchhHHHHHHHHhhhhccCCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT--QSSEEKRKFVTRWRHLTRRNTL 158 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~--~~~~~~~~f~~~~~~~~~~~~~ 158 (481)
..+..+++++.+.|+.. .++....+... ... ........|++...... ...+..+.|.+.|++.+..
T Consensus 201 ~~~~~~~~~~~~~g~~~---~~~~~~~~~~~-~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--- 269 (340)
T cd06349 201 NDGAPIARQARAVGLDI---PVVASSSVYSP-KFI----ELGGDAVEGVYTPTAFFPGDPRPEVQSFVSAYEAKYGA--- 269 (340)
T ss_pred chHHHHHHHHHHcCCCC---cEEccCCcCCH-HHH----HHhHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHCC---
Confidence 89999999999988753 34444322111 110 11123456666554332 2356788999998876642
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHH--HhcccCceee
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNI--LQVNMTGVTG 236 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l--~~v~f~g~sG 236 (481)
.++.++...||++.+++.|+++.- . . .......+ .+..+.+..|
T Consensus 270 ----~p~~~~~~~y~~~~~~~~a~~~ag---~-------------------------~--~~~~~~~~~~~~~~~~~~~g 315 (340)
T cd06349 270 ----QPDAFAAQAYDAVGILAAAVRRAG---T-------------------------D--RRAARDGFAKAEDVYSGVTG 315 (340)
T ss_pred ----CcchhhhhHHHHHHHHHHHHHHhC---C-------------------------C--CHHHHHHHHHhccCcccceE
Confidence 234578899999999999998731 0 0 11122223 4455789999
Q ss_pred eEEEccC-CCCCCCcEEEEEeecC
Q 011629 237 PIKFTSD-RDLINPAYEVINVIGT 259 (481)
Q Consensus 237 ~v~Fd~~-Gd~~~~~y~I~~~~~~ 259 (481)
.++|+.+ ++.. ..|-++.++.+
T Consensus 316 ~i~~~~~~~~~~-~~~~~~~~~~g 338 (340)
T cd06349 316 STKFDPNTRRVI-KRFVPLVVRNG 338 (340)
T ss_pred eEEECCCCCCcc-CceEEEEEeCC
Confidence 9999986 6554 57777766544
No 67
>cd06357 PBP1_AmiC Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. This group includes the periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. AmiC controls expression of the amidase operon by the ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon are induced.
Probab=99.49 E-value=5.4e-12 Score=123.09 Aligned_cols=223 Identities=13% Similarity=0.084 Sum_probs=158.9
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~ 82 (481)
++++.+..-+=++|++|+.|+++|+...+.+.+.+++.|+.+.....++......|+..++.+++++++++|++.+....
T Consensus 122 ~~~~~~~~~~~~~v~~i~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~~~d~s~~v~~l~~~~pd~V~~~~~~~~ 201 (360)
T cd06357 122 PLADYLLRHYGKRVFLVGSNYIYPYESNRIMRDLLEQRGGEVLGERYLPLGASDEDFARIVEEIREAQPDFIFSTLVGQS 201 (360)
T ss_pred HHHHHHHhcCCcEEEEECCCCcchHHHHHHHHHHHHHcCCEEEEEEEecCCCchhhHHHHHHHHHHcCCCEEEEeCCCCC
Confidence 56665554333899999999999999999999999999999887655665533458999999999999999999988889
Q ss_pred HHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeee--cCCchhHHHHHHHHhhhhccCCCCC
Q 011629 83 GLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMY--TQSSEEKRKFVTRWRHLTRRNTLNG 160 (481)
Q Consensus 83 ~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~--~~~~~~~~~f~~~~~~~~~~~~~~~ 160 (481)
+..+++++.++|+... ...+.+...... ... ....+...|+++.... ....+..+.|.+.|++.+...
T Consensus 202 ~~~~~~~~~~~G~~~~-~~~~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~g~~---- 271 (360)
T cd06357 202 SYAFYRAYAAAGFDPA-RMPIASLTTSEA-EVA----AMGAEAAAGHITAAPYFSSIDTPANRAFVARYRARFGED---- 271 (360)
T ss_pred hHHHHHHHHHcCCCcc-CceeEEeeccHH-HHh----hcchHhhCCcEEecccccccCChhHHHHHHHHHHHcCCC----
Confidence 9999999999997533 233333321111 110 1112445676665432 224577889999998877421
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEEE
Q 011629 161 PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKF 240 (481)
Q Consensus 161 ~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~F 240 (481)
..++.++...||++++++.|+++.-. .+ +..+.+.|+++.|.+..|.+.|
T Consensus 272 -~~~~~~~~~~yda~~~l~~Al~~ag~----------------------------~~-~~~v~~aL~~~~~~~~~g~~~f 321 (360)
T cd06357 272 -APVSACAEAAYFQVHLFARALQRAGS----------------------------DD-PEDVLAALLGFSFDAPQGPVRI 321 (360)
T ss_pred -CCCCcHHHHHHHHHHHHHHHHHHcCC----------------------------CC-HHHHHHHhccCcccCCCcceEE
Confidence 11345778999999999999987310 12 6789999999999999999999
Q ss_pred ccCCCCCCCcEEEEEe-ecCceEEEE
Q 011629 241 TSDRDLINPAYEVINV-IGTGSRRIG 265 (481)
Q Consensus 241 d~~Gd~~~~~y~I~~~-~~~~~~~VG 265 (481)
|..++.......+.++ +.++++.+.
T Consensus 322 ~~~~~~~~~~~~~~~~~~~G~~~~~~ 347 (360)
T cd06357 322 DPDNNHTYLWPRIARVNADGQFDIVR 347 (360)
T ss_pred eCCCCeeeeeeEEEEEcCCCCEEEEE
Confidence 9766543244445565 455665554
No 68
>cd06332 PBP1_aromatic_compounds_like Type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes. This group includes the type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well characterized, however. Members also exhibit close similarity to active transport systems for short chain amides and/or urea found in bacteria and archaea.
Probab=99.49 E-value=2.5e-12 Score=124.26 Aligned_cols=201 Identities=15% Similarity=0.224 Sum_probs=147.6
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
+.+++.+...||++|++|+.++.+|....+.+.+.++ ..+.....++.... ++...++++++.++++|++.....
T Consensus 123 ~~~~~~l~~~g~~~v~il~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~--d~~~~i~~l~~~~~d~i~~~~~~~ 197 (333)
T cd06332 123 EAMGKYAADKGYKKVVIIAPDYAAGKDAVAGFKRTFK---GEVVEEVYTPLGQL--DFSAELAQIRAAKPDAVFVFLPGG 197 (333)
T ss_pred HHHHHHHHHhCCceEEEEecCcchhHHHHHHHHHhhc---EEEeeEEecCCCCc--chHHHHHHHHhcCCCEEEEecccc
Confidence 4678888889999999999989999888889988887 34544444544333 688889999999999999988878
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecC--CchhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQ--SSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
.+..+++++.+.|+. +...++.+..+... ... ........|++...+..+ ..+..++|.+.|++.++.
T Consensus 198 ~~~~~~~~~~~~g~~-~~~~~~~~~~~~~~-~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~---- 267 (333)
T cd06332 198 MAVNFVKQYDQAGLK-KKIPLYGPGFLTDQ-DTL----PAQGDAAVGVLTALHWAPDLDNPANKRFVAAYKAAYGR---- 267 (333)
T ss_pred hHHHHHHHHHHcCcc-cCCceeccCCCCCH-HHH----HhhchhhcCeeeeeccCCCCCCHHHHHHHHHHHHHhCC----
Confidence 889999999998874 24456665544322 110 122244566666544332 356788999999887742
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIK 239 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~ 239 (481)
.+..++...||++++++.|+++.-.. ..++..+.+.|++++|.|+.|++.
T Consensus 268 ---~~~~~~~~~yda~~~~~~a~~~ag~~---------------------------~~~~~~v~~al~~~~~~~~~g~i~ 317 (333)
T cd06332 268 ---VPSVYAAQGYDAAQLLDAALRAVGGD---------------------------LSDKDALRAALRAADFDSPRGPFK 317 (333)
T ss_pred ---CCcHHHHHHHHHHHHHHHHHHHhcCC---------------------------CCCHHHHHHHHhcCceecCcccee
Confidence 24557889999999999999874110 112567999999999999999999
Q ss_pred EccCCCCC
Q 011629 240 FTSDRDLI 247 (481)
Q Consensus 240 Fd~~Gd~~ 247 (481)
|+++|+..
T Consensus 318 f~~~~~~~ 325 (333)
T cd06332 318 FNPNHNPI 325 (333)
T ss_pred ECCCCCcc
Confidence 99999865
No 69
>PF13458 Peripla_BP_6: Periplasmic binding protein; PDB: 4EVS_A 4EY3_A 4EYG_B 4EYK_A 3H5L_B 3TD9_A 3EAF_A 1Z18_A 1Z17_A 2LIV_A ....
Probab=99.48 E-value=3.6e-12 Score=123.69 Aligned_cols=213 Identities=18% Similarity=0.242 Sum_probs=161.3
Q ss_pred hHhHHH-HHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 2 AAIADI-VDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~l-l~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.++++. ++++|.++|++|+.++.+|....+.+++.+++.|+.+.....++... .++..+++++++.++++|++++..
T Consensus 123 ~~~~~~~~~~~g~~~v~iv~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~~~~l~~~~~d~v~~~~~~ 200 (343)
T PF13458_consen 123 AALAEYLAKKLGAKKVAIVYPDDPYGRSLAEAFRKALEAAGGKVVGEIRYPPGD--TDFSALVQQLKSAGPDVVVLAGDP 200 (343)
T ss_dssp HHHHHHHHHTTTTSEEEEEEESSHHHHHHHHHHHHHHHHTTCEEEEEEEE-TTS--SHHHHHHHHHHHTTTSEEEEESTH
T ss_pred HHHHHHHHHHcCCcEEEEEecCchhhhHHHHHHHHHHhhcCceeccceeccccc--ccchHHHHHHhhcCCCEEEEeccc
Confidence 467775 56699999999999999999999999999999999998788887654 489999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEecc-ccccccCCccccccccccceeeEEEeeecC--CchhHHHHHHHHhhhhccCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDW-LSSILDTDSQLHSEKMDDIQGVLTLRMYTQ--SSEEKRKFVTRWRHLTRRNT 157 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~-~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~f~~~~~~~~~~~~ 157 (481)
..+..+++++.+.|...+ .+.+.... +..... ........|++......+ ..+..++|.+.|++.++..
T Consensus 201 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~------~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~- 272 (343)
T PF13458_consen 201 ADAAAFLRQLRQLGLKPP-RIPLFGTSLDDASLQ------QLGGDALEGVYIVSPWFPDPDSPAVKQFQERYRAAYGEE- 272 (343)
T ss_dssp HHHHHHHHHHHHTTGCSC-TEEEEEGGGSSHHHH------HHHGGGGTTEEEEESGGGTGGSHHHHHHHHHHHHHHSST-
T ss_pred hhHHHHHHHHHhhccccc-cceeeccccCcHHHH------HhhhhhccCceeecccCCCCCCHHHHHHHHHHHHHcCCC-
Confidence 999999999999886532 24444322 211110 111234667766655433 4577889999999888521
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeee
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGP 237 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~ 237 (481)
-.++.++...||++.+++.|+++.- ..+ +..+.+.|+.+.|+|+.|+
T Consensus 273 ----~~~~~~~~~~yda~~~~~~al~~~g----------------------------~~~-~~~v~~al~~~~~~g~~g~ 319 (343)
T PF13458_consen 273 ----PPPSLYAAQGYDAARLLAQALERAG----------------------------SLD-REAVREALESLKYDGLFGP 319 (343)
T ss_dssp ----GGTCHHHHHHHHHHHHHHHHHHHHT----------------------------SHH-HHHHHHHHHTSEEEETTEE
T ss_pred ----CCCchhHHHHHHHHHHHHHHHHHhC----------------------------CCC-HHHHHHHHHhCCCcccccc
Confidence 1256688999999999999998751 022 7899999999999999999
Q ss_pred EEEccCCCCCCCcEEEEEee
Q 011629 238 IKFTSDRDLINPAYEVINVI 257 (481)
Q Consensus 238 v~Fd~~Gd~~~~~y~I~~~~ 257 (481)
+.|+..+......+.|++++
T Consensus 320 ~~~~~~~~~~~~~~~i~~v~ 339 (343)
T PF13458_consen 320 ISFDPPDHQANKPVYIVQVK 339 (343)
T ss_dssp EEEETTTSBEEEEEEEEEEE
T ss_pred eEEeCCCCccccCeEEEEEe
Confidence 99976544445777777776
No 70
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.46 E-value=1.7e-13 Score=126.04 Aligned_cols=109 Identities=20% Similarity=0.297 Sum_probs=91.6
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.++|+|++.. +++||.+.+. +|++.|+++|++++|++++|++++|. . .+|+.++.++.+|++|+++++
T Consensus 20 ~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~~~~--~-------~~~~~~~~~l~~g~~D~~~~~ 87 (243)
T PRK15007 20 AETIRFATEA--SYPPFESIDA-NNQIVGFDVDLAQALCKEIDATCTFS--N-------QAFDSLIPSLKFRRVEAVMAG 87 (243)
T ss_pred CCcEEEEeCC--CCCCceeeCC-CCCEEeeeHHHHHHHHHHhCCcEEEE--e-------CCHHHHhHHHhCCCcCEEEEc
Confidence 4689999986 7999999875 78999999999999999999775554 3 359999999999999998888
Q ss_pred eeeccccccceeeccceeecceEEEEecCCCCcCccccccCcc
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
++.+++|++.++||.||+..+.+++.++.. ...+.+|+..+
T Consensus 88 ~~~~~~r~~~~~fs~p~~~~~~~~v~~~~~--~~~~~dL~g~~ 128 (243)
T PRK15007 88 MDITPEREKQVLFTTPYYDNSALFVGQQGK--YTSVDQLKGKK 128 (243)
T ss_pred CccCHHHhcccceecCccccceEEEEeCCC--CCCHHHhCCCe
Confidence 899999999999999999999888876553 44555565544
No 71
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=99.46 E-value=6.4e-12 Score=122.50 Aligned_cols=213 Identities=10% Similarity=0.048 Sum_probs=148.5
Q ss_pred HhHHHHH-HcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 3 AIADIVD-YFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 3 Ai~~ll~-~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++++.+. ..|.++|++++.|++||....+.+++.+++.|+.|+....++... .|+..++++|+++++++|++.....
T Consensus 123 ~~~~~~~~~~g~k~v~~l~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~D~s~~v~~l~~~~pDav~~~~~~~ 200 (359)
T TIGR03407 123 PAVDYLLSKKGAKRFFLLGSDYVFPRTANKIIKAYLKSLGGTVVGEDYTPLGH--TDFQTIINKIKAFKPDVVFNTLNGD 200 (359)
T ss_pred HHHHHHHhccCCceEEEecCccHHHHHHHHHHHHHHHHcCCEEEeeEEecCCh--HhHHHHHHHHHHhCCCEEEEeccCC
Confidence 4455444 469999999999999999989999999999999998887776543 4899999999999999998877777
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEee--ecCCchhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRM--YTQSSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~--~~~~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
....+++++.+.|+.......+.+........ ....+...|+.+... .....+..+.|.+.+++.+..
T Consensus 201 ~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~------~~g~~~~~G~~~~~~~~~~~~~~~~~~f~~~~~~~~~~---- 270 (359)
T TIGR03407 201 SNVAFFKQLKNAGITAKDVPVVSFSVAEEEIR------GIGPENLVGHLAAWNYFQSVDTPANKKFVKAFKAKYGD---- 270 (359)
T ss_pred CHHHHHHHHHHcCCCccCCcEEEeecCHHHHh------hcChHhhCCeEEeccchhcCCCHHHHHHHHHHHHHcCC----
Confidence 77889999999997543333444322111100 111133456544321 123457788899888877632
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIK 239 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~ 239 (481)
......++...|||+++++.|+++.-. .+ +..+.+.|+.++|.++.|+++
T Consensus 271 -~~~~~~~~~~~y~a~~~~~~A~~~ag~----------------------------~~-~~~i~~al~~~~~~~~~G~i~ 320 (359)
T TIGR03407 271 -DRVTNDPMEAAYLGVYLWKAAVEKAGS----------------------------FD-VDAVRDAAIGIEFDAPEGKVK 320 (359)
T ss_pred -CCCCCcHHHHHHHHHHHHHHHHHHhCC----------------------------CC-HHHHHHHhcCCcccCCCccEE
Confidence 111233456789999999999987410 22 788999999999999999999
Q ss_pred EccCCCCCCCcEEEEEee
Q 011629 240 FTSDRDLINPAYEVINVI 257 (481)
Q Consensus 240 Fd~~Gd~~~~~y~I~~~~ 257 (481)
|++++......+.+.++.
T Consensus 321 f~~~~~~~~~~~~~~~~~ 338 (359)
T TIGR03407 321 VDGKNHHLTKTVRIGEIR 338 (359)
T ss_pred EeCCCCeeeeeeEEEEEc
Confidence 997432222344444443
No 72
>cd06330 PBP1_Arsenic_SBP_like Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa.
Probab=99.46 E-value=3.7e-12 Score=123.77 Aligned_cols=201 Identities=13% Similarity=0.050 Sum_probs=145.5
Q ss_pred hHhHHHHHHcC--CcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEE--EecCCCCChhHHHHHHHHhccCCceEEEEE
Q 011629 2 AAIADIVDYFG--WRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHK--VPLSPKGSRNQIIDTLLTVSSMMSRILILH 77 (481)
Q Consensus 2 ~Ai~~ll~~fg--W~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~--~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~ 77 (481)
.++++++++++ |++|++|+.++++|....+.+++.+++.|+++... ..++. ...++...+.+|++.++++|+++
T Consensus 125 ~~~~~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~g~~~~~v~~~~~~~--~~~d~~~~v~~i~~~~~d~ii~~ 202 (346)
T cd06330 125 VAGALYAAKLDKKAKTWATINPDYAYGQDAWADFKAALKRLRPDVEVVSEQWPKL--GAPDYGSEITALLAAKPDAIFSS 202 (346)
T ss_pred HHHHHHHHHhCcCccEEEEECCchHHHHHHHHHHHHHHHHhCCCCeecccccCCC--CCcccHHHHHHHHhcCCCEEEEe
Confidence 46778888774 99999999999999999999999999997665433 32332 23478899999999999999998
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEee--ecC--CchhHHHHHHHHhhhh
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRM--YTQ--SSEEKRKFVTRWRHLT 153 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~--~~~--~~~~~~~f~~~~~~~~ 153 (481)
+...+...+++++.+.|+.. +..|+.+........ ........|++.... ... ..+..++|.+.|++.+
T Consensus 203 ~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~~------~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~ 275 (346)
T cd06330 203 LWGGDLVTFVRQANARGLFD-GTTVVLTLTGAPELA------PLGDEMPEGVIIGGRGPYFIPPDTPENKAFVDAYQEKY 275 (346)
T ss_pred cccccHHHHHHHHHhcCccc-CceEEeeccchhhhh------hhhcccCCceEEeccccCCCCCCChHHHHHHHHHHHHH
Confidence 88888899999999998753 567887654322210 111233445443321 111 4677899999998877
Q ss_pred ccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCc
Q 011629 154 RRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTG 233 (481)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g 233 (481)
+. .++.++...||++.+++.|++++...... .. ...+.+.|+++.|.|
T Consensus 276 g~-------~p~~~~~~~y~a~~~l~~a~~~a~~~~~~------------------------~~-~~~v~~al~~~~~~~ 323 (346)
T cd06330 276 GD-------YPTYGAYGAYQAVMALAAAVEKAGATDGG------------------------AP-PEQIAAALEGLSFET 323 (346)
T ss_pred CC-------CCChHHHHHHHHHHHHHHHHHHhcCCCCC------------------------Cc-HHHHHHHHcCCCccC
Confidence 42 23446789999999999999875321100 11 256999999999999
Q ss_pred eeeeEEEccC
Q 011629 234 VTGPIKFTSD 243 (481)
Q Consensus 234 ~sG~v~Fd~~ 243 (481)
+.|++.|+++
T Consensus 324 ~~G~~~f~~~ 333 (346)
T cd06330 324 PGGPITMRAA 333 (346)
T ss_pred CCCceeeecC
Confidence 9999999874
No 73
>cd06327 PBP1_SBP_like_1 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are predicted to have a similar function to an active transport system for short chain amides and urea by sequence comparison and phylogenetic analysis. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus may also be involved in transport of amino acids.
Probab=99.44 E-value=4e-12 Score=122.81 Aligned_cols=201 Identities=13% Similarity=0.099 Sum_probs=148.9
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
+++++.+..-++++|++++.++.+|......+++.+++.|++|.....++... .|+..++.++++.++++|++.+...
T Consensus 124 ~~~~~~~~~~~~~~v~~i~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~l~~~~~d~v~~~~~~~ 201 (334)
T cd06327 124 NGTAPALVKAGGKKWFFLTADYAFGHSLERDARKVVKANGGKVVGSVRHPLGT--SDFSSYLLQAQASGADVLVLANAGA 201 (334)
T ss_pred HHHHHHHHHhcCCeEEEEecchHHhHHHHHHHHHHHHhcCCEEcCcccCCCCC--ccHHHHHHHHHhCCCCEEEEeccch
Confidence 46777666567999999999999999999999999999999999888787653 3799999999999999999999999
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec--CCchhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT--QSSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~--~~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
.+..+++++.+.|+. ....++....+... .. ....+...|++...... ...+..++|.+.|++.+..
T Consensus 202 ~~~~~~~~~~~~g~~-~~~~~~~~~~~~~~--~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~---- 270 (334)
T cd06327 202 DTVNAIKQAAEFGLT-KGQKLAGLLLFLTD--VH----SLGLDAAQGLYLTTAWYWDLPNDETRAFVKRFQAKYGK---- 270 (334)
T ss_pred hHHHHHHHHHHhCCc-cCCcEEEecccHHH--HH----hhchhhhcCeEEeeeccccCCCHHHHHHHHHHHHHHCc----
Confidence 999999999999875 22333332221111 00 11123456666554432 3367788999999887742
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcc-cCceeeeE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVN-MTGVTGPI 238 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~-f~g~sG~v 238 (481)
.+..++...||++++++.|+++.-. .+ +..+.+.|+++. +.++.|++
T Consensus 271 ---~p~~~~~~~Y~~~~~~~~A~~~ag~----------------------------~~-~~~v~~al~~~~~~~~~~g~~ 318 (334)
T cd06327 271 ---MPSMVQAGAYSAVLHYLKAVEAAGT----------------------------DD-ADKVVAKMKETPIYDLFAGNG 318 (334)
T ss_pred ---CCCcHHHHHHHHHHHHHHHHHHHCC----------------------------CC-hHHHHHhccccceeccCCCCc
Confidence 2445788999999999999987521 12 566899999875 57788899
Q ss_pred EEcc-CCCCC
Q 011629 239 KFTS-DRDLI 247 (481)
Q Consensus 239 ~Fd~-~Gd~~ 247 (481)
+|+. +++..
T Consensus 319 ~~~~~~~~~~ 328 (334)
T cd06327 319 YIRACDHQMV 328 (334)
T ss_pred eeeccccchh
Confidence 9986 66543
No 74
>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=99.44 E-value=2.5e-13 Score=123.22 Aligned_cols=94 Identities=31% Similarity=0.494 Sum_probs=85.5
Q ss_pred EEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeee
Q 011629 320 LRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAI 399 (481)
Q Consensus 320 l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~ 399 (481)
|+||+.. +++||.+.++ ++++.|+++|+++++++++|+++++...+ |.+++.+|.+|++|+++++++.
T Consensus 1 l~V~~~~--~~~P~~~~~~-~~~~~G~~~dl~~~i~~~~g~~~~~~~~~---------~~~~~~~l~~g~~D~~~~~~~~ 68 (225)
T PF00497_consen 1 LRVGVDE--DYPPFSYIDE-DGEPSGIDVDLLRAIAKRLGIKIEFVPMP---------WSRLLEMLENGKADIIIGGLSI 68 (225)
T ss_dssp EEEEEES--EBTTTBEEET-TSEEESHHHHHHHHHHHHHTCEEEEEEEE---------GGGHHHHHHTTSSSEEESSEB-
T ss_pred CEEEEcC--CCCCeEEECC-CCCEEEEhHHHHHHHHhhcccccceeecc---------cccccccccccccccccccccc
Confidence 6889965 8999999987 89999999999999999999886666555 9999999999999999988999
Q ss_pred ccccccceeeccceeecceEEEEecC
Q 011629 400 TTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 400 t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
|++|.+.++||.||+..+.++++++.
T Consensus 69 ~~~r~~~~~~s~p~~~~~~~~~~~~~ 94 (225)
T PF00497_consen 69 TPERAKKFDFSDPYYSSPYVLVVRKG 94 (225)
T ss_dssp BHHHHTTEEEESESEEEEEEEEEETT
T ss_pred cccccccccccccccchhheeeeccc
Confidence 99999999999999999999999965
No 75
>cd06329 PBP1_SBP_like_3 Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=99.44 E-value=7.7e-12 Score=121.24 Aligned_cols=195 Identities=13% Similarity=0.098 Sum_probs=147.3
Q ss_pred hHhHHHHHHcC-CcEEEEEEEeCCcccchHHHHHHHHHh--cCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEe
Q 011629 2 AAIADIVDYFG-WRNVIALYVDDDHGRNGIAALGDKLAE--KRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 2 ~Ai~~ll~~fg-W~~V~ii~~dd~~g~~~~~~l~~~l~~--~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
.++++++...+ |++|++++.|+.||....+.+++.+++ .|++|.....++... ..|+..++.++++.++++|++..
T Consensus 131 ~~l~~~~~~~~~~k~v~i~~~~~~~g~~~~~~~~~~~~~~~~G~~vv~~~~~~~~~-~~d~~~~i~~l~~~~~d~v~~~~ 209 (342)
T cd06329 131 EALASYIKKQPDGKKVYLINQDYSWGQDVAAAFKAMLAAKRPDIQIVGEDLHPLGK-VKDFSPYVAKIKASGADTVITGN 209 (342)
T ss_pred HHHHHHHHhcccCceEEEEeCChHHHHHHHHHHHHHHHhhcCCcEEeceeccCCCC-CCchHHHHHHHHHcCCCEEEEcc
Confidence 46778887776 999999999999999999999999999 999998877776543 13789999999999999999988
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec--CCchhHHHHHHHHhhhhccC
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT--QSSEEKRKFVTRWRHLTRRN 156 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~--~~~~~~~~f~~~~~~~~~~~ 156 (481)
....+..+++++.+.|+.. .++........ .. ....+...|.+...... ...+..++|.+.|++.+..
T Consensus 210 ~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~--~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~- 279 (342)
T cd06329 210 WGNDLLLLVKQAADAGLKL---PFYTPYLDQPG--NP----AALGEAGLGLVVAVAYWHPNDTPANRAFVEAFKAKYGR- 279 (342)
T ss_pred cCchHHHHHHHHHHcCCCc---eEEeccccchh--HH----HhhcccccceEEeeeccCCCCCHHHHHHHHHHHHHhCC-
Confidence 8888899999999998742 34444332211 10 11223345655543322 2357788999999877642
Q ss_pred CCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceee
Q 011629 157 TLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTG 236 (481)
Q Consensus 157 ~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG 236 (481)
.++.++...||++++++.|+++.-. .+ +..+.+.|++++|.|..|
T Consensus 280 ------~~~~~~~~~y~~~~~~~~a~~~ag~----------------------------~~-~~~v~~al~~~~~~~~~g 324 (342)
T cd06329 280 ------VPDYYEGQAYNGIQMLADAIEKAGS----------------------------TD-PEAVAKALEGMEVDTPVG 324 (342)
T ss_pred ------CCCchHHHHHHHHHHHHHHHHHhCC----------------------------CC-HHHHHHHHhCCccccCCC
Confidence 2345678899999999999986310 12 678999999999999999
Q ss_pred eEEEcc
Q 011629 237 PIKFTS 242 (481)
Q Consensus 237 ~v~Fd~ 242 (481)
++.|+.
T Consensus 325 ~~~~~~ 330 (342)
T cd06329 325 PVTMRA 330 (342)
T ss_pred CeEEcc
Confidence 999984
No 76
>cd06358 PBP1_NHase Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified int
Probab=99.43 E-value=6.5e-12 Score=121.30 Aligned_cols=198 Identities=13% Similarity=0.099 Sum_probs=145.9
Q ss_pred HHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHH
Q 011629 6 DIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLE 85 (481)
Q Consensus 6 ~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~ 85 (481)
.+.+..||++|++++.|+.+|+...+.+++.+++.|+.|.....++.. ..|+...+.++++.++++|++.........
T Consensus 125 ~~~~~~g~~~v~i~~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~ 202 (333)
T cd06358 125 WLAEEKGARRWYLIGNDYVWPRGSLAAAKRYIAELGGEVVGEEYVPLG--TTDFTSVLERIAASGADAVLSTLVGQDAVA 202 (333)
T ss_pred HHHHhcCCCeEEEEeccchhhHHHHHHHHHHHHHcCCEEeeeeeecCC--hHHHHHHHHHHHHcCCCEEEEeCCCCchHH
Confidence 345668999999999999999999999999999999999988778754 348999999999999999998888878889
Q ss_pred HHHHHHHcCCccCCeEEEE-eccccccccCCccccccccccceeeEEEeeec--CCchhHHHHHHHHhhhhccCCCCCCC
Q 011629 86 VLNAAKHLRMMESGYVWIV-TDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT--QSSEEKRKFVTRWRHLTRRNTLNGPI 162 (481)
Q Consensus 86 il~~a~~~g~~~~~~~wI~-~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~--~~~~~~~~f~~~~~~~~~~~~~~~~~ 162 (481)
+++++.+.|+..+ ++. ...+.... .. ........|++...... ...+..++|.+.|++.+.. +..
T Consensus 203 ~~~~~~~~G~~~~---~~~~~~~~~~~~-~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~----~~~ 270 (333)
T cd06358 203 FNRQFAAAGLRDR---ILRLSPLMDENM-LL----ASGAEAAEGLYSSSGYFASLQTPANAAFLARYRARFGD----DAP 270 (333)
T ss_pred HHHHHHHcCCCcc---CceeecccCHHH-HH----hcChHhhCCcEEeccchhhcCCHHHHHHHHHHHHHcCC----CCC
Confidence 9999999987542 222 21121110 00 11112345655543322 2457788999999887742 112
Q ss_pred CCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEEEcc
Q 011629 163 GLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKFTS 242 (481)
Q Consensus 163 ~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~Fd~ 242 (481)
.++.++...||++.+++.|+++.- ..+ +..|.+.|++++|.|.+|++.|++
T Consensus 271 ~~~~~~~~~yda~~~~~~A~~~ag----------------------------~~~-~~~v~~al~~~~~~~~~G~~~~~~ 321 (333)
T cd06358 271 PLNSLSESCYEAVHALAAAAERAG----------------------------SLD-PEALIAALEDVSYDGPRGTVTMRG 321 (333)
T ss_pred CCChHHHHHHHHHHHHHHHHHHhC----------------------------CCC-HHHHHHHhccCeeeCCCcceEEcc
Confidence 245577889999999999998521 022 678999999999999999999998
Q ss_pred CCCC
Q 011629 243 DRDL 246 (481)
Q Consensus 243 ~Gd~ 246 (481)
++..
T Consensus 322 ~~~~ 325 (333)
T cd06358 322 RHAR 325 (333)
T ss_pred cccc
Confidence 8654
No 77
>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=99.43 E-value=3.4e-13 Score=126.35 Aligned_cols=108 Identities=24% Similarity=0.279 Sum_probs=91.6
Q ss_pred CCceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCc-ccEEEEeCCCCCCCCCHHHHHHHHHcccccEEE
Q 011629 316 NGRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYA-VPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAV 394 (481)
Q Consensus 316 ~~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~ 394 (481)
..++|+|++. +++||.+.++ +|++.|+++||++++++++|.+ +++... .|+.++..|.+|++|+++
T Consensus 31 ~~~~l~v~~~---~~pP~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~~~~~~~---------~w~~~~~~l~~G~~Di~~ 97 (275)
T TIGR02995 31 EQGFARIAIA---NEPPFTYVGA-DGKVSGAAPDVARAIFKRLGIADVNASIT---------EYGALIPGLQAGRFDAIA 97 (275)
T ss_pred hCCcEEEEcc---CCCCceeECC-CCceecchHHHHHHHHHHhCCCceeeccC---------CHHHHHHHHHCCCcCEEe
Confidence 4578999986 6899999875 7899999999999999999975 344444 499999999999999988
Q ss_pred eeeeeccccccceeeccceeecceEEEEecCCC-CcCcccccc
Q 011629 395 GDFAITTERTKMVDFTQPYIESGLVVVAPIKKL-NSNAWAFLN 436 (481)
Q Consensus 395 ~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~-~~~~~~~l~ 436 (481)
+++++|++|++.++||.||+.++.++++++++. .+..+.+|.
T Consensus 98 ~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~~~i~~~~dl~ 140 (275)
T TIGR02995 98 AGLFIKPERCKQVAFTQPILCDAEALLVKKGNPKGLKSYKDIA 140 (275)
T ss_pred ecccCCHHHHhccccccceeecceeEEEECCCCCCCCCHHHhc
Confidence 888999999999999999999999999998762 244455553
No 78
>TIGR03669 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization.
Probab=99.43 E-value=1.7e-11 Score=119.65 Aligned_cols=212 Identities=10% Similarity=0.075 Sum_probs=148.4
Q ss_pred HhHHHHH-HcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 3 AIADIVD-YFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 3 Ai~~ll~-~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++++.+. ..+ ++|++|+.|++||+.....+++.+++.|+.|.....++.... |+..++.+|+++++++|++.....
T Consensus 123 ~~~~~~~~~~g-~~va~l~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~g~~--Df~~~l~~i~~~~pD~V~~~~~g~ 199 (374)
T TIGR03669 123 TVVPYMVEEYG-KKIYTIAADYNFGQLSADWVRVIAKENGAEVVGEEFIPLSVS--QFSSTIQNIQKADPDFVMSMLVGA 199 (374)
T ss_pred HHHHHHHHcCC-CeEEEEcCCcHHHHHHHHHHHHHHHHcCCeEEeEEecCCCcc--hHHHHHHHHHHcCCCEEEEcCcCC
Confidence 4556554 467 579999999999999999999999999999988888876543 899999999999999999988777
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec--CCchhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT--QSSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~--~~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
+...+++++.++|+..+ .+............ ........|+++..... ...+..+.|.+.|++.+...+
T Consensus 200 ~~~~~~kq~~~~G~~~~---~~~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~F~~~y~~~~g~~p-- 270 (374)
T TIGR03669 200 NHASFYEQAASANLNLP---MGTSTAMAQGYEHK----RFEPPALKDVYAGVNYMEEIDTPENEAFVERFYAKFPDAP-- 270 (374)
T ss_pred cHHHHHHHHHHcCCCCc---ccchhhhhhhhhhh----hcCchhhCCcEEeeeccccCCCHHHHHHHHHHHHHcCCCC--
Confidence 88899999999997532 12111111100000 00112234444333222 245778999999998874211
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHh-cccCceeeeE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQ-VNMTGVTGPI 238 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~-v~f~g~sG~v 238 (481)
.++.++...|||+++++.|+++.-+ .+ +..+.+.|++ .+|.+..|++
T Consensus 271 ---~~~~~a~~~Yda~~~l~~Ai~~AGs----------------------------~d-~~av~~aL~~~~~~~~~~G~i 318 (374)
T TIGR03669 271 ---YINQEAENNYFSVYMYKQAVEEAGT----------------------------TD-QDAVRDVLESGVEMDAPEGKV 318 (374)
T ss_pred ---CCChHHHHHHHHHHHHHHHHHHhCC----------------------------CC-HHHHHHHHHcCCeEECCCccE
Confidence 1244678899999999999987410 22 7889999987 6789999999
Q ss_pred EEccCCCCCCCcEEEEEeec
Q 011629 239 KFTSDRDLINPAYEVINVIG 258 (481)
Q Consensus 239 ~Fd~~Gd~~~~~y~I~~~~~ 258 (481)
+||++++.....+.|.++..
T Consensus 319 ~fd~~~~~~~~~~~v~~~~~ 338 (374)
T TIGR03669 319 CIDGATHHMSHTMRLARADA 338 (374)
T ss_pred EEcCCCCeeeeeeEEEEEcC
Confidence 99977654323444555543
No 79
>PRK11260 cystine transporter subunit; Provisional
Probab=99.42 E-value=5.7e-13 Score=124.22 Aligned_cols=114 Identities=24% Similarity=0.352 Sum_probs=94.9
Q ss_pred CCCceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEE
Q 011629 315 NNGRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAV 394 (481)
Q Consensus 315 ~~~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~ 394 (481)
...++|+|++.. +++||.+.++ +|++.|+.+|++++|++++|.++++ ++ ..|.+++.+|.+|++|+++
T Consensus 38 ~~~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~e~--~~-------~~~~~~~~~l~~G~~D~~~ 105 (266)
T PRK11260 38 KERGTLLVGLEG--TYPPFSFQGE-DGKLTGFEVEFAEALAKHLGVKASL--KP-------TKWDGMLASLDSKRIDVVI 105 (266)
T ss_pred hcCCeEEEEeCC--CcCCceEECC-CCCEEEehHHHHHHHHHHHCCeEEE--Ee-------CCHHHHHHHHhcCCCCEEE
Confidence 356799999876 7999998875 7899999999999999999977544 44 3499999999999999998
Q ss_pred eeeeeccccccceeeccceeecceEEEEecCC-CCcCccccccCcch
Q 011629 395 GDFAITTERTKMVDFTQPYIESGLVVVAPIKK-LNSNAWAFLNPFTP 440 (481)
Q Consensus 395 ~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~-~~~~~~~~l~pf~~ 440 (481)
++++.+++|.+.+.||.||+..+.++++++.+ ..+..+.+|+..+.
T Consensus 106 ~~~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~dL~g~~I 152 (266)
T PRK11260 106 NQVTISDERKKKYDFSTPYTVSGIQALVKKGNEGTIKTAADLKGKKV 152 (266)
T ss_pred eccccCHHHHhccccCCceeecceEEEEEcCCcCCCCCHHHcCCCEE
Confidence 88899999999999999999999999998765 23455555554433
No 80
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=99.41 E-value=2.7e-11 Score=118.19 Aligned_cols=213 Identities=16% Similarity=0.120 Sum_probs=154.8
Q ss_pred HhHHHH-HHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 3 AIADIV-DYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 3 Ai~~ll-~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++++.+ +.++.++|++|++|+.||++..+.+++.+++.|..+...+.+.+... ++..++.+|+++++++|++.+...
T Consensus 137 ~~~~~l~~~~~~k~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~~~~~~~~~~--~~~~~v~~i~~~~~d~v~~~~~~~ 214 (366)
T COG0683 137 AAADYLVKKGGKKRVAIIGDDYAYGEGLADAFKAALKALGGEVVVEEVYAPGDT--DFSALVAKIKAAGPDAVLVGGYGP 214 (366)
T ss_pred HHHHHHHHhcCCcEEEEEeCCCCcchhHHHHHHHHHHhCCCeEEEEEeeCCCCC--ChHHHHHHHHhcCCCEEEECCCCc
Confidence 456554 56777899999999999999999999999999998665566665544 499999999999999999999999
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccce--eeEEEe-eecCCchhHHHHHHHHhhhhccCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQ--GVLTLR-MYTQSSEEKRKFVTRWRHLTRRNTL 158 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~--g~l~~~-~~~~~~~~~~~f~~~~~~~~~~~~~ 158 (481)
+...+++++.++|+.. ...++.......... ....... +.+... ......|..+.|.+.|++.+.
T Consensus 215 ~~~~~~r~~~~~G~~~-~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~~g---- 282 (366)
T COG0683 215 DAALFLRQAREQGLKA-KLIGGDGAGTAEFEE-------IAGAGGAGAGLLATAYSTPDDSPANKKFVEAYKAKYG---- 282 (366)
T ss_pred cchHHHHHHHHcCCCC-ccccccccCchhhhh-------hcccCccccEEEEecccccccCcchHHHHHHHHHHhC----
Confidence 9999999999998643 233332221111100 0011111 222222 222344566779999998874
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcc-cCceeee
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVN-MTGVTGP 237 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~-f~g~sG~ 237 (481)
+....+.++...|||+++++.|+++... . .+ +..+.+.|+... +.+.+|.
T Consensus 283 -~~~~~~~~~~~~y~a~~~~~~ai~~a~~---~------------------------~d-~~~v~~al~~~~~~~~~~G~ 333 (366)
T COG0683 283 -DPAAPSYFAAAAYDAVKLLAKAIEKAGK---S------------------------SD-REAVAEALKGGKFFDTAGGP 333 (366)
T ss_pred -CCCCcccchHHHHHHHHHHHHHHHHHhc---C------------------------CC-HHHHHHHHhhCCCCccCCcc
Confidence 1223455788999999999999998632 0 22 677999999887 6888899
Q ss_pred EEEccCCCCCCCcEEEEEeec
Q 011629 238 IKFTSDRDLINPAYEVINVIG 258 (481)
Q Consensus 238 v~Fd~~Gd~~~~~y~I~~~~~ 258 (481)
+.||++|++....+.|.+++.
T Consensus 334 v~~~~~~~~~~~~~~i~~~~~ 354 (366)
T COG0683 334 VTFDEKGDRGSKPVYVGQVQK 354 (366)
T ss_pred eeECCCCCcCCCceEEEEEEe
Confidence 999999998888888888874
No 81
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.38 E-value=9.6e-13 Score=121.65 Aligned_cols=109 Identities=24% Similarity=0.349 Sum_probs=92.8
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF 397 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 397 (481)
++|+|++.. +++||.+.++ +|++.|+++|+++++++.+|.+ +++++ .+|..++.+|.+|++|++++++
T Consensus 24 ~~l~v~~~~--~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~--~~~~~-------~~~~~~~~~l~~G~~D~~~~~~ 91 (250)
T TIGR01096 24 GSVRIGTET--GYPPFESKDA-NGKLVGFDVDLAKALCKRMKAK--CKFVE-------QNFDGLIPSLKAKKVDAIMATM 91 (250)
T ss_pred CeEEEEECC--CCCCceEECC-CCCEEeehHHHHHHHHHHhCCe--EEEEe-------CCHHHHHHHHhCCCcCEEEecC
Confidence 789999975 7999999876 7899999999999999999977 55555 3599999999999999998788
Q ss_pred eeccccccceeeccceeecceEEEEecCCCCcCccccccCc
Q 011629 398 AITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPF 438 (481)
Q Consensus 398 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf 438 (481)
+.+++|++.+.||.|++..+..+++++++.....+.+|+..
T Consensus 92 ~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~~~~~~dl~g~ 132 (250)
T TIGR01096 92 SITPKRQKQIDFSDPYYATGQGFVVKKGSDLAKTLEDLDGK 132 (250)
T ss_pred ccCHHHhhccccccchhcCCeEEEEECCCCcCCChHHcCCC
Confidence 89999999999999999999999998876433445555443
No 82
>cd06337 PBP1_ABC_ligand_binding_like_4 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.37 E-value=1.8e-11 Score=119.22 Aligned_cols=197 Identities=15% Similarity=0.086 Sum_probs=137.6
Q ss_pred hHhHHHHHHcC-CcEEEEEEEeCCcccchHHHHH---HHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEE
Q 011629 2 AAIADIVDYFG-WRNVIALYVDDDHGRNGIAALG---DKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILH 77 (481)
Q Consensus 2 ~Ai~~ll~~fg-W~~V~ii~~dd~~g~~~~~~l~---~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~ 77 (481)
+++++.++..+ .++|++++.|+.||....+.+. +.+++.|+.|...+.++.... |+..++++|+++++++|++.
T Consensus 133 ~~~~~~~~~~~~~k~v~ii~~~~~~g~~~~~~~~~~~~~~~~~G~~vv~~~~~~~~~~--D~~~~v~~ik~a~pD~v~~~ 210 (357)
T cd06337 133 ATYVGMWKQLETNKKVGILYPNDPDGNAFADPVIGLPAALADAGYKLVDPGRFEPGTD--DFSSQINAFKREGVDIVTGF 210 (357)
T ss_pred HHHHHHHHhCCCCceEEEEeecCchhHHHHHhhhcccHHHHhCCcEEecccccCCCCC--cHHHHHHHHHhcCCCEEEeC
Confidence 35566667777 9999999999999987766554 567779999998888876544 89999999999999999998
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEe-ccccccccCCccccccccccceeeEEEeeecCC--------chhHHHHHHH
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVT-DWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQS--------SEEKRKFVTR 148 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~-~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~--------~~~~~~f~~~ 148 (481)
+....+..+++++.++|...+ ++.. ...... ... ....+...|++......+. .+..++|.+.
T Consensus 211 ~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 282 (357)
T cd06337 211 AIPPDFATFWRQAAQAGFKPK---IVTIAKALLFP-EDV----EALGDRGDGMSTEVWWSPSHPFRSSLTGQSAAELADA 282 (357)
T ss_pred CCccHHHHHHHHHHHCCCCCC---eEEEeccccCH-HHH----HHhhhhhcCccccceeccCCCcccccCCccHHHHHHH
Confidence 888899999999999886432 2222 111111 010 0111122444433221111 2357889988
Q ss_pred HhhhhccCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHh
Q 011629 149 WRHLTRRNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQ 228 (481)
Q Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~ 228 (481)
|++.+... +.....+.|+++++++.|+++.-. ..++..|.+.|++
T Consensus 283 y~~~~g~~-------~~~~~~~~~~~~~~l~~Ai~~Ags----------------------------~~d~~~v~~aL~~ 327 (357)
T cd06337 283 YEAATGRQ-------WTQPLGYAHALFEVGVKALVRADD----------------------------PDDPAAVADAIAT 327 (357)
T ss_pred HHHHhCCC-------ccCcchHHHHHHHHHHHHHHHcCC----------------------------CCCHHHHHHHHHc
Confidence 88777421 123456789999999999986311 1126789999999
Q ss_pred cccCceeeeEEEccC
Q 011629 229 VNMTGVTGPIKFTSD 243 (481)
Q Consensus 229 v~f~g~sG~v~Fd~~ 243 (481)
++|.++.|++.|+++
T Consensus 328 ~~~~~~~G~~~f~~~ 342 (357)
T cd06337 328 LKLDTVVGPVDFGNS 342 (357)
T ss_pred CCcccceeeeecCCC
Confidence 999999999999865
No 83
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.34 E-value=7.6e-11 Score=114.48 Aligned_cols=201 Identities=16% Similarity=0.162 Sum_probs=140.3
Q ss_pred hHhHHHH-HHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 2 AAIADIV-DYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~ll-~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.++++.+ ++.+|++|++++.+++||....+.+++.+++.|+++.....++.... ++...+++|+++++++|++.+..
T Consensus 126 ~~~a~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~~--d~s~~i~~i~~~~~d~v~~~~~~ 203 (347)
T cd06335 126 PFLVDEAVKRGGFKKVALLLDNTGWGRSNRKDLTAALAARGLKPVAVEWFNWGDK--DMTAQLLRAKAAGADAIIIVGNG 203 (347)
T ss_pred HHHHHHHHHhcCCCeEEEEeccCchhhhHHHHHHHHHHHcCCeeEEEeeecCCCc--cHHHHHHHHHhCCCCEEEEEecC
Confidence 3567755 56779999999999999999999999999999999998888876533 79999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec---CCchhHHHHHHHHhhhhccCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT---QSSEEKRKFVTRWRHLTRRNT 157 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~---~~~~~~~~f~~~~~~~~~~~~ 157 (481)
.....+++++.+.|+.. .++..+........ ........|++...... ...+..++|.+.|++.+...+
T Consensus 204 ~~~~~~~~~~~~~g~~~----~~~~~~~~~~~~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~ 275 (347)
T cd06335 204 PEGAQIANGMAKLGWKV----PIISHWGLSGGNFI----EGAGPAANDALMIQTFIFEPPSNPKAKAFLAAYHKKYPEKK 275 (347)
T ss_pred hHHHHHHHHHHHcCCCC----cEecccCCcCchhh----hccchhhcCcEEEEeeccccCCCHHHHHHHHHHHHHhCCCc
Confidence 99999999999988742 22222111111110 11112345555443221 256788999999998875321
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhc--ccCcee
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQV--NMTGVT 235 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v--~f~g~s 235 (481)
.. ...++.++...||++++++.|+++.-. .. +..+.+.|+++ .+.|+.
T Consensus 276 ~~-~~~~~~~~~~aYd~~~~l~~A~~~ag~----------------------------~~-~~~v~~al~~~~~~~~G~~ 325 (347)
T cd06335 276 PA-DIPAPVGAAHAYDAVHLLAAAIKQAGS----------------------------TD-GRAIKRALENLKKPVEGLV 325 (347)
T ss_pred cc-ccCcchhHHHHHHHHHHHHHHHHHhcC----------------------------CC-HHHHHHHHHhccCCceeee
Confidence 11 112344567899999999999987410 11 35678888765 456766
Q ss_pred e--eEEEcc
Q 011629 236 G--PIKFTS 242 (481)
Q Consensus 236 G--~v~Fd~ 242 (481)
| .+.|+.
T Consensus 326 ~~~~~~~~~ 334 (347)
T cd06335 326 KTYDKPFSK 334 (347)
T ss_pred cccCCCCCh
Confidence 6 345654
No 84
>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=99.34 E-value=1.6e-12 Score=119.57 Aligned_cols=100 Identities=17% Similarity=0.255 Sum_probs=79.5
Q ss_pred eEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHH---HHHHcccccEEEe
Q 011629 319 HLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLL---RLVSEEVYDAAVG 395 (481)
Q Consensus 319 ~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~---~~l~~g~~d~~~~ 395 (481)
+|+||+.. ++|||.+.+ + .||++||+++||+++|++++ +++ .+|++++ ..|.+|++|+++
T Consensus 1 ~l~vg~~~--~~pPf~~~~---~--~Gfdvdl~~~ia~~lg~~~~--~~~-------~~~~~~~~~~~~L~~g~~Dii~- 63 (246)
T TIGR03870 1 TLRVCAAT--KEAPYSTKD---G--SGFENKIAAALAAAMGRKVV--FVW-------LAKPAIYLVRDGLDKKLCDVVL- 63 (246)
T ss_pred CeEEEeCC--CCCCCccCC---C--CcchHHHHHHHHHHhCCCeE--EEE-------eccchhhHHHHHHhcCCccEEE-
Confidence 47899987 899999964 2 69999999999999997744 444 3488876 699999999997
Q ss_pred eeeeccccccceeeccceeecceEEEEecCCC-CcCccc--cccCc
Q 011629 396 DFAITTERTKMVDFTQPYIESGLVVVAPIKKL-NSNAWA--FLNPF 438 (481)
Q Consensus 396 ~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~-~~~~~~--~l~pf 438 (481)
++++|++| +.||.||+.++.++++++++. .+..+. .|+..
T Consensus 64 ~~~~t~~r---~~fS~PY~~~~~~~v~~k~~~~~~~~~~d~~L~g~ 106 (246)
T TIGR03870 64 GLDTGDPR---VLTTKPYYRSSYVFLTRKDRNLDIKSWNDPRLKKV 106 (246)
T ss_pred eCCCChHH---HhcccCcEEeeeEEEEeCCCCCCCCCccchhhccC
Confidence 58888877 679999999999999998762 334332 35554
No 85
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=99.31 E-value=1.8e-10 Score=111.23 Aligned_cols=192 Identities=11% Similarity=0.047 Sum_probs=136.1
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-H
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-W 82 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~ 82 (481)
+++.+... +++|++|+.|++||....+.+++.+++.|++|+....++.... |+...+.+|+++++++|++..... .
T Consensus 128 ~~~~~~~~-~~~v~~i~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~--d~~~~v~~l~~~~pd~V~~~~~~~~~ 204 (333)
T cd06328 128 AAAALGKP-GKKIATLAQDYAFGRDGVAAFKAALEKLGAAIVTEEYAPTDTT--DFTPYAQRLLDALKKVLFVIWAGAGG 204 (333)
T ss_pred HHHHHHhc-CCeEEEEecCccccHHHHHHHHHHHHhCCCEEeeeeeCCCCCc--chHHHHHHHHhcCCCEEEEEecCchh
Confidence 34444444 8999999999999999999999999999999998888876443 799999999999999988765444 5
Q ss_pred HHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec-CCchhHHHHHHHHhhhhccCCCCCC
Q 011629 83 GLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT-QSSEEKRKFVTRWRHLTRRNTLNGP 161 (481)
Q Consensus 83 ~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~-~~~~~~~~f~~~~~~~~~~~~~~~~ 161 (481)
+..+++++...|... .............. ........+........ +..+..+.|.+.|++.+..
T Consensus 205 ~~~~~~~~~~~g~~~---~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g~------ 270 (333)
T cd06328 205 PWPKLQQMGVLGYGI---EITLAGDILANLTM-----YKAGPGMSGASYYYHYFLPKNPVNDWLVEEHKARFGS------ 270 (333)
T ss_pred HHHHHHHhhhhcCCC---eEEecccccCcccc-----ccccccccceeeeecCCCCCCHHHHHHHHHHHHHhCC------
Confidence 666777776665432 11111111111100 11122344544443332 4567778899888887631
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEEEc
Q 011629 162 IGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKFT 241 (481)
Q Consensus 162 ~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~Fd 241 (481)
.++.++...||++.+++.|+.+.- ..+ +..+.+.|++..|.++.|+++|+
T Consensus 271 -~p~~~~~~~y~a~~~l~~Ai~~ag----------------------------~~~-~~~v~~aL~~~~~~~~~g~~~f~ 320 (333)
T cd06328 271 -PPDLFTAGGMSAAIAVVEALEETG----------------------------DTD-TEALIAAMEGMSFETPKGTMTFR 320 (333)
T ss_pred -CcchhhHHHHHHHHHHHHHHHHhC----------------------------CCC-HHHHHHHHhCCeeecCCCceEEC
Confidence 245578899999999999998741 022 67899999999999999999998
Q ss_pred c
Q 011629 242 S 242 (481)
Q Consensus 242 ~ 242 (481)
.
T Consensus 321 ~ 321 (333)
T cd06328 321 K 321 (333)
T ss_pred c
Confidence 5
No 86
>cd06339 PBP1_YraM_LppC_lipoprotein_like Periplasmic binding component of lipoprotein LppC, an immunodominant antigen. This subgroup includes periplasmic binding component of lipoprotein LppC, an immunodominant antigen, whose molecular function is not characterized. Members of this subgroup are predicted to be involved in transport of lipid compounds, and they are sequence similar to the family of ABC-type hydrophobic amino acid transporters (HAAT).
Probab=99.31 E-value=2.9e-11 Score=116.75 Aligned_cols=195 Identities=13% Similarity=0.017 Sum_probs=134.8
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC------------
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM------------ 69 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s------------ 69 (481)
+++++.+...|+++|++++.+++||....+.+++.+++.|+.|.....++.. ..|+...+++|++.
T Consensus 113 ~~~~~~~~~~g~k~vaii~~~~~~g~~~~~~f~~~~~~~G~~vv~~~~~~~~--~~d~~~~i~~i~~~~~~~~~~~~~~~ 190 (336)
T cd06339 113 RRAAEYARSQGKRRPLVLAPDGAYGQRVADAFRQAWQQLGGTVVAIESYDPS--PTDLSDAIRRLLGVDDSEQRIAQLKS 190 (336)
T ss_pred HHHHHHHHhcCccceEEEecCChHHHHHHHHHHHHHHHcCCceeeeEecCCC--HHHHHHHHHHHhccccchhhhhhhhh
Confidence 4567777667999999999999999999999999999999999988888754 34899999999987
Q ss_pred ---------CceEEEEEeCcH-HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCc
Q 011629 70 ---------MSRILILHTYDI-WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSS 139 (481)
Q Consensus 70 ---------~~~vIvl~~~~~-~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~ 139 (481)
+++.|++.+... .+..+..++...+....+..++.++.|...... ........|+...... .
T Consensus 191 ~~~~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-----~~~g~~~~g~~~~~~~---~ 262 (336)
T cd06339 191 LESEPRRRQDIDAIDAVALPDGEARLIKPQLLFYYGVPGDVPLYGTSRWYSGTPA-----PLRDPDLNGAWFADPP---W 262 (336)
T ss_pred cccCccccCCCCcEEEEecChhhhhhhcchhhhhccCcCCCCEEEeccccCCCCC-----cccCcccCCcEEeCCC---c
Confidence 899998888776 666666666554321124467777766543111 1112334565544331 1
Q ss_pred hhHHHHHHHHhhhhccCCCCCCCCC-ChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCc
Q 011629 140 EEKRKFVTRWRHLTRRNTLNGPIGL-NSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNG 218 (481)
Q Consensus 140 ~~~~~f~~~~~~~~~~~~~~~~~~~-~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 (481)
....+|.+.|++.+.. .+ ..+++..|||+.+++.+++..- .+
T Consensus 263 ~~~~~f~~~y~~~~~~-------~p~~~~~a~~YDa~~l~~~~~~~~~-----------------------------~~- 305 (336)
T cd06339 263 LLDANFELRYRAAYGW-------PPLSRLAALGYDAYALAAALAQLGQ-----------------------------GD- 305 (336)
T ss_pred ccCcchhhhHHHHhcC-------CCCchHHHHHHhHHHHHHHHHHccc-----------------------------cc-
Confidence 1223677777776642 23 5688999999999887665420 00
Q ss_pred cHHHHHHHHhcccCceeeeEEEccCCCCC
Q 011629 219 GKMLLDNILQVNMTGVTGPIKFTSDRDLI 247 (481)
Q Consensus 219 ~~~L~~~l~~v~f~g~sG~v~Fd~~Gd~~ 247 (481)
. ..++...|.|++|+++||++|+..
T Consensus 306 ~----al~~~~~~~g~~G~~~f~~~g~~~ 330 (336)
T cd06339 306 A----ALTPGAGFSGVTGVLRLDPDGVIE 330 (336)
T ss_pred c----ccCCCCccccCcceEEECCCCeEE
Confidence 1 112234689999999999999763
No 87
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.28 E-value=6.4e-12 Score=126.56 Aligned_cols=112 Identities=18% Similarity=0.177 Sum_probs=90.7
Q ss_pred CCCceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEE
Q 011629 315 NNGRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAV 394 (481)
Q Consensus 315 ~~~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~ 394 (481)
.+.++|+|++.. +|+.+.++ ++...||++||+++|++++|+++++... .+|+.++.+|.+|++|+++
T Consensus 40 ~~~g~LrVg~~~----~P~~~~~~-~~~~~G~~~DLl~~ia~~LGv~~e~v~~--------~~~~~ll~aL~~G~iDi~~ 106 (482)
T PRK10859 40 QERGELRVGTIN----SPLTYYIG-NDGPTGFEYELAKRFADYLGVKLEIKVR--------DNISQLFDALDKGKADLAA 106 (482)
T ss_pred HhCCEEEEEEec----CCCeeEec-CCCcccHHHHHHHHHHHHhCCcEEEEec--------CCHHHHHHHHhCCCCCEEe
Confidence 356799999973 45555544 3445999999999999999977555422 4699999999999999998
Q ss_pred eeeeeccccccceeeccceeecceEEEEecCCCCcCccccccCcc
Q 011629 395 GDFAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 395 ~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
+++++|++|++.++||.||+..+.+++++++...+....+|+..+
T Consensus 107 ~~lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~~~i~~l~dL~Gk~ 151 (482)
T PRK10859 107 AGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQPRPRSLGDLKGGT 151 (482)
T ss_pred ccCcCChhhhccCcccCCceeeeEEEEEeCCCCCCCCHHHhCCCe
Confidence 899999999999999999999999999988764455566666544
No 88
>cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.25 E-value=4.3e-10 Score=109.09 Aligned_cols=214 Identities=12% Similarity=0.122 Sum_probs=146.8
Q ss_pred hHhHHHHHHcC-----CcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEE
Q 011629 2 AAIADIVDYFG-----WRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILIL 76 (481)
Q Consensus 2 ~Ai~~ll~~fg-----W~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl 76 (481)
.++++.+...+ -++|++|+.|+.||....+.+++.+++.|++|.....++...+ |+..++.+|++.++++|++
T Consensus 124 ~~l~~~~~~~~~~~~~~~kvaiv~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~--D~~~~v~~i~~~~pd~V~~ 201 (351)
T cd06334 124 RALVQYIAEQEGGKLKGKKIALVYHDSPFGKEPIEALKALAEKLGFEVVLEPVPPPGPN--DQKAQWLQIRRSGPDYVIL 201 (351)
T ss_pred HHHHHHHHHhcccCCCCCeEEEEeCCCccchhhHHHHHHHHHHcCCeeeeeccCCCCcc--cHHHHHHHHHHcCCCEEEE
Confidence 45677776555 6999999999999999999999999999999998888876544 8999999999999999999
Q ss_pred EeCcHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec--CCchhHHHHHHHHhhhhc
Q 011629 77 HTYDIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT--QSSEEKRKFVTRWRHLTR 154 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~--~~~~~~~~f~~~~~~~~~ 154 (481)
.+...+...+++++.++|+. ..++.+.... ...+. ........|+++..... ...|..++|.+.+++.+.
T Consensus 202 ~~~~~~~~~~~~~~~~~G~~---~~~~~~~~~~-~~~~~----~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~~ 273 (351)
T cd06334 202 WGWGVMNPVAIKEAKRVGLD---DKFIGNWWSG-DEEDV----KPAGDAAKGYKGVTPFAGGADDPVGKEIVKEVYDKGK 273 (351)
T ss_pred ecccchHHHHHHHHHHcCCC---ceEEEeeccC-cHHHH----HHhhhhhcCcEEeecccCCCCchHHHHHHHHHHHccC
Confidence 99988999999999999873 2344443221 11111 11223456665554332 356788999999888764
Q ss_pred cCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCce
Q 011629 155 RNTLNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGV 234 (481)
Q Consensus 155 ~~~~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~ 234 (481)
..+.. +...+.++...|||+++++.||+++-+....... ........-...++.+++....|.
T Consensus 274 ~~~~~-~~~~~~~~~~gy~a~~~l~~Al~~ag~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~g~ 336 (351)
T cd06334 274 GSGND-KEIGSVYYNRGVVNAMIMVEAIRRAQEKGGETTI----------------AGEEQLENLKLDAARLEELGAEGL 336 (351)
T ss_pred CCCCc-ccccccHHHHHHHHHHHHHHHHHHHHHhcCCCCC----------------cHHHHHHhhhhhhhhhhhcCcccc
Confidence 21110 1223457889999999999999987554321100 000000002234456677777788
Q ss_pred eeeEEEcc
Q 011629 235 TGPIKFTS 242 (481)
Q Consensus 235 sG~v~Fd~ 242 (481)
.|+++|..
T Consensus 337 ~~~~~~~~ 344 (351)
T cd06334 337 GPPVSVSC 344 (351)
T ss_pred cCCceecc
Confidence 88888864
No 89
>cd06356 PBP1_Amide_Urea_BP_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
Probab=99.22 E-value=7.4e-10 Score=106.96 Aligned_cols=201 Identities=9% Similarity=0.068 Sum_probs=142.0
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.++++.+..-+=++|++|+.|++||....+.+++.+++.|+.+.....++... .|+...+++|+++++++|++.....
T Consensus 121 ~~~~~~~~~~~~~~vail~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~l~~~~pd~v~~~~~~~ 198 (334)
T cd06356 121 STLVPYMMEKYGKKVYTIAADYNFGQISAEWVRKIVEENGGEVVGEEFIPLDV--SDFGSTIQKIQAAKPDFVMSILVGA 198 (334)
T ss_pred HHHHHHHHHccCCeEEEECCCchhhHHHHHHHHHHHHHcCCEEEeeeecCCCc--hhHHHHHHHHHhcCCCEEEEeccCC
Confidence 35666555432278999999999999999999999999999999888887653 3899999999999999999988777
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec--CCchhHHHHHHHHhhhhccCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT--QSSEEKRKFVTRWRHLTRRNTLN 159 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~--~~~~~~~~f~~~~~~~~~~~~~~ 159 (481)
....+++++.+.|+ . ....+.+.......... .......+|++...... ...+..++|.+.|++++...
T Consensus 199 ~~~~~~~~~~~~G~-~-~~~~~~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~--- 269 (334)
T cd06356 199 NHLSFYRQWAAAGL-G-NIPMASSTLGAQGYEHK----RLKPPALKDMYATANYIEELDTPANKAFVERFRAKFPDA--- 269 (334)
T ss_pred cHHHHHHHHHHcCC-c-cCceeeeecccchhHHh----ccCchhcCCeEEecchhhhcCCHHHHHHHHHHHHHcCCC---
Confidence 88899999999987 1 11122211110110000 00113345655543322 23567889999999877421
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHh-cccCceeeeE
Q 011629 160 GPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQ-VNMTGVTGPI 238 (481)
Q Consensus 160 ~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~-v~f~g~sG~v 238 (481)
-..+..+...||++++++.|+++.-. .+ +..|.+.|+. ..|+|+.|++
T Consensus 270 --p~~~~~~~~~y~a~~~~~~A~~~ag~----------------------------~~-~~~v~~aL~~~~~~~~~~g~~ 318 (334)
T cd06356 270 --PYINEEAENNYEAIYLYKEAVEKAGT----------------------------TD-RDAVIEALESGLVCDGPEGKV 318 (334)
T ss_pred --CCCCchhHHHHHHHHHHHHHHHHHCC----------------------------CC-HHHHHHHHHhCCceeCCCceE
Confidence 01245678999999999999987410 22 6789999997 5788999999
Q ss_pred EEccCC
Q 011629 239 KFTSDR 244 (481)
Q Consensus 239 ~Fd~~G 244 (481)
.|+..+
T Consensus 319 ~~~~~~ 324 (334)
T cd06356 319 CIDGKT 324 (334)
T ss_pred EEecCC
Confidence 999644
No 90
>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=99.16 E-value=8.5e-11 Score=109.70 Aligned_cols=96 Identities=17% Similarity=0.147 Sum_probs=81.7
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHC-CCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEe
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELL-PYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVG 395 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~ 395 (481)
.++|+++.. +||||.+.+. ++...|+..|+++++++++ ++++++...+ |++++.++ .|+.|+++.
T Consensus 17 ~~~l~~~~~---~~pPf~~~~~-~~~~~G~~~~i~~~i~~~~~~~~~~~~~~p---------w~r~l~~l-~~~~d~~~~ 82 (268)
T TIGR02285 17 KEAITWIVN---DFPPFFIFSG-PSKGRGVFDVILQEIRRALPQYEHRFVRVS---------FARSLKEL-QGKGGVCTV 82 (268)
T ss_pred cceeEEEec---ccCCeeEeCC-CCCCCChHHHHHHHHHHHcCCCceeEEECC---------HHHHHHHH-hcCCCeEEe
Confidence 468888886 7999999864 6788999999999999998 8776666555 99999999 788888877
Q ss_pred eeeeccccccceeeccceee-cceEEEEecCC
Q 011629 396 DFAITTERTKMVDFTQPYIE-SGLVVVAPIKK 426 (481)
Q Consensus 396 ~~~~t~~r~~~~~fs~p~~~-~~~~~~~~~~~ 426 (481)
++++|++|++.++||.||+. ....+++++++
T Consensus 83 ~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~ 114 (268)
T TIGR02285 83 NLLRTPEREKFLIFSDPTLRALPVGLVLRKEL 114 (268)
T ss_pred eccCCcchhhceeecCCccccCCceEEEccch
Confidence 89999999999999999985 57888888764
No 91
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.14 E-value=1.5e-10 Score=108.57 Aligned_cols=123 Identities=24% Similarity=0.264 Sum_probs=100.9
Q ss_pred CCceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEe
Q 011629 316 NGRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVG 395 (481)
Q Consensus 316 ~~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~ 395 (481)
..+.++|++... ..+|+.+.+.+.+++.||++|+++++++.++....+.+.+ ..|.++++.|..|++|++++
T Consensus 32 ~~~~~~v~~~~~-~~~p~~~~~~~~~~~~G~dvdl~~~ia~~l~~~~~~~~~~-------~~~~~~~~~l~~g~~D~~~~ 103 (275)
T COG0834 32 ARGKLRVGTEAT-YAPPFEFLDAKGGKLVGFDVDLAKAIAKRLGGDKKVEFVP-------VAWDGLIPALKAGKVDIIIA 103 (275)
T ss_pred hcCeEEEEecCC-CCCCcccccCCCCeEEeeeHHHHHHHHHHhCCcceeEEec-------cchhhhhHHHhcCCcCEEEe
Confidence 346788888851 4569999986336999999999999999998653244444 46999999999999999999
Q ss_pred eeeeccccccceeeccceeecceEEEEecCCCC-cCccccccCcchhHHHHH
Q 011629 396 DFAITTERTKMVDFTQPYIESGLVVVAPIKKLN-SNAWAFLNPFTPKMWCVT 446 (481)
Q Consensus 396 ~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~-~~~~~~l~pf~~~~W~~~ 446 (481)
++++|++|.+.++||.||+..+..+++++++.. .....+|+..+..+....
T Consensus 104 ~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~~~~~~~~DL~gk~v~v~~gt 155 (275)
T COG0834 104 GMTITPERKKKVDFSDPYYYSGQVLLVKKDSDIGIKSLEDLKGKKVGVQLGT 155 (275)
T ss_pred ccccCHHHhccccccccccccCeEEEEECCCCcCcCCHHHhCCCEEEEEcCc
Confidence 999999999999999999999999999987733 567888888766655543
No 92
>cd04509 PBP1_ABC_transporter_GCPR_C_like Family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA receptor, G-protein-coupled receptors, metabotropic glutamate, GABA-B, calcium sensing, phermone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. The glutamate receptors that form cation-selective ion channels, iGluR, can be classified into three different subgroups according to their binding-affinity for the agonists NMDA (N-methyl-D-asparate), AMPA (alpha-amino-3-dihydro-5-methyl-3-oxo-4-isoxazolepropionic acid), and kainate. L-glutamate is a major neurotransmitter in the brain of vertebrates and acts th
Probab=99.13 E-value=4.7e-10 Score=106.23 Aligned_cols=165 Identities=19% Similarity=0.223 Sum_probs=118.4
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++++++++++||++|++++.++.++....+.+++.+++.|+++.....++... .++...++++++.++++|++++...
T Consensus 125 ~~~~~~l~~~~~~~v~iv~~~~~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~~--~~~~~~~~~l~~~~~~~v~~~~~~~ 202 (299)
T cd04509 125 EALADYIKEYNWKKVAILYDDDSYGRGLLEAFKAAFKKKGGTVVGEEYYPLGT--TDFTSLLQKLKAAKPDVIVLCGSGE 202 (299)
T ss_pred HHHHHHHHHcCCcEEEEEecCchHHHHHHHHHHHHHHHcCCEEEEEecCCCCC--ccHHHHHHHHHhcCCCEEEEcccch
Confidence 46788999999999999999988999999999999999999998776665432 3678888999888889999988888
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCCchhH-HHHHHHHhhhhccCCCCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQSSEEK-RKFVTRWRHLTRRNTLNG 160 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~-~~f~~~~~~~~~~~~~~~ 160 (481)
.+..+++++.+.|+. .++.||..+.+...... ....+...|+++........+.. ..+...++..+... .
T Consensus 203 ~~~~~~~~~~~~g~~-~~~~~i~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~ 273 (299)
T cd04509 203 DAATILKQAAEAGLT-GGYPILGITLGLSDVLL-----EAGGEAAEGVLTGTPYFPGDPPPESFFFVRAAAREKKK---Y 273 (299)
T ss_pred HHHHHHHHHHHcCCC-CCCcEEecccccCHHHH-----HHhHHhhcCcEEeeccCCCCCChHHHHHHhHHHHHHHH---h
Confidence 999999999999987 78899998766443211 12235567777776544333322 22221111111100 1
Q ss_pred CCCCChhHHHHHHHHHH
Q 011629 161 PIGLNSFGLYAYDTLWL 177 (481)
Q Consensus 161 ~~~~~~~~~~~ydAV~~ 177 (481)
...++.++.+.|||+++
T Consensus 274 ~~~~~~~~~~~yda~~~ 290 (299)
T cd04509 274 EDQPDYFAALAYDAVLL 290 (299)
T ss_pred CCCCChhhhhhcceeee
Confidence 12356688999999987
No 93
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.11 E-value=2.2e-10 Score=129.37 Aligned_cols=99 Identities=11% Similarity=0.153 Sum_probs=86.5
Q ss_pred CCceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEe
Q 011629 316 NGRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVG 395 (481)
Q Consensus 316 ~~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~ 395 (481)
+.++++|++.. +||||.+.++ +|++.||++|++++|++++|++ +++++. ..|..+..+|.+|++|++.
T Consensus 300 ~~~~l~v~~~~--~~pP~~~~d~-~g~~~G~~~Dll~~i~~~~g~~--~~~v~~------~~~~~~~~~l~~g~~D~i~- 367 (1197)
T PRK09959 300 QHPDLKVLENP--YSPPYSMTDE-NGSVRGVMGDILNIITLQTGLN--FSPITV------SHNIHAGTQLNPGGWDIIP- 367 (1197)
T ss_pred HCCceEEEcCC--CCCCeeEECC-CCcEeeehHHHHHHHHHHHCCe--EEEEec------CCHHHHHHHHHCCCceEee-
Confidence 35789999987 8999999986 7999999999999999999966 666653 4588888999999999874
Q ss_pred eeeeccccccceeeccceeecceEEEEecCC
Q 011629 396 DFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 396 ~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
+++.|++|++.++||.||+.++.+++++++.
T Consensus 368 ~~~~t~~r~~~~~fs~py~~~~~~~v~~~~~ 398 (1197)
T PRK09959 368 GAIYSEDRENNVLFAEAFITTPYVFVMQKAP 398 (1197)
T ss_pred cccCCccccccceeccccccCCEEEEEecCC
Confidence 4678999999999999999999999998754
No 94
>cd06326 PBP1_STKc_like Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins. The type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins, some of which contain a conserved catalytic serine/threonine protein kinase (STKc) domain in the N-terminal region. Members of this group are sequence-similar to the branched-chain amino acid ABC transporter leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=99.11 E-value=3.3e-09 Score=102.60 Aligned_cols=200 Identities=13% Similarity=0.164 Sum_probs=139.9
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.++++.+.+.||++|++|+.++.+|....+.+++.+++.|+++.....++.. ..++...+.+++++++++|++..+..
T Consensus 125 ~~~~~~l~~~g~~~v~~l~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~--~~d~~~~~~~l~~~~~dav~~~~~~~ 202 (336)
T cd06326 125 AAIVRHLVTLGLKRIAVFYQDDAFGKDGLAGVEKALAARGLKPVATASYERN--TADVAAAVAQLAAARPQAVIMVGAYK 202 (336)
T ss_pred HHHHHHHHHhCCceEEEEEecCcchHHHHHHHHHHHHHcCCCeEEEEeecCC--cccHHHHHHHHHhcCCCEEEEEcCcH
Confidence 4677888889999999999988899999999999999999998777666643 23788899999988899999888877
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEee----ecCCchhHHHHHHHHhhhhccCC
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRM----YTQSSEEKRKFVTRWRHLTRRNT 157 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~----~~~~~~~~~~f~~~~~~~~~~~~ 157 (481)
.+..+++++.++|+.. ...+ ....... ... ........|++.... .....+..+.|.+.|++.+..
T Consensus 203 ~a~~~i~~~~~~G~~~-~~~~--~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-- 272 (336)
T cd06326 203 AAAAFIRALRKAGGGA-QFYN--LSFVGAD-ALA----RLLGEYARGVIVTQVVPNPWSRTLPIVREYQAAMKAYGPG-- 272 (336)
T ss_pred HHHHHHHHHHhcCCCC-cEEE--EeccCHH-HHH----HHhhhhhcceEEEEEecCccccCCHHHHHHHHHHHhhCCC--
Confidence 8899999999998742 2222 2221111 010 111123445543221 112356778888888876531
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceee-
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTG- 236 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG- 236 (481)
..++.++...||++++++.|+++.-. + . ++..+.+.|+++...+..|
T Consensus 273 ----~~~~~~~~~~y~~~~~~~~a~~~~g~---~------------------------~-~~~~v~~al~~~~~~~~~g~ 320 (336)
T cd06326 273 ----APPSYVSLEGYIAAKVLVEALRRAGP---D------------------------P-TRESLLAALEAMGKFDLGGF 320 (336)
T ss_pred ----CCCCeeeehhHHHHHHHHHHHHHcCC---C------------------------C-CHHHHHHHHHhcCCCCCCCe
Confidence 12344567899999999999986310 0 1 2778999999987765555
Q ss_pred eEEEccCCCC
Q 011629 237 PIKFTSDRDL 246 (481)
Q Consensus 237 ~v~Fd~~Gd~ 246 (481)
.+.|+. +|+
T Consensus 321 ~~~~~~-~~h 329 (336)
T cd06326 321 RLDFSP-GNH 329 (336)
T ss_pred EEecCc-ccc
Confidence 899964 554
No 95
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.08 E-value=3.1e-10 Score=128.16 Aligned_cols=100 Identities=13% Similarity=0.174 Sum_probs=86.4
Q ss_pred CCceEEEeecCCCCCcCcEEe-cCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEE
Q 011629 316 NGRHLRIGVPSQVIYPEFVAQ-GKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAV 394 (481)
Q Consensus 316 ~~~~l~v~~~~~~~~~p~~~~-~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~ 394 (481)
+.++|+||+.. +++|+.+. ++ +|++.||.+|+++.||+.+|++ +++++. .+|++++.+|++|++|+++
T Consensus 54 ~~~~l~vgv~~--~~~p~~~~~~~-~g~~~G~~~D~l~~ia~~lG~~--~e~v~~------~~~~~~l~~l~~g~iDl~~ 122 (1197)
T PRK09959 54 SKKNLVIAVHK--SQTATLLHTDS-QQRVRGINADYLNLLKRALNIK--LTLREY------ADHQKAMDALEEGEVDIVL 122 (1197)
T ss_pred hCCeEEEEecC--CCCCCceeecC-CCccceecHHHHHHHHHhcCCc--eEEEeC------CCHHHHHHHHHcCCCcEec
Confidence 45789999986 66555444 44 8999999999999999999966 667662 4799999999999999998
Q ss_pred eeeeeccccccceeeccceeecceEEEEecCC
Q 011629 395 GDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 395 ~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
+.++.|++|.+.++||.||+.+..+++++++.
T Consensus 123 ~~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~ 154 (1197)
T PRK09959 123 SHLVASPPLNDDIAATKPLIITFPALVTTLHD 154 (1197)
T ss_pred CccccccccccchhcCCCccCCCceEEEeCCC
Confidence 88999999999999999999999999998755
No 96
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=99.05 E-value=7e-09 Score=97.39 Aligned_cols=214 Identities=14% Similarity=0.075 Sum_probs=142.0
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~ 82 (481)
++--++.+||-+++.+|-+|..|+....+.+++.+.+.|+.|.....+|.+. +++..++++|++.++++|+--...+.
T Consensus 124 l~~~~~~~~G~~r~~lvGSdYv~pre~Nri~r~~l~~~GgevvgE~Y~plg~--td~~~ii~~I~~~~Pd~V~stlvG~s 201 (363)
T PF13433_consen 124 LIDYLLENFGAKRFYLVGSDYVYPRESNRIIRDLLEARGGEVVGERYLPLGA--TDFDPIIAEIKAAKPDFVFSTLVGDS 201 (363)
T ss_dssp HHHHHHHHS--SEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE-S-H--HHHHHHHHHHHHHT-SEEEEE--TTC
T ss_pred HHHHHHhccCCceEEEecCCccchHHHHHHHHHHHHHcCCEEEEEEEecCCc--hhHHHHHHHHHhhCCCEEEEeCcCCc
Confidence 3445789999999999999999999999999999999999999998888754 58999999999999999987777778
Q ss_pred HHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeee--cCCchhHHHHHHHHhhhhccCCCCC
Q 011629 83 GLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMY--TQSSEEKRKFVTRWRHLTRRNTLNG 160 (481)
Q Consensus 83 ~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~--~~~~~~~~~f~~~~~~~~~~~~~~~ 160 (481)
...|+++..+.|+. +...=|.+-..... ... .-..+...|.+....+ +-..|..+.|++.|++.+..
T Consensus 202 ~~aF~r~~~~aG~~-~~~~Pi~S~~~~E~-E~~----~~g~~~~~Gh~~~~~YFqsidtp~N~~Fv~~~~~~~g~----- 270 (363)
T PF13433_consen 202 NVAFYRAYAAAGLD-PERIPIASLSTSEA-ELA----AMGAEAAAGHYTSAPYFQSIDTPENQAFVARFRARYGD----- 270 (363)
T ss_dssp HHHHHHHHHHHH-S-SS---EEESS--HH-HHT----TS-HHHHTT-EEEES--TT-SSHHHHHHHHHHHTTS-T-----
T ss_pred HHHHHHHHHHcCCC-cccCeEEEEecCHH-HHh----hcChhhcCCcEEeehhhhhCCcHHHHHHHHHHHHHhCC-----
Confidence 88999999998876 44455555322111 000 1112345666666543 34568999999999988742
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccCceeeeEEE
Q 011629 161 PIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMTGVTGPIKF 240 (481)
Q Consensus 161 ~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~g~sG~v~F 240 (481)
....+...-.+|.+|+++|.|+++.-+ .+ ...+.++|..+.|....|.|++
T Consensus 271 ~~v~s~~~eaaY~~v~l~a~Av~~ags----------------------------~d-~~~vr~al~g~~~~aP~G~v~i 321 (363)
T PF13433_consen 271 DRVTSDPMEAAYFQVHLWAQAVEKAGS----------------------------DD-PEAVREALAGQSFDAPQGRVRI 321 (363)
T ss_dssp T----HHHHHHHHHHHHHHHHHHHHTS-------------------------------HHHHHHHHTT--EEETTEEEEE
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHHhCC----------------------------CC-HHHHHHHhcCCeecCCCcceEE
Confidence 112344556799999999999998511 23 7899999999999999999999
Q ss_pred ccCCCCCCCcEEEEEeecCceEEEEEeeC
Q 011629 241 TSDRDLINPAYEVINVIGTGSRRIGYWSN 269 (481)
Q Consensus 241 d~~Gd~~~~~y~I~~~~~~~~~~VG~~~~ 269 (481)
|..-... .....||..+.
T Consensus 322 d~~n~H~-----------~l~~rIg~~~~ 339 (363)
T PF13433_consen 322 DPDNHHT-----------WLPPRIGRVNA 339 (363)
T ss_dssp -TTTSBE-----------EB--EEEEE-T
T ss_pred cCCCCee-----------cccceEEEEcC
Confidence 9733221 13456777664
No 97
>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=99.04 E-value=4.6e-10 Score=102.44 Aligned_cols=90 Identities=20% Similarity=0.234 Sum_probs=73.4
Q ss_pred eEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeee
Q 011629 319 HLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFA 398 (481)
Q Consensus 319 ~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~ 398 (481)
.|+|++.. +++||.+.+ ..||++||++++++++|.++++...+ ..+..++..+.+|++|++++
T Consensus 1 ~l~v~~~~--~~~P~~~~~-----~~G~~~el~~~i~~~~g~~i~~~~~~-------~~~~~~~~~l~~g~~Di~~~--- 63 (232)
T TIGR03871 1 ALRVCADP--NNLPFSNEK-----GEGFENKIAQLLADDLGLPLEYTWFP-------QRRGFVRNTLNAGRCDVVIG--- 63 (232)
T ss_pred CeEEEeCC--CCCCccCCC-----CCchHHHHHHHHHHHcCCceEEEecC-------cchhhHHHHHhcCCccEEEe---
Confidence 37888886 899998632 36999999999999999886665555 22444667899999999865
Q ss_pred eccccccceeeccceeecceEEEEecCC
Q 011629 399 ITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 399 ~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
+++|.+.++||.||+..+.++++++++
T Consensus 64 -~~~r~~~~~fs~py~~~~~~lv~~~~~ 90 (232)
T TIGR03871 64 -VPAGYEMVLTTRPYYRSTYVFVTRKDS 90 (232)
T ss_pred -ccCccccccccCCcEeeeEEEEEeCCC
Confidence 578999999999999999999998874
No 98
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=99.02 E-value=2.1e-10 Score=79.14 Aligned_cols=47 Identities=26% Similarity=0.591 Sum_probs=36.7
Q ss_pred CCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCC-----CCCCHHHHHHHHHc
Q 011629 339 GTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGH-----NSPKRFDLLRLVSE 387 (481)
Q Consensus 339 ~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~~ 387 (481)
++.+++|||+||+++||+.++|+ |++..++|++ .+++|+||+++|.+
T Consensus 14 g~~~~eGyciDll~~la~~l~F~--y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 14 GNDRYEGYCIDLLEELAEELNFT--YEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp GGGGEESHHHHHHHHHHHHHT-E--EEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred CCccEEEEHHHHHHHHHHHcCCe--EEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 46789999999999999999988 4455545543 67899999999874
No 99
>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=98.98 E-value=3.3e-08 Score=95.82 Aligned_cols=198 Identities=12% Similarity=0.043 Sum_probs=137.1
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCC-cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 2 AAIADIVDYFGWRNVIALYVDDD-HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.++++.+..-|-+++++|+.++. +|......+++.++++|+.+.....++.. ..++...+.++++.++++|++....
T Consensus 121 ~~~~~~l~~~g~~~~~~i~~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~~~~i~~~~pdaV~~~~~~ 198 (341)
T cd06341 121 TTWGDFAKDQGGTRAVALVTALSAAVSAAAALLARSLAAAGVSVAGIVVITAT--APDPTPQAQQAAAAGADAIITVLDA 198 (341)
T ss_pred HHHHHHHHHcCCcEEEEEEeCCcHHHHHHHHHHHHHHHHcCCccccccccCCC--CCCHHHHHHHHHhcCCCEEEEecCh
Confidence 46777777778999999987775 99999999999999999998776666543 2378899999999999999988888
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeec---CCchhHHHHHHHHhhhhccCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYT---QSSEEKRKFVTRWRHLTRRNT 157 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~---~~~~~~~~f~~~~~~~~~~~~ 157 (481)
..+..+++++.++|+..+. . ........ ... ....+...|++...... ...|..+.|.+.+++....
T Consensus 199 ~~a~~~~~~~~~~G~~~~~-~--~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~-- 268 (341)
T cd06341 199 AVCASVLKAVRAAGLTPKV-V--LSGTCYDP-ALL----AAPGPALAGVYIAVFYRPFESGTPAVALYLAAMARYAPQ-- 268 (341)
T ss_pred HHHHHHHHHHHHcCCCCCE-E--EecCCCCH-HHH----HhcCcccCceEEEeeeccccCCCHHHHHHHHHHHHhCCC--
Confidence 8999999999999975432 2 22211111 010 12224567766654433 2457777777765543321
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHH-HHHHHHhcccCceee
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKM-LLDNILQVNMTGVTG 236 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-L~~~l~~v~f~g~sG 236 (481)
....++.++...||++++++.|+++.-. ..++.. +.+.|+++......|
T Consensus 269 --~~~~~~~~~~~~yda~~~~~~a~~~ag~----------------------------~~~~~~~v~~al~~~~~~~~~g 318 (341)
T cd06341 269 --LDPPEQGFALIGYIAADLFLRGLSGAGG----------------------------CPTRASQFLRALRAVTDYDAGG 318 (341)
T ss_pred --CCCCcchHHHHHHHHHHHHHHHHHhcCC----------------------------CCChHHHHHHHhhcCCCCCCCC
Confidence 1123566889999999999999987411 011555 999999987665555
Q ss_pred -eEEEc
Q 011629 237 -PIKFT 241 (481)
Q Consensus 237 -~v~Fd 241 (481)
...++
T Consensus 319 ~~~~~~ 324 (341)
T cd06341 319 LTPPCD 324 (341)
T ss_pred cccCcc
Confidence 44443
No 100
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=98.96 E-value=3.1e-09 Score=95.14 Aligned_cols=109 Identities=25% Similarity=0.364 Sum_probs=91.2
Q ss_pred EEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeee
Q 011629 320 LRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAI 399 (481)
Q Consensus 320 l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~ 399 (481)
|+|++.. .++||.+.++ +|++.|+.+|+++.+++++|.+ +++.. ..|.++..+|.+|++|++++....
T Consensus 1 l~i~~~~--~~~p~~~~~~-~g~~~G~~~~~~~~~~~~~g~~--~~~~~-------~~~~~~~~~l~~g~~D~~~~~~~~ 68 (218)
T cd00134 1 LTVGTAG--TYPPFSFRDA-NGELTGFDVDLAKAIAKELGVK--VKFVE-------VDWDGLITALKSGKVDLIAAGMTI 68 (218)
T ss_pred CEEecCC--CCCCeeEECC-CCCEEeeeHHHHHHHHHHhCCe--EEEEe-------CCHHHHHHHHhcCCcCEEeecCcC
Confidence 4677776 8999999875 8999999999999999999966 55555 339999999999999999887778
Q ss_pred ccccccceeeccceeecceEEEEecCCCCcCccccccCcchh
Q 011629 400 TTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFTPK 441 (481)
Q Consensus 400 t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~~~ 441 (481)
+++|.+.+.|+.|+...+..+++++++. .....+|+..+..
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~dl~g~~i~ 109 (218)
T cd00134 69 TPERAKQVDFSDPYYKSGQVILVKKGSP-IKSVKDLKGKKVA 109 (218)
T ss_pred CHHHHhhccCcccceeccEEEEEECCCC-CCChHHhCCCEEE
Confidence 9999999999999999999999998773 3356666655443
No 101
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=98.89 E-value=6.3e-09 Score=93.04 Aligned_cols=108 Identities=26% Similarity=0.397 Sum_probs=90.8
Q ss_pred eEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeee
Q 011629 319 HLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFA 398 (481)
Q Consensus 319 ~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~ 398 (481)
+|+|++.. .++|+.+.++ +|.+.|+.+|+++.+.+++|++ +++.+ ..|..+..++.+|++|+++++..
T Consensus 1 ~l~v~~~~--~~~p~~~~~~-~g~~~G~~~~~~~~~~~~~g~~--~~~~~-------~~~~~~~~~l~~g~~D~~~~~~~ 68 (219)
T smart00062 1 TLRVGTNG--DYPPFSFADE-DGELTGFDVDLAKAIAKELGLK--VEFVE-------VSFDNLLTALKSGKIDVVAAGMT 68 (219)
T ss_pred CEEEEecC--CCCCcEEECC-CCCcccchHHHHHHHHHHhCCe--EEEEe-------ccHHHHHHHHHCCcccEEecccc
Confidence 47888875 8999998875 7889999999999999999966 55555 35999999999999999988777
Q ss_pred eccccccceeeccceeecceEEEEecCCCCcCccccccCcc
Q 011629 399 ITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 399 ~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
.+++|+..+.|+.|++..+..+++++++ ....+++|+..+
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~dL~g~~ 108 (219)
T smart00062 69 ITPERAKQVDFSDPYYKSGQVILVRKDS-PIKSLEDLKGKK 108 (219)
T ss_pred CCHHHHhheeeccceeeceeEEEEecCC-CCCChHHhCCCE
Confidence 7889999999999999999999998876 355666665543
No 102
>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=98.88 E-value=5.7e-08 Score=92.91 Aligned_cols=162 Identities=15% Similarity=0.134 Sum_probs=113.5
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
+++++.+...||++|++++.++.+|....+.+++.+++.|+++.....++... .++...+.+++..++++|++.....
T Consensus 122 ~~~~~~l~~~g~~~vail~~~~~~~~~~~~~~~~~~~~~G~~v~~~~~~~~~~--~d~~~~~~~l~~~~pdaIi~~~~~~ 199 (312)
T cd06333 122 EAILADMKKRGVKTVAFIGFSDAYGESGLKELKALAPKYGIEVVADERYGRTD--TSVTAQLLKIRAARPDAVLIWGSGT 199 (312)
T ss_pred HHHHHHHHHcCCCEEEEEecCcHHHHHHHHHHHHHHHHcCCEEEEEEeeCCCC--cCHHHHHHHHHhCCCCEEEEecCCc
Confidence 45677788899999999999888999899999999999999998776775433 3677888888888899988887777
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEee------ec----CCchhHHHHHHHHhh
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRM------YT----QSSEEKRKFVTRWRH 151 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~------~~----~~~~~~~~f~~~~~~ 151 (481)
.+..+++++.+.|+..+ ++ .++..... ... ....+...|+..... .. ...+..++|.+.+++
T Consensus 200 ~~~~~~~~l~~~g~~~p--~~-~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~f~~~~~~ 271 (312)
T cd06333 200 PAALPAKNLRERGYKGP--IY-QTHGVASP-DFL----RLAGKAAEGAILPAGPVLVADQLPDSDPQKKVALDFVKAYEA 271 (312)
T ss_pred HHHHHHHHHHHcCCCCC--EE-eecCcCcH-HHH----HHhhHhhcCcEeecccceeeeeCCCCCcchHHHHHHHHHHHH
Confidence 77789999999886432 33 33322211 110 111234456544321 11 123568889988888
Q ss_pred hhccCCCCCCCCCChhHHHHHHHHHHHH
Q 011629 152 LTRRNTLNGPIGLNSFGLYAYDTLWLLA 179 (481)
Q Consensus 152 ~~~~~~~~~~~~~~~~~~~~ydAV~~~a 179 (481)
.+... .+..++...|||+++++
T Consensus 272 ~~g~~------~~~~~~~~~Yda~~~~~ 293 (312)
T cd06333 272 KYGAG------SVSTFGGHAYDALLLLA 293 (312)
T ss_pred HhCCC------CCCchhHHHHHHHHHHH
Confidence 76421 24557899999999998
No 103
>cd06268 PBP1_ABC_transporter_LIVBP_like Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC
Probab=98.76 E-value=1.9e-07 Score=88.16 Aligned_cols=161 Identities=20% Similarity=0.189 Sum_probs=116.2
Q ss_pred hHhHHHHHHcC-CcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 2 AAIADIVDYFG-WRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 2 ~Ai~~ll~~fg-W~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+++++++...+ |++|++++.+++++....+.+.+.+++.|+++.....++... .++...+++++..++++|++.+..
T Consensus 123 ~~~~~~~~~~~~~~~i~~v~~~~~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~~--~~~~~~~~~l~~~~~~~vi~~~~~ 200 (298)
T cd06268 123 AALADYLAEKGKVKKVAIIYDDYAYGRGLAAAFREALKKLGGEVVAEETYPPGA--TDFSPLIAKLKAAGPDAVFLAGYG 200 (298)
T ss_pred HHHHHHHHHhcCCCEEEEEEcCCchhHHHHHHHHHHHHHcCCEEEEEeccCCCC--ccHHHHHHHHHhcCCCEEEEcccc
Confidence 56788888888 999999999988999999999999999999988776665432 367888999988888999988887
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEeeecCC--chhHHHHH-HHHhhhhccCC
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRMYTQS--SEEKRKFV-TRWRHLTRRNT 157 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~--~~~~~~f~-~~~~~~~~~~~ 157 (481)
..+..+++++.+.|+ +..|+..+.+...... ........|++........ .+....|. ..|++.+.
T Consensus 201 ~~~~~~~~~~~~~g~---~~~~~~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--- 269 (298)
T cd06268 201 GDAALFLKQAREAGL---KVPIVGGDGAAAPALL-----ELAGDAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAKYG--- 269 (298)
T ss_pred chHHHHHHHHHHcCC---CCcEEecCccCCHHHH-----HhhhHhhCCcEEeccCCCCCCChhhhHHHHHHHHHHhC---
Confidence 888999999999876 4577777655432111 1122345666666543322 23333443 55555442
Q ss_pred CCCCCCCChhHHHHHHHHHHHH
Q 011629 158 LNGPIGLNSFGLYAYDTLWLLA 179 (481)
Q Consensus 158 ~~~~~~~~~~~~~~ydAV~~~a 179 (481)
..++.++...||++++++
T Consensus 270 ----~~~~~~~~~~y~~~~~~~ 287 (298)
T cd06268 270 ----RPPDSYAAAAYDAVRLLA 287 (298)
T ss_pred ----CCcccchHHHHHHHHHHc
Confidence 234557889999999998
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=98.62 E-value=7.6e-07 Score=85.87 Aligned_cols=184 Identities=14% Similarity=0.143 Sum_probs=119.0
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCC--hhHHHHHHHHhccCCceEEEEEeC
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGS--RNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~--~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
+++++.+..-|.++|++|+.|++||....+.+++.+++.|+.|...+.++...+ ..++.......+.+++++|++...
T Consensus 117 ~ala~~~~~~g~kkvaii~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~~~~~d~s~~~~~~~~s~pDvv~~~~~ 196 (347)
T TIGR03863 117 DALAQYLAAKRWRRILLIQGPLPADALYADAFRRSAKRFGAKIVAERPFTFSGDPRRTDQSEVPLFTQGADYDVVVVADE 196 (347)
T ss_pred HHHHHHHHHcCCCEEEEEeCCCcccHHHHHHHHHHHHHCCCEEEEeEEeccCCchhhhhcccCceeecCCCCCEEEEecc
Confidence 567777766699999999999999999999999999999999998888875422 123332223344578999988654
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEeccccccccCCccccccccccceeeEEEee-ecCCchhHHHHHHHHhhhhccCCC
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVTDWLSSILDTDSQLHSEKMDDIQGVLTLRM-YTQSSEEKRKFVTRWRHLTRRNTL 158 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~~~~~~~~~~~~~~~g~l~~~~-~~~~~~~~~~f~~~~~~~~~~~~~ 158 (481)
..+....+... .+. ....+.. .|+..... .....+..++|.+.|++.++.
T Consensus 197 ~~~~~~~~~~~--~~~---~~~~~g~---------------------~G~~~~~~~~~~~~~~~~~f~~~f~~~~g~--- 247 (347)
T TIGR03863 197 AGEFARYLPYA--TWL---PRPVAGS---------------------AGLVPTAWHRAWERWGATQLQSRFEKLAGR--- 247 (347)
T ss_pred hhhHhhhcccc--ccc---ccccccc---------------------cCccccccCCcccchhHHHHHHHHHHHhCC---
Confidence 33221111000 000 0000100 11110000 111235678899999887742
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHhhhhcCCCccccCCcccccccCCCcccccccccCccHHHHHHHHhcccC--ceee
Q 011629 159 NGPIGLNSFGLYAYDTLWLLAHAIGAFFDQGGNISFSEDSKLSELSRGDMRFSSVSIFNGGKMLLDNILQVNMT--GVTG 236 (481)
Q Consensus 159 ~~~~~~~~~~~~~ydAV~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~v~f~--g~sG 236 (481)
.+..+++.+||||++++.|+++.-+ .+ +..+.++|+...+. +..|
T Consensus 248 ----~p~~~~a~aY~av~~~a~Ai~~AGs----------------------------~d-~~aV~~aL~~~~~~~~~~~g 294 (347)
T TIGR03863 248 ----PMTELDYAAWLAVRAVGEAVTRTRS----------------------------AD-PATLRDYLLSDEFELAGFKG 294 (347)
T ss_pred ----CCChHHHHHHHHHHHHHHHHHHhcC----------------------------CC-HHHHHHHHcCCCceecccCC
Confidence 2344678899999999999998511 23 88999999998774 6777
Q ss_pred -eEEEcc-CCCCC
Q 011629 237 -PIKFTS-DRDLI 247 (481)
Q Consensus 237 -~v~Fd~-~Gd~~ 247 (481)
+++|.+ ++...
T Consensus 295 ~~~~~R~~Dhq~~ 307 (347)
T TIGR03863 295 RPLSFRPWDGQLR 307 (347)
T ss_pred CcceeeCCCcccc
Confidence 799985 56544
No 105
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=98.61 E-value=3.3e-08 Score=90.79 Aligned_cols=111 Identities=14% Similarity=0.110 Sum_probs=94.0
Q ss_pred CCceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEe
Q 011629 316 NGRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVG 395 (481)
Q Consensus 316 ~~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~ 395 (481)
..++|+|++.. .|.++... ++...|++++|++++|+.||.+ .+..+. .+-+.+..+|.+|++|++++
T Consensus 21 ~rGvLrV~tin----sp~sy~~~-~~~p~G~eYelak~Fa~yLgV~--Lki~~~------~n~dqLf~aL~ng~~DL~Aa 87 (473)
T COG4623 21 ARGVLRVSTIN----SPLSYFED-KGGPTGLEYELAKAFADYLGVK--LKIIPA------DNIDQLFDALDNGNADLAAA 87 (473)
T ss_pred hcCeEEEEeec----Cccceecc-CCCccchhHHHHHHHHHHhCCe--EEEEec------CCHHHHHHHHhCCCcceecc
Confidence 35799999985 46666554 6778899999999999999966 555552 46899999999999999999
Q ss_pred eeeeccccccceeeccceeecceEEEEecCCCCcCccccccCcc
Q 011629 396 DFAITTERTKMVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 396 ~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
++...++|.+.+.....|+..+.+++.++....+..+..|..-+
T Consensus 88 gl~~~~~~l~~~~~gP~y~svs~qlVyRkG~~Rp~~l~~L~g~~ 131 (473)
T COG4623 88 GLLYNSERLKNFQPGPTYYSVSQQLVYRKGQYRPRSLGQLKGRQ 131 (473)
T ss_pred cccCChhHhcccCCCCceecccHHHHhhcCCCCCCCHHHccCce
Confidence 99999999999988888999999999999997788887777643
No 106
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=97.72 E-value=0.00037 Score=64.18 Aligned_cols=105 Identities=16% Similarity=0.141 Sum_probs=79.4
Q ss_pred hHhHHHHHHcCCcEEEEEEEeC-CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC-CceEEEEEeC
Q 011629 2 AAIADIVDYFGWRNVIALYVDD-DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM-MSRILILHTY 79 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd-~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s-~~~vIvl~~~ 79 (481)
+++++++.+.+|+++++++.+. ..+....+.+++.+++.|+++......+... ..++....+.+++. ++++|+++++
T Consensus 113 ~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~i~~~~~ 191 (269)
T cd01391 113 EAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGIEVVAIEYGDLDT-EKGFQALLQLLKAAPKPDAIFACND 191 (269)
T ss_pred HHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHHhcCcEEEeccccCCCc-cccHHHHHHHHhcCCCCCEEEEcCc
Confidence 5788999999999999999877 6677788999999999997776544433222 13566777777776 6888888776
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEeccc
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVTDWL 108 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~~~~ 108 (481)
..+..+++++.+.|+...++.|+..+.+
T Consensus 192 -~~a~~~~~~~~~~g~~~~~~~ii~~~~~ 219 (269)
T cd01391 192 -EMAAGALKAAREAGLTPGDISIIGFDGS 219 (269)
T ss_pred -hHHHHHHHHHHHcCCCCCCCEEEecccc
Confidence 8889999999999986345666666554
No 107
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=97.38 E-value=0.0003 Score=65.00 Aligned_cols=103 Identities=10% Similarity=-0.062 Sum_probs=73.7
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.++|+||+.. .++|+.+ .+...++.+.+++++|.+ +++... .+|+.++..+.+|++|+++.+
T Consensus 31 ~~~l~vg~~~--~~~~~~~--------~~~~~~l~~~l~~~~g~~--v~~~~~------~~~~~~~~~l~~g~~Di~~~~ 92 (254)
T TIGR01098 31 PKELNFGILP--GENASNL--------TRRWEPLADYLEKKLGIK--VQLFVA------TDYSAVIEAMRFGRVDIAWFG 92 (254)
T ss_pred CCceEEEECC--CCCHHHH--------HHHHHHHHHHHHHHhCCc--EEEEeC------CCHHHHHHHHHcCCccEEEEC
Confidence 4579999986 5555432 344579999999999976 555441 469999999999999999866
Q ss_pred eeecc---ccccceeeccceeec------ceEEEEecCCCCcCccccccCc
Q 011629 397 FAITT---ERTKMVDFTQPYIES------GLVVVAPIKKLNSNAWAFLNPF 438 (481)
Q Consensus 397 ~~~t~---~r~~~~~fs~p~~~~------~~~~~~~~~~~~~~~~~~l~pf 438 (481)
..... +|.....|+.|+... ..++++++++ .+..+.+|+.-
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~-~i~~~~dL~gk 142 (254)
T TIGR01098 93 PSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADS-PIKSLKDLKGK 142 (254)
T ss_pred cHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCC-CCCChHHhcCC
Confidence 54333 566678888886643 3578888766 45666676644
No 108
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=96.49 E-value=0.024 Score=57.99 Aligned_cols=86 Identities=8% Similarity=0.006 Sum_probs=59.3
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
+.+++.+..-|+++..||+.++++|....+.|.+...+.|..+.....+.. ..++...++.-...+.+.|++.+++.
T Consensus 334 ~q~A~~a~~~g~~~alvl~p~~~~g~R~~~aF~~~W~~~gg~~~~~~~~~~---~~~~~~~i~~r~r~d~D~ifl~a~~~ 410 (536)
T PF04348_consen 334 RQAAQKAFQDGYRRALVLAPQNAWGQRMAEAFNQQWQALGGQVAEVSYYGS---PADLQAAIQPRRRQDIDAIFLVANPE 410 (536)
T ss_dssp HHHHHHHHHTT--S-EEEEESSHHHHHHHHHHHHHHHHHHSS--EEEEESS---TTHHHHHHHHS--TT--EEEE---HH
T ss_pred HHHHHHHHhcCCCCEEEEcCCChHHHHHHHHHHHHHHHcCCCceeeEecCC---HHHHHHHHhhcCCCCCCEEEEeCCHH
Confidence 457788888899999999999999999999999999999888766666653 23677777755556799999999988
Q ss_pred HHHHHHHHH
Q 011629 82 WGLEVLNAA 90 (481)
Q Consensus 82 ~~~~il~~a 90 (481)
+++.|--..
T Consensus 411 ~ar~ikP~l 419 (536)
T PF04348_consen 411 QARLIKPQL 419 (536)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHhhhc
Confidence 887775543
No 109
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=96.19 E-value=0.0061 Score=57.24 Aligned_cols=66 Identities=15% Similarity=0.065 Sum_probs=55.2
Q ss_pred CCHHHHHHHHHcccccEEEeeeeeccccccceeeccc--eeecceEEEEecCCCCcCccccccCcchhH
Q 011629 376 PKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQP--YIESGLVVVAPIKKLNSNAWAFLNPFTPKM 442 (481)
Q Consensus 376 ~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p--~~~~~~~~~~~~~~~~~~~~~~l~pf~~~~ 442 (481)
.+|.++...|.+|++|+++++++++.+|.+.++|+.| |....++++++++. .....++|+..+..+
T Consensus 51 ~~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~-~i~sl~DL~Gk~ia~ 118 (287)
T PRK00489 51 LRPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDS-DWQGVEDLAGKRIAT 118 (287)
T ss_pred ECcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCC-CCCChHHhCCCEEEE
Confidence 3589999999999999999999999999999999998 77888888888776 355677777665544
No 110
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=94.95 E-value=0.049 Score=51.26 Aligned_cols=100 Identities=12% Similarity=-0.001 Sum_probs=62.7
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF 397 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 397 (481)
.+|+|++.. ...+ .+....+ -.+.+.+++++|.+ +++... .+|..++.++.+|++|+++.+.
T Consensus 27 ~~l~vg~~~--~~~~-------~~~~~~~-~~l~~~l~~~~g~~--v~~~~~------~~~~~~~~al~~g~~D~~~~~~ 88 (288)
T TIGR03431 27 KELNFGIIP--TENA-------SDLKQRW-EPLADYLSKKLGVK--VKLFFA------TDYAGVIEGMRFGKVDIAWYGP 88 (288)
T ss_pred CeEEEEEcC--CCCH-------HHHHHHH-HHHHHHHHHHhCCc--EEEEeC------CCHHHHHHHHHcCCccEEEECh
Confidence 578999874 1111 1112223 34788999999966 554331 4799999999999999997553
Q ss_pred e---ecccccccee--------eccceeecceEEEEecCCCCcCccccccCcc
Q 011629 398 A---ITTERTKMVD--------FTQPYIESGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 398 ~---~t~~r~~~~~--------fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
. ...+|.+... ++.||. ..+++++++ .+..+.+|+.-+
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~---~~lvv~~ds-~i~sl~DL~Gk~ 137 (288)
T TIGR03431 89 SSYAEAYQKANAEAFAIEVNADGSTGYY---SVLIVKKDS-PIKSLEDLKGKT 137 (288)
T ss_pred HHHHHHHHhcCCeEEEEeccCCCCCceE---EEEEEeCCC-CCCcHHHhCCCE
Confidence 1 1225555433 455554 467777765 466777776543
No 111
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=93.92 E-value=0.66 Score=42.04 Aligned_cols=88 Identities=14% Similarity=0.089 Sum_probs=69.4
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCC-------CChhHHHHHHHHhccCCceEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPK-------GSRNQIIDTLLTVSSMMSRIL 74 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~-------~~~~~~~~~l~~i~~s~~~vI 74 (481)
.|+++-|+++|-++|++++ .|-....+.+.+.+++.|+.|.....+... .+.+.+.+.++++...+++.|
T Consensus 109 ~A~~~AL~alg~~RIalvT---PY~~~v~~~~~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAi 185 (239)
T TIGR02990 109 SAAVDGLAALGVRRISLLT---PYTPETSRPMAQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADAL 185 (239)
T ss_pred HHHHHHHHHcCCCEEEEEC---CCcHHHHHHHHHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEE
Confidence 5889999999999999998 366678899999999999999876555432 133455666666667789999
Q ss_pred EEEeCcHHHHHHHHHHHH
Q 011629 75 ILHTYDIWGLEVLNAAKH 92 (481)
Q Consensus 75 vl~~~~~~~~~il~~a~~ 92 (481)
++.|..-....++.++++
T Consensus 186 fisCTnLrt~~vi~~lE~ 203 (239)
T TIGR02990 186 FLSCTALRAATCAQRIEQ 203 (239)
T ss_pred EEeCCCchhHHHHHHHHH
Confidence 999988888888888755
No 112
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=91.11 E-value=1.7 Score=39.82 Aligned_cols=100 Identities=16% Similarity=0.218 Sum_probs=60.9
Q ss_pred HhHHHHHHcCCcEEEEEEEe---CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHH-hccC-CceEEEEE
Q 011629 3 AIADIVDYFGWRNVIALYVD---DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLT-VSSM-MSRILILH 77 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~d---d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~-i~~s-~~~vIvl~ 77 (481)
++++.|...|.++|+++..+ .+++....+.+++.++++|+.+......+. +..+....+.+ +++. ..+.| ++
T Consensus 106 ~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~ai-~~ 182 (266)
T cd06282 106 DVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAMRAAGLAPLPPVEIPF--NTAALPSALLALLTAHPAPTAI-FC 182 (266)
T ss_pred HHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHHHHcCCCCCccccCCC--cHHHHHHHHHHHhcCCCCCCEE-EE
Confidence 45566666799999999743 235566788899999999876433222221 21222333443 4443 34444 44
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
++...+..++.++.+.|+..++.+-+.+
T Consensus 183 ~~d~~a~g~~~al~~~g~~~p~di~v~g 210 (266)
T cd06282 183 SNDLLALAVIRALRRLGLRVPDDLSVVG 210 (266)
T ss_pred CCcHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 5666677899999998876555554443
No 113
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=90.81 E-value=1.8 Score=39.37 Aligned_cols=101 Identities=13% Similarity=0.055 Sum_probs=63.6
Q ss_pred HhHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcC-CEEEEEEecCCCCChhHHHHHHHHhccCCceEE-EEEe
Q 011629 3 AIADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKR-CRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRIL-ILHT 78 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~g-i~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vI-vl~~ 78 (481)
.+++.+...|-++|+++..+.. ++....+.+++.+++.| ..+...... ..+.++....++++.+..+++- +++.
T Consensus 108 ~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~i~~~ 185 (264)
T cd01537 108 LAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALKEAGPIEIVLVQEG--DWDAEKGYQAAEELLTAHPDPTAIFAA 185 (264)
T ss_pred HHHHHHHHhcCCcEEEEECCCCCCcHHHHHHHHHHHHHHcCCcChhhhccC--CCCHHHHHHHHHHHHhcCCCCCEEEEc
Confidence 4566667778999999986654 55667888999998887 443322222 2233455566666666554332 3334
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
+...+..++.++.+.|+..++.+-|++
T Consensus 186 ~~~~a~~~~~~~~~~g~~i~~~i~i~~ 212 (264)
T cd01537 186 NDDMALGALRALREAGLRVPDDISVIG 212 (264)
T ss_pred CcHHHHHHHHHHHHhCCCCCCCeEEEe
Confidence 445666788888888876555555554
No 114
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=90.68 E-value=2.5 Score=38.45 Aligned_cols=101 Identities=14% Similarity=0.132 Sum_probs=61.4
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCC--ceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMM--SRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~--~~vIvl~~~ 79 (481)
+++.+..-|-++|++++.+.. ++....+.+++.+++.+..+.....+....+.++....++++..+. .+.|+ +.+
T Consensus 107 ~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~ 185 (264)
T cd06267 107 AVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIF-AAN 185 (264)
T ss_pred HHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHHcCCCCCcceEEecccchhhHHHHHHHHHhcCCCCcEEE-EcC
Confidence 445555568999999986654 5666778888999888854332222222222334555666655544 44444 344
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++.++.+.|+..++.+-|++
T Consensus 186 ~~~a~~~~~al~~~g~~~~~~i~i~~ 211 (264)
T cd06267 186 DLMAIGALRALRELGLRVPEDVSVVG 211 (264)
T ss_pred cHHHHHHHHHHHHhCCCCCCceEEEe
Confidence 55667788888888875555555554
No 115
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=90.66 E-value=1.2 Score=43.78 Aligned_cols=76 Identities=8% Similarity=0.010 Sum_probs=58.4
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
+.+.++.+|-+++.+++...-......+.+.+.|++.|+.+.....+.++.+.++..+..+.+++.++++||..+.
T Consensus 22 l~~~~~~~g~~~~livt~~~~~~~g~~~~v~~~L~~~~i~~~~f~~v~~np~~~~v~~~~~~~~~~~~D~IiaiGG 97 (383)
T PRK09860 22 AMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGG 97 (383)
T ss_pred HHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 4567888999999998854333345678899999999998654445555666777888889999999999997765
No 116
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=89.92 E-value=3.7 Score=37.49 Aligned_cols=92 Identities=13% Similarity=0.104 Sum_probs=58.6
Q ss_pred HhHHHHHHc--CCcEEEEEEEeCC--cccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEE
Q 011629 3 AIADIVDYF--GWRNVIALYVDDD--HGRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LIL 76 (481)
Q Consensus 3 Ai~~ll~~f--gW~~V~ii~~dd~--~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl 76 (481)
.+++.+... |=+++++++..+. ++....+.+++.+++. |+++...... ..+..+....++++.+...++ +|+
T Consensus 109 ~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~i~ 186 (267)
T cd01536 109 LAGEYLAKLLGGKGKVAIIEGPPGSSNAQERVKGFRDALKEYPDIEIVAVQDG--NWDREKALQAMEDLLQANPDIDAIF 186 (267)
T ss_pred HHHHHHHHHhCCCceEEEEEcccccchHHHHHHHHHHHHHhCCCcEEEEEecC--CCcHHHHHHHHHHHHHhCCCccEEE
Confidence 345555555 8899999986553 6777888899999988 4665533222 223334556666665443333 344
Q ss_pred EeCcHHHHHHHHHHHHcCCc
Q 011629 77 HTYDIWGLEVLNAAKHLRMM 96 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~ 96 (481)
+++...+..++.++.+.|+.
T Consensus 187 ~~~d~~a~~~~~~l~~~g~~ 206 (267)
T cd01536 187 AANDSMALGAVAALKAAGRK 206 (267)
T ss_pred EecCCchHHHHHHHHhcCCC
Confidence 44556677888888888764
No 117
>cd08192 Fe-ADH7 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to CoA-dependent thiolysis to yield acetyl-CoA and 6-C8-SPC-CoA. The major laundry surfactant in worldwide use is commercial linear alkylbenzenesulfonate (LAS) which contains 20 congeners of linear alkanes (C10 to C13). LAS is fully biodegradable in oxic environments. Degradation involves microbial communities. Parvibaculum lavamentivorans DS-1T is a representative member of many heterotrophic, LAS-degrading communities, in which it catalyzes the first steps of LAS degradation. Strain DS-1T is a small heterotrophic bacterium able to omega-oxygenate the comm
Probab=89.38 E-value=1.8 Score=42.34 Aligned_cols=76 Identities=8% Similarity=-0.051 Sum_probs=57.6
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
+.++++.+|.+++-+|++.........+.+.+.|++.|+++.....+..+.+.+.....++..++.+++.||..+.
T Consensus 15 l~~~l~~~g~~~~liv~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGG 90 (370)
T cd08192 15 LPAECAELGIKRPLIVTDPGLAALGLVARVLALLEDAGLAAALFDEVPPNPTEAAVEAGLAAYRAGGCDGVIAFGG 90 (370)
T ss_pred HHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 4567788899999988855443334678899999999998764444555666677888888899889999997755
No 118
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=89.35 E-value=2.8 Score=38.51 Aligned_cols=101 Identities=20% Similarity=0.152 Sum_probs=59.7
Q ss_pred HhHHHHHHcCCcEEEEEEEeC---CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEE
Q 011629 3 AIADIVDYFGWRNVIALYVDD---DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILH 77 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd---~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~ 77 (481)
.+++.|..-|.++|++|.... ..+....+.|.+.++++++.+.....+....+.++....+.++.++ .+++|+ +
T Consensus 106 ~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~ 184 (268)
T cd06273 106 LAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALAEAGLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVI-C 184 (268)
T ss_pred HHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCcHHHHHHHHHHHHcCCCCCCEEE-E
Confidence 344544445999999997432 2455678889999999986543222222222222333445555432 345544 4
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
++...+..++..+.+.|+..++.+-|.
T Consensus 185 ~~~~~a~~~~~~l~~~g~~~p~~i~vi 211 (268)
T cd06273 185 GNDVLALGALYEARRLGLSVPEDLSIV 211 (268)
T ss_pred cChHHHHHHHHHHHHcCCCCCCceEEE
Confidence 555667788888888887655544443
No 119
>cd08190 HOT Hydroxyacid-oxoacid transhydrogenase (HOT) involved in gamma-hydroxybutyrate metabolism. Hydroxyacid-oxoacid transhydrogenase (HOT), also known as D-2-hydroxyglutarate transhydrogenase. It catalyzes the conversion of gamma-hydroxybutyrate (GHB) to succinic semialdehyde (SSA), coupled to the stoichiometric conversion of alpha-ketoglutarate to D-2-hydroxyglutarate in gamma-Hydroxybutyrate catabolism. Unlike many other alcohols, which are oxidized by NAD-linked dehydrogenases, gamma-hydroxybutyrate is metabolized to succinate semialdehyde by hydroxyacid-oxoacid transhydrogenase which does not require free NAD or NADP, but instead using alpha -ketoglutarate as an acceptor, converting it to d-2-hydroxyglutarate. Alpha-ketoglutarate serves as an intermediate acceptor to regenerate NAD(P) required for the oxidation of GHB. HOT also catalyzes the reversible oxidation of a hydroxyacid obligatorily coupled to the reduction of an oxoacid, and requires no cofactor. In mammals, the HOT
Probab=89.34 E-value=2 Score=42.73 Aligned_cols=77 Identities=8% Similarity=-0.031 Sum_probs=59.0
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.+|.+++.||++.........+.+.+.+++.|+.+.....+..+.+.+.....++..++.++++||..+..
T Consensus 14 l~~~l~~~g~~~vlivt~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (414)
T cd08190 14 VGMDLKNLGARRVCLVTDPNLAQLPPVKVVLDSLEAAGINFEVYDDVRVEPTDESFKDAIAFAKKGQFDAFVAVGGG 90 (414)
T ss_pred HHHHHHHcCCCeEEEEECcchhhcchHHHHHHHHHHcCCcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 45678889999999998655444445788999999999987654445556666678888888899899999987653
No 120
>PF00465 Fe-ADH: Iron-containing alcohol dehydrogenase ; InterPro: IPR001670 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of ethanol to acetaldehyde with the concomitant reduction of NAD. Currently three, structurally and catalytically, different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Iron-containing ADH's have been found in yeast (gene ADH4) [], as well as in Zymomonas mobilis (gene adhB) []. These two iron-containing ADH's are closely related to the following enzymes: Escherichia coli propanediol oxidoreductase (1.1.1.77 from EC) (gene fucO) [], an enzyme involved in the metabolism of fucose and which also seems to contain ferrous ion(s). Clostridium acetobutylicum NADPH- and NADH-dependent butanol dehydrogenases (1.1.1 from EC) (genes adh1, bdhA and bdhB) [], an enzyme which has activity using butanol and ethanol as substrates. E. coli adhE [], an iron-dependent enzyme which harbor three different activities: alcohol dehydrogenase, acetaldehyde dehydrogenase (acetylating) (1.2.1.10 from EC) and pyruvate-formate-lyase deactivase. Bacterial glycerol dehydrogenase (1.1.1.6 from EC) (gene gldA or dhaD) []. Clostridium kluyveri NAD-dependent 4-hydroxybutyrate dehydrogenase (4hbd) (1.1.1.61 from EC). Citrobacter freundii and Klebsiella pneumoniae 1,3-propanediol dehydrogenase (1.1.1.202 from EC) (gene dhaT). Bacillus methanolicus NAD-dependent methanol dehydrogenase (1.1.1.244 from EC) []. E. coli and Salmonella typhimurium ethanolamine utilization protein eutG. E. coli hypothetical protein yiaY. ; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 1RRM_A 2BL4_A 2BI4_A 3BFJ_R 1KQ3_A 1JQ5_A 1JPU_A 1JQA_A 3JZD_A 3UHJ_A ....
Probab=89.34 E-value=1.4 Score=43.13 Aligned_cols=86 Identities=8% Similarity=0.024 Sum_probs=65.0
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI- 81 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~- 81 (481)
.+.+.++.+| ++.+|+..........+.+.+.|++.|+.+.....+....+.++..+.++.+++.+++.||..+...
T Consensus 13 ~l~~~l~~~g--r~lvVt~~~~~~~~~~~~v~~~L~~~~i~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS~ 90 (366)
T PF00465_consen 13 ELGEELKRLG--RVLVVTDPSLSKSGLVDRVLDALEEAGIEVQVFDGVGPNPTLEDVDEAAEQARKFGADCIIAIGGGSV 90 (366)
T ss_dssp GHHHHHHCTT--EEEEEEEHHHHHHTHHHHHHHHHHHTTCEEEEEEEESSS-BHHHHHHHHHHHHHTTSSEEEEEESHHH
T ss_pred HHHHHHHhcC--CEEEEECchHHhCccHHHHHHHHhhCceEEEEEecCCCCCcHHHHHHHHHHHHhcCCCEEEEcCCCCc
Confidence 4567788888 9999996633333468999999999999987777777777778899999999999999999887643
Q ss_pred -HHHHHHHHH
Q 011629 82 -WGLEVLNAA 90 (481)
Q Consensus 82 -~~~~il~~a 90 (481)
++...+...
T Consensus 91 ~D~aK~va~~ 100 (366)
T PF00465_consen 91 MDAAKAVALL 100 (366)
T ss_dssp HHHHHHHHHH
T ss_pred CcHHHHHHhh
Confidence 334444333
No 121
>PRK15454 ethanol dehydrogenase EutG; Provisional
Probab=88.82 E-value=2 Score=42.30 Aligned_cols=77 Identities=10% Similarity=-0.039 Sum_probs=57.9
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.+|.+++-++.+..-...+..+.+.+.|++.|+.+.....+..+.+.+...+.++..++.++++||..+..
T Consensus 40 l~~~~~~~g~~~~lvv~~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~P~~~~v~~~~~~~r~~~~D~IiavGGG 116 (395)
T PRK15454 40 CGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLAVKGIAMTLWPCPVGEPCITDVCAAVAQLRESGCDGVIAFGGG 116 (395)
T ss_pred HHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCcCEEEEeCCh
Confidence 45678889998888776443333456788999999999987644445555666678888889999999999988764
No 122
>PF13377 Peripla_BP_3: Periplasmic binding protein-like domain; PDB: 3K9C_B 3BIL_B 3JVD_B 1ZAY_A 1VPW_A 1DBQ_A 2PUA_A 1QQA_A 1PNR_A 1JHZ_A ....
Probab=88.33 E-value=2.6 Score=35.24 Aligned_cols=98 Identities=16% Similarity=0.181 Sum_probs=62.7
Q ss_pred HHHHHcCCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHH-HHhccCCceEEEEEeCcHH
Q 011629 6 DIVDYFGWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTL-LTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 6 ~ll~~fgW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l-~~i~~s~~~vIvl~~~~~~ 82 (481)
+-|..-|-+++++|.... .+.....+.+++.+++.|+........... ...+..... ..+++..++ .|++++...
T Consensus 2 ~~L~~~G~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~pd-aii~~~~~~ 79 (160)
T PF13377_consen 2 DYLIERGHRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFEELIFFSDD-DSEDAREAQLLWLRRLRPD-AIICSNDRL 79 (160)
T ss_dssp HHHHHTT-SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEEGEEEEESS-SHHHHHHHHHHHHHTCSSS-EEEESSHHH
T ss_pred hHHHHCCCCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCCeeEeecCC-cchhHHHHHHHHHhcCCCc-EEEEcCHHH
Confidence 445667999999999333 334466788899999999986655444333 222222222 223333444 455678888
Q ss_pred HHHHHHHHHHcCCccCCeEEEEe
Q 011629 83 GLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 83 ~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
+..++..+.+.|+..++-+-|++
T Consensus 80 a~~~~~~l~~~g~~vP~di~vv~ 102 (160)
T PF13377_consen 80 ALGVLRALRELGIRVPQDISVVS 102 (160)
T ss_dssp HHHHHHHHHHTTSCTTTTSEEEE
T ss_pred HHHHHHHHHHcCCcccccccEEE
Confidence 99999999999987766555554
No 123
>PRK10624 L-1,2-propanediol oxidoreductase; Provisional
Probab=88.24 E-value=2.5 Score=41.49 Aligned_cols=76 Identities=12% Similarity=0.049 Sum_probs=56.6
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
+.+.++.+|.+++-|+++..-.-....+.+.+.+++.|+.+.....+..+.+.+.....++.+++.++++||..+.
T Consensus 21 l~~~~~~~g~~~~lvvtd~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGG 96 (382)
T PRK10624 21 LTDEVKRRGFKKALIVTDKTLVKCGVVAKVTDVLDAAGLAYEIYDGVKPNPTIEVVKEGVEVFKASGADYLIAIGG 96 (382)
T ss_pred HHHHHHhcCCCEEEEEeCcchhhCcchHHHHHHHHHCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 4567788899999988855433334678899999999987754444555555667788888888889999997765
No 124
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=88.17 E-value=3.9 Score=37.49 Aligned_cols=101 Identities=12% Similarity=0.085 Sum_probs=60.6
Q ss_pred hHHHHHHcCCcEEEEEEEeCC---cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCC-ceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD---HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMM-SRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~---~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~-~~vIvl~~~ 79 (481)
+++.|..-|=++++++..+.. .+....+.+++.++++|+.+..........+.+.....++++.++. .+.|+ +.+
T Consensus 107 ~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ai~-~~~ 185 (268)
T cd06298 107 ATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEALSEANIEFDESLIFEGDYTYESGYELAEELLEDGKPTAAF-VTD 185 (268)
T ss_pred HHHHHHHcCCceEEEEeCCcccccchhHHHHHHHHHHHHcCCCCCHHHeEeCCCChhHHHHHHHHHhcCCCCCEEE-EcC
Confidence 445555568899999985433 4667788889999998865432111111222223334555555443 44444 455
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..+++.+.+.|+..++.+=+++
T Consensus 186 d~~a~~~~~~l~~~g~~vp~di~vvg 211 (268)
T cd06298 186 DELAIGILNAAQDAGLKVPEDFEIIG 211 (268)
T ss_pred cHHHHHHHHHHHHcCCCCccceEEEe
Confidence 56677889999998887665544443
No 125
>cd08193 HVD 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase (HVD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the cyclopentanol metabolism biochemical pathway. It catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. This cyclopentanol (cpn) degradation pathway is present in some bacteria which can use cyclopentanol as sole carbon source. In Comamonas sp. strain NCIMB 9872, this enzyme is encoded by the CpnD gene.
Probab=88.15 E-value=2.4 Score=41.59 Aligned_cols=77 Identities=8% Similarity=-0.010 Sum_probs=57.9
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.+|.+++.+|+...-......+.+.+.+++.|+.+.....+..+.+.+...+.++.+++.+++.||..+..
T Consensus 17 l~~~l~~~~~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 93 (376)
T cd08193 17 LGELLAALGAKRVLVVTDPGILKAGLIDPLLASLEAAGIEVTVFDDVEADPPEAVVEAAVEAARAAGADGVIGFGGG 93 (376)
T ss_pred HHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 45667888999999888554333345788999999999877644455556666778888889998899999987653
No 126
>cd08551 Fe-ADH iron-containing alcohol dehydrogenases (Fe-ADH)-like. Large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. They contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases; insect-type, or short-chain alcohol dehydrogenases; iron-containing alcohol dehydrogenases, and others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H.
Probab=87.82 E-value=3.1 Score=40.72 Aligned_cols=85 Identities=8% Similarity=0.002 Sum_probs=61.6
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc--
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-- 80 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-- 80 (481)
-+.++++.+|-+++.+|++.........+.+.+.+++.|+.+.....+..+.+.++..+.++.++..+++.||..+..
T Consensus 13 ~l~~~l~~~~~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IiaiGGGs~ 92 (370)
T cd08551 13 KLGEEIKNLGGRKALIVTDPGLVKTGVLDKVIDSLKEAGIEVVIFDGVEPNPTLSNVDAAVAAYREEGCDGVIAVGGGSV 92 (370)
T ss_pred HHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCchH
Confidence 355677888999999998654433356788999999999887644445556667778888889988889999977653
Q ss_pred HHHHHHH
Q 011629 81 IWGLEVL 87 (481)
Q Consensus 81 ~~~~~il 87 (481)
-++..++
T Consensus 93 ~D~AK~v 99 (370)
T cd08551 93 LDTAKAI 99 (370)
T ss_pred HHHHHHH
Confidence 3444443
No 127
>PF13685 Fe-ADH_2: Iron-containing alcohol dehydrogenase; PDB: 3CE9_C.
Probab=87.42 E-value=4.5 Score=36.89 Aligned_cols=97 Identities=8% Similarity=0.117 Sum_probs=57.4
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHH
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWG 83 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~ 83 (481)
+-++++.++.+++.+|++.+.+ ....+.+.+.++..|+.+..........+.++...+.+.++..++++||..+.. .+
T Consensus 10 l~~~l~~~~~~~~lvv~d~~t~-~~~g~~v~~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ii~vGgG-~i 87 (250)
T PF13685_consen 10 LPEILSELGLKKVLVVTDENTY-KAAGEKVEESLKSAGIEVAVIEEFVGDADEDEVEKLVEALRPKDADLIIGVGGG-TI 87 (250)
T ss_dssp HHHHHGGGT-SEEEEEEETTHH-HHHHHHHHHHHHTTT-EEEEEE-EE---BHHHHHHHHTTS--TT--EEEEEESH-HH
T ss_pred HHHHHHhcCCCcEEEEEcCCHH-HHHHHHHHHHHHHcCCeEEEEecCCCCCCHHHHHHHHHHhcccCCCEEEEeCCc-HH
Confidence 5578888899999999966544 345678889999999998854433333454556666677776788888888774 34
Q ss_pred HHHHHH-HHHcCCccCCeEEEEe
Q 011629 84 LEVLNA-AKHLRMMESGYVWIVT 105 (481)
Q Consensus 84 ~~il~~-a~~~g~~~~~~~wI~~ 105 (481)
..+-+. |.+++ ..|+=+-|
T Consensus 88 ~D~~K~~A~~~~---~p~isVPT 107 (250)
T PF13685_consen 88 IDIAKYAAFELG---IPFISVPT 107 (250)
T ss_dssp HHHHHHHHHHHT-----EEEEES
T ss_pred HHHHHHHHHhcC---CCEEEecc
Confidence 455444 34443 23555544
No 128
>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=87.37 E-value=0.38 Score=45.51 Aligned_cols=82 Identities=11% Similarity=-0.043 Sum_probs=50.5
Q ss_pred HHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeec-ccccccee----eccceeecceEEEEecCCC
Q 011629 353 AVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAIT-TERTKMVD----FTQPYIESGLVVVAPIKKL 427 (481)
Q Consensus 353 ~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t-~~r~~~~~----fs~p~~~~~~~~~~~~~~~ 427 (481)
.+++++|+++++ ... .++..++.+|.+|++|+++.+.+.. ..+.+..+ +...+......+++++++
T Consensus 20 ~~~k~~Gl~Ve~--~~~------~~~~~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~~~~~lv~~~~s- 90 (300)
T TIGR01729 20 AAAKEAGATIDW--RKF------DSGADISTALASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIGKSEALVAREGS- 90 (300)
T ss_pred chHHhcCCeeEE--Eec------CcHHHHHHHHHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCCccceEEecCCC-
Confidence 566778977444 442 3588999999999999987544322 13333332 222333334577777665
Q ss_pred CcCccccccCcchhHH
Q 011629 428 NSNAWAFLNPFTPKMW 443 (481)
Q Consensus 428 ~~~~~~~l~pf~~~~W 443 (481)
.+....+|+.-+..++
T Consensus 91 ~I~s~~DLkGK~Igv~ 106 (300)
T TIGR01729 91 GIEKPEDLKGKNVAVP 106 (300)
T ss_pred CCCChhHcCCCEEEeC
Confidence 5667788887665443
No 129
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=87.35 E-value=5.9 Score=37.79 Aligned_cols=100 Identities=10% Similarity=0.075 Sum_probs=61.5
Q ss_pred hHHHHHHcCCcEEEEEEEeC--C-cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDD--D-HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd--~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+++.|...|.++++++.... . .+....+.+.+.++++|+.+..........+.++....++++.+..+.. |++.+.
T Consensus 167 a~~~L~~~G~~~I~~i~g~~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~p~a-i~~~~d 245 (329)
T TIGR01481 167 AVGELIAKGHKSIAFVGGPLSDSINGEDRLEGYKEALNKAGIQFGEDLVCEGKYSYDAGYKAFAELKGSLPTA-VFVASD 245 (329)
T ss_pred HHHHHHHCCCCeEEEEecCcccccchHHHHHHHHHHHHHcCCCCCcceEEecCCChHHHHHHHHHHhCCCCCE-EEEcCc
Confidence 34445556999999997432 2 2456788899999999976532211211222223334555555445554 455666
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEE
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
..+..++..+.+.|+..++-+=++
T Consensus 246 ~~A~g~~~al~~~g~~vP~dvsvv 269 (329)
T TIGR01481 246 EMAAGILNAAMDAGIKVPEDLEVI 269 (329)
T ss_pred HHHHHHHHHHHHcCCCCCCceEEE
Confidence 778889999999998766544333
No 130
>cd08194 Fe-ADH6 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions.
Probab=86.86 E-value=3.4 Score=40.52 Aligned_cols=77 Identities=6% Similarity=-0.022 Sum_probs=58.5
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.++-+++.+|++...+..+..+.+.+.|++.|+.+.....+..+.+.+...+.++.++..+++.||..+..
T Consensus 14 l~~~~~~~~~~r~livt~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (375)
T cd08194 14 TGAVLADLGGKRPLIVTDKVMVKLGLVDKLTDSLKKEGIESAIFDDVVSEPTDESVEEGVKLAKEGGCDVIIALGGG 90 (375)
T ss_pred HHHHHHHcCCCeEEEEcCcchhhcchHHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 44567777889999998555443346788999999999987655556666666778888889998899999987653
No 131
>cd08185 Fe-ADH1 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases-like (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase fold and is a member of the iron-containing alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown. They are present in bacteria and archaea.
Probab=86.76 E-value=3.4 Score=40.57 Aligned_cols=75 Identities=4% Similarity=0.002 Sum_probs=56.7
Q ss_pred hHHHHHHcCCcEEEEEEEeCC-cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD-HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
+.++++.+| +++-||++... ......+.+.+.|++.|+.+.....+..+.+.++..+....+++.+++.||..+.
T Consensus 17 l~~~~~~~g-~r~livt~~~~~~~~g~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiavGG 92 (380)
T cd08185 17 LGEEALKPG-KKALIVTGNGSSKKTGYLDRVIELLKQAGVEVVVFDKVEPNPTTTTVMEGAALAREEGCDFVVGLGG 92 (380)
T ss_pred HHHHHHhcC-CeEEEEeCCCchhhccHHHHHHHHHHHcCCeEEEeCCccCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 456677788 99988885443 2445678899999999998765445555666677888888889889999997765
No 132
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=86.69 E-value=5 Score=38.93 Aligned_cols=87 Identities=8% Similarity=-0.002 Sum_probs=67.3
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc--
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-- 80 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-- 80 (481)
.+.+.++.+|++++-||++..-.....++.+.+.|+..|+.+.....+.++.+.+.....+..+++.+++.||.++-.
T Consensus 19 ~l~~~~~~~g~~r~liVTd~~~~~~g~~~~v~~~L~~~~i~~~if~~v~p~P~~~~v~~~~~~~~~~~~D~iIalGGGS~ 98 (377)
T COG1454 19 ELGEEVKRLGAKRALIVTDRGLAKLGLLDKVLDSLDAAGIEYEVFDEVEPEPTIETVEAGAEVAREFGPDTIIALGGGSV 98 (377)
T ss_pred HHHHHHHhcCCCceEEEECCccccchhHHHHHHHHHhcCCeEEEecCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCccH
Confidence 456778889999999999766566678999999999999887766666667776777888889999999999987653
Q ss_pred HHHHHHHHH
Q 011629 81 IWGLEVLNA 89 (481)
Q Consensus 81 ~~~~~il~~ 89 (481)
-++...+.-
T Consensus 99 ~D~AK~i~~ 107 (377)
T COG1454 99 IDAAKAIAL 107 (377)
T ss_pred HHHHHHHHH
Confidence 344444433
No 133
>cd08189 Fe-ADH5 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown.
Probab=86.36 E-value=3.9 Score=40.08 Aligned_cols=84 Identities=7% Similarity=-0.007 Sum_probs=60.2
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc--H
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD--I 81 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~--~ 81 (481)
+.+.++.+|-+++.+|++.........+.+.+.+++.|+.+.....+..+.+.+...+.++.+++.++++||..+.. -
T Consensus 17 l~~~l~~~g~~~~lvvt~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS~~ 96 (374)
T cd08189 17 LPAAISQLGVKKVLIVTDKGLVKLGLLDKVLEALEGAGIEYAVYDGVPPDPTIENVEAGLALYRENGCDAILAVGGGSVI 96 (374)
T ss_pred HHHHHHhcCCCeEEEEeCcchhhcccHHHHHHHHHhcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHH
Confidence 45667888888998888554433345788999999999976654455556666678888889998899999977543 3
Q ss_pred HHHHHH
Q 011629 82 WGLEVL 87 (481)
Q Consensus 82 ~~~~il 87 (481)
++...+
T Consensus 97 D~aK~i 102 (374)
T cd08189 97 DCAKAI 102 (374)
T ss_pred HHHHHH
Confidence 444443
No 134
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=85.83 E-value=9 Score=35.72 Aligned_cols=98 Identities=11% Similarity=0.096 Sum_probs=67.7
Q ss_pred hHHHHHHcCCcE-EEEEEEeCCc--ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEEEeC
Q 011629 4 IADIVDYFGWRN-VIALYVDDDH--GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~-V~ii~~dd~~--g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl~~~ 79 (481)
+++-|..-|-++ |+++..+.+. .....+.+++.++++|+++..........+.++-...++++-+..+.+ .|++++
T Consensus 109 a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~p~idai~~~n 188 (279)
T PF00532_consen 109 ATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPIDEEWIFEGDFDYESGYEAARELLESHPDIDAIFCAN 188 (279)
T ss_dssp HHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCEEEEEEEESSSSHHHHHHHHHHHHHTSTT-SEEEESS
T ss_pred HHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCCCcccccccCCCHHHHHHHHHHHHhhCCCCEEEEEeC
Confidence 345555679999 9999987654 345567789999999997766655544444444445566665544442 456677
Q ss_pred cHHHHHHHHHHHHcC-CccCCeE
Q 011629 80 DIWGLEVLNAAKHLR-MMESGYV 101 (481)
Q Consensus 80 ~~~~~~il~~a~~~g-~~~~~~~ 101 (481)
...+...++.+.+.| ...++.+
T Consensus 189 d~~A~ga~~~l~~~gr~~ip~di 211 (279)
T PF00532_consen 189 DMMAIGAIRALRERGRLKIPEDI 211 (279)
T ss_dssp HHHHHHHHHHHHHTT-TCTTTEE
T ss_pred HHHHHHHHHHHHHcCCcccChhh
Confidence 788889999999998 7666655
No 135
>TIGR02638 lactal_redase lactaldehyde reductase. This clade of genes encoding iron-containing alcohol dehydrogenase (pfam00465) proteins is generally found in apparent operons for the catabolism of rhamnose or fucose. Catabolism of both of these monosaccharides results in lactaldehyde which is reduced by this enzyme to 1,2 propanediol. This protein is alternatively known by the name 1,2 propanediol oxidoreductase. This enzyme is active under anaerobic conditions in E. coli while being inactivated by reactive oxygen species under aerobic conditions. Under aerobic conditions the lactaldehyde product of rhamnose and fucose catabolism is believed to be oxidized to lactate by a separate enzyme, lactaldehyde dehydrogenase.
Probab=85.78 E-value=3.9 Score=40.11 Aligned_cols=77 Identities=14% Similarity=0.053 Sum_probs=56.6
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.+.++.+|-+++-||+.....-.+..+.+.+.+++.|+.+.....+..+.+.+...+..+..++.+++.||..+..
T Consensus 20 l~~~l~~~g~~r~lvvt~~~~~~~g~~~~v~~~L~~~~i~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiaiGGG 96 (379)
T TIGR02638 20 IVDEVKRRGFKKALVVTDKDLIKFGVADKVTDLLDEAGIAYELFDEVKPNPTITVVKAGVAAFKASGADYLIAIGGG 96 (379)
T ss_pred HHHHHHhcCCCEEEEEcCcchhhccchHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCh
Confidence 45678889999999888544332336788999999999876544344445566677888888888899999987653
No 136
>cd08181 PPD-like 1,3-propanediol dehydrogenase-like (PPD). 1,3-propanediol dehydrogenase-like (PPD). This family is a member of the iron-containing alcohol dehydrogenase superfamily, and exhibits a dehydroquinate synthase-like fold. Protein sequence similarity search and other biochemical evidences suggest that they are close to the iron-containing 1,3-propanediol dehydrogenase (EC 1.1.1.202). 1,3-propanediol dehydrogenase catalyzes the oxidation of propane-1,3-diol to 3-hydroxypropanal with the simultaneous reduction of NADP+ to NADPH. The protein structure of Thermotoga maritima TM0920 gene contains one NADP+ and one iron ion.
Probab=84.93 E-value=4.6 Score=39.24 Aligned_cols=76 Identities=8% Similarity=0.056 Sum_probs=56.1
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcc-cchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHG-RNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g-~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.+| +++-+|++...+- .+..+.+.+.+++.|+.+.....+..+.+.++..+..+..++.++++||..+..
T Consensus 17 l~~~~~~~g-~r~lvVt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 93 (357)
T cd08181 17 HGEELAALG-KRALIVTGKSSAKKNGSLDDVTKALEELGIEYEIFDEVEENPSLETIMEAVEIAKKFNADFVIGIGGG 93 (357)
T ss_pred HHHHHHHcC-CEEEEEeCCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 346678888 8888887544322 234688899999999987654445556666778888889999999999988754
No 137
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=84.51 E-value=8.5 Score=35.25 Aligned_cols=97 Identities=13% Similarity=0.091 Sum_probs=55.7
Q ss_pred hHHHHHHcCCcEEEEEEEeCCc--ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc--CCceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDDH--GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS--MMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~--g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~--s~~~vIvl~~~ 79 (481)
+++.+...|.++++++..+..+ .....+.+++.+++.|+.+..........+.++-...++++.+ ...+.|+ +++
T Consensus 109 a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~ 187 (270)
T cd01545 109 MTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAGLPLDPELVAQGDFTFESGLEAAEALLALPDRPTAIF-ASN 187 (270)
T ss_pred HHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHhCCCCCCEEE-EcC
Confidence 4455555699999999865543 2344677888888888765211111111111122233444432 3345444 556
Q ss_pred cHHHHHHHHHHHHcCCccCCeE
Q 011629 80 DIWGLEVLNAAKHLRMMESGYV 101 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~ 101 (481)
...+..+++.+.+.|...++.+
T Consensus 188 d~~a~~~~~~~~~~g~~~p~~i 209 (270)
T cd01545 188 DDMAAGVLAVAHRRGLRVPDDL 209 (270)
T ss_pred cHHHHHHHHHHHHcCCCCCCce
Confidence 6777788999988887555444
No 138
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=83.89 E-value=9.7 Score=34.79 Aligned_cols=101 Identities=14% Similarity=0.082 Sum_probs=57.2
Q ss_pred HhHHHHHHcCCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEe
Q 011629 3 AIADIVDYFGWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHT 78 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~ 78 (481)
.+++.+..-|.++++++..+. ..+....+.|.+.++++|+.+..........+.+.....++++-+. ..+. |++.
T Consensus 105 ~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~ 183 (267)
T cd06284 105 LAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGLPADEELIQEGDFSLESGYAAARRLLALPDRPTA-IFCF 183 (267)
T ss_pred HHHHHHHHcCCceEEEEcCCccchhHHHHHHHHHHHHHHcCCCCCcceEEeCCCChHHHHHHHHHHHhCCCCCcE-EEEc
Confidence 445555556999999997642 3455677888899998885432211111111222233444444322 2344 4445
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
+...+..+++++.+.|+..++.+-++
T Consensus 184 ~~~~a~g~~~al~~~g~~~p~~v~v~ 209 (267)
T cd06284 184 SDEMAIGAISALKELGLRVPEDISVV 209 (267)
T ss_pred CcHHHHHHHHHHHHcCCCCccceeEE
Confidence 55667788888888886544444333
No 139
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=83.80 E-value=9.5 Score=34.85 Aligned_cols=101 Identities=17% Similarity=0.128 Sum_probs=59.0
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC-C-ceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM-M-SRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s-~-~~vIvl~~~ 79 (481)
+++.+...|-++++++..... .+....+.+++.++++|+.+.....+....+.+.....++++-+. . .++ |++.+
T Consensus 111 a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~ 189 (268)
T cd06271 111 AVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTA-IVCSS 189 (268)
T ss_pred HHHHHHHcCCCcEEEecCccccchHHHHHHHHHHHHHHhCCCCCCceEEeCCCChHHHHHHHHHHHhCCCCCCE-EEEcC
Confidence 444445568999999975432 344567888899998887542211222222222333445554332 2 343 44455
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..+++.+.+.|+..++.+-|++
T Consensus 190 d~~a~g~~~al~~~g~~vp~~i~iig 215 (268)
T cd06271 190 ELMALGVLAALAEAGLRPGRDVSVVG 215 (268)
T ss_pred cHHHHHHHHHHHHhCCCCCcceeEEE
Confidence 66777888888898877666555554
No 140
>cd08188 Fe-ADH4 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown.
Probab=83.76 E-value=6.1 Score=38.73 Aligned_cols=77 Identities=9% Similarity=0.003 Sum_probs=55.7
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.+|-+++.+|++.........+.+.+.+++.|+.+.....+..+.+.++..+.+...++.+++.||..+..
T Consensus 19 l~~~l~~~g~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 95 (377)
T cd08188 19 AGRYARRLGAKKVLLVSDPGVIKAGWVDRVIESLEEAGLEYVVFSDVSPNPRDEEVMAGAELYLENGCDVIIAVGGG 95 (377)
T ss_pred HHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 45667888999999988544333335788899999999876544345445566677788888888889999987653
No 141
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=83.64 E-value=11 Score=35.94 Aligned_cols=102 Identities=8% Similarity=0.039 Sum_probs=60.8
Q ss_pred hHHHHHHcCCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCce-EEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSR-ILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~-vIvl~~~~ 80 (481)
+++.|..-|-+++++|.... .......+.+.+.++++|+.+.....+....+.+.....++++.+...+ -.|++++.
T Consensus 165 a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d 244 (327)
T PRK10423 165 ATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLALPLRPQAVFTGND 244 (327)
T ss_pred HHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCCCcceEEeCCCChHHHHHHHHHHhcCCCCCCEEEEcCc
Confidence 34555556999999997433 2345567888999999997643221122121212223344444332222 24556666
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
..+..++..+.+.|...++-+-|++
T Consensus 245 ~~A~g~~~~l~~~g~~vP~dvsvig 269 (327)
T PRK10423 245 AMAVGVYQALYQAGLSVPQDIAVIG 269 (327)
T ss_pred HHHHHHHHHHHHcCCCCCCceEEEE
Confidence 7778899999999887766665554
No 142
>cd08191 HHD 6-hydroxyhexanoate dehydrogenase (HHD) catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. 6-hydroxyhexanoate dehydrogenase (HHD). The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. Some bacteria can grow on cyclic ketones, cyclohexylamine, and alcohols as sole carbon source. Cyclohexylamine is an insecticide and antiseptic in various industries and is considered a possible environmental pollutant. The degradation of these chemical compounds are through the cyclohexanol and cyclohexanone biological oxidation pathway. The intermediates of this pathway include cyclohexanol, cyclohexanone, e-caprolactone, 6-hydroxyhexanoate, 6-oxohexanoate and adipate. The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate.
Probab=83.34 E-value=6.3 Score=38.77 Aligned_cols=76 Identities=13% Similarity=0.113 Sum_probs=52.5
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.+| +++-||++.........+.+.+.+++.|+.+.....+....+.++....+...++.+++.||..+..
T Consensus 14 l~~~~~~~g-~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~~~~~~v~~~~~~~~~~~~D~IIaiGGG 89 (386)
T cd08191 14 LPRLAARLG-SRALIVTDERMAGTPVFAELVQALAAAGVEVEVFDGVLPDLPRSELCDAASAAARAGPDVIIGLGGG 89 (386)
T ss_pred HHHHHHHcC-CeEEEEECcchhhcchHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 446778889 9998888443333356788999999999876544334333344456666777777889999987653
No 143
>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=83.11 E-value=2.8 Score=39.86 Aligned_cols=84 Identities=7% Similarity=-0.045 Sum_probs=52.1
Q ss_pred HHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeecc------------ccccceeeccceee
Q 011629 348 IDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITT------------ERTKMVDFTQPYIE 415 (481)
Q Consensus 348 ~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~------------~r~~~~~fs~p~~~ 415 (481)
.++.+.++++++ ++++++.+. +.....+..|.+|++|+++....... .+.+.+....+++.
T Consensus 48 ~~la~~~~~~~~-~i~v~~~~~------~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 120 (320)
T TIGR02122 48 GAIAQLINKKSG-KLRVRVQST------GGSVENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFEGPVEKLRALASLYP 120 (320)
T ss_pred HHHHHHHhccCC-CeeEEEEeC------cchHHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccCCCCccHHhHHHhcc
Confidence 567788888876 134666651 34567899999999999876532211 11122222234566
Q ss_pred cceEEEEecCCCCcCccccccCcc
Q 011629 416 SGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 416 ~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
....+++++++ ....+.+|++..
T Consensus 121 ~~~~lvv~~d~-~i~sl~dL~gk~ 143 (320)
T TIGR02122 121 EYIQIVVRKDS-GIKTVADLKGKR 143 (320)
T ss_pred ccEEEEEECCC-CCCcHHHcCCCE
Confidence 67778888775 456677777544
No 144
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=82.97 E-value=9.1 Score=36.81 Aligned_cols=101 Identities=8% Similarity=0.011 Sum_probs=59.8
Q ss_pred HHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCce-EEEEEeCcH
Q 011629 5 ADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSR-ILILHTYDI 81 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~-vIvl~~~~~ 81 (481)
++-|...|-+++++|..... ......+.+++.++++|+.+..........+.+.-...++++.+...+ -.|++.+..
T Consensus 168 ~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~nD~ 247 (343)
T PRK10727 168 TRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLGRGRNFTAVACYNDS 247 (343)
T ss_pred HHHHHHCCCccEEEEeCCccccchHHHHHHHHHHHHHCCCCCChhhEEeCCCChhHHHHHHHHHHhCCCCCCEEEEcCcH
Confidence 34444459999999975432 345567888999999997543211111111222223344444332222 245566777
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEe
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
.+..++..+.++|+..++-+-|++
T Consensus 248 ~A~g~~~al~~~G~~vP~disVig 271 (343)
T PRK10727 248 MAAGAMGVLNDNGIDVPGEISLIG 271 (343)
T ss_pred HHHHHHHHHHHcCCCCCcceeEEe
Confidence 788999999999987766555543
No 145
>cd08170 GlyDH Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway . In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=82.39 E-value=5.5 Score=38.63 Aligned_cols=74 Identities=9% Similarity=0.016 Sum_probs=55.4
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.++ +++-||+....+. ...+.+.+.+++.|+.+.+. .+..+.+.++....++..++.+++.||..+..
T Consensus 14 l~~~~~~~~-~r~livt~~~~~~-~~~~~v~~~L~~~~i~~~~~-~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 87 (351)
T cd08170 14 LGEYLARLG-KRALIIADEFVLD-LVGAKIEESLAAAGIDARFE-VFGGECTRAEIERLAEIARDNGADVVIGIGGG 87 (351)
T ss_pred HHHHHHHhC-CeEEEEECHHHHH-HHHHHHHHHHHhCCCeEEEE-EeCCcCCHHHHHHHHHHHhhcCCCEEEEecCc
Confidence 446677787 8988888443333 67888889999999987654 35555666678888888888899999987654
No 146
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=82.35 E-value=13 Score=35.86 Aligned_cols=101 Identities=10% Similarity=-0.057 Sum_probs=61.0
Q ss_pred hHHHHHHcCCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
.++.|..-|-+++++|.... .......+.+++.++++|+.+..........+.+.-...++++.+. .+. .|++++
T Consensus 167 a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-ai~~~n 245 (346)
T PRK10401 167 ATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRNLQLT-AVFAYN 245 (346)
T ss_pred HHHHHHHCCCCeEEEEeCCCcCcchHHHHHHHHHHHHHcCCCCChhheecCCCChHHHHHHHHHHHcCCCCCc-EEEECC
Confidence 34445556999999997543 2345677889999999997543221111122222222344444332 244 455667
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++..+.++|+..|+-+-|++
T Consensus 246 d~~A~g~~~al~~~G~~vP~disvig 271 (346)
T PRK10401 246 DNMAAGALTALKDNGIAIPLHLSIIG 271 (346)
T ss_pred cHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 77788999999999987766555543
No 147
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=82.20 E-value=9.5 Score=34.92 Aligned_cols=101 Identities=10% Similarity=0.040 Sum_probs=59.1
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
+++.+..-|-++++++..+.. ......+.+.+.++++|+.+..........+..+....++++.+. ..+.| ++.+
T Consensus 107 a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~ 185 (269)
T cd06288 107 ATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGIPFDPDLVVHGDWSADDGYEAAAALLDLDDRPTAI-FCGN 185 (269)
T ss_pred HHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCCCCCHHHeEeCCCChHHHHHHHHHHHhCCCCCCEE-EEeC
Confidence 344444459999999985543 234567888889988886532111111111212233444454333 34444 4566
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++..+.+.|+..++.+.+++
T Consensus 186 d~~a~~~~~~l~~~g~~vp~di~v~g 211 (269)
T cd06288 186 DRMAMGAYQALLERGLRIPQDVSVVG 211 (269)
T ss_pred cHHHHHHHHHHHHcCCCCcccceEEe
Confidence 67777888888888876666666665
No 148
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=81.94 E-value=12 Score=34.53 Aligned_cols=87 Identities=11% Similarity=0.090 Sum_probs=57.6
Q ss_pred HhHHHHHHc--CCcEEEEEEEeC-CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 3 AIADIVDYF--GWRNVIALYVDD-DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 3 Ai~~ll~~f--gW~~V~ii~~dd-~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
++++.+... |-+++++++.+. .++....+.+++.+++.|+.+.... .. ..+++...++++.+. .++|+ +..
T Consensus 119 ~~~~~l~~~~~g~~~i~~l~~~~~~~~~~r~~g~~~~~~~~g~~~~~~~-~~---~~~~~~~~~~~~~~~-~dai~-~~~ 192 (281)
T cd06325 119 TQLELLKKLLPDAKTVGVLYNPSEANSVVQVKELKKAAAKLGIEVVEAT-VS---SSNDVQQAAQSLAGK-VDAIY-VPT 192 (281)
T ss_pred HHHHHHHHHCCCCcEEEEEeCCCCccHHHHHHHHHHHHHhCCCEEEEEe-cC---CHHHHHHHHHHhccc-CCEEE-EcC
Confidence 445566554 999999998544 3666778899999999998876532 21 233566677777653 45544 444
Q ss_pred cHHHHHHHHHHHHcCC
Q 011629 80 DIWGLEVLNAAKHLRM 95 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~ 95 (481)
...+..++.++.+.++
T Consensus 193 d~~a~~~~~~~~~~~~ 208 (281)
T cd06325 193 DNTVASAMEAVVKVAN 208 (281)
T ss_pred chhHHhHHHHHHHHHH
Confidence 5566677777777654
No 149
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=81.71 E-value=12 Score=34.25 Aligned_cols=100 Identities=16% Similarity=0.055 Sum_probs=58.7
Q ss_pred HhHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCce-EEEEEeC
Q 011629 3 AIADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSR-ILILHTY 79 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~-vIvl~~~ 79 (481)
.+++.|..-|-++++++..+.. .+....+.+.+.++++|+.+.....+....+.+.....++++.+...+ ..|++.+
T Consensus 104 ~a~~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~ 183 (265)
T cd06285 104 LATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEVPPERIVYSGFDIEGGEAAAEKLLRSDSPPTAIFAVN 183 (265)
T ss_pred HHHHHHHHCCCccEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhhEEeCCCCHHHHHHHHHHHHcCCCCCCEEEEcC
Confidence 3455555568999999985432 345667888888988887643211121122222233445554332222 3455566
Q ss_pred cHHHHHHHHHHHHcCCccCCeEE
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVW 102 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~w 102 (481)
...+..+++.+.+.|+..++-+=
T Consensus 184 d~~a~g~~~~l~~~g~~~p~di~ 206 (265)
T cd06285 184 DFAAIGVMGAARDRGLRVPDDVA 206 (265)
T ss_pred cHHHHHHHHHHHHcCCCCCcceE
Confidence 67778899999998876554443
No 150
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=81.50 E-value=15 Score=35.19 Aligned_cols=96 Identities=6% Similarity=-0.013 Sum_probs=56.0
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCce-EEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSR-ILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~-vIvl~~~~ 80 (481)
+++.|...|.++++++..... ......+.+.+.++++|+.+.....+....+.+.....++++-+...+ -.|++.+.
T Consensus 173 a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~nd 252 (342)
T PRK10014 173 LTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVVCYNE 252 (342)
T ss_pred HHHHHHHCCCCEEEEEcCCcccccHHHHHHHHHHHHHHcCCCCCcceEecCCCChHHHHHHHHHHHcCCCCCCEEEECCc
Confidence 445555569999999975432 223466788999999997643222221111222233444444333222 23456667
Q ss_pred HHHHHHHHHHHHcCCccCC
Q 011629 81 IWGLEVLNAAKHLRMMESG 99 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~ 99 (481)
..+..++..+.+.|+..+.
T Consensus 253 ~~A~g~~~~l~~~g~~vp~ 271 (342)
T PRK10014 253 TIAMGAWFGLLRAGRQSGE 271 (342)
T ss_pred HHHHHHHHHHHHcCCCCCC
Confidence 7788888888888876553
No 151
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=81.39 E-value=21 Score=34.26 Aligned_cols=98 Identities=13% Similarity=0.064 Sum_probs=65.4
Q ss_pred hHhHHHHHHcCCcEEEEEEEe--CCcccchHHHHHHHHHhcCCEE--EEEEecCCCCChhHHHHHHHHhccCC-c-eEEE
Q 011629 2 AAIADIVDYFGWRNVIALYVD--DDHGRNGIAALGDKLAEKRCRL--SHKVPLSPKGSRNQIIDTLLTVSSMM-S-RILI 75 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v--~~~~~~~~~~~~~~~~~~l~~i~~s~-~-~vIv 75 (481)
+.+++.|..-|-++++++... ...+....+.+.+.++++|+.. .....- ..+.++-...+.++.... . --.|
T Consensus 164 ~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~i~~~--~~~~~~g~~~~~~ll~~~~~~ptAi 241 (333)
T COG1609 164 YLATEHLIELGHRRIAFIGGPLDSSASRERLEGYRAALREAGLPINPEWIVEG--DFSEESGYEAAERLLARGEPRPTAI 241 (333)
T ss_pred HHHHHHHHHCCCceEEEEeCCCccccHhHHHHHHHHHHHHCCCCCCcceEEec--CCChHHHHHHHHHHHhcCCCCCcEE
Confidence 345667777899999999976 3456778899999999999885 222211 112223334444444322 2 3456
Q ss_pred EEeCcHHHHHHHHHHHHcCCccCCeE
Q 011629 76 LHTYDIWGLEVLNAAKHLRMMESGYV 101 (481)
Q Consensus 76 l~~~~~~~~~il~~a~~~g~~~~~~~ 101 (481)
+|++...+..++.++.+.|...++-+
T Consensus 242 f~~nD~~Alg~l~~~~~~g~~vP~di 267 (333)
T COG1609 242 FCANDLMALGALRALRELGLRVPEDL 267 (333)
T ss_pred EEcCcHHHHHHHHHHHHcCCCCCCee
Confidence 67888899999999999988766533
No 152
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=81.20 E-value=12 Score=34.00 Aligned_cols=102 Identities=12% Similarity=-0.022 Sum_probs=60.3
Q ss_pred HhHHHHHHcCCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEe
Q 011629 3 AIADIVDYFGWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHT 78 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~ 78 (481)
.+++.|..-|-++++++..+. .......+.+.+.+.++|+.+.....+....+.++....++.+.+. ..+. |+++
T Consensus 104 ~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~ 182 (260)
T cd06286 104 EALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLLKMKDRPDA-IFTG 182 (260)
T ss_pred HHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCCCChHheEeCCCCHHHHHHHHHHHHcCCCCCCE-EEEc
Confidence 344555556999999997543 3344567888889999886543211111111222333445554432 3443 4566
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
+...+..++..+.++|...++.+-|++
T Consensus 183 ~d~~a~~~~~~l~~~g~~ip~di~v~g 209 (260)
T cd06286 183 SDEVAAGIITEAKKQGIRVPEDLAIIG 209 (260)
T ss_pred chHHHHHHHHHHHHcCCCCCcceEEEe
Confidence 667778889999998876555554443
No 153
>cd08182 HEPD Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP). Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP) with either NADH or NADPH as a cofactor. NADH is the preferred cofactor. PnAA is a biosynthetic intermediate for several phosphonates such as the antibiotic fosfomycin, phosphinothricin tripeptide (PTT), and 2-aminoethylphosphonate (AEP). This enzyme is named PhpC in PTT biosynthesis pathway in Streptomyces hygroscopicus and S. viridochromogenes. Members of this family are only found in bacteria.
Probab=81.18 E-value=8 Score=37.77 Aligned_cols=82 Identities=9% Similarity=0.036 Sum_probs=57.8
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc--H
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD--I 81 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~--~ 81 (481)
+.++++.+|-+++.+|++...+ ....+.+.+++.|+.+.....+..+.+.+...+.++.+++.++++||..+.. -
T Consensus 14 l~~~~~~~g~~~~livtd~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGGs~~ 90 (367)
T cd08182 14 LPSLLKGLGGKRVLLVTGPRSA---IASGLTDILKPLGTLVVVFDDVQPNPDLEDLAAGIRLLREFGPDAVLAVGGGSVL 90 (367)
T ss_pred HHHHHHhcCCCeEEEEeCchHH---HHHHHHHHHHHcCCeEEEEcCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCcHHH
Confidence 4567788899999999855443 4566788888888776544455555566678888888888889999977653 3
Q ss_pred HHHHHHH
Q 011629 82 WGLEVLN 88 (481)
Q Consensus 82 ~~~~il~ 88 (481)
++..++.
T Consensus 91 D~aK~ia 97 (367)
T cd08182 91 DTAKALA 97 (367)
T ss_pred HHHHHHH
Confidence 4444443
No 154
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=81.04 E-value=25 Score=30.76 Aligned_cols=88 Identities=8% Similarity=0.033 Sum_probs=65.1
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCC-------ChhHHHHHHHHhccCCceEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKG-------SRNQIIDTLLTVSSMMSRIL 74 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~-------~~~~~~~~l~~i~~s~~~vI 74 (481)
-|+++=|+.+|-++|.+++ .|-....+...+.++++|+.|.....+-... +.....++.+++...+++.|
T Consensus 107 ~Avv~aL~al~a~ri~vlT---PY~~evn~~e~ef~~~~Gfeiv~~~~Lgi~dn~eigr~~P~~~y~lAk~~~~~~~Dai 183 (238)
T COG3473 107 TAVVEALNALGAQRISVLT---PYIDEVNQREIEFLEANGFEIVDFKGLGITDNLEIGRQEPWAVYRLAKEVFTPDADAI 183 (238)
T ss_pred HHHHHHHHhhCcceEEEec---cchhhhhhHHHHHHHhCCeEEEEeeccCCcccchhcccChHHHHHHHHHhcCCCCCeE
Confidence 4788889999999999998 4555678889999999999998776654321 12234566778888889999
Q ss_pred EEEeCcHHHHHHHHHHHH
Q 011629 75 ILHTYDIWGLEVLNAAKH 92 (481)
Q Consensus 75 vl~~~~~~~~~il~~a~~ 92 (481)
++-|..-....++....+
T Consensus 184 FiSCTnlRt~eii~~lE~ 201 (238)
T COG3473 184 FISCTNLRTFEIIEKLER 201 (238)
T ss_pred EEEeeccccHHHHHHHHH
Confidence 988876555556555543
No 155
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=81.03 E-value=16 Score=33.33 Aligned_cols=101 Identities=13% Similarity=0.014 Sum_probs=57.7
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
.++.|...|-++++++..+.. ......+.+++.+++.|.............+.+.....++++-++ ..+.| ++++
T Consensus 107 ~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~ 185 (268)
T cd01575 107 MARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAV-FCSN 185 (268)
T ss_pred HHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCCCCceeEeccCCCHHHHHHHHHHHHhCCCCCCEE-EECC
Confidence 444555568899999986542 344567788889988886432222222222222333444454332 34443 3455
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..+++.+.+.|...++.+-+++
T Consensus 186 d~~a~~~~~~l~~~g~~~p~di~vig 211 (268)
T cd01575 186 DDLALGALFECQRRGISVPEDIAIAG 211 (268)
T ss_pred cHHHHHHHHHHHHhCCCCCcceEEEe
Confidence 56667788888888865555554443
No 156
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=80.98 E-value=13 Score=34.26 Aligned_cols=98 Identities=16% Similarity=0.100 Sum_probs=58.6
Q ss_pred HHHHHcCCcEEEEEEEeC--C------cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCce-EEEE
Q 011629 6 DIVDYFGWRNVIALYVDD--D------HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSR-ILIL 76 (481)
Q Consensus 6 ~ll~~fgW~~V~ii~~dd--~------~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~-vIvl 76 (481)
.|++. .+.++++.... . .+....+.+++.+++.|+.+.....+....+.++....++++-+...+ -.|+
T Consensus 108 ~L~~~--~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~ 185 (269)
T cd06297 108 YLADF--PGRIGAITVEEEPDRAFRRTVFAERRAGFQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLAVF 185 (269)
T ss_pred HHHHh--CCceEEEeCccccccccccccHHHHHHHHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHcCCCCCcEEE
Confidence 34444 68999886432 2 345668888999999988643221121122222334455555433222 2445
Q ss_pred EeCcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 77 HTYDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
+.+...+..+++.+.+.|...++.+-|++
T Consensus 186 ~~~d~~a~g~~~~l~~~g~~vP~di~vvg 214 (269)
T cd06297 186 ASADQQALGALQEAVELGLTVGEDVRVVG 214 (269)
T ss_pred EcCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 55666778889999999887777666664
No 157
>cd08176 LPO Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. Lactadehyde:propanediol oxidoreductase (LPO) is a member of the group III iron-activated dehydrogenases which catalyze the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. L-Fucose and L-rhamnose is used by Escherichia coli through an inducible pathway mediated by the fucose regulon comprising four linked oeprons fucO, fucA, fucPIK, and fucR. The fucA-encoded aldolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Under anaerobic conditions, with NADH as a cofactor, lactaldehyde is converted by a fucO-encoded Lactadehyde:propanediol oxidoreductase (LPO) to L-1,2-propanediol, which is excreted as a fermentation product. In mutant strains, E. coli adapted to grow on L-1,2-propanediol, FucO catalyzes the oxidation of the polyol to
Probab=80.61 E-value=7.7 Score=38.04 Aligned_cols=77 Identities=13% Similarity=0.093 Sum_probs=56.1
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.+.++.+|-+++-+|++....-....+.+.+.+++.|+.+.....+..+.+.+...+..+..++.+++.||..+..
T Consensus 19 l~~~l~~~g~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 95 (377)
T cd08176 19 IGDELKNLGFKKALIVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVKPNPTITNVKDGLAVFKKEGCDFIISIGGG 95 (377)
T ss_pred HHHHHHHhCCCeEEEECCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 45677888888888887443322256788999999999876544445555666678888888888899999987653
No 158
>cd08187 BDH Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. The butanol dehydrogenase (BDH) is involved in the final step of the butanol formation pathway in anaerobic micro-organism. Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. Activity in the reverse direction was 50-fold lower than that in the forward direction. The NADH-BDH had higher activity with longer chained aldehydes and was inhibited by metabolites containing an adenine moiety. This protein family belongs to the so-called iron-containing alcohol dehydrogenase superfamily. Since members of this superfamily use different divalent ions, preferentially iron or zinc, it has been suggested to be renamed to family III metal-dependent polyol dehydrogenases.
Probab=80.40 E-value=8.4 Score=37.87 Aligned_cols=77 Identities=8% Similarity=0.083 Sum_probs=55.5
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCc-ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 3 AIADIVDYFGWRNVIALYVDDDH-GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~-g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.+.++++.++ +++.||++.... .....+.+.+.|++.|+++.....+..+.+.+.....+...++.+++.||..+..
T Consensus 19 ~l~~~~~~~~-~r~livt~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 96 (382)
T cd08187 19 ELGKELKKYG-KKVLLVYGGGSIKKNGLYDRVIASLKEAGIEVVELGGVEPNPRLETVREGIELCKEEKVDFILAVGGG 96 (382)
T ss_pred HHHHHHHHhC-CEEEEEeCCcHHHhcCcHHHHHHHHHHcCCeEEEECCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCh
Confidence 3456777786 898888754322 2345688999999999987654445555566678888888898899999977653
No 159
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=79.89 E-value=19 Score=32.98 Aligned_cols=102 Identities=12% Similarity=0.063 Sum_probs=58.5
Q ss_pred HhHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCC--ceEEEEEe
Q 011629 3 AIADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMM--SRILILHT 78 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~--~~vIvl~~ 78 (481)
.+++.|...|-++++++..+.. ......+.+++.++++|+.+..........+.++....++++.++. .++ |+++
T Consensus 106 ~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~ 184 (268)
T cd06270 106 LATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGIALDESLIIEGDFTEEGGYAAMQELLARGAPFTA-VFCA 184 (268)
T ss_pred HHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCCCcceEEECCCCHHHHHHHHHHHHhCCCCCCE-EEEc
Confidence 4556666668999999975432 2334567788889888876422111111222223344555544333 444 3444
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
+...+..+++.+.+.|...++.+=|.+
T Consensus 185 ~d~~a~g~~~~l~~~g~~ip~di~v~g 211 (268)
T cd06270 185 NDEMAAGAISALREHGISVPQDVSIIG 211 (268)
T ss_pred CcHHHHHHHHHHHHcCCCCCCceeEEE
Confidence 555667788888888876555444443
No 160
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor
Probab=79.76 E-value=12 Score=34.13 Aligned_cols=103 Identities=11% Similarity=-0.068 Sum_probs=58.5
Q ss_pred HhHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCc-eEEEEEeC
Q 011629 3 AIADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMS-RILILHTY 79 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~-~vIvl~~~ 79 (481)
.+++.+..-|-++|+++..... ......+.+++.+++.|+.+..........+.+.....++++.+... --.|++++
T Consensus 101 ~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~ 180 (261)
T cd06272 101 LAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENGISISDSHIDVDGLSAEGGDNAAKKLLKESDLPTAIICGS 180 (261)
T ss_pred HHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCCHHHHHHHHHHHHcCCCCCCEEEECC
Confidence 3455555568899999975433 33445678888998888643221111111122233344454433322 22355566
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..+++.+.+.|+..++.+-+++
T Consensus 181 d~~a~~~~~~l~~~g~~vp~dv~vvg 206 (261)
T cd06272 181 YDIALGVLSALNKQGISIPEDIEIIS 206 (261)
T ss_pred cHHHHHHHHHHHHhCCCCCCceEEEe
Confidence 66777888888888876665554443
No 161
>cd08171 GlyDH-like2 Glycerol dehydrogenase-like. Glycerol dehydrogenases-like. The proteins in this family have not been characterized, but they show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=79.61 E-value=8.2 Score=37.32 Aligned_cols=75 Identities=5% Similarity=0.085 Sum_probs=53.2
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.+.++.+| +++-+|++...+ ....+.+.+.+++.|+.+.....+..+.+.+...+..+..++.++++||..+..
T Consensus 14 l~~~~~~~~-~r~liv~d~~~~-~~~~~~v~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~iiavGGG 88 (345)
T cd08171 14 IPEVCEKYG-KKVVVIGGKTAL-AAAKDKIKAALEQSGIEITDFIWYGGESTYENVERLKKNPAVQEADMIFAVGGG 88 (345)
T ss_pred HHHHHHhcC-CEEEEEeCHHHH-HHHHHHHHHHHHHCCCeEEEEEecCCCCCHHHHHHHHHHHhhcCCCEEEEeCCc
Confidence 345677788 888888754333 345677888888899877644455555566677777888888889999987653
No 162
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=79.59 E-value=14 Score=34.75 Aligned_cols=101 Identities=9% Similarity=0.069 Sum_probs=60.1
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
.++.|...|-++++++..... ......+.|++.+++.|+.+.....+....+.+.....++++.+. ..+.|+ +++
T Consensus 143 a~~~l~~~G~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~ 221 (309)
T PRK11041 143 AVNYLHELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITVDPQYIARGDFTFEAGAKALKQLLDLPQPPTAVF-CHS 221 (309)
T ss_pred HHHHHHHcCCceEEEEeCCccccchHHHHHHHHHHHHHcCCCCCHHHeEeCCCCHHHHHHHHHHHHcCCCCCCEEE-EcC
Confidence 344444569999999974433 234567888899998887653211112122222334455555433 245544 456
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++....+.|+..++-+.|++
T Consensus 222 d~~a~gv~~al~~~g~~ip~di~vvg 247 (309)
T PRK11041 222 DVMALGALSQAKRMGLRVPQDLSIIG 247 (309)
T ss_pred cHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 66677888888888876666666665
No 163
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=79.41 E-value=21 Score=32.63 Aligned_cols=101 Identities=14% Similarity=0.044 Sum_probs=59.1
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc--CCceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS--MMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~--s~~~vIvl~~~ 79 (481)
+++.|..-|-++++++..+.. ......+.+++.+++.|+.+..........+.+.....+.++-+ ...+ .|++++
T Consensus 107 ~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-ai~~~~ 185 (269)
T cd06293 107 ATRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPT-AIFAAS 185 (269)
T ss_pred HHHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHHHcCCCCChheEEecCCCHHHHHHHHHHHHcCCCCCC-EEEEcC
Confidence 445555569999999975433 23355788899998888643211111112222233344444432 2244 355566
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++..+.+.|...++.+-|++
T Consensus 186 d~~a~g~~~al~~~g~~vp~di~i~g 211 (269)
T cd06293 186 DEIAIGLLEVLRERGLSIPGDMSLVG 211 (269)
T ss_pred cHHHHHHHHHHHHcCCCCccceEEEe
Confidence 67777888888888876666666554
No 164
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=79.08 E-value=19 Score=32.93 Aligned_cols=101 Identities=17% Similarity=0.134 Sum_probs=56.0
Q ss_pred hHHHHHHcCCcEEEEEEEeCCc--ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDH--GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~--g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl~~~~ 80 (481)
+++.|...|-++|+++.....+ .....+.|++.+++.|+.+..........+.+.....+.++.++..++ .|++.+.
T Consensus 113 ~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d 192 (270)
T cd06294 113 ATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIVATDD 192 (270)
T ss_pred HHHHHHHcCCccEEEecCCcccHHHHHHHHHHHHHHHHcCCCCCcceEEecCCchHHHHHHHHHHHhCCCCCCEEEECCh
Confidence 3444444589999999754432 334577888999988853211111111112223334444443333333 2334455
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEE
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
..+..++..+.+.|+..++.+-++
T Consensus 193 ~~a~g~~~al~~~g~~iP~dv~vi 216 (270)
T cd06294 193 LLALGVLKVLNELGLKVPEDLSII 216 (270)
T ss_pred HHHHHHHHHHHHcCCCCCcceEEE
Confidence 677788888888887665554433
No 165
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=78.95 E-value=15 Score=35.29 Aligned_cols=100 Identities=10% Similarity=0.090 Sum_probs=58.7
Q ss_pred HHHHHHcCCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeCc
Q 011629 5 ADIVDYFGWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTYD 80 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~~ 80 (481)
++.|..-|-+++++|..+. .......+.+.+.++++|+.+..........+.++....++++.++ ..+. |++++.
T Consensus 170 ~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~nd 248 (341)
T PRK10703 170 GRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVPEEWIVQGDFEPESGYEAMQQILSQKHRPTA-VFCGGD 248 (341)
T ss_pred HHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHHcCCCCChHHeEeCCCCHHHHHHHHHHHHhCCCCCCE-EEECCc
Confidence 3444445889999996432 3344567888889998997654221111122222333445454333 2344 445666
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
..+..++..+.+.|...++.+.|++
T Consensus 249 ~~a~g~~~al~~~g~~ip~dv~vvg 273 (341)
T PRK10703 249 IMAMGAICAADEMGLRVPQDISVIG 273 (341)
T ss_pred HHHHHHHHHHHHcCCCCCCceEEEE
Confidence 7777888888888876666665554
No 166
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=78.88 E-value=2.9 Score=39.74 Aligned_cols=99 Identities=14% Similarity=0.030 Sum_probs=57.2
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHC-CCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEe
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELL-PYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVG 395 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~ 395 (481)
.++|+||... ...+ .+-.+....+.++. +. ++++++. .+...++.+|.+|++|+++.
T Consensus 26 ~~~lrIg~~~--~~~~------------~~l~~~~~~~~~~~p~v--~ie~~~~------~~~~~~~~aL~~G~iDia~~ 83 (314)
T PRK11553 26 PEALRIGYQK--GSIG------------LVLAKSHQLLEKRFPQT--KISWVEF------PAGPQMLEALNVGSIDLGST 83 (314)
T ss_pred CCeEEEEeCC--CchH------------HHHHHhhCHHHHhCCCC--eeEEEEC------CCcHHHHHHHHcCCCCEEcc
Confidence 4678988863 1110 12234444555554 54 4666652 23578999999999999875
Q ss_pred eeeeccccc--c----ceeeccceeecceEEEEecCCCCcCccccccCcc
Q 011629 396 DFAITTERT--K----MVDFTQPYIESGLVVVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 396 ~~~~t~~r~--~----~~~fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~ 439 (481)
+ ..++.+. . .+..+.++...+..+++++++ .+..+.+|+...
T Consensus 84 ~-~~~~~~~~~~g~~~~~v~~~~~~~~~~~lvv~~~s-~i~s~~dL~Gk~ 131 (314)
T PRK11553 84 G-DIPPIFAQAAGADLVYVGVEPPKPKAEVILVAENS-PIKTVADLKGHK 131 (314)
T ss_pred C-CHHHHHHHhCCCCEEEEEEecCCCcceEEEEeCCC-CCCCHHHhCCCE
Confidence 4 2323321 1 122245555566788888765 455677776543
No 167
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=78.78 E-value=18 Score=33.21 Aligned_cols=102 Identities=15% Similarity=0.033 Sum_probs=58.7
Q ss_pred HhHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 3 AIADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.+++.|...|-++++++....+ ......+.+++.++++|+.......+....+.+.....++++....++. |++.+.
T Consensus 112 ~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~a-i~~~~d 190 (273)
T cd06292 112 LAVRHLVALGHRRIGFASGPGRTVPRRRKIAGFRAALEEAGLEPPEALVARGMFSVEGGQAAAVELLGSGPTA-IVAASD 190 (273)
T ss_pred HHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhheEeCCCCHHHHHHHHHHHhcCCCCE-EEEcCc
Confidence 3445555669999999975432 2445678888899888863211111111112222334444443333554 445566
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
..+..+++.+.+.|+..++.+-|.+
T Consensus 191 ~~a~g~~~~l~~~g~~ip~di~ii~ 215 (273)
T cd06292 191 LMALGAIRAARRRGLRVPEDVSVVG 215 (273)
T ss_pred HHHHHHHHHHHHcCCCCCcceEEEe
Confidence 6777888888888876666555554
No 168
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=78.59 E-value=38 Score=30.95 Aligned_cols=98 Identities=7% Similarity=-0.028 Sum_probs=55.5
Q ss_pred hHHHHHHc--CCcEEEEEEEeCCc--ccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEEE
Q 011629 4 IADIVDYF--GWRNVIALYVDDDH--GRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LILH 77 (481)
Q Consensus 4 i~~ll~~f--gW~~V~ii~~dd~~--g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl~ 77 (481)
+++.+... |.++++++....++ .....+.+++.++++ |+.+... .....+.++....+.++.++..++ .|++
T Consensus 112 ~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~ 189 (273)
T cd06310 112 AAEALAELLGKKGKVAVISFVPGSSTTDQREEGFLEGLKEYPGIEIVAT--QYSDSDYAKALDITEDLLTANPDLKGIFG 189 (273)
T ss_pred HHHHHHHHcCCCceEEEEeCCCCCccHHHHHHHHHHHHHhCCCcEEEec--ccCCcCHHHHHHHHHHHHHhCCCceEEEe
Confidence 34444444 89999999754333 334567888889888 7765431 111112223334455544333333 3444
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
.+...+..+++.+.+.|+. .+...+.
T Consensus 190 ~~d~~a~g~~~~l~~~g~~-~di~vig 215 (273)
T cd06310 190 ANEGSAVGAARAVRQAGKA-GKVKVVG 215 (273)
T ss_pred cCchhHHHHHHHHHhcCCC-CCeEEEE
Confidence 5566788888888888864 3433333
No 169
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=78.37 E-value=26 Score=32.19 Aligned_cols=91 Identities=11% Similarity=0.058 Sum_probs=53.3
Q ss_pred hHHHHH-Hc-CCcEEEEEEEeCC--cccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEE-
Q 011629 4 IADIVD-YF-GWRNVIALYVDDD--HGRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILH- 77 (481)
Q Consensus 4 i~~ll~-~f-gW~~V~ii~~dd~--~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~- 77 (481)
+++.+. +. |.++++++....+ ......+.+.+.++++ |+.+.... ....+.++....++++.++..++-.++
T Consensus 111 ~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~ 188 (275)
T cd06320 111 GAEWIIDKLAEGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGIEVVASQ--PADWDREKAYDVATTILQRNPDLKAIYC 188 (275)
T ss_pred HHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCcEEEEec--CCCccHHHHHHHHHHHHHhCCCccEEEE
Confidence 344443 33 8999999985332 2345568889999998 88765432 112222334445555544334443334
Q ss_pred eCcHHHHHHHHHHHHcCCc
Q 011629 78 TYDIWGLEVLNAAKHLRMM 96 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~ 96 (481)
.+...+..+++.+.+.|..
T Consensus 189 ~~d~~a~~~~~al~~~g~~ 207 (275)
T cd06320 189 NNDTMALGVVEAVKNAGKQ 207 (275)
T ss_pred CCchhHHHHHHHHHhcCCC
Confidence 4455666788888888763
No 170
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=78.06 E-value=18 Score=33.04 Aligned_cols=100 Identities=10% Similarity=0.015 Sum_probs=55.8
Q ss_pred hHHHHHHcCCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCC--ceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMM--SRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~--~~vIvl~~~ 79 (481)
+++.|..-|-+.|+++..+. .......+.+.+.+.+.|+.+.....+....+.+.....++++.++. .+. |++++
T Consensus 106 ~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-ii~~~ 184 (265)
T cd06290 106 ATQHLIDLGHRRIAHITGPRGHIDARDRLAGYRKALEEAGLEVQPDLIVQGDFEEESGLEAVEELLQRGPDFTA-IFAAN 184 (265)
T ss_pred HHHHHHHCCCCeEEEEeCccccchhhHHHHHHHHHHHHcCCCCCHHHEEecCCCHHHHHHHHHHHHcCCCCCCE-EEEcC
Confidence 34434444889999997543 23335677788888888765432111111111112233444443322 344 44566
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
...+..+++.+.+.|+..++.+=|+
T Consensus 185 ~~~a~~~~~~l~~~g~~ip~di~vi 209 (265)
T cd06290 185 DQTAYGARLALYRRGLRVPEDVSLI 209 (265)
T ss_pred cHHHHHHHHHHHHcCCCCCcceEEe
Confidence 6777888888888887655544333
No 171
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=77.66 E-value=18 Score=33.32 Aligned_cols=102 Identities=15% Similarity=0.078 Sum_probs=57.6
Q ss_pred HhHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEe
Q 011629 3 AIADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHT 78 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~ 78 (481)
..++.|...|.+.|+++..+.. .+....+.+.+.+.+.|+.+..........+.+.....+.++-++ ..+.|+ ++
T Consensus 115 ~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~ 193 (275)
T cd06295 115 LATEHLLARGRRRIAFLGGPQDMPEGEERLEGYREALAEAGLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVF-AA 193 (275)
T ss_pred HHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHcCCCCChhhEEeccCCHHHHHHHHHHHHhCCCCCCEEE-EC
Confidence 3455555679999999975432 344567888999988886543211122222222223334443322 344433 34
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
+...+..++..+.+.|...++.+-|++
T Consensus 194 ~~~~a~g~~~~l~~~g~~ip~~i~ii~ 220 (275)
T cd06295 194 SDLMALGALRALREAGRRVPEDVAVVG 220 (275)
T ss_pred CcHHHHHHHHHHHHhCCCCccceEEEe
Confidence 445667788888888876555555554
No 172
>cd07766 DHQ_Fe-ADH Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH). Dehydroquinate synthase-like. This superfamily divides into two subgroups: the dehydroquinate synthase-like, and a large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. Dehydroquinate synthase-like group includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. The alcohol dehydrogenases in this superfamily contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alc
Probab=77.57 E-value=11 Score=36.05 Aligned_cols=83 Identities=7% Similarity=0.037 Sum_probs=56.0
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc--H
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD--I 81 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~--~ 81 (481)
+.++++.+|.+++.+|++.... ....+.+.+.+++. +.+........+.+.++..+.+..+++.+++.||..+.. -
T Consensus 14 l~~~~~~~g~~~~liv~~~~~~-~~~~~~v~~~l~~~-~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs~~ 91 (332)
T cd07766 14 IGEEIKRGGFDRALVVSDEGVV-KGVGEKVADSLKKL-IAVHIFDGVGPNPTFEEVKEAVERARAAEVDAVIAVGGGSTL 91 (332)
T ss_pred HHHHHHhcCCCeEEEEeCCchh-hhHHHHHHHHHHhc-CcEEEeCCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCchHH
Confidence 4456777899999999854433 35677888888877 665444334334566678888888888889999877653 3
Q ss_pred HHHHHHH
Q 011629 82 WGLEVLN 88 (481)
Q Consensus 82 ~~~~il~ 88 (481)
++..++.
T Consensus 92 D~aK~ia 98 (332)
T cd07766 92 DTAKAVA 98 (332)
T ss_pred HHHHHHH
Confidence 4444443
No 173
>cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar bindi
Probab=77.32 E-value=20 Score=32.86 Aligned_cols=100 Identities=10% Similarity=0.038 Sum_probs=57.8
Q ss_pred hHHHHHHcCCcEEEEEEEeCC-------cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHh-ccC---Cce
Q 011629 4 IADIVDYFGWRNVIALYVDDD-------HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTV-SSM---MSR 72 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~-------~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i-~~s---~~~ 72 (481)
+++.+..-|-++++++..... ......+.+.+.++++|+. .....+....+.++....++++ ++. ..+
T Consensus 103 ~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 181 (270)
T cd01544 103 ALDYLLELGHTRIGFIGGEEKTTDGHEYIEDPRETAFREYMKEKGLY-DPELIYIGDFTVESGYQLMKEALKSLGDNLPT 181 (270)
T ss_pred HHHHHHHcCCCcEEEECCCcccccccchhhhHHHHHHHHHHHHcCCC-ChheEeeCCCCHHHHHHHHHHHHhccCCCCCC
Confidence 344455569999999985542 2345577888899988842 1111111111222223344443 322 133
Q ss_pred EEEEEeCcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 73 ILILHTYDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 73 vIvl~~~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
.|++++...+..++..+.+.|+..++-+-|++
T Consensus 182 -ai~~~~d~~a~g~~~~l~~~g~~vp~di~v~g 213 (270)
T cd01544 182 -AFFIASDPMAIGALRALQEAGIKVPEDVSVIS 213 (270)
T ss_pred -EEEEcCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 45566677788888889888887665555554
No 174
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=76.99 E-value=23 Score=32.47 Aligned_cols=84 Identities=13% Similarity=0.039 Sum_probs=49.9
Q ss_pred CCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEEEeCcHHHHHHHH
Q 011629 12 GWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LILHTYDIWGLEVLN 88 (481)
Q Consensus 12 gW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl~~~~~~~~~il~ 88 (481)
|-++|+++.... ..+....+.+++.++++|+.+.... .....+.++....++++.++.++. .|++.+...+..++.
T Consensus 124 g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~ 202 (277)
T cd06319 124 ADGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCDLAGIR-QQKDFSYQETFDYTNDLLTANPDIRAIWLQGSDRYQGALD 202 (277)
T ss_pred CCCcEEEEeccCCCccHHHHHHHHHHHHHhcCCceEeec-cCCCCCHHHHHHHHHHHHHhCCCCCEEEECCCccchHHHH
Confidence 668999997432 3456778889999999998654221 111222223334455544333443 333444455667888
Q ss_pred HHHHcCCc
Q 011629 89 AAKHLRMM 96 (481)
Q Consensus 89 ~a~~~g~~ 96 (481)
++.+.|+.
T Consensus 203 al~~~g~~ 210 (277)
T cd06319 203 AIATAGKT 210 (277)
T ss_pred HHHHcCCC
Confidence 88888864
No 175
>cd08186 Fe-ADH8 Iron-containing alcohol dehydrogenase. Type III Iron-containing alcohol dehydrogenases (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. The ADH of hyperthermophilic archaeon Thermococcus hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols preferentially from C2 to C8 but is also active towards methanol and glycerol and stereospecific for monoterpenes. It was suggested that the type III ADHs in microorganisms are involved in acetaldehyde detoxication rather than in alcohol turnover.
Probab=76.92 E-value=13 Score=36.47 Aligned_cols=76 Identities=12% Similarity=0.090 Sum_probs=54.1
Q ss_pred hHHHHHHc---CCcEEEEEEEeCCcc-cchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 4 IADIVDYF---GWRNVIALYVDDDHG-RNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~f---gW~~V~ii~~dd~~g-~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
+.++++.+ |-+++-+|++..... .+..+.+.+.+++.|+.+.....+..+.+.+......+.+++.++++||..+.
T Consensus 14 l~~~l~~~~~~g~kr~livtd~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGG 93 (383)
T cd08186 14 IGEILKDLKSKGISKVLLVTGKSAYKKSGAWDKVEPALDEHGIEYVLYNKVTPNPTVDQVDEAAKLGREFGAQAVIAIGG 93 (383)
T ss_pred HHHHHHHhcccCCCEEEEEcCccHHhhcChHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 34566776 889999888544332 23468889999999987654434555556667888888888888999987754
No 176
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=76.80 E-value=15 Score=33.60 Aligned_cols=102 Identities=16% Similarity=0.104 Sum_probs=56.6
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCce-EEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSR-ILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~-vIvl~~~~ 80 (481)
.++.+..-|.++++++..... ......+.|.+.+++.|+.+..........+.+.....++++.++... ..|++.+.
T Consensus 108 a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d 187 (270)
T cd06296 108 ATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAALAEAGIPVDPALVREGDFSTESGFRAAAELLALPERPTAIFAGND 187 (270)
T ss_pred HHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHHHHcCCCCChHHheeCCCCHHHHHHHHHHHHhCCCCCcEEEEcCc
Confidence 344444459999999975332 334567888888888876543211111111222233344444332222 23445566
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
..+..+++.+.+.|...++.+-|++
T Consensus 188 ~~a~~~~~~l~~~g~~~p~~i~v~~ 212 (270)
T cd06296 188 LMALGVYEAARERGLRIPEDLSVVG 212 (270)
T ss_pred HHHHHHHHHHHHhCCCCCCceEEEE
Confidence 6777888888888876555554443
No 177
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=76.78 E-value=13 Score=34.12 Aligned_cols=92 Identities=10% Similarity=-0.022 Sum_probs=55.4
Q ss_pred HhHHHH-HHc-CCcEEEEEEEeC--CcccchHHHHHHHHHhcC-CEEEEEEecCCCCChhHHHHHHHHhccCCceEE-EE
Q 011629 3 AIADIV-DYF-GWRNVIALYVDD--DHGRNGIAALGDKLAEKR-CRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRIL-IL 76 (481)
Q Consensus 3 Ai~~ll-~~f-gW~~V~ii~~dd--~~g~~~~~~l~~~l~~~g-i~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vI-vl 76 (481)
.+++.| ++. |=+++++|..+. ..+....+.+++.+.+++ +.+... .....+.++..+.++++.++..++. |+
T Consensus 113 ~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~g~~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~ 190 (272)
T cd06300 113 QGAEWLVKELGGKGNVLVVRGLAGHPVDEDRYAGAKEVLKEYPGIKIVGE--VYGDWDQAVAQKAVADFLASNPDVDGIW 190 (272)
T ss_pred HHHHHHHHHcCCCceEEEEECCCCCcchHHHHHHHHHHHHHCCCcEEEee--cCCCCCHHHHHHHHHHHHHhCCCcCEEE
Confidence 344444 443 778999997432 345567788899998887 776532 2222233345566666655444333 33
Q ss_pred EeCcHHHHHHHHHHHHcCCcc
Q 011629 77 HTYDIWGLEVLNAAKHLRMME 97 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~~ 97 (481)
+.+.. +..+++.+.+.|+..
T Consensus 191 ~~~d~-A~g~~~al~~~g~~~ 210 (272)
T cd06300 191 TQGGD-AVGAVQAFEQAGRDI 210 (272)
T ss_pred ecCCC-cHHHHHHHHHcCCCC
Confidence 33444 888899998888643
No 178
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=76.63 E-value=3.6 Score=37.39 Aligned_cols=83 Identities=14% Similarity=0.047 Sum_probs=48.2
Q ss_pred HHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeec-cc--cccceeecccee-----ecceE
Q 011629 348 IDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAIT-TE--RTKMVDFTQPYI-----ESGLV 419 (481)
Q Consensus 348 ~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t-~~--r~~~~~fs~p~~-----~~~~~ 419 (481)
-.+...|++.+|.+ +++... .+...+..++.+|++|++..+-..- .. +....-+-.+.. .....
T Consensus 17 ~~l~~~L~~~~g~~--v~~~~~------~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ 88 (243)
T PF12974_consen 17 APLADYLSKQLGVP--VELVPA------DDYAEFIEALRSGEIDLAFMGPLPYVQARQRAGVEPLATPVGPDGSPSYRSV 88 (243)
T ss_dssp HHHHHHHHHHHTSE--EEEE--------SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHSSEEEEEEEEETTT-SCEEEE
T ss_pred HHHHHHHHHHhCCC--EEEEEc------CCHHHHHHHHHcCCccEEEECcHHHHHHhhcCcEEEEEEecccCCCcceeEE
Confidence 46788899999976 555442 4799999999999999997643211 11 112222222222 34667
Q ss_pred EEEecCCCCcCccccccCcc
Q 011629 420 VVAPIKKLNSNAWAFLNPFT 439 (481)
Q Consensus 420 ~~~~~~~~~~~~~~~l~pf~ 439 (481)
|++++++ .++..++|+.-+
T Consensus 89 ivv~~ds-~i~~l~dL~Gk~ 107 (243)
T PF12974_consen 89 IVVRADS-PITSLADLKGKR 107 (243)
T ss_dssp EEEETTS-S--SHHHHGGSE
T ss_pred EEEECCC-CCCChhhcCCCE
Confidence 8888876 466666665443
No 179
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription
Probab=76.60 E-value=27 Score=31.85 Aligned_cols=100 Identities=11% Similarity=0.035 Sum_probs=56.5
Q ss_pred hHHHHHHcCCcEEEEEEEeCC---cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCce-EEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD---HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSR-ILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~---~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~-vIvl~~~ 79 (481)
+++.|..-|.++++++....+ ......+.+.+.++++|+.+.... .....+.++....++++-+...+ -.|++++
T Consensus 103 ~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~ 181 (265)
T cd06291 103 AAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEVRIIE-IQENFDDAEKKEEIKELLEEYPDIDGIFASN 181 (265)
T ss_pred HHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHcCCCCChhe-eeccccchHHHHHHHHHHhCCCCCCEEEECC
Confidence 444455559999999974332 344567888999998887653221 11111111123344444322222 2344445
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
...+..++..+.+.|...++.+-++
T Consensus 182 d~~a~~~~~al~~~g~~vp~di~v~ 206 (265)
T cd06291 182 DLTAILVLKEAQQRGIRVPEDLQII 206 (265)
T ss_pred hHHHHHHHHHHHHcCCCCCcceEEe
Confidence 5667788888888887655544444
No 180
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=76.49 E-value=20 Score=32.73 Aligned_cols=101 Identities=9% Similarity=0.081 Sum_probs=58.5
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
+++.+...|-++|+++..... ......+.+.+.++++|+.+..........+.+.....++.+-+..++. |++++..
T Consensus 107 ~~~~l~~~g~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a-v~~~~d~ 185 (265)
T cd06299 107 AVSLLVALGHKKIGYISGPQDTSTGRERLEAFRQACASLGLEVNEDLVVLGGYSQESGYAGATKLLDQGATA-IIAGDSM 185 (265)
T ss_pred HHHHHHHcCCCcEEEEeCCCCcccHHHHHHHHHHHHHHCCCCCChHhEEecCcchHHHHHHHHHHHcCCCCE-EEEcCcH
Confidence 344555568899999965432 2345567888888888854322111111112222334455544333444 5556666
Q ss_pred HHHHHHHHHHHcCCccCCeEEEEe
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
.+..++..+.+.|+..++.+-|++
T Consensus 186 ~a~gv~~al~~~g~~vp~dv~v~g 209 (265)
T cd06299 186 MTIGAIRAIHDAGLVIGEDISLIG 209 (265)
T ss_pred HHHHHHHHHHHhCCCCCcceeEEE
Confidence 777888888888877666565554
No 181
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=76.35 E-value=13 Score=36.30 Aligned_cols=74 Identities=9% Similarity=0.007 Sum_probs=53.9
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.+.++.+| +++-+|++...+ ....+.+.+.+++.|+.+.+. .++.+.+.+.....++.+++.++++||..+..
T Consensus 21 l~~~l~~~g-~~~livtd~~~~-~~~~~~v~~~l~~~~~~~~~~-~~~~ep~~~~v~~~~~~~~~~~~d~IIavGGG 94 (366)
T PRK09423 21 LGEYLKPLG-KRALVIADEFVL-GIVGDRVEASLKEAGLTVVFE-VFNGECSDNEIDRLVAIAEENGCDVVIGIGGG 94 (366)
T ss_pred HHHHHHHcC-CEEEEEEChhHH-HHHHHHHHHHHHhCCCeEEEE-EeCCCCCHHHHHHHHHHHHhcCCCEEEEecCh
Confidence 456788889 998888843333 336778888899999887554 35555566677788888888889999987654
No 182
>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=76.14 E-value=39 Score=31.13 Aligned_cols=100 Identities=13% Similarity=0.044 Sum_probs=60.6
Q ss_pred hHHHHHHcCCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
+++.|...|-+++++|.... .......+.+++.++++|+..... .+....+.++-...++++.+. ..+ .|++.+
T Consensus 109 a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~-ai~~~~ 186 (269)
T cd06287 109 LLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHGMPPVVL-RVDEAGGEEAGYAACAQLLAQHPDLD-ALCVPV 186 (269)
T ss_pred HHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcCCCccee-EecCCCChHHHHHHHHHHHhCCCCCC-EEEEcC
Confidence 34445556999999997432 234456778889999988754321 122122222333445554332 234 455667
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++..+.+.|+..++-+=|++
T Consensus 187 d~~A~gvl~al~~~gl~vP~dvsvig 212 (269)
T cd06287 187 DAFAVGAVRAATELGRAVPDQLRVVT 212 (269)
T ss_pred cHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 77888999999999987776555543
No 183
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=75.75 E-value=50 Score=28.19 Aligned_cols=92 Identities=8% Similarity=-0.047 Sum_probs=56.1
Q ss_pred HHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhc--CCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHH
Q 011629 6 DIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEK--RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWG 83 (481)
Q Consensus 6 ~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~--gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~ 83 (481)
+.+..-++ +|.++-.+++ .++.+.+.+.+. |+.|+-.. +...+.++...+++.|+++++++|++......-
T Consensus 42 ~~~~~~~~-~ifllG~~~~----~~~~~~~~l~~~yP~l~ivg~~--~g~f~~~~~~~i~~~I~~~~pdiv~vglG~PkQ 114 (172)
T PF03808_consen 42 RRAEQRGK-RIFLLGGSEE----VLEKAAANLRRRYPGLRIVGYH--HGYFDEEEEEAIINRINASGPDIVFVGLGAPKQ 114 (172)
T ss_pred HHHHHcCC-eEEEEeCCHH----HHHHHHHHHHHHCCCeEEEEec--CCCCChhhHHHHHHHHHHcCCCEEEEECCCCHH
Confidence 33334445 6777775554 466677777766 56655432 222233466788999999999999988766555
Q ss_pred HHHHHHHHHcCCccCCeEEEEecc
Q 011629 84 LEVLNAAKHLRMMESGYVWIVTDW 107 (481)
Q Consensus 84 ~~il~~a~~~g~~~~~~~wI~~~~ 107 (481)
..++.+..+. + +..+||..+.
T Consensus 115 E~~~~~~~~~-l--~~~v~i~vG~ 135 (172)
T PF03808_consen 115 ERWIARHRQR-L--PAGVIIGVGG 135 (172)
T ss_pred HHHHHHHHHH-C--CCCEEEEECc
Confidence 5555554442 2 2237777654
No 184
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=75.48 E-value=39 Score=30.86 Aligned_cols=96 Identities=16% Similarity=0.078 Sum_probs=53.1
Q ss_pred HHHHHc-CCcEEEEEEEeCCc--ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHh-cc--CCceEEEEEeC
Q 011629 6 DIVDYF-GWRNVIALYVDDDH--GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTV-SS--MMSRILILHTY 79 (481)
Q Consensus 6 ~ll~~f-gW~~V~ii~~dd~~--g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i-~~--s~~~vIvl~~~ 79 (481)
.+++++ |=++|+++....++ +....+.+++.++++|..+..........+.++....++++ .+ ...+.|+ +++
T Consensus 117 ~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~-~~~ 195 (275)
T cd06317 117 AMCKALGGKGQIVVIAGQPGNGTAIERQKGFEDELAEVCPGVEVLDTQPADWDREKAQVAMEALITKFGDDIDGVY-AGD 195 (275)
T ss_pred HHHHHcCCCceEEEEecCCCCchHHHHHHHHHHHHHhhCCCCEEEeccCCCCCHHHHHHHHHHHHHhCCCCccEEE-ECC
Confidence 344444 67899999864433 34556788899988875433322222122222222334433 22 2345544 455
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
...+..++.++.+.|+. +.+-|.
T Consensus 196 d~~a~g~~~~l~~~g~~--~dv~v~ 218 (275)
T cd06317 196 DNMARGALNAAKEAGLA--GGIVIV 218 (275)
T ss_pred CcHHHHHHHHHHhcCCc--CCcEEE
Confidence 56677889999888865 334444
No 185
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=75.09 E-value=10 Score=34.58 Aligned_cols=78 Identities=12% Similarity=0.014 Sum_probs=56.1
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC-cHHHHHHHHHHHH
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY-DIWGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~-~~~~~~il~~a~~ 92 (481)
|++|.. ++.|.....+.+++.+++.|+.+... .+...+.+.....++++.+.+++.||+... ...+..++.++.+
T Consensus 1 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~--~~~~~d~~~q~~~i~~~i~~~~d~Iiv~~~~~~~~~~~l~~~~~ 78 (257)
T PF13407_consen 1 IGVIVPSMDNPFWQQVIKGAKAAAKELGYEVEIV--FDAQNDPEEQIEQIEQAISQGVDGIIVSPVDPDSLAPFLEKAKA 78 (257)
T ss_dssp EEEEESSSSSHHHHHHHHHHHHHHHHHTCEEEEE--EESTTTHHHHHHHHHHHHHTTESEEEEESSSTTTTHHHHHHHHH
T ss_pred cEEEeCCCCCHHHHHHHHHHHHHHHHcCCEEEEe--CCCCCCHHHHHHHHHHHHHhcCCEEEecCCCHHHHHHHHHHHhh
Confidence 455553 34567778889999999999998875 233334445567777777788999888754 4567788999988
Q ss_pred cCC
Q 011629 93 LRM 95 (481)
Q Consensus 93 ~g~ 95 (481)
.|+
T Consensus 79 ~gI 81 (257)
T PF13407_consen 79 AGI 81 (257)
T ss_dssp TTS
T ss_pred cCc
Confidence 764
No 186
>cd08183 Fe-ADH2 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria.
Probab=75.00 E-value=15 Score=35.96 Aligned_cols=72 Identities=14% Similarity=0.119 Sum_probs=52.2
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+-++++.++ +++.||++.... ..+.+.+.|++.|+.+.... +..+.+.+...+.++..++.++++||..+..
T Consensus 14 l~~~l~~~~-~r~livtd~~~~---~~~~v~~~L~~~g~~~~~~~-~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 85 (374)
T cd08183 14 LPALAAELG-RRVLLVTGASSL---RAAWLIEALRAAGIEVTHVV-VAGEPSVELVDAAVAEARNAGCDVVIAIGGG 85 (374)
T ss_pred HHHHHHHcC-CcEEEEECCchH---HHHHHHHHHHHcCCeEEEec-CCCCcCHHHHHHHHHHHHhcCCCEEEEecCc
Confidence 445677776 888888844332 67778888999998765433 4445566678888888998899999987654
No 187
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a
Probab=74.85 E-value=23 Score=32.38 Aligned_cols=103 Identities=11% Similarity=0.055 Sum_probs=58.5
Q ss_pred HhHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCce-EEEEEeC
Q 011629 3 AIADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSR-ILILHTY 79 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~-vIvl~~~ 79 (481)
.+++.|..-|-++++++..... ......+.+.+.++++|+.+..........+.+.....++++.+...+ -.|++++
T Consensus 107 ~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~ 186 (269)
T cd06275 107 LATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPVNPGWIVEGDFECEGGYEAMQRLLAQPKRPTAVFCGN 186 (269)
T ss_pred HHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCCCHHHhccCCCChHHHHHHHHHHHcCCCCCcEEEECC
Confidence 3445555568999999974322 234556778888888887643211111122222333445554333222 2344555
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++..+.+.|...++.+-+++
T Consensus 187 d~~a~g~~~~l~~~g~~vp~di~vvg 212 (269)
T cd06275 187 DLMAMGALCAAQEAGLRVPQDLSIIG 212 (269)
T ss_pred hHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 66667888888888876665555554
No 188
>cd08550 GlyDH-like Glycerol_dehydrogenase-like. Families of proteins related to glycerol dehydrogenases. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site. Some subfamilies have not been characterized till now.
Probab=74.84 E-value=13 Score=35.89 Aligned_cols=74 Identities=16% Similarity=0.152 Sum_probs=51.2
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.+| +++.+|++...+ ....+.+.+.+++.|+.+.... +..+.+.+...+.++..++.+++.||..+..
T Consensus 14 l~~~~~~~g-~~~liv~~~~~~-~~~~~~v~~~l~~~~i~~~~~~-~~~~p~~~~v~~~~~~~~~~~~d~IIavGGG 87 (349)
T cd08550 14 IAAILSTFG-SKVAVVGGKTVL-KKSRPRFEAALAKSIIVVDVIV-FGGECSTEEVVKALCGAEEQEADVIIGVGGG 87 (349)
T ss_pred HHHHHHHcC-CeEEEEEChHHH-HHHHHHHHHHHHhcCCeeEEEE-cCCCCCHHHHHHHHHHHHhcCCCEEEEecCc
Confidence 456788889 888777743332 3456788888988888654433 4444455567777888888889999877653
No 189
>PRK09526 lacI lac repressor; Reviewed
Probab=74.42 E-value=45 Score=31.85 Aligned_cols=99 Identities=15% Similarity=0.076 Sum_probs=59.3
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
+++.|...|-++++++..... ......+.+++.+++.|+.+... +....+.+.-...+.++.+. ..+ .|++++
T Consensus 172 a~~~L~~~G~~~I~~l~g~~~~~~~~~R~~Gf~~al~~~gi~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~-ai~~~~ 248 (342)
T PRK09526 172 GVEHLVELGHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQPIAV--REGDWSAMSGYQQTLQMLREGPVPS-AILVAN 248 (342)
T ss_pred HHHHHHHCCCCeEEEEeCCCccccHHHHHHHHHHHHHHcCCCcceE--EeCCCchHHHHHHHHHHhcCCCCCc-EEEEcC
Confidence 445555569999999975432 23455778899999999864322 11121222222334444332 233 455566
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++..+.+.|+..++-+-|++
T Consensus 249 d~~A~g~~~al~~~g~~vP~disvig 274 (342)
T PRK09526 249 DQMALGVLRALHESGLRVPGQISVIG 274 (342)
T ss_pred cHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 67788899999999987766554443
No 190
>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=73.79 E-value=20 Score=30.27 Aligned_cols=70 Identities=20% Similarity=0.189 Sum_probs=47.9
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++.+.. ++...+...+.+|++|+++.. .+.....+. ..+.......+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~---~~~~~~~~~-~~~l~~~~~~~v~~~ 80 (193)
T cd08442 13 VRLPPLLAAYHARYP-KVDLSLST-------GTTGALIQAVLEGRLDGAFVA---GPVEHPRLE-QEPVFQEELVLVSPK 80 (193)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCccEEEEe---CCCCCCCcE-EEEeecCcEEEEecC
Confidence 344688888888763 24566665 457789999999999998753 233333343 357778888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 81 ~~ 82 (193)
T cd08442 81 GH 82 (193)
T ss_pred CC
Confidence 54
No 191
>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=73.61 E-value=26 Score=29.64 Aligned_cols=70 Identities=13% Similarity=0.072 Sum_probs=48.4
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++.++.+... ++++.+.. +...++...|.+|++|+++... +.....+ .+.|+......+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~-~~~~l~~~~~~~v~~~ 80 (196)
T cd08415 13 SLLPRAIARFRARHP-DVRISLHT-------LSSSTVVEAVLSGQADLGLASL---PLDHPGL-ESEPLASGRAVCVLPP 80 (196)
T ss_pred cccHHHHHHHHHHCC-CcEEEEEe-------cchHHHHHHHHcCCccEEEEeC---CCCCCcc-eeeeecccceEEEEcC
Confidence 445788888888762 35566665 4577899999999999997532 2222334 3477888888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
..
T Consensus 81 ~~ 82 (196)
T cd08415 81 GH 82 (196)
T ss_pred CC
Confidence 43
No 192
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=73.12 E-value=39 Score=31.29 Aligned_cols=93 Identities=18% Similarity=0.166 Sum_probs=53.1
Q ss_pred hHHHHHHcCC--cEEEEEEE-eC--CcccchHHHHHHHHHhcCCEEEEEEecCCC-CChhHHHHHHHHhccC--CceE-E
Q 011629 4 IADIVDYFGW--RNVIALYV-DD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPK-GSRNQIIDTLLTVSSM--MSRI-L 74 (481)
Q Consensus 4 i~~ll~~fgW--~~V~ii~~-dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~-~~~~~~~~~l~~i~~s--~~~v-I 74 (481)
+++.+..-|+ ..+++|.. .. .......+.+++.+++.|+........... .+.+.....++.+..+ ..+. +
T Consensus 118 l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~G~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 197 (289)
T cd01540 118 IADEMKKRGWDPKEVGALRITYDELDTAKPRTDGALEALKAPGFPEANIFQAPQKTTDTEGAFDAAASTLTKNPNVKNWI 197 (289)
T ss_pred HHHHHHhhcCCCcceEEEEecCCCCcchhhHHHHHHHHHhcCCCCcceEecccccCcchhhHHHHHHHHHHhCCCcCeeE
Confidence 3334445688 78888752 22 345667888899998888753222111111 1111222344444322 2343 5
Q ss_pred EEEeCcHHHHHHHHHHHHcCCc
Q 011629 75 ILHTYDIWGLEVLNAAKHLRMM 96 (481)
Q Consensus 75 vl~~~~~~~~~il~~a~~~g~~ 96 (481)
|++.+...+..++..+.+.|..
T Consensus 198 i~~~~d~~a~g~~~al~~~g~~ 219 (289)
T cd01540 198 IYGLNDETVLGAVRATEQSGIA 219 (289)
T ss_pred EEeCCcHHHHHHHHHHHHcCCC
Confidence 6666667788888888888876
No 193
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=72.44 E-value=38 Score=34.14 Aligned_cols=46 Identities=17% Similarity=0.094 Sum_probs=35.6
Q ss_pred HHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEec
Q 011629 5 ADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPL 50 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~ 50 (481)
++-+-.=|-+...++...+++|++..+.|.++..+.|...+....|
T Consensus 375 A~~l~~qG~R~plvlvPr~~lG~Rv~~AF~~~Wq~~gg~~v~~~~f 420 (604)
T COG3107 375 ANHLWDQGKRNPLVLVPRNDLGDRVANAFNQEWQKLGGGTVLQQKF 420 (604)
T ss_pred HHHHHHccccCceEEecchHHHHHHHHHHHHHHHHhcCCchhHhhc
Confidence 3444455888899999999999999999999999988744433333
No 194
>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=72.43 E-value=22 Score=30.55 Aligned_cols=84 Identities=18% Similarity=0.187 Sum_probs=58.5
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.++|++|+.. .+. ..+-.+++..+.++.. ++++.+.. ++...+...|.+|++|+++..
T Consensus 5 ~~~l~Ig~~~--~~~------------~~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~ 62 (209)
T PF03466_consen 5 RGTLRIGASP--SFA------------SSLLPPLLAEFRERHP-NIRIEIRE-------GDSDELIEALRSGELDLAITF 62 (209)
T ss_dssp EEEEEEEEEH--HHH------------HHTHHHHHHHHHHHST-TEEEEEEE-------ESHHHHHHHHHTTSSSEEEES
T ss_pred ceEEEEEEEh--HHH------------HHHHHHHHHHHHHHCC-CcEEEEEe-------ccchhhhHHHhcccccEEEEE
Confidence 3578888864 211 1234678888887774 35566665 457899999999999999654
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
. +.....+.+ .|+....+.+++++..
T Consensus 63 ~---~~~~~~~~~-~~l~~~~~~~~~~~~~ 88 (209)
T PF03466_consen 63 G---PPPPPGLES-EPLGEEPLVLVVSPDH 88 (209)
T ss_dssp S---SSSSTTEEE-EEEEEEEEEEEEETTS
T ss_pred e---ecccccccc-ccccceeeeeeeeccc
Confidence 3 334455544 7888999999998765
No 195
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=71.98 E-value=25 Score=32.06 Aligned_cols=100 Identities=13% Similarity=0.153 Sum_probs=53.7
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
+++.+..-|=++|+++..+.. ......+.+.+.+++.|+.+.....+....+.+.....++++-+. ..++ |++.+
T Consensus 108 ~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-i~~~~ 186 (268)
T cd06289 108 ATEHLISLGHRRIAFIGGLEDSSTRRERLAGYRAALAEAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTA-IVCFN 186 (268)
T ss_pred HHHHHHHCCCCCEEEecCCccccchHHHHHHHHHHHHHcCCCCCchhEEecCcchhhHHHHHHHHHcCCCCCCE-EEEcC
Confidence 344444458889998874332 345567888888888875322111111111222223334443322 2344 33445
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
...+..+++.+.+.|+..++.+-|+
T Consensus 187 ~~~a~~~~~al~~~g~~~p~di~ii 211 (268)
T cd06289 187 DLVAFGAMSGLRRAGLTPGRDIAVV 211 (268)
T ss_pred cHHHHHHHHHHHHcCCCCCcceEEE
Confidence 5567778888888887655444443
No 196
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=71.93 E-value=24 Score=32.26 Aligned_cols=77 Identities=9% Similarity=-0.017 Sum_probs=51.0
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC-cHHHHHHHHHHHH
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY-DIWGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~-~~~~~~il~~a~~ 92 (481)
|+++.. ++.|.....+.+++.+++.|+++.... ...+.+.....++.+...+.+.||+... ......++..+.+
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~~~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~~~i~~~~~ 78 (273)
T cd06305 2 IAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYD---AGGDDAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRALD 78 (273)
T ss_pred eEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEEC---CCCCHHHHHHHHHHHHHcCCCEEEEecCChhhhHHHHHHHHH
Confidence 677765 455666788899999999999987642 2223333445666666668898888753 3334566777777
Q ss_pred cCC
Q 011629 93 LRM 95 (481)
Q Consensus 93 ~g~ 95 (481)
.|+
T Consensus 79 ~~i 81 (273)
T cd06305 79 AGI 81 (273)
T ss_pred cCC
Confidence 653
No 197
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=71.72 E-value=28 Score=31.68 Aligned_cols=98 Identities=10% Similarity=0.120 Sum_probs=59.0
Q ss_pred hHHHHHHcCCcEEEEEEEeC-CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHh-ccC-CceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDD-DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTV-SSM-MSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd-~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i-~~s-~~~vIvl~~~~ 80 (481)
+++.|...|-++++++.... .......+.+++.+.++|+...... +. .+.++....++++ +.. .+. .|++.+.
T Consensus 106 a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~-~~--~~~~~~~~~~~~~l~~~~~~~-ai~~~~d 181 (263)
T cd06280 106 LVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAPDARF-VA--PTAEAAEAALAAWLAAPERPE-ALVASNG 181 (263)
T ss_pred HHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHHcCCCCChhh-cc--cCHHHHHHHHHHHhcCCCCCc-EEEECCc
Confidence 45556666999999987532 2234557788889988887643211 11 1222223334443 332 233 3555667
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
..+..++..+.+.|+..++-+.|.+
T Consensus 182 ~~a~g~~~~l~~~g~~~p~di~iig 206 (263)
T cd06280 182 LLLLGALRAVRAAGLRIPQDLALAG 206 (263)
T ss_pred HHHHHHHHHHHHcCCCCCCcEEEEE
Confidence 7788899999999887666665554
No 198
>PRK07377 hypothetical protein; Provisional
Probab=71.71 E-value=12 Score=31.89 Aligned_cols=63 Identities=21% Similarity=0.255 Sum_probs=46.0
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
..++|+|+.. .. ++ .+...+-.++.++.+.+..+.+ ++++++ .+-..+..++.+|++|++++.
T Consensus 74 s~~~Rlgv~~--~~------~~-~~~~~~~l~~~l~~~~~~y~~r--lElv~y------~~~~~l~~aL~~~eVh~~c~~ 136 (184)
T PRK07377 74 SLVMRLGVLE--IE------TE-TSSVFDQLIDQLRTILDKYHLR--LELVVY------PDLQALEQALRDKEVHAICLE 136 (184)
T ss_pred ccEEEEEEEe--cc------cc-ccccHHHHHHHHHHHHHHhCce--eeEEec------CCHHHHHHHHhcCCccEEecC
Confidence 3578999875 21 11 2334455788899999999966 666663 578999999999999988663
No 199
>KOG3857 consensus Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=71.71 E-value=22 Score=33.60 Aligned_cols=75 Identities=9% Similarity=0.035 Sum_probs=60.5
Q ss_pred HHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 5 ADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
.+=++..|-+++.+|++.+-.-....+..++.|+++||.++.......+.+..++...++-.|+...+.+|..+.
T Consensus 62 g~dikn~gaKk~llvTDkni~~~~~~~~a~~~L~~~~I~~~vyD~v~~ePtv~s~~~alefak~~~fDs~vaiGG 136 (465)
T KOG3857|consen 62 GDDIKNLGAKKTLLVTDKNIAKLGLVKVAQDSLEENGINVEVYDKVQPEPTVGSVTAALEFAKKKNFDSFVAIGG 136 (465)
T ss_pred HHHHHhcCccceEEeeCCChhhcccHHHHHHHHHHcCCceEEecCccCCCchhhHHHHHHHHHhcccceEEEEcC
Confidence 345788999999999977766667788899999999999988777777777677888888888877777776654
No 200
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=71.33 E-value=55 Score=29.69 Aligned_cols=100 Identities=15% Similarity=0.068 Sum_probs=58.9
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCc--ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCC-ceEEEEEeC
Q 011629 3 AIADIVDYFGWRNVIALYVDDDH--GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMM-SRILILHTY 79 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~--g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~-~~vIvl~~~ 79 (481)
.+++.+...|-++|+++..+... .....+.+.+.+++.|+.+... +....+.+.....++++.++. .+ .|++++
T Consensus 106 ~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~-ai~~~~ 182 (264)
T cd01574 106 LATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIAPPPV--LEGDWSAESGYRAGRELLREGDPT-AVFAAN 182 (264)
T ss_pred HHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHHHHCCCCccee--eecCCCHHHHHHHHHHHHhCCCCc-EEEEcC
Confidence 44555556788999999754332 2345677888888888765432 211222223334444444332 33 345556
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++..+.+.|...++.+-|++
T Consensus 183 d~~a~g~~~~~~~~g~~ip~~i~ii~ 208 (264)
T cd01574 183 DQMALGVLRALHELGLRVPDDVSVVG 208 (264)
T ss_pred cHHHHHHHHHHHHcCCCCccceEEec
Confidence 66777888888888865555555554
No 201
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=71.15 E-value=50 Score=30.01 Aligned_cols=101 Identities=13% Similarity=0.027 Sum_probs=58.5
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHh-ccC--CceEEEEEe
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTV-SSM--MSRILILHT 78 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i-~~s--~~~vIvl~~ 78 (481)
+++.+..-|-++++++..... ......+.+++.++++|+.+..........+.+.....++++ ++. ..+. |+++
T Consensus 107 ~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~a-i~~~ 185 (264)
T cd06274 107 LTRELLAAPPEEVLFLGGLPELSPSRERLAGFRQALADAGLPVQPDWIYAEGYSPESGYQLMAELLARLGRLPRA-LFTT 185 (264)
T ss_pred HHHHHHHCCCCcEEEEeCCCcccchHHHHHHHHHHHHHcCCCCCcceeecCCCChHHHHHHHHHHHccCCCCCcE-EEEc
Confidence 344444568899999975433 344567888889998886432221111122222233444444 332 2444 4455
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
+...+..++..+.+.|+..++.+-|++
T Consensus 186 ~d~~A~g~~~al~~~g~~ip~dv~v~g 212 (264)
T cd06274 186 SYTLLEGVLRFLRERPGLAPSDLRIAT 212 (264)
T ss_pred ChHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 666777888888888876666666554
No 202
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=70.86 E-value=48 Score=30.07 Aligned_cols=102 Identities=16% Similarity=0.124 Sum_probs=57.3
Q ss_pred hHHHHHHcCCcEEEEEEEeCC-c--ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD-H--GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~-~--g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl~~~ 79 (481)
+++.|..-|-++++++..... . .....+.+++.++++|+............+.......++++.++..++ .|++.+
T Consensus 107 ~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~ 186 (267)
T cd06283 107 AVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALAEHGIGVNEELIEIDDEDADELDERLRQLLNKPKKKTAIFAAN 186 (267)
T ss_pred HHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHHHcCCCCCcceeEecccchHHHHHHHHHHHcCCCCCCEEEEcC
Confidence 445555568899999975432 1 124567788888888753222111111112223445555654443222 344455
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++..+.+.|+..++.+-|.+
T Consensus 187 d~~a~g~~~~l~~~g~~vp~di~v~g 212 (267)
T cd06283 187 GLILLEVLKALKELGIRIPEDVGLIG 212 (267)
T ss_pred cHHHHHHHHHHHHcCCCCccceEEEE
Confidence 56677888888888876665555544
No 203
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=70.80 E-value=27 Score=29.61 Aligned_cols=70 Identities=16% Similarity=0.133 Sum_probs=48.4
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++++.. ++...+...|.+|++|+++.. .+.....+. +.|+......+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~---~~~~~~~~~-~~~l~~~~~~~~~~~ 80 (198)
T cd08412 13 YYLPGLLRRFREAYP-GVEVRVVE-------GNQEELEEGLRSGELDLALTY---DLDLPEDIA-FEPLARLPPYVWLPA 80 (198)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEc---CCCCCcccc-eeeeeccceEEEecC
Confidence 445688888887763 34566665 457788999999999998753 222233443 378888888888866
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 81 ~~ 82 (198)
T cd08412 81 DH 82 (198)
T ss_pred CC
Confidence 54
No 204
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=70.69 E-value=7.2 Score=35.69 Aligned_cols=97 Identities=16% Similarity=0.114 Sum_probs=57.9
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
..+|+||....+.+.|+ .+-.-+.+.++.|+++++... .++..++.+|.+|++|++..
T Consensus 5 ~~~l~ig~~~~~~~~p~-------------~~a~~~g~f~~~G~~ve~~~~--------~~g~~~~~al~~G~iD~a~~- 62 (252)
T PF13379_consen 5 PTTLRIGYLPGPDYAPL-------------YVAQEKGLFEKEGLDVEWVQF--------ASGADILEALAAGEIDIAFV- 62 (252)
T ss_dssp ESEEEEEETSSGGGHHH-------------HHHHHTTHHHHTTSCEEEEEE--------SSHHHHHHHHHCTSSSEEEE-
T ss_pred CcEEEEEeecchHHHHH-------------HHHHHcChHHHcCCEEEEEEc--------CCHHHHHHHHHcCCCCEEEe-
Confidence 45789888742222222 122224567777977554444 47999999999999999866
Q ss_pred eee---cccccc-----ceeeccceeecceEEEEecCC---CCcCccccc
Q 011629 397 FAI---TTERTK-----MVDFTQPYIESGLVVVAPIKK---LNSNAWAFL 435 (481)
Q Consensus 397 ~~~---t~~r~~-----~~~fs~p~~~~~~~~~~~~~~---~~~~~~~~l 435 (481)
... -..+-. .+-.-......+..++++++- .....+.+|
T Consensus 63 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~lvv~~~~~~~~~~~~~~dl 112 (252)
T PF13379_consen 63 LAPALIAIAKGAGGPDVDIVVLAGLSQNGNALVVRNDLKDASDIKSLADL 112 (252)
T ss_dssp CTHHHHHHHTTTTT----EEEEEECSBSSEEEEECGGGTTCSTTCCGHHH
T ss_pred chHHHHHHHcCCCCcccceEEeeccCCCceEEEEcCccccCCCccCHHHH
Confidence 211 112222 222333456678888888751 346667777
No 205
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=70.18 E-value=35 Score=32.47 Aligned_cols=100 Identities=11% Similarity=0.012 Sum_probs=56.3
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
+++-|...|.++++++..... ......+.+.+.++.+|+ +.....+....+.+.....++++.+. .++ .|++++
T Consensus 165 a~~~l~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~g~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-ai~~~~ 242 (327)
T PRK10339 165 IIDFYINQGVNRIGFIGGEDEPGKADIREVAFAEYGRLKQV-VREEDIWRGGFSSSSGYELAKQMLAREDYPK-ALFVAS 242 (327)
T ss_pred HHHHHHHCCCCeEEEeCCccccchhhHHHHHHHHHHHHcCC-CChhheeecCcChhHHHHHHHHHHhCCCCCC-EEEECC
Confidence 344445559999999964332 233456677788888876 11111111111112223344444332 233 466667
Q ss_pred cHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
...+..++..+.++|...++-+-|++
T Consensus 243 D~~A~g~~~al~~~g~~vP~di~vig 268 (327)
T PRK10339 243 DSIAIGVLRAIHERGLNIPQDISLIS 268 (327)
T ss_pred cHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 77888899999999987665554443
No 206
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=69.99 E-value=37 Score=30.73 Aligned_cols=99 Identities=13% Similarity=0.060 Sum_probs=58.0
Q ss_pred HhHHHHHHcCCcEEEEEEEe-C--CcccchHHHHHHHHHhcCC-EEEEEEecCCCCChhHHHHHHHHhccCC-ceEEEEE
Q 011629 3 AIADIVDYFGWRNVIALYVD-D--DHGRNGIAALGDKLAEKRC-RLSHKVPLSPKGSRNQIIDTLLTVSSMM-SRILILH 77 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~d-d--~~g~~~~~~l~~~l~~~gi-~v~~~~~~~~~~~~~~~~~~l~~i~~s~-~~vIvl~ 77 (481)
.+++.|..-|-++++++... + ..+....+.+++.+++.|. .+.. .....+.+.....+.++.+.. .+. |++
T Consensus 104 ~~~~~l~~~g~~~i~~v~~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~~-i~~ 179 (259)
T cd01542 104 ELGEYLAQQGHKNIAYLGVSESDIAVGILRKQGYLDALKEHGICPPNI---VETDFSYESAYEAAQELLEPQPPDA-IVC 179 (259)
T ss_pred HHHHHHHHcCCCcEEEEcCCcccchhHHHHHHHHHHHHHHcCCChHHe---eeccCchhhHHHHHHHHhcCCCCCE-EEE
Confidence 34555555688999998643 2 2234567888899988887 2111 111112223334444444333 343 444
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
.+...+..++..+.+.|+..++.+.+++
T Consensus 180 ~~d~~a~g~~~~l~~~g~~vp~di~v~g 207 (259)
T cd01542 180 ATDTIALGAMKYLQELGRRIPEDISVAG 207 (259)
T ss_pred cCcHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 5556777888888888887666666664
No 207
>cd08178 AAD_C C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD). Alcohol dehydrogenase domain located on the C-terminal of a bifunctional two-domain protein. The N-terminal of the protein contains an acetaldehyde-CoA dehydrogenase domain. This protein is involved in pyruvate metabolism. Pyruvate is converted to acetyl-CoA and formate by pyruvate formate-lysase (PFL). Under anaerobic condition, acetyl-CoA is reduced to acetaldehyde and ethanol by this two-domain protein. Acetyl-CoA is first converted into an enzyme-bound thiohemiacetal by the N-terminal acetaldehyde dehydrogenase domain. The enzyme-bound thiohemiacetal is subsequently reduced by the C-terminal NAD+-dependent alcohol dehydrogenase domain. In E. coli, this protein is called AdhE and was shown pyruvate formate-lysase (PFL) deactivase activity, which is involved in the inactivation of PFL, a key enzyme in anaerobic metabolism. In Escherichi
Probab=69.13 E-value=22 Score=35.21 Aligned_cols=79 Identities=10% Similarity=-0.011 Sum_probs=54.6
Q ss_pred HcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc--HHHHHHH
Q 011629 10 YFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD--IWGLEVL 87 (481)
Q Consensus 10 ~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~--~~~~~il 87 (481)
..+-+++.+|++.........+.+.+.|++.|+.+.....+..+.+.+...+.+..+++.++++||..+.. -++..++
T Consensus 18 ~~~~~k~liVtd~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS~iD~AK~i 97 (398)
T cd08178 18 LKGKKRAFIVTDRFMVKLGYVDKVIDVLKRRGVETEVFSDVEPDPSLETVRKGLELMNSFKPDTIIALGGGSPMDAAKIM 97 (398)
T ss_pred hcCCCeEEEEcChhHHhCccHHHHHHHHHHCCCeEEEecCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHHH
Confidence 34668888887433333346788899999999987654455556666677888888888899999977543 3444444
Q ss_pred H
Q 011629 88 N 88 (481)
Q Consensus 88 ~ 88 (481)
.
T Consensus 98 A 98 (398)
T cd08178 98 W 98 (398)
T ss_pred H
Confidence 3
No 208
>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=68.99 E-value=26 Score=29.26 Aligned_cols=69 Identities=23% Similarity=0.299 Sum_probs=47.1
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.++++.+.++.. ++++++.. .+...++..|.+|++|+++..... ....+.+ .++......++++++
T Consensus 14 ~l~~~i~~~~~~~p-~i~i~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~~-~~l~~~~~~~~~~~~ 81 (197)
T cd05466 14 LLPPLLAAFRQRYP-GVELSLVE-------GGSSELLEALLEGELDLAIVALPV---DDPGLES-EPLFEEPLVLVVPPD 81 (197)
T ss_pred HhHHHHHHHHHHCC-CCEEEEEE-------CChHHHHHHHHcCCceEEEEcCCC---CCCcceE-eeeeccceEEEecCC
Confidence 34567777776653 35566665 456789999999999999764332 3334443 577788888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 82 ~ 82 (197)
T cd05466 82 H 82 (197)
T ss_pred C
Confidence 4
No 209
>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=68.26 E-value=29 Score=29.75 Aligned_cols=73 Identities=19% Similarity=0.195 Sum_probs=48.3
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++.++.++.. ++++.+.. .+...++..|.+|++|+++........-...+.+ .+.......+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~ 83 (202)
T cd08468 13 AVMPRLMARLEELAP-SVRLNLVH-------AEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEE-RDWWEDTYVVIASR 83 (202)
T ss_pred HHhHHHHHHHHhhCC-CCEEEEEE-------CChHhHHHHHHCCCccEEEecccccccCCCCEEE-EEEecCcEEEEEeC
Confidence 345678888888762 35576665 5678999999999999987633211101233444 57777778888766
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 84 ~h 85 (202)
T cd08468 84 DH 85 (202)
T ss_pred CC
Confidence 54
No 210
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=68.14 E-value=77 Score=28.99 Aligned_cols=88 Identities=11% Similarity=-0.050 Sum_probs=48.2
Q ss_pred HHHHcCC--cEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc--CCceEEEEEeCc
Q 011629 7 IVDYFGW--RNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS--MMSRILILHTYD 80 (481)
Q Consensus 7 ll~~fgW--~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~--s~~~vIvl~~~~ 80 (481)
|++.+|. ++++++..... ......+.+++.+++++..+..........+.++....++++.+ ...+.|+...+
T Consensus 117 l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d- 195 (275)
T cd06307 117 IGRFLGRRPGKVAVLAGSHRFRGHEEREMGFRSVLREEFPGLRVLETLEGLDDPARAYEATRKLLARHPDLVGIYNAGG- 195 (275)
T ss_pred HHHHhCCCCCeEEEEecCCCCcchHHHHHHHHHHHHhhCCCcEEEeeccCCCChHHHHHHHHHHHHhCCCceEEEECCC-
Confidence 4444465 58998875432 23455778888988877654433222222222233344444432 23455544443
Q ss_pred HHHHHHHHHHHHcCCc
Q 011629 81 IWGLEVLNAAKHLRMM 96 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~ 96 (481)
. +..++..+.+.|+.
T Consensus 196 ~-~~g~~~al~~~g~~ 210 (275)
T cd06307 196 G-NRGVIRALREAGRA 210 (275)
T ss_pred C-hHHHHHHHHHcCCC
Confidence 3 46788888888863
No 211
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=67.67 E-value=73 Score=29.36 Aligned_cols=84 Identities=13% Similarity=0.067 Sum_probs=50.4
Q ss_pred cCCcEEEEEEEeC-CcccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEEEeCcHHHHHHH
Q 011629 11 FGWRNVIALYVDD-DHGRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LILHTYDIWGLEVL 87 (481)
Q Consensus 11 fgW~~V~ii~~dd-~~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl~~~~~~~~~il 87 (481)
-|-++++++.... .......+.+++.++++ |+.+... .....+.++....++++-+...++ .|++++...+..++
T Consensus 129 ~g~~~i~~l~~~~~~~~~~R~~gf~~al~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~nd~~A~g~l 206 (280)
T cd06303 129 PNHARYAMLYFSPGYISTARGDTFIDCVHARNNWTLTSE--FYTDATRQKAYQATSDILSNNPDVDFIYACSTDIALGAS 206 (280)
T ss_pred CCCcEEEEEECCCCcchhHHHHHHHHHHHhCCCceEEEe--ecCCCCHHHHHHHHHHHHHhCCCCcEEEECCcHHHHHHH
Confidence 6899999997543 22345577888889887 7654322 222222223334444443332222 35566667777899
Q ss_pred HHHHHcCCc
Q 011629 88 NAAKHLRMM 96 (481)
Q Consensus 88 ~~a~~~g~~ 96 (481)
..+.+.|+.
T Consensus 207 ~al~~~G~~ 215 (280)
T cd06303 207 DALKELGRE 215 (280)
T ss_pred HHHHHcCCC
Confidence 999998874
No 212
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=67.03 E-value=61 Score=29.39 Aligned_cols=90 Identities=12% Similarity=0.082 Sum_probs=51.2
Q ss_pred hHHHHHHc--CCcEEEEEEEeC--CcccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEEE
Q 011629 4 IADIVDYF--GWRNVIALYVDD--DHGRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LILH 77 (481)
Q Consensus 4 i~~ll~~f--gW~~V~ii~~dd--~~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl~ 77 (481)
+++.|... |-++++++..+. ..+....+.+++.++++ |+.+.... ....+.++....+.++.+...+. .|++
T Consensus 110 ~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~ 187 (268)
T cd06323 110 AAEYLVKLLGGKGKVVELQGIPGASAARERGKGFHEVVDKYPGLKVVASQ--PADFDRAKGLNVMENILQAHPDIKGVFA 187 (268)
T ss_pred HHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHHHHhCCCcEEEecc--cCCCCHHHHHHHHHHHHHHCCCcCEEEE
Confidence 44444444 779999998643 34556678888888884 77654221 11122223333444443322322 3444
Q ss_pred eCcHHHHHHHHHHHHcCC
Q 011629 78 TYDIWGLEVLNAAKHLRM 95 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~ 95 (481)
.+...+..++.++.+.|.
T Consensus 188 ~~d~~a~~~~~~l~~~g~ 205 (268)
T cd06323 188 QNDEMALGAIEALKAAGK 205 (268)
T ss_pred cCCchHHHHHHHHHHcCC
Confidence 555666678888888876
No 213
>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=66.70 E-value=28 Score=29.50 Aligned_cols=68 Identities=24% Similarity=0.277 Sum_probs=47.9
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-.+++..+.++.. ++++++.. ++...++..|.+|++|+++.. .+.....+.+ .+.....+.++++++.
T Consensus 15 l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~---~~~~~~~~~~-~~l~~~~~~~v~~~~~ 82 (198)
T cd08421 15 LPEDLASFLAAHP-DVRIDLEE-------RLSADIVRAVAEGRADLGIVA---GNVDAAGLET-RPYRTDRLVVVVPRDH 82 (198)
T ss_pred hHHHHHHHHHHCC-CceEEEEe-------cCcHHHHHHHhcCCceEEEEe---cCCCCCCcEE-EEeecCcEEEEeCCCC
Confidence 3578888887762 35566665 457789999999999998753 2333444544 6888888888887654
No 214
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=66.36 E-value=40 Score=31.40 Aligned_cols=83 Identities=12% Similarity=0.201 Sum_probs=56.5
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF 397 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 397 (481)
++++|++.. .. ...+-.+++..+.++.. ++.+.+.. .+...++..|.+|++|+++..
T Consensus 91 ~~i~I~~~~--~~------------~~~~l~~~l~~~~~~~p-~~~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~- 147 (296)
T PRK11242 91 GSLRLAMTP--TF------------TAYLIGPLIDAFHARYP-GITLTIRE-------MSQERIEALLADDELDVGIAF- 147 (296)
T ss_pred eEEEEEecc--ch------------hhhhhHHHHHHHHHHCC-CCEEEEEe-------CCHHHHHHHHHCCCCcEEEEe-
Confidence 578888863 11 12345678888888753 45566665 456788999999999999753
Q ss_pred eeccccccceeeccceeecceEEEEecCC
Q 011629 398 AITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 398 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
.+.+.+.+. +.++....+.++++++.
T Consensus 148 --~~~~~~~l~-~~~l~~~~~~~~~~~~~ 173 (296)
T PRK11242 148 --APVHSPEIE-AQPLFTETLALVVGRHH 173 (296)
T ss_pred --cCCCCccee-EEEeeeccEEEEEcCCC
Confidence 233334443 47888888888887654
No 215
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=65.78 E-value=55 Score=30.25 Aligned_cols=102 Identities=18% Similarity=0.120 Sum_probs=58.2
Q ss_pred HhHHHHHHcCCcEEEEEEEeC-------------------CcccchHHHHHHHHHhcCCEEEEEEecCC-CCChhHHHHH
Q 011629 3 AIADIVDYFGWRNVIALYVDD-------------------DHGRNGIAALGDKLAEKRCRLSHKVPLSP-KGSRNQIIDT 62 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd-------------------~~g~~~~~~l~~~l~~~gi~v~~~~~~~~-~~~~~~~~~~ 62 (481)
..++.|...|-++++++..+. .......+.+.+.++++|+.+.....+.. ..+.+.....
T Consensus 106 ~~~~~L~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (283)
T cd06279 106 EAARHLLDLGHRRIGILGLRLGRDRNTGRVTDERLASATFSVARERLEGYLEALEEAGIDISDVPIWEIPENDRASGEEA 185 (283)
T ss_pred HHHHHHHHcCCCcEEEecCcccccccccccccccccccccccHHHHHHHHHHHHHHcCCCCChheEEecCCCchHHHHHH
Confidence 345566667899999997532 12335577788899888865422111111 1122233445
Q ss_pred HHHhccCCceE-EEEEeCcHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 63 LLTVSSMMSRI-LILHTYDIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 63 l~~i~~s~~~v-Ivl~~~~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
++++-++..++ .|++++...+..+++.+.+.|+..++.+=|+
T Consensus 186 ~~~~l~~~~~~~ai~~~~d~~a~gv~~al~~~g~~ip~di~vi 228 (283)
T cd06279 186 ARELLDASPRPTAILCMSDVLALGALQVARELGLRVPEDLSVV 228 (283)
T ss_pred HHHHHcCCCCCcEEEECCcHHHHHHHHHHHHcCCCCCCceEEe
Confidence 55553332222 3445556677788888888887655544333
No 216
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=65.07 E-value=92 Score=29.47 Aligned_cols=97 Identities=10% Similarity=-0.055 Sum_probs=57.7
Q ss_pred HHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeCc
Q 011629 5 ADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTYD 80 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~~ 80 (481)
++-|...|-++|+++....+ .+....+.+.+.++++|+.+... .....+.++-...++++-+. .++. |++++.
T Consensus 171 ~~~L~~~G~r~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d 247 (328)
T PRK11303 171 AESLLKFPAESILLLGALPELSVSFEREQGFRQALKDDPREVHYL--YANSFEREAGAQLFEKWLETHPMPDA-LFTTSY 247 (328)
T ss_pred HHHHHHCCCCeEEEEeCccccccHHHHHHHHHHHHHHcCCCceEE--EeCCCChHHHHHHHHHHHcCCCCCCE-EEEcCc
Confidence 33344458899999975432 34556788899999998754322 11111222233444444332 2343 555666
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEE
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
..+..++.++.+.|+..++-+=|+
T Consensus 248 ~~A~g~~~al~~~g~~vP~disv~ 271 (328)
T PRK11303 248 TLLQGVLDVLLERPGELPSDLAIA 271 (328)
T ss_pred HHHHHHHHHHHHcCCCCCCceEEE
Confidence 677788888888887766555444
No 217
>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=64.54 E-value=41 Score=28.31 Aligned_cols=70 Identities=9% Similarity=0.016 Sum_probs=48.3
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++++.. ++...+...+.+|++|+++.. .+.....+.+ .+.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Di~i~~---~~~~~~~~~~-~~l~~~~~~~~~~~ 80 (197)
T cd08448 13 RGLPRILRAFRAEYP-GIEVALHE-------MSSAEQIEALLRGELDLGFVH---SRRLPAGLSA-RLLHREPFVCCLPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe-------CCHHHHHHHHHcCCcceEEEe---CCCCCcCceE-EEEecCcEEEEeeC
Confidence 344678888887762 35566665 468889999999999998752 2233334444 67888888888776
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
..
T Consensus 81 ~h 82 (197)
T cd08448 81 GH 82 (197)
T ss_pred CC
Confidence 53
No 218
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=64.27 E-value=70 Score=30.38 Aligned_cols=100 Identities=10% Similarity=-0.022 Sum_probs=58.6
Q ss_pred hHHHHHHcCCcEEEEEEEeCC-cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCC--ceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDD-HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMM--SRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~--~~vIvl~~~~ 80 (481)
+++-|...|-++++++....+ ......+.+++.+.++|+..... .+....+.+.-...++++.+.. .. .|++++.
T Consensus 171 a~~~L~~~Gh~~I~~i~~~~~~~~~~R~~Gf~~al~~~g~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~-ai~~~nD 248 (331)
T PRK14987 171 MTTAIIARGHRHIAYLGARLDERTIIKQKGYEQAMLDAGLVPYSV-MVEQSSSYSSGIELIRQARREYPQLD-GVFCTND 248 (331)
T ss_pred HHHHHHHCCCceEEEEcCCCcccHHHHHHHHHHHHHHcCCCccce-eecCCCChhhHHHHHHHHHhcCCCCC-EEEECCc
Confidence 344444569999999964322 23345678888999988732111 1111111112233445543332 33 4556677
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
..+..++..+.+.|+..|+-+-|++
T Consensus 249 ~~A~g~~~al~~~g~~vP~disvig 273 (331)
T PRK14987 249 DLAVGAAFECQRLGLKVPDDMAIAG 273 (331)
T ss_pred HHHHHHHHHHHHcCCCCCCccEEEe
Confidence 7888889999999988776666554
No 219
>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=64.26 E-value=42 Score=28.13 Aligned_cols=70 Identities=19% Similarity=0.292 Sum_probs=48.1
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.++++.+.++.. ++++++.. .+...+...|.+|++|+++.. .+.....+.+ .++......+++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~---~~~~~~~~~~-~~l~~~~~~~~~~~ 80 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRD-------VSAEQVIEAVRSGEVDFGIGS---EPEADPDLEF-EPLLRDPFVLVCPK 80 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEe-------CChHHHHHHHHcCCccEEEEe---CCCCCCCeeE-EEeecccEEEEecC
Confidence 445688888887763 35566665 457789999999999999753 2223333433 67788888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 81 ~~ 82 (197)
T cd08440 81 DH 82 (197)
T ss_pred CC
Confidence 54
No 220
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=63.75 E-value=39 Score=31.77 Aligned_cols=86 Identities=19% Similarity=0.189 Sum_probs=55.0
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF 397 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 397 (481)
+++++|+.. .. ...+-.+++..+.+... ++++.+.. .....+...|.+|++|+++..-
T Consensus 95 g~l~ig~~~--~~------------~~~~~~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 152 (305)
T CHL00180 95 GTLIIGASQ--TT------------GTYLMPRLIGLFRQRYP-QINVQLQV-------HSTRRIAWNVANGQIDIAIVGG 152 (305)
T ss_pred ceEEEEEcC--cc------------hHhHHHHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHcCCccEEEEcC
Confidence 578888874 11 11234677788877653 34466654 4578899999999999997632
Q ss_pred eeccccccceeeccceeecceEEEEecCC
Q 011629 398 AITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 398 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
....+..+.+ .+.++....+.++++++.
T Consensus 153 ~~~~~~~~~~-~~~~l~~~~~~~v~~~~~ 180 (305)
T CHL00180 153 EVPTELKKIL-EITPYVEDELALIIPKSH 180 (305)
T ss_pred ccCcccccce-eEEEeccCcEEEEECCCC
Confidence 2111111233 347888888899987654
No 221
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=63.72 E-value=40 Score=30.79 Aligned_cols=77 Identities=10% Similarity=0.018 Sum_probs=51.5
Q ss_pred EEEEEEEe--CCcccchHHHHHHHHHh-cCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-HHHHHHHHH
Q 011629 15 NVIALYVD--DDHGRNGIAALGDKLAE-KRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-WGLEVLNAA 90 (481)
Q Consensus 15 ~V~ii~~d--d~~g~~~~~~l~~~l~~-~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~~~~il~~a 90 (481)
+|++|..+ +.|.....+.+.+.+++ .|+.+..... ..+.+...+.++.+.+.+.+.||+.+... ....++.++
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~l 77 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFEDA---KNDVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVKAA 77 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEeCC---CCCHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHHHH
Confidence 36777754 55677778888999999 8988876422 22333455677777777889888866443 345666766
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.+
T Consensus 78 ~~~~ 81 (272)
T cd06301 78 NAAG 81 (272)
T ss_pred HHCC
Confidence 6654
No 222
>cd06353 PBP1_BmpA_Med_like Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type I periplasmic sugar-binding protein-like fold.
Probab=63.70 E-value=63 Score=29.64 Aligned_cols=83 Identities=10% Similarity=0.038 Sum_probs=52.7
Q ss_pred EEEEEEE----eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHH-HHH
Q 011629 15 NVIALYV----DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEV-LNA 89 (481)
Q Consensus 15 ~V~ii~~----dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~i-l~~ 89 (481)
+|+++++ |..+.+...+.+++..++.|+.+...+..+ +.+++.+.++.+.+.+.++||..+. ..... ...
T Consensus 1 kva~l~~g~~~D~~~n~~~~~G~~~~~~~~gv~~~~~e~~~---~~~~~~~~i~~~~~~g~dlIi~~g~--~~~~~~~~v 75 (258)
T cd06353 1 KVAFVYVGPIGDQGWNYAHDEGRKAAEKALGVEVTYVENVP---EGADAERVLRELAAQGYDLIFGTSF--GFMDAALKV 75 (258)
T ss_pred CEEEEEeCCCCccchhHHHHHHHHHHHHhcCCeEEEEecCC---chHhHHHHHHHHHHcCCCEEEECch--hhhHHHHHH
Confidence 3777775 223444456777777777899888776543 2346778888888888999888433 33344 444
Q ss_pred HHHcCCccCCeEEEEec
Q 011629 90 AKHLRMMESGYVWIVTD 106 (481)
Q Consensus 90 a~~~g~~~~~~~wI~~~ 106 (481)
|.+. ++..|+..+
T Consensus 76 A~~~----p~~~F~~~d 88 (258)
T cd06353 76 AKEY----PDVKFEHCS 88 (258)
T ss_pred HHHC----CCCEEEECC
Confidence 4442 456676654
No 223
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=63.65 E-value=66 Score=30.46 Aligned_cols=96 Identities=10% Similarity=0.030 Sum_probs=56.9
Q ss_pred HHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC---CceEEEEEeCc
Q 011629 6 DIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM---MSRILILHTYD 80 (481)
Q Consensus 6 ~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s---~~~vIvl~~~~ 80 (481)
+-|..-|-++++++....+ ......+.+++.+.++|+.+... +....+.++-...++++.+. .+. .|++++.
T Consensus 171 ~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~~-Ai~~~~D 247 (327)
T TIGR02417 171 ERLLSQHADEFWYLGAQPELSVSRDRLAGFRQALKQATLEVEWV--YGGNYSRESGYQMFAKLCARLGRLPQ-ALFTTSY 247 (327)
T ss_pred HHHHHCCCCeEEEEeCcccchhHHHHHHHHHHHHHHcCCChHhE--EeCCCChHHHHHHHHHHHhcCCCCCc-EEEEcCc
Confidence 3344458899999975432 34456788889999888753221 11111222233445554332 234 4555666
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
..+..++..+.++| ..++-+-|++
T Consensus 248 ~~A~g~~~al~~~g-~vP~dvsvig 271 (327)
T TIGR02417 248 TLLEGVLDYMLERP-LLDSQLHLAT 271 (327)
T ss_pred HHHHHHHHHHHHcC-CCCCcceEEE
Confidence 77888899999988 6665554443
No 224
>cd08175 G1PDH Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner. Glycerol-1-phosphate dehydrogenase (G1PDH) plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires a Ni++ ion. In Bacillus subtilis, it has been described as AraM gene in L-arabinose (ara) operon. AraM protein forms homodimer. This family is bacteria specific.
Probab=63.56 E-value=32 Score=33.24 Aligned_cols=75 Identities=9% Similarity=0.116 Sum_probs=49.9
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCC--CChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPK--GSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~--~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.+|-+++.+|++.... ....+.+.+.+++.|+.+......... .+.+.....++.+++ ++++||..+..
T Consensus 14 l~~~~~~~~~~~~livtd~~~~-~~~~~~v~~~l~~~~i~~~~~~~~~~~~~pt~~~v~~~~~~~~~-~~d~IIaIGGG 90 (348)
T cd08175 14 LPEILKEFGYKKALIVADENTY-AAAGKKVEALLKRAGVVVLLIVLPAGDLIADEKAVGRVLKELER-DTDLIIAVGSG 90 (348)
T ss_pred HHHHHHhcCCCcEEEEECCcHH-HHHHHHHHHHHHHCCCeeEEeecCCCcccCCHHHHHHHHHHhhc-cCCEEEEECCc
Confidence 4466777888998888743322 223577888999999866443333332 455567777777777 78998877653
No 225
>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=63.17 E-value=46 Score=28.26 Aligned_cols=72 Identities=15% Similarity=0.098 Sum_probs=46.3
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++.+.. .....+..+|.+|++|+++............+. +.+.....+.++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~-~~~l~~~~~~~v~~~~ 84 (200)
T cd08453 14 VLPELVRRFREAYP-DVELQLRE-------ATSDVQLEALLAGEIDAGIVIPPPGASAPPALA-YRPLLSEPLVLAVPAA 84 (200)
T ss_pred HHHHHHHHHHHhCC-CceEEEEe-------CCHHHHHHHHHcCCCCEEEEecCcccCCCccee-EEEeeeCceEEEEECC
Confidence 44677888877762 34566665 457789999999999998753211111123343 3677788888887765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 85 h 85 (200)
T cd08453 85 W 85 (200)
T ss_pred C
Confidence 4
No 226
>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=62.89 E-value=27 Score=30.73 Aligned_cols=80 Identities=19% Similarity=0.047 Sum_probs=51.4
Q ss_pred HHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeecc-ccccceee---ccceeecceEEEEecCCCCcCc
Q 011629 356 ELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITT-ERTKMVDF---TQPYIESGLVVVAPIKKLNSNA 431 (481)
Q Consensus 356 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~-~r~~~~~f---s~p~~~~~~~~~~~~~~~~~~~ 431 (481)
++-|++ ++++.. .+....+.+|.+|++|++++....-. .|.+..+. -..+......+++++++ .+..
T Consensus 17 ~~~gl~--ve~~~~------~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s-~i~~ 87 (216)
T PF09084_consen 17 KEEGLD--VEIVFF------GGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPNALVVRKDS-GIKS 87 (216)
T ss_dssp HHTTEE--EEEEEE------SSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCEEEEEETTT-S-SS
T ss_pred ccCeEE--EEEEEe------cChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCceEEEEeccC-CCCC
Confidence 455655 555542 46889999999999999987664322 34443333 23344556678887766 5888
Q ss_pred cccccCcchhHHH
Q 011629 432 WAFLNPFTPKMWC 444 (481)
Q Consensus 432 ~~~l~pf~~~~W~ 444 (481)
+.+|+.-+..+.-
T Consensus 88 ~~DLkGK~i~v~~ 100 (216)
T PF09084_consen 88 PADLKGKKIGVSR 100 (216)
T ss_dssp GGGGTTSEEEEST
T ss_pred HHHhCCCEEEEec
Confidence 9999977665443
No 227
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=62.69 E-value=79 Score=28.78 Aligned_cols=91 Identities=11% Similarity=-0.020 Sum_probs=48.8
Q ss_pred HHHHH-cCCcEEEEEEEeC-CcccchHHHHHHHHHhcC-CEEEEEEecCCCCChhHHHHHHHHhccCCceE---EEEEeC
Q 011629 6 DIVDY-FGWRNVIALYVDD-DHGRNGIAALGDKLAEKR-CRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI---LILHTY 79 (481)
Q Consensus 6 ~ll~~-fgW~~V~ii~~dd-~~g~~~~~~l~~~l~~~g-i~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v---Ivl~~~ 79 (481)
.|++. -|-++|+++...+ .......+.+.+.+++.+ +.+..........+.++....++++.....++ .|++.+
T Consensus 112 ~l~~~~~g~~~i~~i~~~~~~~~~~R~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~~ 191 (273)
T cd06305 112 QLVKDLGGKGNVGYVNVAGFPPLDRRYDVWQAVLKAYPGIKEVAELGDVSNNTAQDAAAQVEAVLKKYPKGGIDAIWAAW 191 (273)
T ss_pred HHHHHhCCCCCEEEEEccCCchHHHHHHHHHHHHHHCCCcEEecccccccccchhHHHHHHHHHHHHCCCcccCeEEEcC
Confidence 34443 4889999997542 123345567777888777 55432211111112223334454443333333 344445
Q ss_pred cHHHHHHHHHHHHcCCc
Q 011629 80 DIWGLEVLNAAKHLRMM 96 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~ 96 (481)
...+..++..+.+.|..
T Consensus 192 d~~a~g~~~~l~~~g~~ 208 (273)
T cd06305 192 DEFAKGAKQALDEAGRT 208 (273)
T ss_pred hhhhHHHHHHHHHcCCC
Confidence 55677788888888764
No 228
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=62.59 E-value=76 Score=28.96 Aligned_cols=102 Identities=13% Similarity=0.208 Sum_probs=58.2
Q ss_pred HhHHHHHHcCCcEEEEEEEeCC-cccchHHHHHHHHHhcCCEEEEEE--ecCCCCChhHHHHHHHHhccC--CceEEEEE
Q 011629 3 AIADIVDYFGWRNVIALYVDDD-HGRNGIAALGDKLAEKRCRLSHKV--PLSPKGSRNQIIDTLLTVSSM--MSRILILH 77 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v~~~~--~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~ 77 (481)
.+++.|..-|.++++++...+. .+....+.+++.+++.|+.+.... ..............++.+-+. ..+. |++
T Consensus 111 ~~~~~l~~~G~~~i~~l~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-v~~ 189 (273)
T cd01541 111 KATEYLIELGHRKIAGIFKADDLQGVKRMKGFIKAYREHGIPFNPSNVITYTTEEKEEKLFEKIKEILKRPERPTA-IVC 189 (273)
T ss_pred HHHHHHHHcCCcCEEEecCCCcccHHHHHHHHHHHHHHcCCCCChHHEEeccccchhhHHHHHHHHHHcCCCCCCE-EEE
Confidence 3455555669999998874332 234556778888888886432211 111111112233444444332 2343 455
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
.+...+..++..+.+.|+..++.+-|++
T Consensus 190 ~~d~~a~g~~~al~~~g~~~p~dv~vvg 217 (273)
T cd01541 190 YNDEIALRVIDLLKELGLKIPEDISVVG 217 (273)
T ss_pred cCcHHHHHHHHHHHHcCCCCCCcEEEEE
Confidence 6666777888889998876666555554
No 229
>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=62.51 E-value=36 Score=28.66 Aligned_cols=70 Identities=19% Similarity=0.169 Sum_probs=48.2
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.++++.+.+... ++++.+.. ++-..+...|.+|++|+++.... .....+.+ .++....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~L~~~~~Dl~i~~~~---~~~~~~~~-~~l~~~~~~~v~~~ 80 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVE-------YGGKKVEQAVLNGELDVGITVLP---VDEEEFDS-QPLCNEPLVAVLPR 80 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEE-------cCcHHHHHHHHcCCCCEEEEecc---cccCCcee-EEeccccEEEEecC
Confidence 345688888888763 35566665 45778899999999999975322 22233433 57778888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 81 ~~ 82 (197)
T cd08438 81 GH 82 (197)
T ss_pred CC
Confidence 54
No 230
>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=62.16 E-value=44 Score=28.28 Aligned_cols=68 Identities=13% Similarity=0.172 Sum_probs=46.8
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-..++..+.++.. ++++.+.. .....+...|.+|++|+++.. .+.....+.+ .++....+.++++++.
T Consensus 16 l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~---~~~~~~~~~~-~~l~~~~~~~v~~~~~ 83 (197)
T cd08425 16 IGPLIDRFHARYP-GIALSLRE-------MPQERIEAALADDRLDLGIAF---APVRSPDIDA-QPLFDERLALVVGATH 83 (197)
T ss_pred hHHHHHHHHHHCC-CcEEEEEE-------CcHHHHHHHHHcCCccEEEEe---cCCCCCCcEE-EEeccccEEEEecCCC
Confidence 3677888877753 45577765 346788899999999999753 2333334433 6788888888887654
No 231
>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=62.07 E-value=45 Score=28.47 Aligned_cols=69 Identities=10% Similarity=0.060 Sum_probs=47.1
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++.++.++.- ++++++.. ++...+...|.+|++|+++..- +.....++ +.+.....+.++++++
T Consensus 15 ~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~l~~~l~~g~~D~~~~~~---~~~~~~~~-~~~l~~~~~~lv~~~~ 82 (198)
T cd08486 15 SLPLLLRAFLTSTP-TATVSLTH-------MTKDEQVEGLLAGTIHVGFSRF---FPRHPGIE-IVNIAQEDLYLAVHRS 82 (198)
T ss_pred HHHHHHHHHHHhCC-CeEEEEEE-------CCHHHHHHHHHcCCceEEEecC---CCCCCceE-EEEEeeccEEEEecCC
Confidence 34677888877762 35566665 5688999999999999997532 22223343 3667778888888764
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 83 h 83 (198)
T cd08486 83 Q 83 (198)
T ss_pred C
Confidence 3
No 232
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=62.01 E-value=44 Score=30.50 Aligned_cols=99 Identities=10% Similarity=0.027 Sum_probs=55.8
Q ss_pred HHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhc-c-CCceEEEEEeCc
Q 011629 5 ADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVS-S-MMSRILILHTYD 80 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~-~-s~~~vIvl~~~~ 80 (481)
++.|...|-++++++..... .+....+.+.+.++++|+.+.......... .+.....+.++- + ...+.|+ +.+.
T Consensus 108 ~~~l~~~G~~~i~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~ai~-~~~d 185 (269)
T cd06281 108 VEYLISLGHRRIALVGGGSNTRPGRERLEGYKAAFAAAGLPPDPALVRLSTP-AASGFDATRALLALPDRPTAII-AGGT 185 (269)
T ss_pred HHHHHHCCCcEEEEecCccccccHHHHHHHHHHHHHHcCCCCCHHHeecCcH-HHHHHHHHHHHHcCCCCCcEEE-EcCc
Confidence 33344459999999975432 234556788889998887542111111111 222233444433 2 2345554 4456
Q ss_pred HHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 81 IWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 81 ~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
..+..+++.+.+.|+..++.+-|++
T Consensus 186 ~~a~g~~~~l~~~g~~ip~dv~iig 210 (269)
T cd06281 186 QVLVGVLRALREAGLRIPRDLSVIS 210 (269)
T ss_pred HHHHHHHHHHHHcCCCCCcceeEEE
Confidence 6677888888888877665554443
No 233
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=61.94 E-value=1.2e+02 Score=27.77 Aligned_cols=99 Identities=12% Similarity=0.064 Sum_probs=55.5
Q ss_pred hHHHHHHc--CCcEEEEEEEeCC--cccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhccCC---ceEEE
Q 011629 4 IADIVDYF--GWRNVIALYVDDD--HGRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSSMM---SRILI 75 (481)
Q Consensus 4 i~~ll~~f--gW~~V~ii~~dd~--~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~---~~vIv 75 (481)
+++.|... |-.+++++..+.+ ......+.+++.++++ ++.+... .....+.++....++++.++. .+. |
T Consensus 113 ~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~a-I 189 (273)
T cd06309 113 AADWLAKATGGKGNIVELQGTVGSSVAIDRKKGFAEVIKKYPNMKIVAS--QTGDFTRAKGKEVMEALLKAHGDDIDA-V 189 (273)
T ss_pred HHHHHHHHcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHCCCCEEeec--cCCcccHHHHHHHHHHHHHhCCCCccE-E
Confidence 33444444 7889999975432 2234577788888877 4554321 111122223334444443332 333 3
Q ss_pred EEeCcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 76 LHTYDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 76 l~~~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
++.+...+..++..+.+.|+..++.+-|.+
T Consensus 190 ~~~~d~~a~g~~~a~~~~g~~ip~di~iig 219 (273)
T cd06309 190 YAHNDEMALGAIQAIKAAGKKPGKDIKIVS 219 (273)
T ss_pred EECCcHHHHHHHHHHHHcCCCCCCCeEEEe
Confidence 444556666788888888887666665555
No 234
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=61.70 E-value=33 Score=30.87 Aligned_cols=76 Identities=8% Similarity=0.061 Sum_probs=49.3
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++... +.++......+++.+++.|+.+.... ...+.+.....++++.+.+++.||+..........+..+.+.
T Consensus 2 ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~---~~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~l~~~ 78 (264)
T cd01537 2 IGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLAN---SQNDAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARKA 78 (264)
T ss_pred eEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEe---CCCCHHHHHHHHHHHHHcCCCEEEEecCCCcchhHHHHhhhc
Confidence 6777754 56777888999999999998876542 222333456677777777788888766543333345555544
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 79 ~ 79 (264)
T cd01537 79 G 79 (264)
T ss_pred C
Confidence 3
No 235
>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=61.47 E-value=42 Score=28.48 Aligned_cols=71 Identities=8% Similarity=0.052 Sum_probs=48.2
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++.++.++.. ++++++.. .+...+...|.+|++|+++... ..+.....+.+ .+..+....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~-~~~~~~~~l~~-~~l~~~~~~~~~~~~ 83 (198)
T cd08437 14 YFPKLAKDLIKTGL-MIQIDTYE-------GGSAELLEQLLQGDLDIALLGS-LTPLENSALHS-KIIKTQHFMIIVSKD 83 (198)
T ss_pred HhHHHHHHHHHhCC-ceEEEEEE-------cCHHHHHHHHHcCCCCEEEecC-CCCCCcccceE-EEeecceEEEEecCC
Confidence 34577888887763 45576665 4578899999999999997521 11223344544 678888888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 84 h 84 (198)
T cd08437 84 H 84 (198)
T ss_pred C
Confidence 4
No 236
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=60.95 E-value=43 Score=30.17 Aligned_cols=76 Identities=11% Similarity=-0.002 Sum_probs=50.8
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++..+ +.+.....+.+++.+++.|+.+... ....+.+.....++++.+.+.+.||+......... +..+.+.
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~---~~~~~~~~~~~~~~~~~~~~~d~iii~~~~~~~~~-~~~~~~~ 77 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSVLLC---NSDEDPEKEREALELLLSRRVDGIILAPSRLDDEL-LEELAAL 77 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEEEEE---cCCCCHHHHHHHHHHHHHcCcCEEEEecCCcchHH-HHHHHHc
Confidence 5666644 6777788889999999999887653 22223334456677777778898888766544444 6666665
Q ss_pred CC
Q 011629 94 RM 95 (481)
Q Consensus 94 g~ 95 (481)
|.
T Consensus 78 ~i 79 (264)
T cd06267 78 GI 79 (264)
T ss_pred CC
Confidence 53
No 237
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=60.73 E-value=37 Score=31.33 Aligned_cols=79 Identities=13% Similarity=0.034 Sum_probs=48.7
Q ss_pred EEEEEEe---CCcccchHHHHHHHHHhcCCEEEEEEecCCC-CChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHH
Q 011629 16 VIALYVD---DDHGRNGIAALGDKLAEKRCRLSHKVPLSPK-GSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAK 91 (481)
Q Consensus 16 V~ii~~d---d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~-~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~ 91 (481)
|++|..+ +.|.....+.+.+.+++.|+.+......+.. .+.+.....++.+...+++.||+..........+..+.
T Consensus 2 Igvi~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIv~~~~~~~~~~~~~l~ 81 (280)
T cd06303 2 IAVIYPGQQISDYWVRNIASFTARLEELNIPYELTQFSSRPGIDHRLQSQQLNEALQSKPDYLIFTLDSLRHRKLIERVL 81 (280)
T ss_pred eeEEecCccHHHHHHHHHHHHHHHHHHcCCcEEEEEeccCcccCHHHHHHHHHHHHHcCCCEEEEcCCchhhHHHHHHHH
Confidence 6777754 3566677888899999999877654222211 12223345667777778998888654332334555555
Q ss_pred HcC
Q 011629 92 HLR 94 (481)
Q Consensus 92 ~~g 94 (481)
+.+
T Consensus 82 ~~~ 84 (280)
T cd06303 82 ASG 84 (280)
T ss_pred hCC
Confidence 543
No 238
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=60.73 E-value=41 Score=28.56 Aligned_cols=69 Identities=17% Similarity=0.207 Sum_probs=47.1
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.- ++++++.. ++...+...|.+|++|+++.. .+.....+. +.++....+.++++++
T Consensus 14 ~l~~~l~~f~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~---~~~~~~~~~-~~~l~~~~~~lv~~~~ 81 (200)
T cd08466 14 LLPRLLARLKQLAP-NISLRESP-------SSEEDLFEDLRLQEVDLVIDY---VPFRDPSFK-SELLFEDELVCVARKD 81 (200)
T ss_pred HHHHHHHHHHHHCC-CCEEEEec-------CchHhHHHHHHcCCccEEEec---ccCCCCCce-eeeecccceEEEEeCC
Confidence 34577788877762 35566665 557789999999999999752 222223343 3678888888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 82 ~ 82 (200)
T cd08466 82 H 82 (200)
T ss_pred C
Confidence 4
No 239
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=60.38 E-value=11 Score=35.34 Aligned_cols=60 Identities=12% Similarity=0.112 Sum_probs=42.9
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEe
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVG 395 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~ 395 (481)
++|++++.+ . ++..+....---|.+.+.+.+|.++++.+. .+..++++++..|++|++..
T Consensus 35 ~~l~~gi~p--~--------e~~~~~~~~~~pl~~~L~~~lG~~V~~~~a--------~dy~~vieal~~g~~D~A~~ 94 (299)
T COG3221 35 KELRVGIVP--T--------ENPTNLIPAWAPLADYLEKELGIPVEFFVA--------TDYAAVIEALRAGQVDIAWL 94 (299)
T ss_pred cceEEEEcC--C--------CChHHHHHHHHHHHHHHHHHhCCceEEEec--------ccHHHHHHHHhCCCeeEEec
Confidence 578999875 1 112334444566889999999977444433 57999999999999997643
No 240
>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=60.14 E-value=58 Score=27.64 Aligned_cols=68 Identities=12% Similarity=0.065 Sum_probs=46.4
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-.+++..+.++.. ++++++.. +....+...|.+|++|+++.. .+.....+. +.++....+.+++++..
T Consensus 15 l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~---~~~~~~~~~-~~~l~~~~~~lv~~~~h 82 (197)
T cd08452 15 LPPIVREYRKKFP-SVKVELRE-------LSSPDQVEELLKGRIDIGFLH---PPIQHTALH-IETVQSSPCVLALPKQH 82 (197)
T ss_pred HHHHHHHHHHHCC-CcEEEEEe-------cChHHHHHHHHCCCccEEEee---CCCCCCCee-EEEeeeccEEEEEeCCC
Confidence 3577888877763 35566665 457789999999999998752 222333444 35777888888876543
No 241
>cd08549 G1PDH_related Glycerol-1-phosphate_dehydrogenase and related proteins. Bacterial and archeal glycerol-1-phosphate dehydrogenase-like oxidoreductases. The proteins have similarity with glycerol-1-phosphate dehydrogenase (G1PDH). G1PDH plays a role in the synthesis of phosphoglycerolipids in gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires Ni++ ion. It also contains archaeal Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) that plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids.
Probab=60.13 E-value=42 Score=32.23 Aligned_cols=82 Identities=9% Similarity=0.048 Sum_probs=51.0
Q ss_pred hHHHHHHcCC-cEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEE-ecCCCCChhHHHHHHHHhccCCceEEEEEeCc-
Q 011629 4 IADIVDYFGW-RNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKV-PLSPKGSRNQIIDTLLTVSSMMSRILILHTYD- 80 (481)
Q Consensus 4 i~~ll~~fgW-~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~-~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~- 80 (481)
+.++++.++. +++.+|++...... ..+.+.+.+++.|+.+.... ....+.+.+.....++.+++ +.++||..+..
T Consensus 14 l~~~~~~~~~~~kvlivtd~~~~~~-~~~~i~~~L~~~~~~~~i~~~~~~~~p~~~~v~~~~~~~~~-~~d~IIaiGGGs 91 (332)
T cd08549 14 IGPIINKIGVNSKIMIVCGNNTYKV-AGKEIIERLESNNFTKEVLERDSLLIPDEYELGEVLIKLDK-DTEFLLGIGSGT 91 (332)
T ss_pred HHHHHHHcCCCCcEEEEECCcHHHH-HHHHHHHHHHHcCCeEEEEecCCCCCCCHHHHHHHHHHhhc-CCCEEEEECCcH
Confidence 4456777787 78888875444322 34788888988887654321 22223345567777777777 78888877653
Q ss_pred -HHHHHHH
Q 011629 81 -IWGLEVL 87 (481)
Q Consensus 81 -~~~~~il 87 (481)
-++..++
T Consensus 92 v~D~aK~i 99 (332)
T cd08549 92 IIDLVKFV 99 (332)
T ss_pred HHHHHHHH
Confidence 3444444
No 242
>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=59.78 E-value=44 Score=28.58 Aligned_cols=70 Identities=17% Similarity=0.191 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
++-.+++..+.++.- ++++.+.. .+...++..|.+|++|+++.... .....+.. .+.......+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~-------~~~~~~~~~L~~g~~Dl~i~~~~---~~~~~~~~-~~l~~~~~~lv~~~ 80 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQ-------ASREAMLAQVADGEIDLALGVFP---ELPEELHA-ETLFEERFVCLADR 80 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEec-------CChHhHHHHHHCCCccEEEeccc---cCCcCeeE-EEeeeccEEEEEeC
Confidence 344677777766642 35566665 56889999999999999875322 12233444 46777788888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 81 ~h 82 (200)
T cd08465 81 AT 82 (200)
T ss_pred CC
Confidence 54
No 243
>cd08177 MAR Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes. Maleylacetate reductases (MAR) play an important role in the degradation of aromatic compounds in aerobic microbes. In fungi and yeasts, the enzymes are involved in the catabolism of compounds such as phenol, tyrosine, benzoate, 4-hydroxybenzoate and resorcinol. In bacteria, the enzymes contribute to the degradation of resorcinol, 2,4-dihydroxybenzoate ([beta]-resorcylate) and 2,6-dihydroxybenzoate ([gamma]-resorcylate) via hydroxyquinol and maleylacetate. Maleylacetate reductases catalyze NADH- or NADPH-dependent reduction, at the carbon-carbon double bond, of maleylacetate or 2-chloromaleylacetate to 3-oxoadipate. In the case of 2-chloromaleylacetate, Maleylacetate reductases initially catalyses the NAD(P)H-dependent dechlorination to maleylacetate, which is then reduced to 3-oxoadipate. This enzyme is a homodimer. It is inhibited by thiol-blocking reagents such as p-
Probab=59.68 E-value=26 Score=33.74 Aligned_cols=74 Identities=5% Similarity=-0.025 Sum_probs=50.4
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.+.++.+|.+++-+|++...+-. ..+.+.+.+++.++.+ +. .+..+.+.+......+..++.+++.||..+..
T Consensus 14 l~~~l~~~g~~~~livt~~~~~~~-~~~~v~~~l~~~~~~~-~~-~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 87 (337)
T cd08177 14 LAAELERLGASRALVLTTPSLATK-LAERVASALGDRVAGT-FD-GAVMHTPVEVTEAAVAAAREAGADGIVAIGGG 87 (337)
T ss_pred HHHHHHHcCCCeEEEEcChHHHHH-HHHHHHHHhccCCcEE-eC-CCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 456788899999998885443332 5667777787765432 22 34444555677788888888889999977653
No 244
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=58.73 E-value=77 Score=28.81 Aligned_cols=98 Identities=8% Similarity=0.033 Sum_probs=54.1
Q ss_pred HHHHHHcCCcEEEEEEEeCCc--ccchHHHHHHHHHhcCCEEEEEEecCCC-CChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 5 ADIVDYFGWRNVIALYVDDDH--GRNGIAALGDKLAEKRCRLSHKVPLSPK-GSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~~--g~~~~~~l~~~l~~~gi~v~~~~~~~~~-~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++.+...|.++++++..+... .....+.|.+.+++.|+.+......... .....+...++.... ..+. |++.+..
T Consensus 110 ~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~a-i~~~~d~ 187 (268)
T cd06277 110 TEYLIEKGHRKIGFVGDPLYSPSFEERYEGYKKALLDHGIPFNEDYDITEKEEDEEDIGKFIDELKP-LPTA-FFCSNDG 187 (268)
T ss_pred HHHHHHCCCCcEEEECCCCCCcchHHHHHHHHHHHHHcCCCCCcceEEEcchhHHHHHHHHHhcCCC-CCCE-EEECCcH
Confidence 445555699999999755432 2345677888998888754321111111 111223333333222 2343 4455556
Q ss_pred HHHHHHHHHHHcCCccCCeEEEE
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
.+..+++.+.+.|+..++-+-|+
T Consensus 188 ~a~g~~~a~~~~g~~~p~di~vi 210 (268)
T cd06277 188 VAFLLIKVLKEMGIRVPEDVSVI 210 (268)
T ss_pred HHHHHHHHHHHcCCCCCCcceEE
Confidence 66777888888887554444333
No 245
>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=58.72 E-value=53 Score=27.82 Aligned_cols=69 Identities=14% Similarity=0.186 Sum_probs=46.2
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++.+.. .+...++..|.+|++|+++... +.....+.+ .+.......++++++
T Consensus 15 ~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~~-~~l~~~~~~~v~~~~ 82 (200)
T cd08411 15 LLPRLLPALRQAYP-KLRLYLRE-------DQTERLLEKLRSGELDAALLAL---PVDEPGLEE-EPLFDEPFLLAVPKD 82 (200)
T ss_pred hhHHHHHHHHHHCC-CcEEEEEe-------CcHHHHHHHHHcCCccEEEEec---cCCCCCceE-EEeeccceEEEecCC
Confidence 44677888877763 35566665 4577899999999999997532 222233433 567778888887655
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 83 ~ 83 (200)
T cd08411 83 H 83 (200)
T ss_pred C
Confidence 4
No 246
>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=58.56 E-value=94 Score=29.13 Aligned_cols=86 Identities=21% Similarity=0.124 Sum_probs=47.5
Q ss_pred EEEEEEeC--CcccchHHHHHHHHHhcC-CEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeCcHHHHHHHHHH
Q 011629 16 VIALYVDD--DHGRNGIAALGDKLAEKR-CRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTYDIWGLEVLNAA 90 (481)
Q Consensus 16 V~ii~~dd--~~g~~~~~~l~~~l~~~g-i~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~~~~~~~il~~a 90 (481)
++++.... .......+.+++.++++| +.+.. .+....+.+.....++++-++ ..+. |++.+...+..+++++
T Consensus 145 i~~i~~~~~~~~~~~R~~Gf~~~~~~~g~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~A~g~~~al 221 (305)
T cd06324 145 LLAISGDPTTPAAILREAGLRRALAEHPDVRLRQ--VVYAGWSEDEAYEQAENLLKRYPDVRL-IWAANDQMAFGALRAA 221 (305)
T ss_pred EEEEeCCCCChHHHHHHHHHHHHHHHCCCceEee--eecCCCCHHHHHHHHHHHHHHCCCccE-EEECCchHHHHHHHHH
Confidence 66665332 223456777888998887 33322 122222222333444444332 3443 4455666778889999
Q ss_pred HHcCCccCCeEEEE
Q 011629 91 KHLRMMESGYVWIV 104 (481)
Q Consensus 91 ~~~g~~~~~~~wI~ 104 (481)
.+.|+..++.+-|+
T Consensus 222 ~~~g~~vp~di~vi 235 (305)
T cd06324 222 KEAGRKPGRDVLFG 235 (305)
T ss_pred HHcCCCcCCCEEEE
Confidence 98887655544444
No 247
>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=58.41 E-value=59 Score=27.47 Aligned_cols=69 Identities=13% Similarity=0.142 Sum_probs=46.3
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++++.. ++...+...|.+|++|+++... +.....+. +.++....+.++++++
T Consensus 15 ~l~~~i~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~~ 82 (198)
T cd08446 15 TVPRLLRAFLTARP-DVTVSLHN-------MTKDEQIEALRAGRIHIGFGRF---YPVEPDIA-VENVAQERLYLAVPKS 82 (198)
T ss_pred HHHHHHHHHHHHCC-CeEEEEee-------CCHHHHHHHHHCCCccEEEEec---CCCCCCce-eEEeeeccEEEEEeCC
Confidence 34577788877763 35566665 5678899999999999997532 22222232 4677788888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 83 ~ 83 (198)
T cd08446 83 H 83 (198)
T ss_pred C
Confidence 4
No 248
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=58.36 E-value=54 Score=29.75 Aligned_cols=77 Identities=12% Similarity=-0.043 Sum_probs=48.9
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|++|.. .+.|.....+.+++.+++.|+.+... ....+.+.-...++.+.+.+++.||+..........+.++.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~---~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (268)
T cd06289 2 IGLVINDLTNPFFAELAAGLEEVLEEAGYTVFLA---NSGEDVERQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLAES 78 (268)
T ss_pred EEEEecCCCcchHHHHHHHHHHHHHHcCCeEEEe---cCCCChHHHHHHHHHHHHcCCCEEEEeCCCCccHHHHHHHHhc
Confidence 566664 34566677888889999999887532 2222223345667777777888888876443333466666665
Q ss_pred CC
Q 011629 94 RM 95 (481)
Q Consensus 94 g~ 95 (481)
|.
T Consensus 79 ~i 80 (268)
T cd06289 79 GI 80 (268)
T ss_pred CC
Confidence 53
No 249
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=58.03 E-value=1.3e+02 Score=27.40 Aligned_cols=88 Identities=17% Similarity=0.099 Sum_probs=49.3
Q ss_pred HHHHHc-CCcEEEEEEEeCC--cccchHHHHHHHHHhcC-CEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 6 DIVDYF-GWRNVIALYVDDD--HGRNGIAALGDKLAEKR-CRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 6 ~ll~~f-gW~~V~ii~~dd~--~g~~~~~~l~~~l~~~g-i~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
.|++++ |=.+++++....+ ......+.+++.+++.| +.+... .....+.+.....++++-+. ..+. |++.+
T Consensus 115 ~l~~~~~~~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~ 191 (272)
T cd06301 115 YVADKLGGKGNVAILMGPLGQSAQIDRTKGVEEVLAKYPDIKVVEE--QTANWSRAEAMDLMENWLSSGGKIDA-VVANN 191 (272)
T ss_pred HHHHHhCCCccEEEEECCCCCccHHHHHHHHHHHHHHCCCcEEEec--CCCCccHHHHHHHHHHHHHhCCCCCE-EEECC
Confidence 344554 4569999975432 23456788888998888 433221 11122222223344443322 2343 44555
Q ss_pred cHHHHHHHHHHHHcCCc
Q 011629 80 DIWGLEVLNAAKHLRMM 96 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~ 96 (481)
...+..++..+.+.|..
T Consensus 192 d~~a~~~~~~l~~~g~~ 208 (272)
T cd06301 192 DEMALGAIMALKAAGKS 208 (272)
T ss_pred CchHHHHHHHHHHcCCC
Confidence 56777888888888875
No 250
>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.
Probab=57.81 E-value=52 Score=29.95 Aligned_cols=89 Identities=11% Similarity=-0.056 Sum_probs=51.0
Q ss_pred HHHHHHc-CCcEEEEEEEeC-CcccchHHHHHHHHHhcCCEEEEEEecCCCC-ChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 5 ADIVDYF-GWRNVIALYVDD-DHGRNGIAALGDKLAEKRCRLSHKVPLSPKG-SRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 5 ~~ll~~f-gW~~V~ii~~dd-~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~-~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
+.++... |-+++++|..+. .......+.|.+.++++|..+.......... +.+.....++++.+..+++ |++.+..
T Consensus 111 ~~l~~~~~g~~~I~~i~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a-i~~~~d~ 189 (260)
T cd06304 111 GVLAALMTKTGKVGFVGGMPIPEVNRFINGFAAGAKSVNPDITVLVIYTGSFFDPAKGKEAALALIDQGADV-IFAAAGG 189 (260)
T ss_pred HHHHHHhccCCceEEEeccccHHHHHHHHHHHHHHHHhCCCcEEEEEEecCccCcHHHHHHHHHHHhCCCCE-EEEcCCC
Confidence 3566655 889999997532 2234456778888888886433221222111 1122334455544444555 4566666
Q ss_pred HHHHHHHHHHHcC
Q 011629 82 WGLEVLNAAKHLR 94 (481)
Q Consensus 82 ~~~~il~~a~~~g 94 (481)
.+..++.++.++|
T Consensus 190 ~A~gv~~al~~~g 202 (260)
T cd06304 190 TGPGVIQAAKEAG 202 (260)
T ss_pred CchHHHHHHHHcC
Confidence 7777888888766
No 251
>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=57.57 E-value=24 Score=31.24 Aligned_cols=80 Identities=10% Similarity=0.042 Sum_probs=46.8
Q ss_pred HHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcc-cccEEEeeeeecccc---ccceeeccc--eeecceEEE
Q 011629 348 IDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEE-VYDAAVGDFAITTER---TKMVDFTQP--YIESGLVVV 421 (481)
Q Consensus 348 ~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g-~~d~~~~~~~~t~~r---~~~~~fs~p--~~~~~~~~~ 421 (481)
-++++++.++.|++ +.+.. +.-..++..+.+| ++|+.+++=.....+ ...++-..| +....++++
T Consensus 9 ~~~~~~f~~~~gi~--V~~~~-------~gs~~l~~~l~~~~~aDv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~l~ 79 (216)
T TIGR01256 9 KEIAKQFEKRTGNK--VVFSF-------GSSGTLYTQIENGAPADLFISADNKWPKKLVDKGLVVAGSRFTYAGNKLVLI 79 (216)
T ss_pred HHHHHHHHHhhCCe--EEEEe-------CChHHHHHHHHcCCCCcEEEECCHHHHHHHHHCCCCCCCchheEEccEEEEE
Confidence 35777788888866 54443 3355677777776 499987742211212 122332234 667777888
Q ss_pred EecCCCCcCccccccC
Q 011629 422 APIKKLNSNAWAFLNP 437 (481)
Q Consensus 422 ~~~~~~~~~~~~~l~p 437 (481)
+++.. .+..+.+|.|
T Consensus 80 ~~~~~-~~~s~~dL~~ 94 (216)
T TIGR01256 80 SPKNR-VVDDLDILKK 94 (216)
T ss_pred EECCC-CcCcHHHHhh
Confidence 87653 4455666643
No 252
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=57.40 E-value=60 Score=29.28 Aligned_cols=77 Identities=9% Similarity=-0.063 Sum_probs=48.9
Q ss_pred EEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-HHHHHHHHHH
Q 011629 15 NVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-WGLEVLNAAK 91 (481)
Q Consensus 15 ~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~~~~il~~a~ 91 (481)
+|++|..+ +.+.....+.+++.+++.|+.+..... ..+.+.....++++...+.+.||+..... .....+..+.
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~~~~~~l~ 77 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDA---QNDVSKQIQQIEDLIAQGVDGIIISPVDSAALTPALKKAN 77 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEeCCCchhHHHHHHHHH
Confidence 36778754 467777889999999999988765422 22223345667777776888888765433 2233555555
Q ss_pred HcC
Q 011629 92 HLR 94 (481)
Q Consensus 92 ~~g 94 (481)
+.+
T Consensus 78 ~~~ 80 (267)
T cd01536 78 AAG 80 (267)
T ss_pred HCC
Confidence 543
No 253
>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=57.19 E-value=61 Score=27.18 Aligned_cols=68 Identities=15% Similarity=0.129 Sum_probs=46.2
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-.+++..+.+... ++++.+.. ++...+...|.+|++|+++... +.....+.+ .++....+.++++++.
T Consensus 15 l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~~-~~l~~~~~~~v~~~~~ 82 (197)
T cd08414 15 LPRLLRRFRARYP-DVELELRE-------MTTAEQLEALRAGRLDVGFVRP---PPDPPGLAS-RPLLREPLVVALPADH 82 (197)
T ss_pred HHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHcCCccEEEEcC---CCCCCCeeE-EEEeeccEEEEecCCC
Confidence 4577777777653 35566665 4567899999999999997532 222333433 6788888888887654
No 254
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=57.01 E-value=58 Score=29.81 Aligned_cols=80 Identities=11% Similarity=-0.008 Sum_probs=50.0
Q ss_pred EEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHH
Q 011629 15 NVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKH 92 (481)
Q Consensus 15 ~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~ 92 (481)
+|++|..+ +.|.......+++.+++.|+.+.....- ...+.+.....++.+...+++.||+..........+.++.+
T Consensus 1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~-~~~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~ 79 (268)
T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAG-GYPNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVA 79 (268)
T ss_pred CeEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCC-CCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHH
Confidence 36777753 4566677888899999999987654211 11122234456777777789998887644333224566666
Q ss_pred cCC
Q 011629 93 LRM 95 (481)
Q Consensus 93 ~g~ 95 (481)
.|+
T Consensus 80 ~gi 82 (268)
T cd06306 80 ASI 82 (268)
T ss_pred CCC
Confidence 553
No 255
>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=56.92 E-value=51 Score=27.57 Aligned_cols=69 Identities=20% Similarity=0.287 Sum_probs=46.7
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-..++..+.++.. ++++.+.. +....+...+.+|++|+++.. .+.....+.+ .++......++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~---~~~~~~~l~~-~~l~~~~~~~v~~~~ 81 (195)
T cd08434 14 LVPDLIRAFRKEYP-NVTFELHQ-------GSTDELLDDLKNGELDLALCS---PVPDEPDIEW-IPLFTEELVLVVPKD 81 (195)
T ss_pred hhHHHHHHHHHhCC-CeEEEEec-------CcHHHHHHHHHcCCccEEEEc---cCCCCCCeeE-EEeecceEEEEecCC
Confidence 34567777777762 24466655 456788999999999998753 2333344544 678888888888665
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 82 ~ 82 (195)
T cd08434 82 H 82 (195)
T ss_pred C
Confidence 4
No 256
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=56.88 E-value=30 Score=24.92 Aligned_cols=40 Identities=15% Similarity=0.230 Sum_probs=29.0
Q ss_pred HHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEE
Q 011629 5 ADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLS 45 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~ 45 (481)
.++|+.+ =+.|.+.+++|.-|....+.+.+.+.+.|+.+.
T Consensus 36 ~~~L~~~-~~~vii~~D~D~aG~~a~~~~~~~l~~~g~~~~ 75 (79)
T cd03364 36 AELLKRL-AKEVILAFDGDEAGQKAALRALELLLKLGLNVR 75 (79)
T ss_pred HHHHHhc-CCeEEEEECCCHHHHHHHHHHHHHHHHCCCeEE
Confidence 4555554 477777777777788888888888888877654
No 257
>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....
Probab=56.79 E-value=90 Score=25.96 Aligned_cols=71 Identities=8% Similarity=-0.011 Sum_probs=44.3
Q ss_pred EEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHH
Q 011629 15 NVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVL 87 (481)
Q Consensus 15 ~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il 87 (481)
+|+||...+ .-....+...+.|++.|+..... ..+...+.+.+...++++++.+.+|||......-...-+
T Consensus 2 ~V~Ii~gs~-SD~~~~~~a~~~L~~~gi~~~~~-V~saHR~p~~l~~~~~~~~~~~~~viIa~AG~~a~Lpgv 72 (150)
T PF00731_consen 2 KVAIIMGST-SDLPIAEEAAKTLEEFGIPYEVR-VASAHRTPERLLEFVKEYEARGADVIIAVAGMSAALPGV 72 (150)
T ss_dssp EEEEEESSG-GGHHHHHHHHHHHHHTT-EEEEE-E--TTTSHHHHHHHHHHTTTTTESEEEEEEESS--HHHH
T ss_pred eEEEEeCCH-HHHHHHHHHHHHHHHcCCCEEEE-EEeccCCHHHHHHHHHHhccCCCEEEEEECCCcccchhh
Confidence 467776332 22456788888999999776654 344445556677888888887889988876654333333
No 258
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=56.72 E-value=78 Score=29.35 Aligned_cols=76 Identities=9% Similarity=0.033 Sum_probs=51.5
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHHHHH
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~a~~ 92 (481)
|++|..+ +.|.....+.+++.+++.|+.+..... ..+.+.....++.+.+.+++.||+.... ......+.++.+
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~ 78 (288)
T cd01538 2 IGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQNA---NGDPAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAAD 78 (288)
T ss_pred eEEEEeCCCcHHHHHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHH
Confidence 6777753 456677888999999999999876432 2233344566777777789988887543 334567777766
Q ss_pred cC
Q 011629 93 LR 94 (481)
Q Consensus 93 ~g 94 (481)
.|
T Consensus 79 ~~ 80 (288)
T cd01538 79 AG 80 (288)
T ss_pred CC
Confidence 55
No 259
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=56.67 E-value=73 Score=28.99 Aligned_cols=74 Identities=12% Similarity=-0.026 Sum_probs=46.9
Q ss_pred EEEEEEe-----CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHH
Q 011629 16 VIALYVD-----DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAA 90 (481)
Q Consensus 16 V~ii~~d-----d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a 90 (481)
||++..+ +.+.....+.+++.+++.|..+.... .. ...+.....++.+.+.+++.||+...... ..+..+
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~--~~~~~l 76 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKF-VS--DEDEEEFELPSFLEDGKVDGIILLGGIST--EYIKEI 76 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEe-CC--CChHHHHHHHHHHHHCCCCEEEEeCCCCh--HHHHHH
Confidence 6766655 66777888889999999998876543 22 12223344555666677888888764432 235555
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.+
T Consensus 77 ~~~~ 80 (268)
T cd06277 77 KELG 80 (268)
T ss_pred hhcC
Confidence 5544
No 260
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=56.59 E-value=62 Score=31.43 Aligned_cols=84 Identities=10% Similarity=-0.089 Sum_probs=52.7
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEE--ecCCCCChhHHHHHHHHhccCC---ceEEEEEe
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKV--PLSPKGSRNQIIDTLLTVSSMM---SRILILHT 78 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~--~~~~~~~~~~~~~~l~~i~~s~---~~vIvl~~ 78 (481)
+.+.++.++.+++.+|++... .....+.+.+.+++.|+.+.... ....+.+.+.....++.+++.+ .+.||..+
T Consensus 22 l~~~l~~~~~~~~livtd~~~-~~~~~~~v~~~L~~~gi~~~~~~~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~IIavG 100 (358)
T PRK00002 22 LGELLAPLKGKKVAIVTDETV-APLYLEKLRASLEAAGFEVDVVVLPDGEQYKSLETLEKIYDALLEAGLDRSDTLIALG 100 (358)
T ss_pred HHHHHHhcCCCeEEEEECCch-HHHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCCEEEEEc
Confidence 445677778899998885443 34567788888988888665321 1222345556777777777654 47887766
Q ss_pred Cc--HHHHHHHH
Q 011629 79 YD--IWGLEVLN 88 (481)
Q Consensus 79 ~~--~~~~~il~ 88 (481)
.. -++..++.
T Consensus 101 GGsv~D~aK~iA 112 (358)
T PRK00002 101 GGVIGDLAGFAA 112 (358)
T ss_pred CcHHHHHHHHHH
Confidence 53 34444443
No 261
>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=56.51 E-value=53 Score=28.25 Aligned_cols=71 Identities=14% Similarity=0.312 Sum_probs=48.2
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++.++.++.. ++++++... ++.+.+...|.+|++|+++... +...+.+.+ .++.+....+++++
T Consensus 13 ~~~~~~l~~~~~~~P-~~~v~~~~~------~~~~~l~~~L~~g~lDl~i~~~---~~~~~~l~~-~~l~~~~~~lv~~~ 81 (203)
T cd08463 13 LFLPELVARFRREAP-GARLEIHPL------GPDFDYERALASGELDLVIGNW---PEPPEHLHL-SPLFSDEIVCLMRA 81 (203)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEeC------CcchhHHHHHhcCCeeEEEecc---ccCCCCcEE-eEeecCceEEEEeC
Confidence 345688888887763 355666641 2467899999999999997532 222233444 67888888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 82 ~h 83 (203)
T cd08463 82 DH 83 (203)
T ss_pred CC
Confidence 54
No 262
>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=56.42 E-value=61 Score=27.36 Aligned_cols=71 Identities=24% Similarity=0.227 Sum_probs=46.9
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-..++..+.++.. ++++++.. .+...+...|.+|++|+++..... ..+...+.+ .+.....+.++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~-~~~~~~~~~-~~l~~~~~~~v~~~~ 83 (201)
T cd08418 14 LMPAVINRFKEQFP-DVQISIYE-------GQLSSLLPELRDGRLDFAIGTLPD-EMYLKELIS-EPLFESDFVVVARKD 83 (201)
T ss_pred hhHHHHHHHHHHCC-CceEEEEe-------CcHHHHHHHHHcCCCcEEEEecCC-CCCCcceeE-EeecCCceEEEeCCC
Confidence 34577777777762 35566665 457789999999999999753211 111233444 677788888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 84 ~ 84 (201)
T cd08418 84 H 84 (201)
T ss_pred C
Confidence 4
No 263
>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=56.40 E-value=64 Score=27.45 Aligned_cols=70 Identities=17% Similarity=0.108 Sum_probs=48.0
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++.+.. +....+...|.+|++|+++.... ......+.+ .+.......++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~v~~~~-------~~~~~~~~~l~~g~~D~~i~~~~--~~~~~~~~~-~~l~~~~~~~v~~~~ 82 (198)
T cd08413 14 VLPPVIAAFRKRYP-KVKLSLHQ-------GTPSQIAEMVLKGEADIAIATEA--LDDHPDLVT-LPCYRWNHCVIVPPG 82 (198)
T ss_pred hccHHHHHHHHhCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEEccC--CCCCCCcEE-EEeeeeeEEEEecCC
Confidence 44678888888763 35566665 56788999999999999975221 122233443 678888888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 83 h 83 (198)
T cd08413 83 H 83 (198)
T ss_pred C
Confidence 4
No 264
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=55.71 E-value=61 Score=29.63 Aligned_cols=78 Identities=5% Similarity=-0.117 Sum_probs=50.6
Q ss_pred EEEEEEEe---CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-HHHHHHHHH
Q 011629 15 NVIALYVD---DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-WGLEVLNAA 90 (481)
Q Consensus 15 ~V~ii~~d---d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~~~~il~~a 90 (481)
+|+++..+ +.|.....+.+++.+++.|+.+.... +...+.+.....++++...+++.||+..... .....+..+
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~--~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~l~~~ 78 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRG--PETFDVADMARLIEAAIAAKPDGIVVTIPDPDALDPAIKRA 78 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEEC--CCCCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHHHH
Confidence 36666643 46777788899999999999886542 2211333445667777777899888876433 234556666
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.|
T Consensus 79 ~~~~ 82 (271)
T cd06312 79 VAAG 82 (271)
T ss_pred HHCC
Confidence 6654
No 265
>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=55.08 E-value=64 Score=26.98 Aligned_cols=71 Identities=20% Similarity=0.124 Sum_probs=47.2
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++.+.. .+...+...|.+|++|+++..... .....+.+ .+.......+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~~~-~~l~~~~~~~~~~~ 81 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQ-------AGSDDLLAAVREGRLDLAFVGLPE--RRPPGLAS-RELAREPLVAVVAP 81 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCHHHHHHHHHcCCccEEEEecCC--CCCCCcEE-EEeecceEEEEecC
Confidence 344677777777763 35566665 456788999999999999753221 13344444 67788888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 82 ~~ 83 (194)
T cd08436 82 DH 83 (194)
T ss_pred CC
Confidence 54
No 266
>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=54.92 E-value=76 Score=26.65 Aligned_cols=69 Identities=13% Similarity=0.127 Sum_probs=46.0
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.+... ++++++.. +....+..++.+|++|+++... +.....+. +.+.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~-------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~~~~~ 80 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHT-------RDSPTVEQWLSAQQCDLGLVST---LHEPPGIE-RERLLRIDGVCVLPP 80 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEec---CCCCCCee-EEEeeccCeEEEecC
Confidence 344678888888763 35577665 4567888999999999997532 22223333 356777787777765
Q ss_pred C
Q 011629 425 K 425 (481)
Q Consensus 425 ~ 425 (481)
+
T Consensus 81 ~ 81 (196)
T cd08456 81 G 81 (196)
T ss_pred C
Confidence 4
No 267
>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=54.85 E-value=69 Score=26.96 Aligned_cols=70 Identities=20% Similarity=0.210 Sum_probs=46.2
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-.+++..+.+... ++++.+.. .+-..+...+.+|++|+++... ....+...+.+ .|+....+.++++++.
T Consensus 15 l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~-~~~~~~~~~~~-~~l~~~~~~~~~~~~~ 84 (201)
T cd08435 15 LPPAIARLLARHP-RLTVRVVE-------GTSDELLEGLRAGELDLAIGRL-ADDEQPPDLAS-EELADEPLVVVARPGH 84 (201)
T ss_pred HHHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHcCCccEEEEec-CcccCCCCcEE-EEcccCcEEEEEeCCC
Confidence 3577777777653 35566654 4567889999999999987532 11112334443 6788888888887654
No 268
>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=54.83 E-value=57 Score=28.16 Aligned_cols=71 Identities=13% Similarity=0.106 Sum_probs=44.7
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.++++.+.++.. ++++++.. ++...++..|.+|++|+++......+.-...+ ...|..+..+.++++.+
T Consensus 14 ~l~~~l~~f~~~~P-~v~l~i~~-------~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~ 84 (204)
T cd08429 14 IAYRLLEPAMDLHE-PIRLVCRE-------GKLEQLLADLALHRLDMVLADRPMPSSLDVKG-YSHRLGECGVSFFAAPP 84 (204)
T ss_pred HHHHHHHHHHHhCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEecCCCccccchhe-eeccccccceEEEecCC
Confidence 44677888777763 35566665 67899999999999999875322111101122 23577777777776443
No 269
>cd08173 Gro1PDH Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate using either NADH or NADPH as a coenzyme. Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH, EC 1.1.1.261) plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids. It catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate using either NADH or NADPH as a coenzyme. The activity is zinc-dependent. One characteristic feature of archaea is that their cellular membrane has an ether linkage between the glycerol backbone and the hydrocarbon residues. The polar lipids of the members of Archaea consist of di- and tetraethers of glycerol with isoprenoid alcohols bound at the sn-2 and sn-3 positions of the glycerol moiety. The archaeal polar lipids have the enantiomeric configuration of a glycerophosph
Probab=54.80 E-value=58 Score=31.34 Aligned_cols=72 Identities=4% Similarity=-0.010 Sum_probs=48.9
Q ss_pred HHHHH-HcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 5 ADIVD-YFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 5 ~~ll~-~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.++++ ..+.+++.+|++...+ ....+.+.+.++++| .+... +..+.+.+.+...++.+++.++++||..+..
T Consensus 16 ~~~l~~~~~~~~~liv~d~~~~-~~~~~~v~~~l~~~~-~~~~~--~~~~~~~~~v~~~~~~~~~~~~d~iIaiGGG 88 (339)
T cd08173 16 PNVLRDLLLGGRVLVVTGPTTK-SIAGKKVEALLEDEG-EVDVV--IVEDATYEEVEKVESSARDIGADFVIGVGGG 88 (339)
T ss_pred HHHHHHhCCCCeEEEEECCchH-HHHHHHHHHHHHhcC-CeEEE--EeCCCCHHHHHHHHHHhhhcCCCEEEEeCCc
Confidence 45566 4678999888844333 356677888888888 44322 2234456677888888888889999877653
No 270
>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=54.75 E-value=69 Score=26.93 Aligned_cols=70 Identities=19% Similarity=0.168 Sum_probs=46.6
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.++++.+.++.- ++++++.. ++...+...|.+|++|+++... +.....+. +.+.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~~~~~ 80 (196)
T cd08450 13 QWLPEVLPILREEHP-DLDVELSS-------LFSPQLAEALMRGKLDVAFMRP---EIQSDGID-YQLLLKEPLIVVLPA 80 (196)
T ss_pred hhHHHHHHHHHhhCC-CcEEEEEe-------cChHHHHHHHhcCCccEEEEeC---CCCCCCcE-EEEEEccceEEEecC
Confidence 344677788877763 35566665 4567899999999999987532 21223343 367778888888866
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 81 ~~ 82 (196)
T cd08450 81 DH 82 (196)
T ss_pred CC
Confidence 53
No 271
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=54.71 E-value=1.2e+02 Score=27.58 Aligned_cols=100 Identities=15% Similarity=0.054 Sum_probs=56.0
Q ss_pred hHHHHHHcCCcEEEEEEEeCCc-ccchHHHHHHHHHhcCCEEEEEEec--CCCCChhHHHHHHHHh-ccC-CceEEEEEe
Q 011629 4 IADIVDYFGWRNVIALYVDDDH-GRNGIAALGDKLAEKRCRLSHKVPL--SPKGSRNQIIDTLLTV-SSM-MSRILILHT 78 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~-g~~~~~~l~~~l~~~gi~v~~~~~~--~~~~~~~~~~~~l~~i-~~s-~~~vIvl~~ 78 (481)
+++.+...|-++++++...... .....+.+++.+++.|+.+...... ....+.+.....++++ +.. ..+ .|+++
T Consensus 100 ~~~~l~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-ai~~~ 178 (265)
T cd01543 100 AAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAGYECSFFYRGLSTDAQSWEEEQEELAQWLQSLPKPV-GIFAC 178 (265)
T ss_pred HHHHHHHCCCcEEEEEcCCCCHHHHHHHHHHHHHHHHcCCccccccCccccccccHHHHHHHHHHHHhcCCCCc-EEEec
Confidence 3455556689999998744331 2345678888999998765211111 1111111223334443 332 234 45556
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
+...+..+++.+.+.|+..++.+=|+
T Consensus 179 ~d~~a~g~~~~l~~~g~~vp~di~vi 204 (265)
T cd01543 179 TDARARQLLEACRRAGIAVPEEVAVL 204 (265)
T ss_pred ChHHHHHHHHHHHHhCCCCCCceEEE
Confidence 66777888888888887655444333
No 272
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=54.70 E-value=1.7e+02 Score=26.59 Aligned_cols=98 Identities=16% Similarity=0.017 Sum_probs=53.2
Q ss_pred hHHHHHHc--CCcEEEEEEEeCC-cccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEE
Q 011629 4 IADIVDYF--GWRNVIALYVDDD-HGRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILH 77 (481)
Q Consensus 4 i~~ll~~f--gW~~V~ii~~dd~-~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~ 77 (481)
+++.+... |.++|+++..... ......+.+++.+++. +++.... ......+.+.-...++++-+. ..+. |++
T Consensus 110 ~~~~l~~~~~g~~~i~~i~g~~~~~~~~R~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~ 187 (271)
T cd06321 110 SCQYLADRLGGKGNVAILNGPPVSAVLDRVAGCKAALAKYPGIKLLSD-DQNGKGSRDGGLRVMQGLLTRFPKLDG-VFA 187 (271)
T ss_pred HHHHHHHHhCCCceEEEEeCCCCchHHHHHHHHHHHHHhCCCcEEEee-ecCCCCChhhHHHHHHHHHHhCCCCCE-EEE
Confidence 34444444 9999999975432 2345567788888887 6653221 122122222222334444322 2444 444
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
.+...+..++..+.+.|+ .+...+..
T Consensus 188 ~~d~~a~g~~~al~~~g~--~di~v~g~ 213 (271)
T cd06321 188 INDPTAIGADLAAKQAGR--NDIKITSV 213 (271)
T ss_pred CCchhHHHHHHHHHHcCC--CCcEEEEe
Confidence 555677788888888876 34444443
No 273
>cd08184 Fe-ADH3 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the iron-containing alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron or zinc ions. Members of this family are mainly found in bacteria.
Probab=54.42 E-value=64 Score=31.19 Aligned_cols=73 Identities=15% Similarity=0.080 Sum_probs=48.3
Q ss_pred hHHHHHHcCC--cEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC---CceEEEEEe
Q 011629 4 IADIVDYFGW--RNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM---MSRILILHT 78 (481)
Q Consensus 4 i~~ll~~fgW--~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s---~~~vIvl~~ 78 (481)
+.++++.+|. +.+.+++ |... .. ..+.+.+++.|+.+.....+..+.+.++.....+..++. +++.||..+
T Consensus 14 l~~~~~~~g~~~~~~lvvt-d~~~--~~-~~v~~~L~~~g~~~~~f~~v~~nPt~~~v~~~~~~~~~~~~~~~D~IIaiG 89 (347)
T cd08184 14 LNDLLAPKRKNKDPAVFFV-DDVF--QG-KDLISRLPVESEDMIIWVDATEEPKTDQIDALTAQVKSFDGKLPCAIVGIG 89 (347)
T ss_pred HHHHHHHcCCCCCeEEEEE-Ccch--hh-hHHHHHHHhcCCcEEEEcCCCCCcCHHHHHHHHHHHHhhCCCCCCEEEEeC
Confidence 4456777764 5566666 3322 11 567778888888655444566666666777777888876 899999876
Q ss_pred Cc
Q 011629 79 YD 80 (481)
Q Consensus 79 ~~ 80 (481)
..
T Consensus 90 GG 91 (347)
T cd08184 90 GG 91 (347)
T ss_pred Cc
Confidence 53
No 274
>cd08179 NADPH_BDH NADPH-dependent butanol dehydrogenase involved in the butanol and ethanol formation pathway in bacteria. NADPH-dependent butanol dehydrogenase (BDH) is involved in the butanol and ethanol formation pathway of some bacteria. The fermentation process is characterized by an acid producing growth phase, followed by a solvent producing phase. The latter phase is associated with the induction of solventogenic enzymes such as butanol dehydrogenase. The activity of the enzymes require NADPH as cofactor, as well as divalent ions zinc or iron. This family is a member of the iron-containing alcohol dehydrogenase superfamily. Protein structure has a dehydroquinate synthase-like fold.
Probab=54.40 E-value=67 Score=31.44 Aligned_cols=72 Identities=7% Similarity=-0.021 Sum_probs=50.5
Q ss_pred HHcCCcEEEEEEEeCCcc-cchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 9 DYFGWRNVIALYVDDDHG-RNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 9 ~~fgW~~V~ii~~dd~~g-~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
..++-+++.+|++....- ....+.+.+.+++.|+.+.....+..+.+.+.....++.+++.+++.||..+..
T Consensus 19 ~~~~~~r~livt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 91 (375)
T cd08179 19 KTLKGKKAFIVTGGGSMKKFGFLDKVEAYLKEAGIEVEVFEGVEPDPSVETVLKGAEAMREFEPDWIIALGGG 91 (375)
T ss_pred HHhcCCeEEEEeCchHHHhCChHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 344458888887443222 245678888999999987644445555666678888889999899999987653
No 275
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=54.39 E-value=1.2e+02 Score=28.56 Aligned_cols=78 Identities=9% Similarity=0.105 Sum_probs=52.6
Q ss_pred CCcEEEEEEEeCC-cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc---HHHHHHH
Q 011629 12 GWRNVIALYVDDD-HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD---IWGLEVL 87 (481)
Q Consensus 12 gW~~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~---~~~~~il 87 (481)
+=+++|++|..++ ......+.|++++++.|+.|... .++... +....++.+.. ++++|++-++. .....++
T Consensus 158 nak~Igv~Y~p~E~ns~~l~eelk~~A~~~Gl~vve~-~v~~~n---di~~a~~~l~g-~~d~i~~p~dn~i~s~~~~l~ 232 (322)
T COG2984 158 NAKSIGVLYNPGEANSVSLVEELKKEARKAGLEVVEA-AVTSVN---DIPRAVQALLG-KVDVIYIPTDNLIVSAIESLL 232 (322)
T ss_pred CCeeEEEEeCCCCcccHHHHHHHHHHHHHCCCEEEEE-ecCccc---ccHHHHHHhcC-CCcEEEEecchHHHHHHHHHH
Confidence 7899999997665 56678899999999999998754 333222 45555666653 47777776654 2344556
Q ss_pred HHHHHcC
Q 011629 88 NAAKHLR 94 (481)
Q Consensus 88 ~~a~~~g 94 (481)
..|.+.+
T Consensus 233 ~~a~~~k 239 (322)
T COG2984 233 QVANKAK 239 (322)
T ss_pred HHHHHhC
Confidence 6666644
No 276
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=54.01 E-value=1.5e+02 Score=27.10 Aligned_cols=88 Identities=6% Similarity=-0.094 Sum_probs=50.4
Q ss_pred hHHHHHHcCC-----cEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc--CCceEE
Q 011629 4 IADIVDYFGW-----RNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS--MMSRIL 74 (481)
Q Consensus 4 i~~ll~~fgW-----~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~--s~~~vI 74 (481)
+++.|...|- .+|+++....+ ......+.+++.+++.++.+... .....+.+.....++.+-+ ...++|
T Consensus 111 ~~~~l~~~g~~~~~~~~i~~l~g~~~~~~~~~R~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i 188 (268)
T cd06306 111 AGEYLAQRHPKGSKPAKVAWFPGPKGAGWVKAVEKGFRDALAGSAIEISAI--KYGDTGKEVQRKLVEEALEAHPDIDYI 188 (268)
T ss_pred HHHHHHHHhhcCCCCceEEEEeCCCCCchHHHHHHHHHHHHhhcCcEEeee--ccCCccHHHHHHHHHHHHHhCCCcCEE
Confidence 3444444454 78998875333 34456777888888888876432 2212222233344444432 235555
Q ss_pred EEEeCcHHHHHHHHHHHHcCC
Q 011629 75 ILHTYDIWGLEVLNAAKHLRM 95 (481)
Q Consensus 75 vl~~~~~~~~~il~~a~~~g~ 95 (481)
+ +....+..++..+.+.|+
T Consensus 189 ~--~~d~~a~~~~~~l~~~g~ 207 (268)
T cd06306 189 V--GSAVAAEAAVGILRQRGL 207 (268)
T ss_pred e--ecchhhhHHHHHHHhcCC
Confidence 4 346667778888888775
No 277
>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=53.99 E-value=65 Score=27.06 Aligned_cols=70 Identities=16% Similarity=0.139 Sum_probs=46.6
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++.+.. .+-..+..+|.+|++|+++... +.....+.+ .+.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~~~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~~-~~l~~~~~~~v~~~ 80 (201)
T cd08420 13 YLLPRLLARFRKRYP-EVRVSLTI-------GNTEEIAERVLDGEIDLGLVEG---PVDHPDLIV-EPFAEDELVLVVPP 80 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCccEEEecC---CCCCcceEE-EeecCccEEEEecC
Confidence 344677888887762 34466665 3466788999999999987532 222333433 67788888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 81 ~~ 82 (201)
T cd08420 81 DH 82 (201)
T ss_pred CC
Confidence 54
No 278
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=53.90 E-value=70 Score=30.55 Aligned_cols=85 Identities=15% Similarity=0.054 Sum_probs=56.0
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.+.++||+.. .. ...+-.+++..+.++.- ++++.+.. ++...+..+|.+|++|+++..
T Consensus 92 ~g~lrIg~~~--~~------------~~~~l~~~l~~f~~~~P-~v~i~l~~-------~~~~~~~~~l~~g~~Dl~i~~ 149 (327)
T PRK12680 92 QGQLTLTTTH--TQ------------ARFVLPPAVAQIKQAYP-QVSVHLQQ-------AAESAALDLLGQGDADIAIVS 149 (327)
T ss_pred ceEEEEEecc--hh------------HHHhhHHHHHHHHHHCC-CcEEEEEe-------CChHHHHHHHHCCCCcEEEEe
Confidence 3678999874 21 11234678888887764 34566665 567899999999999999753
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-.. ....... ..|++.....++++++.
T Consensus 150 ~~~--~~~~~~~-~~~l~~~~~~l~~~~~h 176 (327)
T PRK12680 150 TAG--GEPSAGI-AVPLYRWRRLVVVPRGH 176 (327)
T ss_pred cCC--CCCCcce-EEEeeccceEEEEeCCC
Confidence 111 1112233 47888888888887654
No 279
>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=53.86 E-value=67 Score=27.03 Aligned_cols=71 Identities=21% Similarity=0.193 Sum_probs=46.6
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++++.. .+...+..+|.+|++|+++..-.. .....+.+ .++....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~l~~-~~l~~~~~~~~~~~ 81 (199)
T cd08430 13 SFLPPILERFRAQHP-QVEIKLHT-------GDPADAIDKVLNGEADIAIAARPD--KLPARLAF-LPLATSPLVFIAPN 81 (199)
T ss_pred eeccHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHCCCCCEEEEecCC--CCCcccEE-EeeccceEEEEEeC
Confidence 445678899988873 34566665 467889999999999999753211 11123333 56677777777765
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 82 ~~ 83 (199)
T cd08430 82 IA 83 (199)
T ss_pred Cc
Confidence 43
No 280
>PF13380 CoA_binding_2: CoA binding domain; PDB: 3FF4_A 2D5A_A 2D59_A 2E6U_X 1IUL_A 1IUK_A 1Y81_A 2DUW_A.
Probab=53.73 E-value=21 Score=28.14 Aligned_cols=85 Identities=14% Similarity=0.157 Sum_probs=46.3
Q ss_pred cEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCCh-hHHHHHHHHhc--cCCceEEEEEeCcHHHHHHHHHH
Q 011629 14 RNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSR-NQIIDTLLTVS--SMMSRILILHTYDIWGLEVLNAA 90 (481)
Q Consensus 14 ~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~-~~~~~~l~~i~--~s~~~vIvl~~~~~~~~~il~~a 90 (481)
+.|++|-..++-+.- ...+.+.+.+.|..|... .+.... .. ......+. -...+.++++..+.....++.++
T Consensus 1 ksiAVvGaS~~~~~~-g~~v~~~l~~~G~~v~~V---np~~~~i~G-~~~y~sl~e~p~~iDlavv~~~~~~~~~~v~~~ 75 (116)
T PF13380_consen 1 KSIAVVGASDNPGKF-GYRVLRNLKAAGYEVYPV---NPKGGEILG-IKCYPSLAEIPEPIDLAVVCVPPDKVPEIVDEA 75 (116)
T ss_dssp -EEEEET--SSTTSH-HHHHHHHHHHTT-EEEEE---STTCSEETT-EE-BSSGGGCSST-SEEEE-S-HHHHHHHHHHH
T ss_pred CEEEEEcccCCCCCh-HHHHHHHHHhCCCEEEEE---CCCceEECc-EEeeccccCCCCCCCEEEEEcCHHHHHHHHHHH
Confidence 467777755544433 344444555588765533 222110 00 01223344 35789999999999999999999
Q ss_pred HHcCCccCCeEEEEec
Q 011629 91 KHLRMMESGYVWIVTD 106 (481)
Q Consensus 91 ~~~g~~~~~~~wI~~~ 106 (481)
.++| .+.+|+.++
T Consensus 76 ~~~g---~~~v~~~~g 88 (116)
T PF13380_consen 76 AALG---VKAVWLQPG 88 (116)
T ss_dssp HHHT----SEEEE-TT
T ss_pred HHcC---CCEEEEEcc
Confidence 9886 568999987
No 281
>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=53.63 E-value=22 Score=31.76 Aligned_cols=82 Identities=21% Similarity=0.149 Sum_probs=53.5
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcc-cccEEEeeeeecccc---cccee--eccceeecce
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEE-VYDAAVGDFAITTER---TKMVD--FTQPYIESGL 418 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g-~~d~~~~~~~~t~~r---~~~~~--fs~p~~~~~~ 418 (481)
+..-++++.+.+..|+++++.... -..+...|..| ++|+.+.+-....++ ...+. -..|+..+.+
T Consensus 11 ~~~~~l~~~f~~~~g~~v~v~~~~---------s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~ 81 (230)
T PF13531_consen 11 PALEELAEAFEKQPGIKVEVSFGG---------SGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLARSPL 81 (230)
T ss_dssp HHHHHHHHHHHHHHCEEEEEEEEC---------HHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEEEEE
T ss_pred HHHHHHHHHHHhccCCeEEEEECC---------hHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCcccccccCce
Confidence 344578888888889665555443 66788888876 899987754222222 12344 5578999999
Q ss_pred EEEEecCC-CCcCccccc
Q 011629 419 VVVAPIKK-LNSNAWAFL 435 (481)
Q Consensus 419 ~~~~~~~~-~~~~~~~~l 435 (481)
+++++++. ..+..+.+|
T Consensus 82 vl~~~~~~~~~~~~~~dL 99 (230)
T PF13531_consen 82 VLAVPKGNPKGIRSWADL 99 (230)
T ss_dssp EEEEETTSTTSTTCHHHH
T ss_pred EEEeccCcccccCCHHHH
Confidence 99999887 344455554
No 282
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=53.59 E-value=76 Score=28.74 Aligned_cols=75 Identities=9% Similarity=-0.102 Sum_probs=49.8
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|++|.. ++.|.....+.+.+.+++.|+.+..... ..+.+.....++.+.+.+.+-||+....... ..+.++.+.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~-~~~~~l~~~ 77 (265)
T cd06299 2 IGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNS---DENPETENRYLDNLLSQRVDGIIVVPHEQSA-EQLEDLLKR 77 (265)
T ss_pred EEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeC---CCCHHHHHHHHHHHHhcCCCEEEEcCCCCCh-HHHHHHHhC
Confidence 677775 3556677888999999999988775422 2233344567777888888988887543332 346677665
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
|
T Consensus 78 ~ 78 (265)
T cd06299 78 G 78 (265)
T ss_pred C
Confidence 5
No 283
>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=53.52 E-value=57 Score=27.37 Aligned_cols=71 Identities=21% Similarity=0.201 Sum_probs=46.9
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++.+.. ++.+.+...|.+|++|+++..-. .......+. +.+.....+.++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~-~~~l~~~~~~~v~~~~ 83 (195)
T cd08427 14 LLPRALARLRRRHP-DLEVHIVP-------GLSAELLARVDAGELDAAIVVEP-PFPLPKDLV-WTPLVREPLVLIAPAE 83 (195)
T ss_pred HhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCCCEEEEcCC-CCccccCce-EEEcccCcEEEEECCC
Confidence 44677888877763 34566665 45789999999999999975321 111123333 4677888888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 84 ~ 84 (195)
T cd08427 84 L 84 (195)
T ss_pred C
Confidence 4
No 284
>PRK09492 treR trehalose repressor; Provisional
Probab=53.08 E-value=1e+02 Score=28.90 Aligned_cols=87 Identities=15% Similarity=0.031 Sum_probs=53.0
Q ss_pred HHHHHHcCCcEEEEEEEe-C--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 5 ADIVDYFGWRNVIALYVD-D--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~d-d--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++-|..-|-++++++... . ..+....+.+++.+++.|+.+... .. ..+.+.-...++++.+..+..| ++.+..
T Consensus 167 ~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~-~~~~~~~~~~~~~~l~~~~~ai-~~~~D~ 242 (315)
T PRK09492 167 MQRLYDQGHRHISYLGVDHSDVTTGKRRHQAYLAFCKQHKLTPVAA--LG-GLSMQSGYELVAKVLTPETTAL-VCATDT 242 (315)
T ss_pred HHHHHHcCCCeEEEEcCCcccchhHHHHHHHHHHHHHHcCCCceee--cC-CCCchHHHHHHHHHhhcCCCEE-EEcCcH
Confidence 333444599999999632 2 234567888999999999865421 11 1121222334444433445554 456667
Q ss_pred HHHHHHHHHHHcCC
Q 011629 82 WGLEVLNAAKHLRM 95 (481)
Q Consensus 82 ~~~~il~~a~~~g~ 95 (481)
.+..++..+.+.|.
T Consensus 243 ~A~g~~~al~~~g~ 256 (315)
T PRK09492 243 LALGASKYLQEQGR 256 (315)
T ss_pred HHHHHHHHHHHcCC
Confidence 78888988888875
No 285
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=52.93 E-value=84 Score=28.52 Aligned_cols=76 Identities=11% Similarity=0.054 Sum_probs=49.3
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-HHHHHHHHHHH
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-WGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~~~~il~~a~~ 92 (481)
||++..+ +.|.....+.+++.+++.|+.+.... . ..+.+.....++.+.+.+++.||+..... .....+.++.+
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~--~-~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSI--A-NQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKK 78 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEec--C-CCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHH
Confidence 5666644 45666788999999999998876432 1 22333445667777777889888865432 23455666666
Q ss_pred cC
Q 011629 93 LR 94 (481)
Q Consensus 93 ~g 94 (481)
.|
T Consensus 79 ~~ 80 (267)
T cd06322 79 AG 80 (267)
T ss_pred CC
Confidence 55
No 286
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial. This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA.
Probab=52.80 E-value=80 Score=26.67 Aligned_cols=67 Identities=15% Similarity=0.083 Sum_probs=44.7
Q ss_pred CCcEEEEEEEeCCccc---chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhc-cCCceEEEEEeCc
Q 011629 12 GWRNVIALYVDDDHGR---NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVS-SMMSRILILHTYD 80 (481)
Q Consensus 12 gW~~V~ii~~dd~~g~---~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~-~s~~~vIvl~~~~ 80 (481)
..-+|++|...|+-+. .....+...+++.|+.+.....++. +.+.+.+.+++.. ....++||..+..
T Consensus 3 ~~~rv~vit~~d~~~~~~d~n~~~l~~~L~~~G~~v~~~~iv~D--d~~~i~~~l~~~~~~~~~DlVIttGGt 73 (163)
T TIGR02667 3 IPLRIAILTVSDTRTEEDDTSGQYLVERLTEAGHRLADRAIVKD--DIYQIRAQVSAWIADPDVQVILITGGT 73 (163)
T ss_pred CccEEEEEEEeCcCCccCCCcHHHHHHHHHHCCCeEEEEEEcCC--CHHHHHHHHHHHHhcCCCCEEEECCCc
Confidence 3457888876664332 3456778888999999888777754 3345667776653 3468888886643
No 287
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=52.54 E-value=99 Score=28.27 Aligned_cols=89 Identities=12% Similarity=-0.102 Sum_probs=49.8
Q ss_pred HHHHHH-cCCcEEEEEEEeCC-cccchHHHHHHHHHhcC---CEEEEEEecCCCCC-hhHHHHHHHHhccCCceEEEEEe
Q 011629 5 ADIVDY-FGWRNVIALYVDDD-HGRNGIAALGDKLAEKR---CRLSHKVPLSPKGS-RNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 5 ~~ll~~-fgW~~V~ii~~dd~-~g~~~~~~l~~~l~~~g---i~v~~~~~~~~~~~-~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
+.++.. .|-++++++..+.. ......+.+++.+++.| ..+..........+ .++....++++.+..+++ |++.
T Consensus 112 ~~ll~~~~G~~~I~~i~~~~~~~~~~r~~gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~pda-I~~~ 190 (265)
T cd06354 112 GYLAALMTKTGKVGFIGGMDIPLIRRFEAGFEAGVKYVNPGVPDIEVLVQYAGSFNDPAKGKEIAQAMYDQGADV-IFAA 190 (265)
T ss_pred HHHHHhhcCCCeEEEEecccChHHHHHHHHHHHHHHHHhccCCCceEEEEEcCcccCHHHHHHHHHHHHHCCCcE-EEEC
Confidence 355553 38899999975332 11222367788888888 65433222221111 123334455554444665 5555
Q ss_pred CcHHHHHHHHHHHHcC
Q 011629 79 YDIWGLEVLNAAKHLR 94 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g 94 (481)
+...+..+++.+++.|
T Consensus 191 nd~~A~gv~~al~~~g 206 (265)
T cd06354 191 AGGTGNGVFQAAKEAG 206 (265)
T ss_pred CCCCchHHHHHHHhcC
Confidence 6667778888888876
No 288
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=52.37 E-value=74 Score=28.99 Aligned_cols=79 Identities=14% Similarity=0.059 Sum_probs=49.2
Q ss_pred EEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHHHHH
Q 011629 15 NVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLNAAK 91 (481)
Q Consensus 15 ~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~~a~ 91 (481)
+||+|..+ +.|.....+.+++.++++|+.+.....-. ..+.......++++...+.+-||+...... ....+..+.
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgvii~~~~~~~~~~~l~~~~ 79 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQGPAS-ETDVAGQVNLLENAIARGPDAILLAPTDAKALVPPLKEAK 79 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHHcCCEEEEecCcc-CCCHHHHHHHHHHHHHhCCCEEEEcCCChhhhHHHHHHHH
Confidence 47777754 45666778888899999999877542111 112233456666776667888887654332 245666665
Q ss_pred HcC
Q 011629 92 HLR 94 (481)
Q Consensus 92 ~~g 94 (481)
+.+
T Consensus 80 ~~~ 82 (273)
T cd06310 80 DAG 82 (273)
T ss_pred HCC
Confidence 544
No 289
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=52.11 E-value=1.8e+02 Score=27.29 Aligned_cols=87 Identities=14% Similarity=-0.049 Sum_probs=53.3
Q ss_pred HHHHHHcCCcEEEEEEEe-C--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 5 ADIVDYFGWRNVIALYVD-D--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~d-d--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++.|..-|-+++++|... . ..+....+.+++.+++.|+.... .....+.++....++++-+.++. .|+|++..
T Consensus 164 ~~~L~~~Ghr~I~~i~~~~~~~~~~~~R~~gf~~a~~~~gi~~~~---~~~~~~~~~~~~~~~~~l~~~~t-Ai~~~~D~ 239 (311)
T TIGR02405 164 MANLYQQGHRHISFLGVDPSDKTTGLMRHNAYLAYCESANLEPIY---QTGQLSHESGYVLTDKVLKPETT-ALVCATDT 239 (311)
T ss_pred HHHHHHcCCCcEEEEccCcccchhHHHHHHHHHHHHHHcCCCcee---eeCCCCHHHHHHHHHHHHhcCCC-EEEECCcH
Confidence 444444599999999732 2 23456788899999999985321 11111222233344444333444 45677778
Q ss_pred HHHHHHHHHHHcCC
Q 011629 82 WGLEVLNAAKHLRM 95 (481)
Q Consensus 82 ~~~~il~~a~~~g~ 95 (481)
.+..++..+.+.|.
T Consensus 240 ~A~g~~~~l~~~g~ 253 (311)
T TIGR02405 240 LALGAAKYLQELDR 253 (311)
T ss_pred HHHHHHHHHHHcCC
Confidence 88888999988874
No 290
>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=51.98 E-value=74 Score=27.60 Aligned_cols=69 Identities=14% Similarity=0.171 Sum_probs=46.7
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++.+.. .+...+...|.+|++|+++... +.....+.+ .|.......++++++
T Consensus 14 ~l~~~l~~f~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~Di~i~~~---~~~~~~l~~-~~l~~~~~~~v~~~~ 81 (221)
T cd08469 14 LLPALVRRLETEAP-GIDLRIRP-------VTRLDLAEQLDLGRIDLVIGIF---EQIPPRFRR-RTLFDEDEVWVMRKD 81 (221)
T ss_pred HHHHHHHHHHHHCC-CcEEEEee-------CChhhHHHHHHCCCccEEEecC---CCCCcccee-eeeeccceEEEEeCC
Confidence 34567777777653 35566665 4567899999999999997632 222344544 688888888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 82 ~ 82 (221)
T cd08469 82 H 82 (221)
T ss_pred C
Confidence 4
No 291
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=51.96 E-value=1.5e+02 Score=27.03 Aligned_cols=97 Identities=12% Similarity=0.049 Sum_probs=55.4
Q ss_pred HhHHHHHH-cCCcEEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCce-EEEEEe
Q 011629 3 AIADIVDY-FGWRNVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSR-ILILHT 78 (481)
Q Consensus 3 Ai~~ll~~-fgW~~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~-vIvl~~ 78 (481)
++++.|.. -|-++++++..+. ..+....+.+.+.++.+++.+.. +....+.++....++++-++..+ ..|++.
T Consensus 114 ~~~~~l~~~~g~~~i~~i~g~~~~~~~~~r~~g~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~~aI~~~ 190 (271)
T cd06312 114 AAGERLAELKGGKNVLCVIHEPGNVTLEDRCAGFADGLGGAGITEEV---IETGADPTEVASRIAAYLRANPDVDAVLTL 190 (271)
T ss_pred HHHHHHHHhcCCCeEEEEecCCCCccHHHHHHHHHHHHHhcCceeeE---eecCCCHHHHHHHHHHHHHhCCCccEEEEe
Confidence 45555555 6889999997533 33456788888888888765432 11122222334445544332222 234444
Q ss_pred CcHHHHHHHHHHHHcCCccCCeEEEE
Q 011629 79 YDIWGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 79 ~~~~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
+...+..++..+.+.|+. +.+-|.
T Consensus 191 ~d~~a~g~~~al~~~g~~--~di~vv 214 (271)
T cd06312 191 GAPSAAPAAKALKQAGLK--GKVKLG 214 (271)
T ss_pred CCccchHHHHHHHhcCCC--CCeEEE
Confidence 556677788888888764 334444
No 292
>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=51.94 E-value=73 Score=26.86 Aligned_cols=69 Identities=12% Similarity=0.061 Sum_probs=46.2
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++.+.. .+...+...+.+|++|+++... +.....+.+ .+.......++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~~~-~~l~~~~~~~v~~~~ 81 (199)
T cd08426 14 LLPSLIARFRQRYP-GVFFTVDV-------ASTADVLEAVLSGEADIGLAFS---PPPEPGIRV-HSRQPAPIGAVVPPG 81 (199)
T ss_pred HHHHHHHHHHHhCC-CeEEEEEe-------CCcHHHHHHHHCCCccEEEecC---CCCCCCeEE-EeeccCcEEEEecCC
Confidence 34577777777652 34566665 4567899999999999997532 222233443 678888888888665
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 82 h 82 (199)
T cd08426 82 H 82 (199)
T ss_pred C
Confidence 4
No 293
>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=51.92 E-value=53 Score=27.90 Aligned_cols=69 Identities=16% Similarity=0.138 Sum_probs=46.7
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++.+.. ++.+.+...|.+|++|+++.... .....+. +.|.....+.++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~v~i~~-------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~l~-~~~l~~~~~~~v~~~~ 81 (201)
T cd08459 14 FLPRLLAALREVAP-GVRIETVR-------LPVDELEEALESGEIDLAIGYLP---DLGAGFF-QQRLFRERYVCLVRKD 81 (201)
T ss_pred HHHHHHHHHHHHCC-CCeEEEEe-------cCccCHHHHhhCCCceEEEEcCC---CCcccce-EEEeecCceEEEEcCC
Confidence 34577888887763 35566665 45668899999999999975322 2223343 4688888888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 82 ~ 82 (201)
T cd08459 82 H 82 (201)
T ss_pred C
Confidence 4
No 294
>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=51.89 E-value=47 Score=28.13 Aligned_cols=69 Identities=25% Similarity=0.289 Sum_probs=46.5
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++.+.. .+...+...|.+|++|+++.. .+.....+. +.++....+.++++++
T Consensus 14 ~~~~~i~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~---~~~~~~~~~-~~~l~~~~~~~v~~~~ 81 (200)
T cd08417 14 LLPPLLARLRQEAP-GVRLRFVP-------LDRDDLEEALESGEIDLAIGV---FPELPPGLR-SQPLFEDRFVCVARKD 81 (200)
T ss_pred HHHHHHHHHHhhCC-CeEEEecc-------CCHHHHHHHHHcCCCCEEEee---cccCCCccc-hhhhhcCceEEEecCC
Confidence 34567777777652 34466654 457789999999999999753 223333343 3678888888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 82 ~ 82 (200)
T cd08417 82 H 82 (200)
T ss_pred C
Confidence 4
No 295
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=51.84 E-value=74 Score=28.77 Aligned_cols=77 Identities=13% Similarity=0.013 Sum_probs=48.4
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++.. ++.|.....+.+.+.+++.|+.+..... ..+.......++++...+.+.||+..........+..+.+.
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATT---DYDAEREADAVETLLRQRVDGLILTVADAATSPALDLLDAE 78 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeC---CCCHHHHHHHHHHHHhcCCCEEEEecCCCCchHHHHHHhhC
Confidence 566664 3456667788899999999998876422 22223345667777777788888764322223456666665
Q ss_pred CC
Q 011629 94 RM 95 (481)
Q Consensus 94 g~ 95 (481)
|.
T Consensus 79 ~i 80 (266)
T cd06282 79 RV 80 (266)
T ss_pred CC
Confidence 53
No 296
>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=51.63 E-value=95 Score=26.37 Aligned_cols=69 Identities=13% Similarity=0.118 Sum_probs=44.5
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.- ++++.+.. ..-+.+..+|.+|++|+++..... ....+.+ .++....+.++++++
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~~-~~l~~~~~~~~~~~~ 82 (198)
T cd08485 15 TLPLLLRQLLSVAP-SATVSLTQ-------MSKNRQIEALDAGTIDIGFGRFYP---YQEGVVV-RNVTNERLFLGAQKS 82 (198)
T ss_pred HHHHHHHHHHHhCC-CcEEEEEE-------CCHHHHHHHHHcCCccEEEecCCC---CCCCeEE-EEeeccceEEEeCCC
Confidence 34677888877652 45566664 456789999999999998753211 1233433 567777777777544
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 83 ~ 83 (198)
T cd08485 83 R 83 (198)
T ss_pred C
Confidence 3
No 297
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=51.50 E-value=1.9e+02 Score=26.36 Aligned_cols=90 Identities=10% Similarity=0.023 Sum_probs=51.3
Q ss_pred hHHHHHHc--CCcEEEEEEEeCCc--ccchHHHHHHHHHhcC-CEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEEE
Q 011629 4 IADIVDYF--GWRNVIALYVDDDH--GRNGIAALGDKLAEKR-CRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LILH 77 (481)
Q Consensus 4 i~~ll~~f--gW~~V~ii~~dd~~--g~~~~~~l~~~l~~~g-i~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl~ 77 (481)
+++.|... |.++|+++..+... .....+.+++.+++.+ +.+... .....+.+.....++++.+...++ .|++
T Consensus 112 ~~~~l~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~ 189 (272)
T cd06313 112 VAQALCNAMGGKGKIAMLQGALGHTGAQGRAQGFNDVIKKYPDIEVVDE--QPANWDVSKAARIWETWLTKYPQLDGAFC 189 (272)
T ss_pred HHHHHHHHcCCCceEEEEECCCCCcchhHHHHHHHHHHHhCCCCEEEec--cCCCCCHHHHHHHHHHHHHhCCCCCEEEE
Confidence 34434334 88999999854322 3356788888888875 554331 222222223334455543322222 3455
Q ss_pred eCcHHHHHHHHHHHHcCC
Q 011629 78 TYDIWGLEVLNAAKHLRM 95 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~ 95 (481)
.+...+..++..+.+.|+
T Consensus 190 ~nd~~a~g~~~al~~~g~ 207 (272)
T cd06313 190 HNDSMALAAYQIMKAAGR 207 (272)
T ss_pred CCCcHHHHHHHHHHHcCC
Confidence 556677788888888876
No 298
>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=51.28 E-value=59 Score=27.74 Aligned_cols=70 Identities=16% Similarity=0.149 Sum_probs=46.3
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++.+.. .........|.+|++|+++... +.....+. ..+.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~ 80 (200)
T cd08467 13 ALLPRLAPRLRERAP-GLDLRLCP-------IGDDLAERGLEQGTIDLAVGRF---AVPPDGLV-VRRLYDDGFACLVRH 80 (200)
T ss_pred HHHHHHHHHHHhhCC-CCEEEEec-------CCcccHHHHhhCCCcCEEEecC---CCCCccce-eEEeeeccEEEEEcC
Confidence 344677888877753 35566665 4567899999999999987521 22223343 357778888888765
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 81 ~h 82 (200)
T cd08467 81 GH 82 (200)
T ss_pred CC
Confidence 43
No 299
>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=50.92 E-value=89 Score=26.26 Aligned_cols=69 Identities=17% Similarity=0.194 Sum_probs=45.9
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.+... ++++.+.. .....+...+.+|++|+++.. .+.....+. +.+.......+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~-------~~~~~~~~~l~~g~~D~~i~~---~~~~~~~~~-~~~l~~~~~~~v~~~ 80 (198)
T cd08447 13 SFLPRLLAAARAALP-DVDLVLRE-------MVTTDQIEALESGRIDLGLLR---PPFARPGLE-TRPLVREPLVAAVPA 80 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHcCCceEEEec---CCCCCCCee-EEEeecCceEEEecC
Confidence 344677888877763 35566655 457889999999999999753 222223332 356777777777765
Q ss_pred C
Q 011629 425 K 425 (481)
Q Consensus 425 ~ 425 (481)
+
T Consensus 81 ~ 81 (198)
T cd08447 81 G 81 (198)
T ss_pred C
Confidence 4
No 300
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=50.61 E-value=78 Score=28.72 Aligned_cols=77 Identities=12% Similarity=-0.083 Sum_probs=47.8
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++..+ +.|.....+.+++.+++.|+.+..... ... ..+.....++.+...+.+.||+..........+..+.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~-~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 79 (270)
T cd01545 2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPC-DSG-SPDLAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEA 79 (270)
T ss_pred EEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeC-CCC-chHHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHHhc
Confidence 5677744 567778889999999999988765432 111 212344556667677788887764332234555555554
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 80 ~ 80 (270)
T cd01545 80 G 80 (270)
T ss_pred C
Confidence 4
No 301
>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=50.55 E-value=63 Score=27.48 Aligned_cols=67 Identities=19% Similarity=0.208 Sum_probs=43.9
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-..++..+.++.. ++++.+.. .+- .+.+.|.+|++|+++..- +.....+.+ .|+......++++++.
T Consensus 15 l~~~i~~~~~~~P-~i~l~i~~-------~~~-~~~~~l~~g~~D~~i~~~---~~~~~~~~~-~~l~~~~~~~v~~~~h 81 (200)
T cd08462 15 LPPVIERVAREAP-GVRFELLP-------PDD-QPHELLERGEVDLLIAPE---RFMSDGHPS-EPLFEEEFVCVVWADN 81 (200)
T ss_pred HHHHHHHHHHHCC-CCEEEEec-------CCh-hHHHHHhcCCeeEEEecC---CCCCCCcee-eeeeccceEEEEcCCC
Confidence 3567777777663 34566664 344 899999999999997532 222233433 5777888888876554
No 302
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=50.29 E-value=85 Score=27.91 Aligned_cols=77 Identities=12% Similarity=0.022 Sum_probs=48.8
Q ss_pred EEEEEEEe---CCcccchHHHHHHHHHh--cCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHH
Q 011629 15 NVIALYVD---DDHGRNGIAALGDKLAE--KRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNA 89 (481)
Q Consensus 15 ~V~ii~~d---d~~g~~~~~~l~~~l~~--~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~ 89 (481)
+||+|..+ +.++....+.+++.+.+ .++.+.... ...+.++....++++...+...||+.........+...
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~ 77 (269)
T cd01391 1 KIGVLLPLSGSAPFGAQLLAGIELAAEEIGRGLEVILAD---SQSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVEL 77 (269)
T ss_pred CceEEeecCCCcHHHHHHHHHHHHHHHHhCCceEEEEec---CCCCHHHHHHHHHHHHHcCCCEEEecCCCHHHHHHHHH
Confidence 36777753 45667778888888888 677665432 22222345566777777778888877665544445666
Q ss_pred HHHcC
Q 011629 90 AKHLR 94 (481)
Q Consensus 90 a~~~g 94 (481)
+.+.+
T Consensus 78 ~~~~~ 82 (269)
T cd01391 78 AAAAG 82 (269)
T ss_pred HHHcC
Confidence 65544
No 303
>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=50.29 E-value=90 Score=26.16 Aligned_cols=71 Identities=13% Similarity=-0.005 Sum_probs=46.9
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-..++..+.++.. ++++.+.. .+...+...|.+|++|+++...... .+...+.+ .+.....+.++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~-~~~~~~~~-~~l~~~~~~~v~~~~ 83 (197)
T cd08449 14 GLGPALRRFKRQYP-NVTVRFHE-------LSPEAQKAALLSKRIDLGFVRFADT-LNDPPLAS-ELLWREPMVVALPEE 83 (197)
T ss_pred hHHHHHHHHHHHCC-CeEEEEEE-------CCHHHHHHHHhCCCccEEEeccccc-CCCCCceE-EEEEEeeEEEEecCC
Confidence 44677888887762 35566665 4578899999999999987532211 01233433 677888888888654
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 84 ~ 84 (197)
T cd08449 84 H 84 (197)
T ss_pred C
Confidence 3
No 304
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=50.28 E-value=1.6e+02 Score=26.58 Aligned_cols=99 Identities=14% Similarity=0.113 Sum_probs=51.7
Q ss_pred hHHHHHHcCCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~ 79 (481)
+++.+...|-++|+++..+.. ......+.+.+.+++.|+.+... ... ..+.++....+.++.+. ..++|+ +.+
T Consensus 106 ~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~l~~~~~~~~i~-~~~ 182 (266)
T cd06278 106 AAELLLAKGCRRIAFIGGPADTSTSRERERGFRDALAAAGVPVVVE-EAG-DYSYEGGYEAARRLLASRPRPDAIF-CAN 182 (266)
T ss_pred HHHHHHHCCCceEEEEcCCCcccchHHHHHHHHHHHHHcCCChhhh-ccC-CCCHHHHHHHHHHHHhcCCCCCEEE-EcC
Confidence 445555568889999985433 34456778888888888764221 111 11222233334443332 344433 344
Q ss_pred cHHHHHHHHHHHHc-CCccCCeEEEEe
Q 011629 80 DIWGLEVLNAAKHL-RMMESGYVWIVT 105 (481)
Q Consensus 80 ~~~~~~il~~a~~~-g~~~~~~~wI~~ 105 (481)
...+..++..+.+. +...++.+-|++
T Consensus 183 ~~~a~~~~~~l~~~~~~~~p~di~i~~ 209 (266)
T cd06278 183 DLLAIGVMDAARQEGGLRVPEDVSVIG 209 (266)
T ss_pred cHHHHHHHHHHHHhcCCCCccceEEEE
Confidence 44556666666654 343344444443
No 305
>cd08180 PDD 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism. 1,3-propanediol dehydrogenase (PPD) plays a role in glycerol metabolism of some bacteria in anaerobic conditions. In this degradation pathway, glycerol is converted in a two-step process to 1,3-propanediol (1,3-PD) which is then excreted into the extracellular medium. The first reaction involves the transformation of glycerol into 3-hydroxypropionaldehyde (3-HPA) by a coenzyme B-12-dependent dehydratase. The second reaction involves the dismutation of the 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol by the NADH-linked 1,3-propanediol dehydrogenase (PPD). The enzyme require iron ion for its function. Because many genes in this pathway are present in the pdu (propanediol utilisation) operon, they are also named pdu genes. PPD is a member of the iron-containing alcohol dehydrogenase superfamily. The PPD structure has a dehydroquinat
Probab=50.21 E-value=78 Score=30.36 Aligned_cols=71 Identities=8% Similarity=0.010 Sum_probs=47.6
Q ss_pred HHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 8 VDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 8 l~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
+..++.+++.+|++.........+.+.+.+++. +.+.....+..+.+.+...+.++.+++.+++.||..+.
T Consensus 17 l~~~~~~~~lvv~~~~~~~~g~~~~v~~~l~~~-~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IiaiGG 87 (332)
T cd08180 17 LKELKNKRVLIVTDPFMVKSGMLDKVTDHLDSS-IEVEIFSDVVPDPPIEVVAKGIKKFLDFKPDIVIALGG 87 (332)
T ss_pred HHHhCCCeEEEEeCchhhhCccHHHHHHHHHhc-CcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEECC
Confidence 355666898888854333333567788888876 65543333444455566778888888888999997765
No 306
>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=49.75 E-value=80 Score=26.56 Aligned_cols=70 Identities=20% Similarity=0.238 Sum_probs=46.8
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.++++++.++.- ++++++.. .+...+...+.+|++|+++..... .....+ -+.+.+...+.++++++
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~v~~~~ 83 (199)
T cd08451 15 LVPGLIRRFREAYP-DVELTLEE-------ANTAELLEALREGRLDAAFVRPPV--ARSDGL-VLELLLEEPMLVALPAG 83 (199)
T ss_pred ccHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHCCCccEEEEecCC--CCCCce-eEEEeecccEEEEecCC
Confidence 44678888887763 34566665 457789999999999999753221 112223 33677888888887654
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 84 ~ 84 (199)
T cd08451 84 H 84 (199)
T ss_pred C
Confidence 3
No 307
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=49.72 E-value=1e+02 Score=28.00 Aligned_cols=75 Identities=16% Similarity=0.002 Sum_probs=46.8
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++.. ++.+.....+.+.+++++.|+.+... ....+.+.....++++.+.+++.||+.+... ....+..+.+.
T Consensus 2 i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~---~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06273 2 IGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVA---SSGYDLDREYAQARKLLERGVDGLALIGLDH-SPALLDLLARR 77 (268)
T ss_pred eEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEe---cCCCCHHHHHHHHHHHHhcCCCEEEEeCCCC-CHHHHHHHHhC
Confidence 567774 35566677888999999999887652 2222333345667777777788777765432 22444555554
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 78 ~ 78 (268)
T cd06273 78 G 78 (268)
T ss_pred C
Confidence 4
No 308
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=49.65 E-value=1.2e+02 Score=29.11 Aligned_cols=80 Identities=8% Similarity=-0.081 Sum_probs=53.6
Q ss_pred cEEEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHHH
Q 011629 14 RNVIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNAA 90 (481)
Q Consensus 14 ~~V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~a 90 (481)
.+++++.. ++.|.....+.+++.+++.|+++... .+...+.+.-...++.+...+.+.|++.... ..+...+.+|
T Consensus 24 ~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~G~~v~~~--~~~~~d~~~q~~~i~~li~~~vdgIiv~~~d~~al~~~l~~a 101 (336)
T PRK15408 24 ERIAFIPKLVGVGFFTSGGNGAKEAGKELGVDVTYD--GPTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALKRA 101 (336)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHHHHHHhCCEEEEE--CCCCCCHHHHHHHHHHHHHcCCCEEEEecCCHHHHHHHHHHH
Confidence 36777774 34677777888899999999888753 2322232223356777777888888886543 4446778888
Q ss_pred HHcCC
Q 011629 91 KHLRM 95 (481)
Q Consensus 91 ~~~g~ 95 (481)
.+.|.
T Consensus 102 ~~~gI 106 (336)
T PRK15408 102 MQRGV 106 (336)
T ss_pred HHCCC
Confidence 87663
No 309
>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=49.16 E-value=93 Score=26.10 Aligned_cols=72 Identities=15% Similarity=0.093 Sum_probs=46.7
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeec--cccccceeeccceeecceEEEEe
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAIT--TERTKMVDFTQPYIESGLVVVAP 423 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t--~~r~~~~~fs~p~~~~~~~~~~~ 423 (481)
+-.+++..+.+... ++++.+.. .+-..+...|.+|++|+++..-... ......+. +.+.......++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~ 84 (200)
T cd08423 14 LLPPALAALRARHP-GLEVRLRE-------AEPPESLDALRAGELDLAVVFDYPVTPPPDDPGLT-RVPLLDDPLDLVLP 84 (200)
T ss_pred hhhHHHHHHHHhCC-CCeEEEEe-------CCHHHHHHHHhcCCccEEEEeccccccCCCCCCcE-EEEeccCcEEEEec
Confidence 34677788887763 35566665 4467889999999999997532110 12233343 46778888888886
Q ss_pred cCC
Q 011629 424 IKK 426 (481)
Q Consensus 424 ~~~ 426 (481)
+..
T Consensus 85 ~~~ 87 (200)
T cd08423 85 ADH 87 (200)
T ss_pred CCC
Confidence 543
No 310
>cd08197 DOIS 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-Deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes neomycin, kanamycin, gentamicin, and ribostamycin. They are important antibacterial agents. DOIS is a homologue of the dehydroquinate synthase which catalyzes the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate (DHQ) in the shikimate pathway.
Probab=49.03 E-value=95 Score=30.15 Aligned_cols=83 Identities=7% Similarity=-0.068 Sum_probs=52.8
Q ss_pred HHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecC---CCCChhHHHHHHHHhccCCce---EEEEEe
Q 011629 5 ADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLS---PKGSRNQIIDTLLTVSSMMSR---ILILHT 78 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~---~~~~~~~~~~~l~~i~~s~~~---vIvl~~ 78 (481)
.++++.+|-+++.+|++.... ....+.+.+.+++.|+.+... .++ .+.+.+.....+..+++.+++ +||..+
T Consensus 15 ~~~l~~~g~~rvlvVtd~~v~-~~~~~~l~~~L~~~g~~~~~~-~~~~~e~~k~~~~v~~~~~~~~~~~~dr~~~IIAvG 92 (355)
T cd08197 15 LGYLPELNADKYLLVTDSNVE-DLYGHRLLEYLREAGAPVELL-SVPSGEEHKTLSTLSDLVERALALGATRRSVIVALG 92 (355)
T ss_pred HHHHHhcCCCeEEEEECccHH-HHHHHHHHHHHHhcCCceEEE-EeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEEEC
Confidence 456677777888888855443 335677888999888865432 233 233445677777888777776 777766
Q ss_pred Cc--HHHHHHHHH
Q 011629 79 YD--IWGLEVLNA 89 (481)
Q Consensus 79 ~~--~~~~~il~~ 89 (481)
.. .++..++..
T Consensus 93 GGsv~D~ak~~A~ 105 (355)
T cd08197 93 GGVVGNIAGLLAA 105 (355)
T ss_pred CcHHHHHHHHHHH
Confidence 53 344444443
No 311
>KOG0025 consensus Zn2+-binding dehydrogenase (nuclear receptor binding factor-1) [Transcription; Energy production and conversion]
Probab=48.95 E-value=1.1e+02 Score=28.67 Aligned_cols=83 Identities=8% Similarity=-0.036 Sum_probs=56.4
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
+|+++|.+++|-+.+.+|-+-+ ..+.|.+.|...|....+++.=-. + -.....+.....+|.-+=|....
T Consensus 175 ~~ViQlaka~GiktinvVRdR~-----~ieel~~~Lk~lGA~~ViTeeel~--~---~~~~k~~~~~~~prLalNcVGGk 244 (354)
T KOG0025|consen 175 QAVIQLAKALGIKTINVVRDRP-----NIEELKKQLKSLGATEVITEEELR--D---RKMKKFKGDNPRPRLALNCVGGK 244 (354)
T ss_pred HHHHHHHHHhCcceEEEeecCc-----cHHHHHHHHHHcCCceEecHHHhc--c---hhhhhhhccCCCceEEEeccCch
Confidence 6889999999999999998655 478999999998887655432111 1 11111123345567667677777
Q ss_pred HHHHHHHHHHHcC
Q 011629 82 WGLEVLNAAKHLR 94 (481)
Q Consensus 82 ~~~~il~~a~~~g 94 (481)
.+..+.+...+-|
T Consensus 245 sa~~iar~L~~Gg 257 (354)
T KOG0025|consen 245 SATEIARYLERGG 257 (354)
T ss_pred hHHHHHHHHhcCc
Confidence 8888888776644
No 312
>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=48.86 E-value=79 Score=26.46 Aligned_cols=69 Identities=20% Similarity=0.297 Sum_probs=46.0
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-..++..+.++.. ++++++.. .....+..+|.+|++|+++.... .....+ -+.+.....+.++++++
T Consensus 13 ~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~~~~~~~ 80 (197)
T cd08419 13 FAPRLLGAFCRRHP-GVEVSLRV-------GNREQVLERLADNEDDLAIMGRP---PEDLDL-VAEPFLDNPLVVIAPPD 80 (197)
T ss_pred HhhHHHHHHHHHCC-CceEEEEE-------CCHHHHHHHHhcCCccEEEecCC---CCCCCe-EEEEeccCCEEEEecCC
Confidence 44677788877752 34566665 45778899999999999975322 112223 34678888888888755
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 81 ~ 81 (197)
T cd08419 81 H 81 (197)
T ss_pred C
Confidence 4
No 313
>PF03830 PTSIIB_sorb: PTS system sorbose subfamily IIB component; InterPro: IPR004720 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This entry is specific for the IIB components of this family of PTS transporters [].; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 3LFJ_B 1BLE_A 3P3V_B 1NRZ_C 3EYE_A 1VSQ_C 2JZH_A 2JZN_C 2JZO_D.
Probab=48.85 E-value=74 Score=26.52 Aligned_cols=79 Identities=18% Similarity=0.098 Sum_probs=56.0
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~ 82 (481)
.+...+++++-+.+.++- |........+.+.+.+.-.|+.+... +.++....+++-...+.+++|++-++.+
T Consensus 16 V~~~W~~~~~~~~IiVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~-------sv~~a~~~l~~~~~~~~~v~ii~k~~~d 87 (151)
T PF03830_consen 16 VATAWVKKLNANRIIVVD-DEVANDPFQKMILKMAAPAGVKLSIF-------SVEEAIEKLKKPEYSKKRVLIIVKSPED 87 (151)
T ss_dssp HHHHHHHHHTTSEEEEE--HHHHHSHHHHHHHHHTSHTTSEEEEE--------HHHHHHHHCGGGGTTEEEEEEESSHHH
T ss_pred eeEEEhhhcccCEEEEEC-HHHhcCHHHHHHHHHhhcCCCceEEE-------EHHHHHHHHHhcccCCceEEEEECCHHH
Confidence 456778889999888665 55555567777777777788887643 2234556666666677899999999988
Q ss_pred HHHHHHH
Q 011629 83 GLEVLNA 89 (481)
Q Consensus 83 ~~~il~~ 89 (481)
+..+...
T Consensus 88 ~~~l~~~ 94 (151)
T PF03830_consen 88 ALRLVEA 94 (151)
T ss_dssp HHHHHHT
T ss_pred HHHHHhc
Confidence 8777764
No 314
>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=48.45 E-value=99 Score=26.00 Aligned_cols=72 Identities=14% Similarity=0.152 Sum_probs=46.4
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
++-.+++.++.++.. ++++.+.. .....+...|.+|++|+++..... +.....+. +.+.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~l~-~~~l~~~~~~~v~~~ 82 (199)
T cd08416 13 NTVPRIIMGLKLRRP-ELDIELTL-------GSNKDLLKKLKDGELDAILVATPE-GLNDPDFE-VVPLFEDDIFLAVPA 82 (199)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEEE-------cCcHHHHHHHhCCCCCEEEEecCC-cCCCCCeE-EEEeecceEEEEECC
Confidence 345677888887773 35566665 456778999999999999763211 11223333 367777788888765
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
..
T Consensus 83 ~h 84 (199)
T cd08416 83 TS 84 (199)
T ss_pred CC
Confidence 43
No 315
>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=48.44 E-value=1.1e+02 Score=26.06 Aligned_cols=70 Identities=17% Similarity=0.226 Sum_probs=47.1
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++++.. .+...+...+.+|++|+++... +.....+. +.++....+.+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~ 81 (203)
T cd08445 14 GLLPELIRRFRQAAP-DVEIELIE-------MTTVQQIEALKEGRIDVGFGRL---RIEDPAIR-RIVLREEPLVVALPA 81 (203)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHcCCCcEEEecC---CCCCCCce-eEEEEeccEEEEeeC
Confidence 345677888877763 34566665 4578999999999999997532 22223343 357788888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 82 ~h 83 (203)
T cd08445 82 GH 83 (203)
T ss_pred CC
Confidence 43
No 316
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=48.33 E-value=1e+02 Score=28.02 Aligned_cols=79 Identities=11% Similarity=-0.019 Sum_probs=49.2
Q ss_pred EEEEEEEe--CCcccchHHHHHHHHHhc---CCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHH
Q 011629 15 NVIALYVD--DDHGRNGIAALGDKLAEK---RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLN 88 (481)
Q Consensus 15 ~V~ii~~d--d~~g~~~~~~l~~~l~~~---gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~ 88 (481)
+|+++..+ +.|.....+.+++.+++. |..+..... ....+.+.....++++...+++.||+...... ....+.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i~-~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~ 79 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIVT-SADGDVAQQIADIRNLIAQGVDAIIINPASPTALNPVIE 79 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEEe-cCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHH
Confidence 36666643 345556788888888888 875544432 22223334567777777778999988765432 344566
Q ss_pred HHHHcC
Q 011629 89 AAKHLR 94 (481)
Q Consensus 89 ~a~~~g 94 (481)
.+.+.|
T Consensus 80 ~~~~~~ 85 (272)
T cd06300 80 EACEAG 85 (272)
T ss_pred HHHHCC
Confidence 666654
No 317
>PF07302 AroM: AroM protein; InterPro: IPR010843 This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL []. The function of this family is unknown.
Probab=48.27 E-value=1.6e+02 Score=26.26 Aligned_cols=74 Identities=11% Similarity=0.107 Sum_probs=48.7
Q ss_pred cEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEe--CcHHHHHHHHHHH
Q 011629 14 RNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHT--YDIWGLEVLNAAK 91 (481)
Q Consensus 14 ~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~--~~~~~~~il~~a~ 91 (481)
.++|+|.-..+. .....+.....+..+.+...-|...+.+++....+++++.++++||+.| ++...+.+++++.
T Consensus 126 ~~vGVivP~~eQ----~~~~~~kW~~l~~~~~~a~asPy~~~~~~l~~Aa~~L~~~gadlIvLDCmGYt~~~r~~~~~~~ 201 (221)
T PF07302_consen 126 HQVGVIVPLPEQ----IAQQAEKWQPLGNPVVVAAASPYEGDEEELAAAARELAEQGADLIVLDCMGYTQEMRDIVQRAL 201 (221)
T ss_pred CeEEEEecCHHH----HHHHHHHHHhcCCCeEEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEECCCCCHHHHHHHHHHh
Confidence 688888866542 3333344455554454443333334566788888999999999999975 5677788887763
No 318
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=47.88 E-value=1.2e+02 Score=28.16 Aligned_cols=79 Identities=6% Similarity=-0.021 Sum_probs=50.7
Q ss_pred CcEEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-HHHHHHHH
Q 011629 13 WRNVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-WGLEVLNA 89 (481)
Q Consensus 13 W~~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~~~~il~~ 89 (481)
=+.++++..+ +.|.....+.+.+.++++|+.+.... ...+.+.....++.+...+++.||+..... .....+..
T Consensus 26 ~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~---~~~d~~~~~~~~~~l~~~~~dgiii~~~~~~~~~~~l~~ 102 (295)
T PRK10653 26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLD---SQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKM 102 (295)
T ss_pred CCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEec---CCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHH
Confidence 4678888853 45666778889999999998876532 122223345667777667788777765433 22355666
Q ss_pred HHHcC
Q 011629 90 AKHLR 94 (481)
Q Consensus 90 a~~~g 94 (481)
+.+.|
T Consensus 103 ~~~~~ 107 (295)
T PRK10653 103 ANQAN 107 (295)
T ss_pred HHHCC
Confidence 66554
No 319
>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2.; GO: 0016021 integral to membrane
Probab=47.76 E-value=27 Score=25.53 Aligned_cols=23 Identities=17% Similarity=0.505 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcc
Q 011629 441 KMWCVTGIFFLVVGVVVWILEHR 463 (481)
Q Consensus 441 ~~W~~~~~~~~~~~~~~~~~~~~ 463 (481)
++|+++++.++++.+++|++.-.
T Consensus 34 gm~~lvI~~iFil~VilwfvCC~ 56 (94)
T PF05393_consen 34 GMWFLVICGIFILLVILWFVCCK 56 (94)
T ss_pred chhHHHHHHHHHHHHHHHHHHHH
Confidence 57777777777778888877543
No 320
>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=47.68 E-value=95 Score=26.11 Aligned_cols=69 Identities=20% Similarity=0.266 Sum_probs=45.9
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.+... ++++.+.. .+-..+...|.+|++|+++.. .+.....+. +.+.....+.++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~---~~~~~~~~~-~~~l~~~~~~~~~~~~ 81 (198)
T cd08433 14 LAVPLLRAVRRRYP-GIRLRIVE-------GLSGHLLEWLLNGRLDLALLY---GPPPIPGLS-TEPLLEEDLFLVGPAD 81 (198)
T ss_pred cchHHHHHHHHHCC-CcEEEEEe-------cCcHHHHHHHhCCCCcEEEEe---CCCCCCCee-EEEeccccEEEEecCC
Confidence 34677888887763 34566664 345688899999999999753 222233332 3677888888888655
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 82 ~ 82 (198)
T cd08433 82 A 82 (198)
T ss_pred C
Confidence 4
No 321
>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=47.49 E-value=79 Score=26.83 Aligned_cols=69 Identities=17% Similarity=0.227 Sum_probs=45.5
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.- ++++++.. ++. .++..|.+|++|+++... +.....+.+ .|.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~v~l~~-------~~~-~~~~~l~~g~~D~~i~~~---~~~~~~~~~-~~l~~~~~~~v~~~ 79 (200)
T cd08460 13 AFGPALLAAVAAEAP-GVRLRFVP-------ESD-KDVDALREGRIDLEIGVL---GPTGPEIRV-QTLFRDRFVGVVRA 79 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec-------Cch-hHHHHHHCCCccEEEecC---CCCCcchhe-eeeeccceEEEEeC
Confidence 445677888887763 35566664 345 788999999999987532 112233443 67778888888765
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 80 ~h 81 (200)
T cd08460 80 GH 81 (200)
T ss_pred CC
Confidence 44
No 322
>PRK00843 egsA NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed
Probab=46.66 E-value=92 Score=30.15 Aligned_cols=80 Identities=8% Similarity=0.025 Sum_probs=51.4
Q ss_pred hHHHHHHcCC-cEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc--
Q 011629 4 IADIVDYFGW-RNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-- 80 (481)
Q Consensus 4 i~~ll~~fgW-~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-- 80 (481)
+.++++.++- +++.+|++...+ ....+.+++.+.+.| .+... +..+.+.+.+...++.+++.+.++||..+..
T Consensus 24 l~~~l~~~~~~~~~livtd~~~~-~~~~~~l~~~l~~~~-~~~~~--~~~~~t~~~v~~~~~~~~~~~~d~IIaiGGGsv 99 (350)
T PRK00843 24 IGDVCSDLKLTGRALIVTGPTTK-KIAGDRVEENLEDAG-DVEVV--IVDEATMEEVEKVEEKAKDVNAGFLIGVGGGKV 99 (350)
T ss_pred HHHHHHHhCCCCeEEEEECCcHH-HHHHHHHHHHHHhcC-CeeEE--eCCCCCHHHHHHHHHHhhccCCCEEEEeCCchH
Confidence 3456777776 788888754443 234567788888777 44322 3334566677888888888788998877653
Q ss_pred HHHHHHH
Q 011629 81 IWGLEVL 87 (481)
Q Consensus 81 ~~~~~il 87 (481)
.++..++
T Consensus 100 ~D~ak~v 106 (350)
T PRK00843 100 IDVAKLA 106 (350)
T ss_pred HHHHHHH
Confidence 3444443
No 323
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=46.24 E-value=1.6e+02 Score=23.86 Aligned_cols=65 Identities=6% Similarity=-0.033 Sum_probs=43.1
Q ss_pred CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH----HHHHHHHHHHHcC
Q 011629 24 DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI----WGLEVLNAAKHLR 94 (481)
Q Consensus 24 ~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~----~~~~il~~a~~~g 94 (481)
|--..+...+...|+..|+.|...... .+ ....++..+++++++|++++... .+..++....+.+
T Consensus 13 D~Hd~g~~iv~~~l~~~GfeVi~lg~~---~s---~e~~v~aa~e~~adii~iSsl~~~~~~~~~~~~~~L~~~g 81 (132)
T TIGR00640 13 DGHDRGAKVIATAYADLGFDVDVGPLF---QT---PEEIARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLG 81 (132)
T ss_pred CccHHHHHHHHHHHHhCCcEEEECCCC---CC---HHHHHHHHHHcCCCEEEEcCchhhhHHHHHHHHHHHHhcC
Confidence 333456777788889999998765433 22 33567777888999999987653 3445555555555
No 324
>PF02502 LacAB_rpiB: Ribose/Galactose Isomerase; InterPro: IPR003500 This entry represents the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB). Galactose-6-phosphate isomerase (5.3.1.26 from EC) is a heteromultimeric protein consisting of subunits LacA and LacB, and catalyses the conversion of D-galactose 6-phosphate to D-tagatose and 6-phosphate in the tagatose 6-phosphate pathway of lactose catabolism []. Galactose-6-phosphate isomerase is induced by galactose or lactose. This entry represents the LacB subunit. Ribose 5-phosphate isomerase (5.3.1.6 from EC) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type alpha/beta/alpha sandwich topology [].; GO: 0005975 carbohydrate metabolic process; PDB: 3HEE_A 3HE8_A 3PH3_B 3PH4_B 3ONO_A 4EM8_B 3S5P_B 1O1X_A 2BES_D 2VVP_D ....
Probab=46.07 E-value=1.5e+02 Score=24.39 Aligned_cols=59 Identities=17% Similarity=0.083 Sum_probs=36.8
Q ss_pred eCCcccchHHHHHHHHHhcCCEEEEEEecCCCC-ChhHH-HHHHHHhccCCc-eEEEEEeCc
Q 011629 22 DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKG-SRNQI-IDTLLTVSSMMS-RILILHTYD 80 (481)
Q Consensus 22 dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~-~~~~~-~~~l~~i~~s~~-~vIvl~~~~ 80 (481)
.|..|....+.+.+.|++.|.+|......+... +..++ ..+.+.+.+... +.|++|++.
T Consensus 6 sDh~g~~lK~~i~~~L~~~g~eV~D~G~~~~~~~dy~~~a~~va~~V~~~~~d~GIliCgtG 67 (140)
T PF02502_consen 6 SDHAGFELKEAIKEYLEEKGYEVIDFGTYSEDSVDYPDFAEKVAEAVASGEADRGILICGTG 67 (140)
T ss_dssp E-GGGHHHHHHHHHHHHHTTEEEEEESESSTST--HHHHHHHHHHHHHTTSSSEEEEEESSS
T ss_pred eCHHHHHHHHHHHHHHHHCCCEEEEeCCCCCCCCCHHHHHHHHHHHHHcccCCeEEEEcCCC
Confidence 566788999999999999999988766555332 11223 233445555444 555555543
No 325
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=46.03 E-value=97 Score=28.56 Aligned_cols=75 Identities=8% Similarity=0.063 Sum_probs=49.4
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHHHHH
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~a~~ 92 (481)
|++|..+ +.+.....+.+.+.+++.|..+... ... +.+.....++.+...+++.||+.... .....++.++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~---~~~-~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~~~~ 77 (289)
T cd01540 2 IGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKI---DVP-DGEKVLSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAKA 77 (289)
T ss_pred eeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEc---cCC-CHHHHHHHHHHHHHcCCCEEEEccCchhhhHHHHHHHHh
Confidence 6667643 4466677888899999999887643 222 22334456677777888888887543 334566777776
Q ss_pred cC
Q 011629 93 LR 94 (481)
Q Consensus 93 ~g 94 (481)
.|
T Consensus 78 ~~ 79 (289)
T cd01540 78 YN 79 (289)
T ss_pred CC
Confidence 65
No 326
>PF13362 Toprim_3: Toprim domain
Probab=45.98 E-value=80 Score=23.65 Aligned_cols=52 Identities=19% Similarity=0.143 Sum_probs=37.9
Q ss_pred cCCcEEEEEEEeCCc--ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHH
Q 011629 11 FGWRNVIALYVDDDH--GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLT 65 (481)
Q Consensus 11 fgW~~V~ii~~dd~~--g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~ 65 (481)
...+.|.|..++|.. |......+.+.+.+.|+.+..... .....|+...++.
T Consensus 39 ~~~~~vii~~D~D~~~~G~~~a~~~~~~~~~~g~~~~~~~p---~~~g~D~ND~l~~ 92 (96)
T PF13362_consen 39 EPGRRVIIAADNDKANEGQKAAEKAAERLEAAGIAVSIVEP---GPEGKDWNDLLQA 92 (96)
T ss_pred CCCCeEEEEECCCCchhhHHHHHHHHHHHHhCCCeEEEECC---CCCCchHHHHHHh
Confidence 477889888877877 889999999999999988775533 1122367766654
No 327
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=45.72 E-value=1.3e+02 Score=27.94 Aligned_cols=78 Identities=6% Similarity=-0.139 Sum_probs=49.8
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHHHHH
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~a~~ 92 (481)
|++|.. ++.|.....+.+++.+++.|+.+... .+...+.+.....++.+...+++-||+.... .....++.++.+
T Consensus 2 I~vi~~~~~~~f~~~i~~gi~~~a~~~g~~v~~~--~~~~~d~~~~~~~i~~~~~~~~DgiIi~~~~~~~~~~~~~~~~~ 79 (298)
T cd06302 2 IAFVPKVTGIPYFNRMEEGAKEAAKELGVDAIYV--GPTTADAAGQVQIIEDLIAQGVDAIAVVPNDPDALEPVLKKARE 79 (298)
T ss_pred EEEEEcCCCChHHHHHHHHHHHHHHHhCCeEEEE--CCCCCCHHHHHHHHHHHHhcCCCEEEEecCCHHHHHHHHHHHHH
Confidence 566663 34566677888999999999887642 1222233344566777767778888887543 334566777766
Q ss_pred cCC
Q 011629 93 LRM 95 (481)
Q Consensus 93 ~g~ 95 (481)
.+.
T Consensus 80 ~~i 82 (298)
T cd06302 80 AGI 82 (298)
T ss_pred CCC
Confidence 553
No 328
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=45.22 E-value=1.1e+02 Score=28.13 Aligned_cols=76 Identities=13% Similarity=-0.009 Sum_probs=48.8
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHHHHH
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~a~~ 92 (481)
|+++.. .+.|.......+.+.+++.|..+.... ...+.+.-...++.+...+++.||+.... ......+..+.+
T Consensus 2 igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~---~~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~ 78 (282)
T cd06318 2 IGFSQYTLNSPFFAALTEAAKAHAKALGYELISTD---AQGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKA 78 (282)
T ss_pred eeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEc---CCCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHH
Confidence 566663 355667788899999999999876432 22232334466777777889888886543 222355666666
Q ss_pred cC
Q 011629 93 LR 94 (481)
Q Consensus 93 ~g 94 (481)
.|
T Consensus 79 ~~ 80 (282)
T cd06318 79 AG 80 (282)
T ss_pred CC
Confidence 54
No 329
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=45.20 E-value=1.5e+02 Score=23.40 Aligned_cols=68 Identities=10% Similarity=0.016 Sum_probs=45.5
Q ss_pred eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH----HHHHHHHHHHHcCC
Q 011629 22 DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI----WGLEVLNAAKHLRM 95 (481)
Q Consensus 22 dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~----~~~~il~~a~~~g~ 95 (481)
.++.-.-+...+...++..|+.|.+... ..+ ....+..+.+.++++|++++... .+..++.+..+.+.
T Consensus 8 ~gd~H~lG~~~~~~~l~~~G~~vi~lG~---~vp---~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~ 79 (122)
T cd02071 8 GLDGHDRGAKVIARALRDAGFEVIYTGL---RQT---PEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELGA 79 (122)
T ss_pred CCChhHHHHHHHHHHHHHCCCEEEECCC---CCC---HHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcCC
Confidence 3444445677788889999999876432 222 33566777788999999987643 45566666666543
No 330
>cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
Probab=45.20 E-value=1e+02 Score=25.64 Aligned_cols=64 Identities=16% Similarity=0.151 Sum_probs=41.7
Q ss_pred EEEEEEEeCC--ccc---chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc-CCceEEEEEeCc
Q 011629 15 NVIALYVDDD--HGR---NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS-MMSRILILHTYD 80 (481)
Q Consensus 15 ~V~ii~~dd~--~g~---~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~-s~~~vIvl~~~~ 80 (481)
++++|...|+ .|+ .....+.+.+++.|..+.....++.+ .+.+.+.+++..+ +.+++||..+..
T Consensus 2 ~~~ii~~~~e~~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd--~~~i~~~l~~~~~~~~~DlVittGG~ 71 (152)
T cd00886 2 RAAVLTVSDTRSAGEAEDRSGPALVELLEEAGHEVVAYEIVPDD--KDEIREALIEWADEDGVDLILTTGGT 71 (152)
T ss_pred EEEEEEEcCcccCCCCccchHHHHHHHHHHcCCeeeeEEEcCCC--HHHHHHHHHHHHhcCCCCEEEECCCc
Confidence 5777766553 222 34557888899999988877666543 3456666665443 368898887643
No 331
>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=45.06 E-value=97 Score=28.88 Aligned_cols=86 Identities=19% Similarity=0.255 Sum_probs=55.9
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.++++||+.. .. . ..+-.+++..+.++.. ++++.+.. .+...++.++.+|++|++++.
T Consensus 92 ~~~l~I~~~~--~~-~-----------~~~~~~~l~~~~~~~P-~~~i~~~~-------~~~~~~~~~l~~g~~D~~i~~ 149 (300)
T TIGR02424 92 GPTVRIGALP--TV-A-----------ARLMPEVVKRFLARAP-RLRVRIMT-------GPNAYLLDQLRVGALDLVVGR 149 (300)
T ss_pred CceEEEeccc--HH-H-----------HhhhHHHHHHHHHhCC-CcEEEEEe-------CchHHHHHHHHCCCCCEEEEe
Confidence 4578888863 11 1 1223577777777764 45566665 457789999999999999853
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
... +.....+.+ .|.......+++++..
T Consensus 150 ~~~-~~~~~~~~~-~~l~~~~~~~~~~~~h 177 (300)
T TIGR02424 150 LGA-PETMQGLSF-EHLYNEPVVFVVRAGH 177 (300)
T ss_pred cCC-cccccceee-eeecCCceEEEEcCCC
Confidence 322 222334444 5788888888887554
No 332
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=45.01 E-value=1.5e+02 Score=28.29 Aligned_cols=78 Identities=10% Similarity=0.053 Sum_probs=52.3
Q ss_pred cEEEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHHHH
Q 011629 14 RNVIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLNAA 90 (481)
Q Consensus 14 ~~V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~~a 90 (481)
..|+++.. ++.|.....+.+++++++.|+.+... ....+.++..+.++.+...+++.||+...... ....+..+
T Consensus 26 ~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~---~~~~~~~~~~~~i~~l~~~~vDGiIi~~~~~~~~~~~l~~~ 102 (330)
T PRK10355 26 VKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQ---SANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVIKEA 102 (330)
T ss_pred ceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEE---CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHHHHH
Confidence 46777773 45678888999999999999987753 22223334556777787788999988764322 23455555
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.+
T Consensus 103 ~~~~ 106 (330)
T PRK10355 103 KQEG 106 (330)
T ss_pred HHCC
Confidence 5544
No 333
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=44.93 E-value=1.3e+02 Score=27.37 Aligned_cols=76 Identities=14% Similarity=0.076 Sum_probs=47.8
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|++|..+ +.+.....+.+.+.+++.|..+..... ..+.+.....++.+.+.+.+-||+.........++..+.+.
T Consensus 2 Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~ 78 (269)
T cd06281 2 IGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIANS---LNDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALASL 78 (269)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEeC---CCChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhC
Confidence 6777743 456667788889999999988765421 22223345667777777788888765433333455555554
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 79 ~ 79 (269)
T cd06281 79 D 79 (269)
T ss_pred C
Confidence 4
No 334
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=44.89 E-value=2.4e+02 Score=25.54 Aligned_cols=98 Identities=9% Similarity=0.103 Sum_probs=55.5
Q ss_pred hHHHHHHc--CCcEEEEEEEeCCc--ccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHh-cc-CCceEEEE
Q 011629 4 IADIVDYF--GWRNVIALYVDDDH--GRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTV-SS-MMSRILIL 76 (481)
Q Consensus 4 i~~ll~~f--gW~~V~ii~~dd~~--g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i-~~-s~~~vIvl 76 (481)
.++.|... |=++|+++...... .....+.+++.++++ |+.+.... ....+.++....++++ ++ .+.+. |+
T Consensus 111 ~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~g~~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~a-I~ 187 (270)
T cd06308 111 AGEYIANLLPGKGNILEIWGLEGSSPAIERHDGFKEALSKYPKIKIVAQQ--DGDWLKEKAEEKMEELLQANPDIDL-VY 187 (270)
T ss_pred HHHHHHHHcCCCceEEEEECCCCCchHHHHHHHHHHHHHHCCCCEEEEec--CCCccHHHHHHHHHHHHHhCCCCcE-EE
Confidence 34444443 78999999754332 334577888899988 88764321 1121222222333433 32 23443 45
Q ss_pred EeCcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 77 HTYDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 77 ~~~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
+.+...+..++..+.+.|+. .+..-+.-
T Consensus 188 ~~~d~~a~g~~~al~~~g~~-~dv~vvg~ 215 (270)
T cd06308 188 AHNDPMALGAYLAAKRAGRE-KEIKFIGI 215 (270)
T ss_pred eCCcHHHHHHHHHHHHcCCC-CCcEEEEe
Confidence 55667777888889888875 33333333
No 335
>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=44.62 E-value=97 Score=26.09 Aligned_cols=68 Identities=18% Similarity=0.211 Sum_probs=44.0
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-..++..+.++.. ++++++.. .....+...|.+|++|+++..- +.....+.+ .++....+.++++++.
T Consensus 15 ~~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~~-~~l~~~~~~~~~~~~~ 82 (198)
T cd08441 15 LMPVLDQFRERWP-DVELDLSS-------GFHFDPLPALLRGELDLVITSD---PLPLPGIAY-EPLFDYEVVLVVAPDH 82 (198)
T ss_pred hHHHHHHHHHhCC-CeEEEEEe-------CCchhHHHHHHcCCceEEEecC---CcCCCCcEE-EEccCCcEEEEEcCCC
Confidence 3577778777763 24466665 4567899999999999997532 222233333 5667777777776543
No 336
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=44.25 E-value=1.3e+02 Score=27.14 Aligned_cols=76 Identities=8% Similarity=-0.016 Sum_probs=48.3
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHHHHHH
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~~a~~ 92 (481)
|++|.. ++.+.....+.+.+.+++.|+.+... ....+.++....++++...+++.||+...... ....+..+.+
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~---~~~~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~~~l~~l~~ 78 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKELGYELTVL---DAQNDAAKQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAANE 78 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHcCceEEec---CCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHH
Confidence 456664 35566778889999999999887542 22223334556777777777888777643322 2455666655
Q ss_pred cC
Q 011629 93 LR 94 (481)
Q Consensus 93 ~g 94 (481)
.+
T Consensus 79 ~~ 80 (268)
T cd06323 79 AG 80 (268)
T ss_pred CC
Confidence 44
No 337
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=44.14 E-value=1.5e+02 Score=27.78 Aligned_cols=78 Identities=15% Similarity=0.109 Sum_probs=49.2
Q ss_pred EEEEEEEe--CCcccchHHHHHHHHHh--cCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHH
Q 011629 15 NVIALYVD--DDHGRNGIAALGDKLAE--KRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNA 89 (481)
Q Consensus 15 ~V~ii~~d--d~~g~~~~~~l~~~l~~--~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~ 89 (481)
+|++|..+ +.|.....+.+++.+++ .|+.+... +...+.+.-...++.+...+++.||+.... ......+.+
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~---~~~~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~ 77 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFY---DAKNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINK 77 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEe---cCCCCHHHHHHHHHHHHHcCCCEEEEecCchhhHHHHHHH
Confidence 36777743 44556677888999998 77776543 222233334466777777889988876533 334566777
Q ss_pred HHHcCC
Q 011629 90 AKHLRM 95 (481)
Q Consensus 90 a~~~g~ 95 (481)
+.+.|.
T Consensus 78 ~~~~gi 83 (303)
T cd01539 78 AKQKNI 83 (303)
T ss_pred HHHCCC
Confidence 766553
No 338
>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=44.09 E-value=42 Score=31.42 Aligned_cols=72 Identities=14% Similarity=0.074 Sum_probs=47.0
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeecccc-------ccceeeccceeecce
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTER-------TKMVDFTQPYIESGL 418 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r-------~~~~~fs~p~~~~~~ 418 (481)
+-.++++++.++.. ++++.+.. +...+++..|.+|++|+++..-...++. ...+. ..|+....+
T Consensus 49 ~lp~~l~~f~~~~P-~i~v~i~~-------~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~-~~~l~~~~l 119 (287)
T TIGR02136 49 LAEAAAEEFQKIHP-GVSVTVQG-------AGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLI-EHKVAVDGL 119 (287)
T ss_pred HHHHHHHHHHhhCC-CceEEEcc-------CCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCce-EEEEEEeeE
Confidence 34567777777773 24466665 5688999999999999987532222211 01133 358888899
Q ss_pred EEEEecCC
Q 011629 419 VVVAPIKK 426 (481)
Q Consensus 419 ~~~~~~~~ 426 (481)
+++++++.
T Consensus 120 ~lvv~~~h 127 (287)
T TIGR02136 120 AVVVNKKN 127 (287)
T ss_pred EEEECCCC
Confidence 99987653
No 339
>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=44.07 E-value=43 Score=30.92 Aligned_cols=79 Identities=14% Similarity=-0.028 Sum_probs=44.0
Q ss_pred HHHHHCC--CcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeec-cccccceeecc--ceee-cceEEEEecCC
Q 011629 353 AVLELLP--YAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAIT-TERTKMVDFTQ--PYIE-SGLVVVAPIKK 426 (481)
Q Consensus 353 ~ia~~l~--~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t-~~r~~~~~fs~--p~~~-~~~~~~~~~~~ 426 (481)
.+-++.| ++ ++++.. .++..++.+|.+|++|+++.+.... ..+.+..++.. .+.. .+..+++++++
T Consensus 20 g~f~~~g~~l~--v~~~~~------~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~~v~~~~~ 91 (288)
T TIGR01728 20 GLLEKELGKTK--VEWVEF------PAGPPALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSDNKATAIVVIKGS 91 (288)
T ss_pred CHHHHhhCCce--EEEEec------CCCcHHHHHHhcCCccccccCCcHHHHHHhcCCCEEEEEEecCCCceEEEECCCC
Confidence 3344445 44 555552 3467899999999999986544311 11111112211 1112 46777777654
Q ss_pred CCcCccccccCcch
Q 011629 427 LNSNAWAFLNPFTP 440 (481)
Q Consensus 427 ~~~~~~~~l~pf~~ 440 (481)
.+..+++|+..+.
T Consensus 92 -~i~s~~dL~Gk~i 104 (288)
T TIGR01728 92 -PIRTVADLKGKRI 104 (288)
T ss_pred -CCCCHHHcCCCEE
Confidence 4566777776554
No 340
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=43.99 E-value=1.7e+02 Score=24.41 Aligned_cols=77 Identities=14% Similarity=0.078 Sum_probs=50.4
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHH
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWG 83 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~ 83 (481)
+...+++++-+.+.++- |..-.....+.+.+.+.-.|+.+... +.++....+++-+..+.|+.+++.++.++
T Consensus 17 ~~~W~~~~~~~~IiVvd-D~~A~D~~~k~~lkma~P~gvk~~i~-------sve~a~~~l~~~~~~~~~v~vl~k~~~da 88 (151)
T TIGR00854 17 GTTWTKVAGANRIIVVN-DDVANDEVRQTLMGIVAPTGFKVRFV-------SLEKTINVIHKPAYHDQTIFLLFRNPQDV 88 (151)
T ss_pred hhhhhcccCCCEEEEEc-ccccCCHHHHHHHHhhCCCCCEEEEE-------EHHHHHHHHhCcCCCCceEEEEECCHHHH
Confidence 34556677777776554 44445556777777776778877643 22244455555455667999999999888
Q ss_pred HHHHH
Q 011629 84 LEVLN 88 (481)
Q Consensus 84 ~~il~ 88 (481)
..++.
T Consensus 89 ~~l~~ 93 (151)
T TIGR00854 89 LTLVE 93 (151)
T ss_pred HHHHH
Confidence 77765
No 341
>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=43.63 E-value=34 Score=32.81 Aligned_cols=104 Identities=8% Similarity=0.013 Sum_probs=57.3
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF 397 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 397 (481)
.++|||+..-+.|.|+....+ .| ++++-.+..|++ ++++.+ .+....+.++.+|++|++..+.
T Consensus 2 ~~~~i~~~~w~G~~p~~lA~~-~G--------~fe~~l~~~Gl~--Ve~~~f------~~~~~~l~Al~aG~iD~~~~g~ 64 (328)
T TIGR03427 2 DKFKVCWSIYAGWMPWGYAAQ-QG--------IVDKWADKYGIT--IEVVQI------NDYVESINQYTAGKFDGCTMTN 64 (328)
T ss_pred CceEEEecCCccHHHHHHHHH-cC--------chhhhHHHcCCe--EEEEEC------CChHHHHHHHHcCCCCEEeecC
Confidence 368888885455555544332 22 234334566866 555553 3578889999999999864332
Q ss_pred ee--cccccccee----eccceeecceEEEEecCCCCcCccccccCcchhH
Q 011629 398 AI--TTERTKMVD----FTQPYIESGLVVVAPIKKLNSNAWAFLNPFTPKM 442 (481)
Q Consensus 398 ~~--t~~r~~~~~----fs~p~~~~~~~~~~~~~~~~~~~~~~l~pf~~~~ 442 (481)
.. .-.+...++ ....+...+..+++++ +...++|+.-+..+
T Consensus 65 ~~~~~~~~a~g~~~~iv~v~~~~~g~~~ivv~~----i~svaDLKGKkIav 111 (328)
T TIGR03427 65 MDALTIPAAGGVDTTALIVGDFSNGNDGIVLKG----GKSLADLKGQKVNL 111 (328)
T ss_pred HHHHHHHHhCCCCeEEEEEEccCCCceEEEECC----CCCHHHcCCCEEec
Confidence 11 111222222 1112233345666642 57788888776644
No 342
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=43.54 E-value=1e+02 Score=28.94 Aligned_cols=83 Identities=13% Similarity=0.175 Sum_probs=54.8
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF 397 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 397 (481)
+.+++++.. .. ..++-..++..+.+... .+++.+.. .+-+.+++.|.+|++|+++...
T Consensus 91 g~l~i~~~~--~~------------~~~~~~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 148 (305)
T PRK11151 91 GPLHIGLIP--TV------------GPYLLPHIIPMLHQTFP-KLEMYLHE-------AQTHQLLAQLDSGKLDCAILAL 148 (305)
T ss_pred ceEEEEecc--hh------------HHHHHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEec
Confidence 578888863 11 11334567777776552 35577765 4567899999999999998632
Q ss_pred eeccccccceeeccceeecceEEEEecCC
Q 011629 398 AITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 398 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
.. . ...+ .+.|+....+.+++++..
T Consensus 149 ~~--~-~~~l-~~~~l~~~~~~~~~~~~h 173 (305)
T PRK11151 149 VK--E-SEAF-IEVPLFDEPMLLAVYEDH 173 (305)
T ss_pred CC--C-CCCe-EEEEeccCcEEEEecCCC
Confidence 22 2 2223 458889999999987654
No 343
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=43.46 E-value=97 Score=28.96 Aligned_cols=86 Identities=12% Similarity=0.059 Sum_probs=51.5
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.+.+++|+.. ... ..+-.+++..+.++.- .+++.+.. ++...++..|.+|++|++++.
T Consensus 91 ~g~l~Ig~~~--~~~------------~~~l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~ 148 (300)
T PRK11074 91 RGQLSIAVDN--IVR------------PDRTRQLIVDFYRHFD-DVELIIRQ-------EVFNGVWDALADGRVDIAIGA 148 (300)
T ss_pred CceEEEEEcC--ccc------------hhHHHHHHHHHHHhCC-CceEEEEe-------hhhhHHHHHHHCCCCCEEEec
Confidence 3688999864 211 1223567777776663 34466554 346788999999999999863
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
.. .......+.+ .++....+.++++++.
T Consensus 149 ~~-~~~~~~~l~~-~~l~~~~~~~v~~~~h 176 (300)
T PRK11074 149 TR-AIPVGGRFAF-RDMGMLSWACVVSSDH 176 (300)
T ss_pred Cc-cCCcccccce-eecccceEEEEEcCCC
Confidence 21 1111222333 4566677777776544
No 344
>PRK09756 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=43.38 E-value=1.9e+02 Score=24.32 Aligned_cols=77 Identities=8% Similarity=-0.022 Sum_probs=49.9
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHH-hcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLA-EKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~-~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
.+...+++.+-+.+.++- |..-.....+.+.+.+. -.|+.+... +.++....+++ +..+-++.+++.++.
T Consensus 20 V~~~W~~~~~~~~IiVvd-D~vA~D~~~k~~lkma~~P~gvk~~i~-------sv~~a~~~l~~-~~~~~~vlvl~~~~~ 90 (158)
T PRK09756 20 VGVTWTSTIGANLLVVVD-DVVANDDIQQKLMGITAETYGFGIRFF-------TIEKTINVIGK-AAPHQKIFLICRTPQ 90 (158)
T ss_pred HHHhhhcccCCCEEEEEc-chhcCCHHHHHHHHhcCCCCCCEEEEE-------EHHHHHHHHHh-ccCCceEEEEECCHH
Confidence 345566777778777654 44444455666666655 567776633 22345566666 556678999999998
Q ss_pred HHHHHHH
Q 011629 82 WGLEVLN 88 (481)
Q Consensus 82 ~~~~il~ 88 (481)
++..++.
T Consensus 91 da~~l~~ 97 (158)
T PRK09756 91 TVRKLVE 97 (158)
T ss_pred HHHHHHH
Confidence 8877765
No 345
>TIGR00249 sixA phosphohistidine phosphatase SixA.
Probab=43.37 E-value=1.2e+02 Score=25.10 Aligned_cols=87 Identities=13% Similarity=-0.039 Sum_probs=44.0
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCC--EEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRC--RLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi--~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
+.+++.|+..+...-.|++|.-....+.++.+.+. .+. .+.....+.+..+..+....++.+.....+.|++++.
T Consensus 32 ~~~~~~l~~~~~~~d~i~sSp~~Ra~qTa~~l~~~---~~~~~~~~~~~~l~p~~~~~~~~~~l~~~~~~~~~~vliVgH 108 (152)
T TIGR00249 32 RLVAQWLKGQGVEIERILVSPFVRAEQTAEIVGDC---LNLPSSAEVLEGLTPCGDIGLVSDYLEALTNEGVASVLLVSH 108 (152)
T ss_pred HHHHHHHHhCCCCCCEEEECCcHHHHHHHHHHHHH---cCCCcceEEccCcCCCCCHHHHHHHHHHHHhcCCCEEEEEeC
Confidence 34566666655544445554444333333333332 243 2333333332233344556666665544556677777
Q ss_pred cHHHHHHHHHHH
Q 011629 80 DIWGLEVLNAAK 91 (481)
Q Consensus 80 ~~~~~~il~~a~ 91 (481)
...+..++....
T Consensus 109 ~P~i~~l~~~l~ 120 (152)
T TIGR00249 109 LPLVGYLVAELC 120 (152)
T ss_pred CCCHHHHHHHHh
Confidence 777777776663
No 346
>cd00001 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate.
Probab=43.23 E-value=1.7e+02 Score=24.35 Aligned_cols=78 Identities=12% Similarity=0.062 Sum_probs=50.9
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~ 82 (481)
.+...+++++-+.+.++- |..-.....+.+.+.+.-.|+.+... +.++....+++-+..+.++.|++-++.+
T Consensus 15 V~~~W~~~~~~~~IvVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~-------sve~a~~~l~~~~~~~~~v~il~k~~~~ 86 (151)
T cd00001 15 VATTWTKELNANRIIVVN-DEVANDELRKTLLKLAAPPGVKLRIF-------TVEKAIEAINSPKYDKQRVFLLFKNPQD 86 (151)
T ss_pred hhhhhhcccCCCEEEEEc-ccccCCHHHHHHHHhhCCCCCeEEEE-------EHHHHHHHHhCcCCCCceEEEEECCHHH
Confidence 345566777777776554 44445556666666666678877643 2224445555545567799999999888
Q ss_pred HHHHHH
Q 011629 83 GLEVLN 88 (481)
Q Consensus 83 ~~~il~ 88 (481)
+..+..
T Consensus 87 ~~~l~~ 92 (151)
T cd00001 87 VLRLVE 92 (151)
T ss_pred HHHHHH
Confidence 877765
No 347
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=43.09 E-value=3.1e+02 Score=26.27 Aligned_cols=88 Identities=8% Similarity=0.005 Sum_probs=50.5
Q ss_pred CCcEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhc-c-CCceEEEEEeCcHHHHHHH
Q 011629 12 GWRNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVS-S-MMSRILILHTYDIWGLEVL 87 (481)
Q Consensus 12 gW~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~-~-s~~~vIvl~~~~~~~~~il 87 (481)
|=.+++++..+.. ......+.+++.+++.|+.+.... . ...+.+.....++++. + ...+.|+ +....+..++
T Consensus 171 g~~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~~i~~~~~~-~-~~~~~~~~~~~~~~~l~~~~~~~ai~--~~d~~A~ga~ 246 (343)
T PRK10936 171 KPLNVALLPGPEGAGGSKAVEQGFRAAIAGSDVRIVDIA-Y-GDNDKELQRNLLQELLERHPDIDYIA--GSAVAAEAAI 246 (343)
T ss_pred CCceEEEEECCCCCchHHHHHHHHHHHHhcCCCEEEEee-c-CCCcHHHHHHHHHHHHHhCCCccEEE--eCCHHHHHHH
Confidence 5789999875432 233457778888888898765421 1 1122222233444443 2 2356554 4556677778
Q ss_pred HHHHHcCCccCCeEEEEe
Q 011629 88 NAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 88 ~~a~~~g~~~~~~~wI~~ 105 (481)
..+.+.|+ ++.+.|++
T Consensus 247 ~al~~~g~--~~di~Vvg 262 (343)
T PRK10936 247 GELRGRNL--TDKIKLVS 262 (343)
T ss_pred HHHHhcCC--CCCeEEEE
Confidence 88888875 44555554
No 348
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=43.05 E-value=1.4e+02 Score=27.60 Aligned_cols=41 Identities=15% Similarity=0.125 Sum_probs=16.3
Q ss_pred HHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEE
Q 011629 7 IVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHK 47 (481)
Q Consensus 7 ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~ 47 (481)
|.+.||.+-+++...+.+-+...+..+.+.++++++.+.+.
T Consensus 183 ~~~~ygl~~~~~~~~~~eps~~~l~~l~~~ik~~~v~~if~ 223 (266)
T cd01018 183 FARDYGLTQIPIEEEGKEPSPADLKRLIDLAKEKGVRVVFV 223 (266)
T ss_pred HHHHcCCEEEecCCCCCCCCHHHHHHHHHHHHHcCCCEEEE
Confidence 44444444444322222223333444444444444444433
No 349
>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=43.02 E-value=1.2e+02 Score=28.47 Aligned_cols=76 Identities=14% Similarity=0.061 Sum_probs=47.9
Q ss_pred EEEEEE---eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeCcHHHHHHHHHH
Q 011629 16 VIALYV---DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTYDIWGLEVLNAA 90 (481)
Q Consensus 16 V~ii~~---dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~~~~~~~il~~a 90 (481)
|+++.. ++.|.....+.+++.+.+.|+.+.... ...+.+.....++.+.+. +++.||+..........+..+
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~---~~~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~ 78 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLY---AERDRFLMLQQARTILQRPDKPDALIFTNEKSVAPELLRLA 78 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEe---CCCCHHHHHHHHHHHHHhccCCCEEEEcCCccchHHHHHHH
Confidence 566663 345666778889999999999876542 122323344566677777 889888865433334556666
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.|
T Consensus 79 ~~~g 82 (305)
T cd06324 79 EGAG 82 (305)
T ss_pred HhCC
Confidence 6654
No 350
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=42.96 E-value=19 Score=32.35 Aligned_cols=93 Identities=11% Similarity=0.116 Sum_probs=53.3
Q ss_pred CCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee-------eeccccccceeeccc
Q 011629 340 TDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF-------AITTERTKMVDFTQP 412 (481)
Q Consensus 340 ~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~-------~~t~~r~~~~~fs~p 412 (481)
+-+++|+.--|.+.+.+ .++++.+-++. .-...+++|.+|++|+++.+- .-....+-.++|..-
T Consensus 23 Sr~YEGLATGl~~~f~~-~~ip~~~aymR--------Ga~~Rie~l~~g~yDfaVvS~lAA~~~i~~~~~l~i~~~fG~~ 93 (232)
T PF14503_consen 23 SRRYEGLATGLYEQFEE-SGIPLNFAYMR--------GAENRIEALKNGRYDFAVVSKLAAEHYIEEGEDLEIVLEFGPG 93 (232)
T ss_dssp SHHHHHHHHHHHCTTT---TS-EEEEE-S---------HHHHHHHHHTTS-SEEEEEHHHHCCCCCC-SSEEEEEE--TT
T ss_pred hhhhHHHHHHHHHHhcc-CCCceEEEeec--------cchHHHHHHHhCCcceEeehHHHHHHHHhhccCeEEEEeeCCC
Confidence 45678988887777766 78777777775 366889999999999998762 112334456888776
Q ss_pred eeecceEEEEecCCCC-c--CccccccCcchh
Q 011629 413 YIESGLVVVAPIKKLN-S--NAWAFLNPFTPK 441 (481)
Q Consensus 413 ~~~~~~~~~~~~~~~~-~--~~~~~l~pf~~~ 441 (481)
-+.++=+++.+++... + ..---++|.|.+
T Consensus 94 sYvs~Hvli~~~~~~~~i~dGmRVGiD~~S~D 125 (232)
T PF14503_consen 94 SYVSEHVLIFRDGEKKEIEDGMRVGIDPSSID 125 (232)
T ss_dssp SSS--EEEEEETT-GGG-----EEEE-TT-HH
T ss_pred CcccceEEEEecCCccceeeeeEeecCCCCcc
Confidence 6777777777776521 1 233455677764
No 351
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT. Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein.
Probab=42.94 E-value=2.6e+02 Score=25.89 Aligned_cols=86 Identities=10% Similarity=0.040 Sum_probs=49.3
Q ss_pred cEEEEEEEeCC--cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc--CCceEEEEEeCcHHHHHHHHH
Q 011629 14 RNVIALYVDDD--HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS--MMSRILILHTYDIWGLEVLNA 89 (481)
Q Consensus 14 ~~V~ii~~dd~--~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~--s~~~vIvl~~~~~~~~~il~~ 89 (481)
.+|+++..... ......+.+++.+++.|+.+... .....+.+.-...++++-+ ...++| +++...+..++..
T Consensus 126 ~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~d~i--~~~d~~a~g~l~a 201 (295)
T TIGR02955 126 TTLAWLPGPKNRGGTKPVTQGFRAALEGSDVEISAI--LWADNDKELQRNLLQDLLKKHPDIDYL--VGSAVAAEAAISE 201 (295)
T ss_pred eeEEEEeCCCcCCchhHHHHHHHHHHhcCCcEEEEE--ecCCCcHHHHHHHHHHHHHhCCCcCEE--EeccHHHHHHHHH
Confidence 46999875443 34456788899998889876542 2222222233344444432 234543 5666667778888
Q ss_pred HHHcCCccCCeEEEEe
Q 011629 90 AKHLRMMESGYVWIVT 105 (481)
Q Consensus 90 a~~~g~~~~~~~wI~~ 105 (481)
+.+.|. ++-+.+.+
T Consensus 202 l~~~g~--~~dv~vvg 215 (295)
T TIGR02955 202 LRSLHM--TQQIKLVS 215 (295)
T ss_pred HHhhCc--cCCeEEEE
Confidence 777664 34455554
No 352
>PF02608 Bmp: Basic membrane protein; InterPro: IPR003760 This is a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. All of these proteins are outer membrane proteins and are thus antigenic in nature when possessed by the pathogenic members of the family []. The Bacillus subtilis degR, a positive regulator of the production of degradative enzymes, is also a member of this group [].; GO: 0005886 plasma membrane; PDB: 2HQB_A 3S99_A 2FQW_A 2FQY_A 2FQX_A.
Probab=42.87 E-value=1.2e+02 Score=28.64 Aligned_cols=87 Identities=13% Similarity=0.115 Sum_probs=55.1
Q ss_pred EEEEEEE----eCCcccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHH
Q 011629 15 NVIALYV----DDDHGRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNA 89 (481)
Q Consensus 15 ~V~ii~~----dd~~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~ 89 (481)
.++++.. |..|.+...+.+++..++. |+.+...+..+. +.+++...++.+.+.+.++||..+... .-.+..-
T Consensus 3 ~v~~~~~g~~~D~g~n~~~~~G~~~~~~~~~~i~~~~~e~~~~--~~~~~~~~~~~~~~~g~dlIi~~g~~~-~~~~~~v 79 (306)
T PF02608_consen 3 KVALLDPGGINDKGFNQSAYEGLKRAEKELDGIEIIYVENVPE--TDADYEEAIRQLADQGYDLIIGHGFEY-SDALQEV 79 (306)
T ss_dssp EEEEESSS-CCCSSHHHHHHHHHHHHHHHCTTEEEEEEES-S---TCHHHHHHHHHHHHTT-SEEEEESGGG-HHHHHHH
T ss_pred EEEEEECCCCCCccHHHHHHHHHHHHHHHcCCceEEEEecCCc--cHHHHHHHHHHHHHcCCCEEEEccHHH-HHHHHHH
Confidence 4555542 4456667777888888888 999888876652 234788888888888999999876543 2233334
Q ss_pred HHHcCCccCCeEEEEeccc
Q 011629 90 AKHLRMMESGYVWIVTDWL 108 (481)
Q Consensus 90 a~~~g~~~~~~~wI~~~~~ 108 (481)
|.+ -|+..|++.+..
T Consensus 80 A~~----yPd~~F~~~d~~ 94 (306)
T PF02608_consen 80 AKE----YPDTKFIIIDGY 94 (306)
T ss_dssp HTC-----TTSEEEEESS-
T ss_pred HHH----CCCCEEEEEecC
Confidence 433 256677776543
No 353
>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=42.79 E-value=92 Score=26.21 Aligned_cols=70 Identities=14% Similarity=0.089 Sum_probs=46.3
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++++.. .+...+...+.+|++|+++... +.....+. +.++....+.+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Di~i~~~---~~~~~~~~-~~~l~~~~~~lv~~~ 80 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRD-------LESDNLEAQLERGEVDLALTTP---EYAPDGLR-SRPLFEERYVCVTRR 80 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEee-------CCcccHHHHHhcCCCcEEEecC---ccCCccce-eeeeecCcEEEEEcC
Confidence 344677888887763 34566654 3456788999999999987521 22223333 467888888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 81 ~~ 82 (198)
T cd08461 81 GH 82 (198)
T ss_pred CC
Confidence 54
No 354
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=42.46 E-value=99 Score=24.95 Aligned_cols=62 Identities=18% Similarity=0.212 Sum_probs=39.9
Q ss_pred EEEEEEeCCc--c---cchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 16 VIALYVDDDH--G---RNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 16 V~ii~~dd~~--g---~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
|++|...|+- | ......+.+.+++.|..+.....++. +.+.+.+.+++..+. +++||..+..
T Consensus 2 v~ii~~G~El~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~D--d~~~i~~~i~~~~~~-~DlvittGG~ 68 (133)
T cd00758 2 VAIVTVSDELSQGQIEDTNGPALEALLEDLGCEVIYAGVVPD--DADSIRAALIEASRE-ADLVLTTGGT 68 (133)
T ss_pred EEEEEeCccccCCceEEchHHHHHHHHHHCCCEEEEeeecCC--CHHHHHHHHHHHHhc-CCEEEECCCC
Confidence 5666554432 2 24466788889999988877655543 334566767666554 8898887543
No 355
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=42.35 E-value=1.3e+02 Score=27.20 Aligned_cols=75 Identities=9% Similarity=0.012 Sum_probs=47.8
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++.. ++.|.....+.+.+.+++.|+++..... ..+.+.....++.+.+.+.+.||+....... ..+..+.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (270)
T cd06296 2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSES---GRRTSPERQWVERLSARRTDGVILVTPELTS-AQRAALRRT 77 (270)
T ss_pred eEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecC---CCchHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHhcC
Confidence 566664 3567778889999999999998765422 2222334566777777788888776543222 345666554
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 78 ~ 78 (270)
T cd06296 78 G 78 (270)
T ss_pred C
Confidence 4
No 356
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=42.30 E-value=1.3e+02 Score=28.52 Aligned_cols=78 Identities=9% Similarity=-0.078 Sum_probs=49.8
Q ss_pred cEEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHH
Q 011629 14 RNVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAK 91 (481)
Q Consensus 14 ~~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~ 91 (481)
+.++++..+ +.|.....+.+.+.+.++|..+.... ...+.+.....++.+...+++.||+..........+..+.
T Consensus 65 ~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~---~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l~ 141 (342)
T PRK10014 65 GVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQ---GGKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMAE 141 (342)
T ss_pred CEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEe---CCCCHHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHHHh
Confidence 468888853 45666778888899999998765431 1223334456677777778888888754332334555555
Q ss_pred HcC
Q 011629 92 HLR 94 (481)
Q Consensus 92 ~~g 94 (481)
+.+
T Consensus 142 ~~~ 144 (342)
T PRK10014 142 EKG 144 (342)
T ss_pred hcC
Confidence 544
No 357
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=42.04 E-value=73 Score=29.77 Aligned_cols=87 Identities=13% Similarity=0.154 Sum_probs=53.0
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.+++++++.. .. ..++-.+++..+.++.. ++++.+.. ++...+...|.+|++|+++..
T Consensus 92 ~g~l~i~~~~--~~------------~~~~l~~~l~~f~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~ 149 (296)
T PRK11062 92 NLLFDVGVAD--AL------------SKRLVSRVLLTAVPEDE-SIHLRCFE-------STHEMLLEQLSQHKLDMILSD 149 (296)
T ss_pred ceEEEEEecc--hh------------hHhhHHHHHHHHHhcCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEec
Confidence 3578888863 11 12455677777766542 34455554 457889999999999998753
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
..........+ ...|+......++++++.
T Consensus 150 ~~~~~~~~~~l-~~~~l~~~~~~~~~~~~~ 178 (296)
T PRK11062 150 CPVDSTQQEGL-FSKKLGECGVSFFCTNPL 178 (296)
T ss_pred CCCccccccch-hhhhhhccCcceEecCCC
Confidence 22111122233 335777777777776554
No 358
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=41.90 E-value=1.3e+02 Score=27.37 Aligned_cols=76 Identities=11% Similarity=-0.005 Sum_probs=47.2
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHHHHHH
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~~a~~ 92 (481)
|++|.. ++.|.....+.+.+.+++.|+.+... ....+.+.-.+.++++...+++.||+...... ....+..+.+
T Consensus 2 i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~---~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~l~~~~~ 78 (277)
T cd06319 2 IAYIVSDLRIPFWQIMGRGVKSKAKALGYDAVEL---SAENSAKKELENLRTAIDKGVSGIIISPTNSSAAVTLLKLAAQ 78 (277)
T ss_pred eEEEeCCCCchHHHHHHHHHHHHHHhcCCeEEEe---cCCCCHHHHHHHHHHHHhcCCCEEEEcCCchhhhHHHHHHHHH
Confidence 566664 35566677888888999999887643 22222223345666666678898887654332 3355666666
Q ss_pred cC
Q 011629 93 LR 94 (481)
Q Consensus 93 ~g 94 (481)
.+
T Consensus 79 ~~ 80 (277)
T cd06319 79 AK 80 (277)
T ss_pred CC
Confidence 54
No 359
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=41.90 E-value=1.4e+02 Score=27.04 Aligned_cols=76 Identities=12% Similarity=-0.063 Sum_probs=48.5
Q ss_pred EEEEEE---eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-HHHHHHHHHH
Q 011629 16 VIALYV---DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-WGLEVLNAAK 91 (481)
Q Consensus 16 V~ii~~---dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~~~~il~~a~ 91 (481)
|++|.. ++.|+....+.+.+.+++.|+.+.... ...+.+.....++.+...+++.||+..... .....+..+.
T Consensus 2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~---~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~l~~~~ 78 (275)
T cd06317 2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVLD---ANGDVARQAAQVEDLIAQKVDGIILWPTDGQAYIPGLRKAK 78 (275)
T ss_pred eEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEEc---CCcCHHHHHHHHHHHHHcCCCEEEEecCCccccHHHHHHHH
Confidence 566663 346777888899999999998876532 222333344566666667789888865432 2345566666
Q ss_pred HcC
Q 011629 92 HLR 94 (481)
Q Consensus 92 ~~g 94 (481)
+.+
T Consensus 79 ~~~ 81 (275)
T cd06317 79 QAG 81 (275)
T ss_pred HCC
Confidence 654
No 360
>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=41.74 E-value=1.1e+02 Score=26.00 Aligned_cols=71 Identities=17% Similarity=0.149 Sum_probs=47.4
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
++-.+++.++.++.. ++++.+.. ++...+.+.|.+|++|+++..-. ......+. +.+.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~--~~~~~~~~-~~~l~~~~~~~~~~~ 81 (198)
T cd08444 13 YALPWVVQAFKEQFP-NVHLVLHQ-------GSPEEIASMLANGQADIGIATEA--LENHPELV-SFPYYDWHHHIIVPV 81 (198)
T ss_pred hhhhHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHCCCccEEEeccc--cCCCcCcE-EeeccccceeEEecC
Confidence 445678888888763 34566665 45778999999999999875211 11222333 467778888888765
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
..
T Consensus 82 ~h 83 (198)
T cd08444 82 GH 83 (198)
T ss_pred CC
Confidence 53
No 361
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=41.74 E-value=1.1e+02 Score=28.49 Aligned_cols=86 Identities=10% Similarity=0.176 Sum_probs=57.5
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.+++++++.. .. ...+-.+++..+.+... ++++.+.. .+..++..+|.+|++|+++..
T Consensus 94 ~g~l~I~~~~--~~------------~~~~l~~~l~~~~~~~p-~i~~~~~~-------~~~~~~~~~l~~g~~Di~i~~ 151 (302)
T PRK09791 94 AGQINIGMGA--SI------------ARSLMPAVISRFHQQHP-QVKVRIME-------GQLVSMINELRQGELDFTINT 151 (302)
T ss_pred ceEEEEEech--HH------------HHhhhHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHCCCccEEEEe
Confidence 4688998874 11 12344678888887774 45566654 457799999999999998752
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
.... .....+.+ .|+....+.++++++.
T Consensus 152 ~~~~-~~~~~~~~-~~l~~~~~~l~~~~~~ 179 (302)
T PRK09791 152 YYQG-PYDHEFTF-EKLLEKQFAVFCRPGH 179 (302)
T ss_pred cCCc-ccccceeE-EEeccceEEEEEcCCC
Confidence 2111 11233555 7888999999987655
No 362
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=41.70 E-value=1.2e+02 Score=28.61 Aligned_cols=85 Identities=15% Similarity=0.153 Sum_probs=55.5
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.++++||+.. .. ...+-.++++.+.+... .+++.+.. ++...+...|.+|++|+++..
T Consensus 92 ~g~lrIg~~~--~~------------~~~~l~~~l~~f~~~~P-~i~l~l~~-------~~~~~~~~~L~~g~~Dl~i~~ 149 (316)
T PRK12679 92 SGVLTIATTH--TQ------------ARYSLPEVIKAFRELFP-EVRLELIQ-------GTPQEIATLLQNGEADIGIAS 149 (316)
T ss_pred CceEEEEech--Hh------------hhcchHHHHHHHHHHCC-CeEEEEec-------CCHHHHHHHHHcCCCCEEEec
Confidence 3678999874 21 12345678888887753 34566654 456789999999999998753
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
.. ......+.+ .++....+.+++++..
T Consensus 150 ~~--~~~~~~l~~-~~l~~~~~~~v~~~~h 176 (316)
T PRK12679 150 ER--LSNDPQLVA-FPWFRWHHSLLVPHDH 176 (316)
T ss_pred cc--CCCCCCceE-EEccCCcEEEEecCCC
Confidence 21 111223443 5788888888887654
No 363
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=41.60 E-value=1.6e+02 Score=26.75 Aligned_cols=76 Identities=8% Similarity=-0.032 Sum_probs=47.7
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHh--cCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHHHH
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAE--KRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLNAA 90 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~--~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~~a 90 (481)
|++|..+ +.|.....+.+.+.+++ .|.++... ....+.+.....++.+...+++.||++..... ....+..+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~ 78 (271)
T cd06321 2 IGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVV---SADYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRA 78 (271)
T ss_pred eEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEc---cCCCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHH
Confidence 6777743 56777788899999999 66665433 22223333456666777777888887654332 34566666
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.+
T Consensus 79 ~~~~ 82 (271)
T cd06321 79 QAAG 82 (271)
T ss_pred HHCC
Confidence 6654
No 364
>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=41.51 E-value=1.3e+02 Score=25.29 Aligned_cols=69 Identities=19% Similarity=0.178 Sum_probs=45.0
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++.+.. +.-..+...|.+|++|+++... +.....+.. .++......+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~~-~~l~~~~~~~~~~~ 80 (196)
T cd08457 13 GFLPRFLAAFLRLRP-NLHLSLMG-------LSSSQVLEAVASGRADLGIADG---PLEERQGFL-IETRSLPAVVAVPM 80 (196)
T ss_pred cccHHHHHHHHHHCC-CeEEEEEe-------cCcHHHHHHHHcCCccEEEecc---CCCCCCcEE-EEeccCCeEEEeeC
Confidence 345688888888763 35566665 3356888899999999997532 222233333 56677777777765
Q ss_pred C
Q 011629 425 K 425 (481)
Q Consensus 425 ~ 425 (481)
+
T Consensus 81 ~ 81 (196)
T cd08457 81 G 81 (196)
T ss_pred C
Confidence 4
No 365
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=41.19 E-value=1.5e+02 Score=26.93 Aligned_cols=78 Identities=6% Similarity=0.029 Sum_probs=47.6
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHHHHH
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~a~~ 92 (481)
+|+|.. ++.+.....+.+.+.+++.|+.+..... +...+...-...++++...+++.||+.... ......+..+.+
T Consensus 2 igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~ 80 (275)
T cd06320 2 YGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAA-PSEGDQQGQLSIAENMINKGYKGLLFSPISDVNLVPAVERAKK 80 (275)
T ss_pred eeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEcc-CCCCCHHHHHHHHHHHHHhCCCEEEECCCChHHhHHHHHHHHH
Confidence 677774 3456667788889999999988775422 111222233456667777778888776543 223345566655
Q ss_pred cC
Q 011629 93 LR 94 (481)
Q Consensus 93 ~g 94 (481)
.+
T Consensus 81 ~~ 82 (275)
T cd06320 81 KG 82 (275)
T ss_pred CC
Confidence 54
No 366
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=41.18 E-value=1.1e+02 Score=25.23 Aligned_cols=50 Identities=12% Similarity=0.062 Sum_probs=35.2
Q ss_pred chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 28 NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 28 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.....+.+.+++.|+++.....++.+ .+++.+.+++..+ ++++||..+..
T Consensus 27 ~n~~~l~~~l~~~G~~v~~~~~v~Dd--~~~i~~~l~~~~~-~~DliIttGG~ 76 (144)
T TIGR00177 27 SNGPLLAALLEEAGFNVSRLGIVPDD--PEEIREILRKAVD-EADVVLTTGGT 76 (144)
T ss_pred CcHHHHHHHHHHCCCeEEEEeecCCC--HHHHHHHHHHHHh-CCCEEEECCCC
Confidence 34668888899999998887766543 3456666666544 58898887643
No 367
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=41.10 E-value=1.4e+02 Score=26.90 Aligned_cols=75 Identities=16% Similarity=0.026 Sum_probs=47.4
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++..+ +.+.....+.+++++++.|+.+.... ...+.+.....++++...+++.+|+...... ..++..+.+.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~~~~~~~~~~i~~l~~~~~dgii~~~~~~~-~~~~~~~~~~ 77 (259)
T cd01542 2 IGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMN---TNFSIEKEIEALELLARQKVDGIILLATTIT-DEHREAIKKL 77 (259)
T ss_pred eEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEe---CCCCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHhcC
Confidence 5666643 34556778889999999999886532 2223334456677777788899888755322 2444555444
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 78 ~ 78 (259)
T cd01542 78 N 78 (259)
T ss_pred C
Confidence 3
No 368
>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=40.97 E-value=1.3e+02 Score=25.06 Aligned_cols=66 Identities=11% Similarity=0.009 Sum_probs=43.3
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-.+++..+.++.- ++++++.. +....+..+|.+|++|+++... + . ..+ -+.+.....+.++++++.
T Consensus 15 l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~---~-~-~~~-~~~~l~~~~~~~v~~~~~ 80 (185)
T cd08439 15 LPFLLNRFASVYP-RLAIEVVC-------KRTPRLMEMLERGEVDLALITH---P-P-PGA-SATILRRSPTVWYCAAGY 80 (185)
T ss_pred HHHHHHHHHHHCC-CeEEEEEE-------CChHHHHHHHHCCCCcEEEEec---c-C-CCC-CceEEEEecCEEEECCCC
Confidence 3567777776652 24466665 4567889999999999987532 1 1 122 246777788888876653
No 369
>PF13955 Fst_toxin: Toxin Fst, type I toxin-antitoxin system; PDB: 2KV5_A.
Probab=40.90 E-value=45 Score=17.26 Aligned_cols=18 Identities=44% Similarity=0.567 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHhhhccc
Q 011629 447 GIFFLVVGVVVWILEHRL 464 (481)
Q Consensus 447 ~~~~~~~~~~~~~~~~~~ 464 (481)
+++=+++++++-+++||+
T Consensus 4 iIaPi~VGvvl~l~~~wL 21 (21)
T PF13955_consen 4 IIAPIVVGVVLTLFDHWL 21 (21)
T ss_dssp HHHHHHHHHHHHHHHHHT
T ss_pred ehhhHHHHHHHHHHHhhC
Confidence 455567788888988874
No 370
>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=40.84 E-value=99 Score=26.01 Aligned_cols=70 Identities=14% Similarity=0.176 Sum_probs=44.9
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
++-..++..+.++.. ++++.+.. .+...+...|.+|++|+++... +.....+. +.+.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~ 80 (200)
T cd08464 13 WLAPPLLAALRAEAP-GVRLVFRQ-------VDPFNVGDMLDRGEIDLAIGVF---GELPAWLK-REVLYTEGYACLFDP 80 (200)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCcccHHHHHhcCcccEEEecC---CCCcccce-eeeecccceEEEEeC
Confidence 344677788877762 35566664 4466888999999999997532 22223333 357777777777755
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
..
T Consensus 81 ~~ 82 (200)
T cd08464 81 QQ 82 (200)
T ss_pred CC
Confidence 43
No 371
>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=40.72 E-value=1.5e+02 Score=25.16 Aligned_cols=71 Identities=17% Similarity=0.120 Sum_probs=47.2
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.. ++++++.. ++...+...+.+|++|+++..- .......+. +.++....+.+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~~~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~--~~~~~~~~~-~~~l~~~~~~~v~~~ 81 (198)
T cd08443 13 YVLPPVIKGFIERYP-RVSLQMHQ-------GSPTQIAEMVSKGLVDFAIATE--ALHDYDDLI-TLPCYHWNRCVVVKR 81 (198)
T ss_pred eECcHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHCCCccEEEEec--cccccCCce-EeeeeeceEEEEEcC
Confidence 455788888887763 34566665 4567899999999999997521 111223343 367788888888765
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 82 ~h 83 (198)
T cd08443 82 DH 83 (198)
T ss_pred CC
Confidence 54
No 372
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=40.64 E-value=1.3e+02 Score=27.52 Aligned_cols=79 Identities=14% Similarity=-0.100 Sum_probs=47.8
Q ss_pred EEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEec-CCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHHHH
Q 011629 15 NVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPL-SPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLNAA 90 (481)
Q Consensus 15 ~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~-~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~~a 90 (481)
+|+++..+ +.|.....+.+.+++++.|.++...... ....+.+...+.++.+.. +++.||+...... ....+.++
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~~~~-~vdgiii~~~~~~~~~~~i~~~ 79 (275)
T cd06307 1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDARIRVRIHFVESFDPAALAAALLRLGA-RSDGVALVAPDHPQVRAAVARL 79 (275)
T ss_pred CeEEEeCCCCChHHHHHHHHHHHHHhhhhccCceEEEEEccCCCHHHHHHHHHHHHh-cCCEEEEeCCCcHHHHHHHHHH
Confidence 46777754 3466677888888899888654332221 112222334566677766 8888887654433 34667777
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.|
T Consensus 80 ~~~~ 83 (275)
T cd06307 80 AAAG 83 (275)
T ss_pred HHCC
Confidence 6655
No 373
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=40.27 E-value=1.2e+02 Score=28.20 Aligned_cols=68 Identities=16% Similarity=0.151 Sum_probs=48.8
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
..+++..+.++.. ++++.+.. .+..+++..|.+|++|+++... +...+.+.+ .|.......++++++.
T Consensus 105 l~~~~~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~l~~-~~l~~~~~~~v~~~~~ 172 (296)
T PRK09906 105 LPKVLPMFRLRHP-DTLIELVS-------LITTQQEEKLRRGELDVGFMRH---PVYSDEIDY-LELLDEPLVVVLPVDH 172 (296)
T ss_pred HHHHHHHHHHHCC-CeEEEEEe-------CCcHHHHHHHHcCCeeEEEecC---CCCCCCceE-EEEecccEEEEecCCC
Confidence 4577787877763 35566665 4567899999999999997533 334445555 7899999999987654
No 374
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=40.22 E-value=76 Score=26.13 Aligned_cols=65 Identities=15% Similarity=0.097 Sum_probs=37.2
Q ss_pred cEEEEEEEeCCc-ccchHHHHHHHHHhc-CCEEEEEEecCCCCCh-hHHHHHHHHhccCCceEEEEEeC
Q 011629 14 RNVIALYVDDDH-GRNGIAALGDKLAEK-RCRLSHKVPLSPKGSR-NQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 14 ~~V~ii~~dd~~-g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~-~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
++|-|+|+.|.- -...+..|.+.|++. |+.|.....-...... .-..-+.+++++. -.|||++..
T Consensus 1 ~kVfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~a-d~Vliv~S~ 68 (150)
T PF08357_consen 1 RKVFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREA-DKVLIVCSP 68 (150)
T ss_pred CeEEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcC-CEEEEEecc
Confidence 367888976543 336688899999999 9988765432211111 1223333444443 455555543
No 375
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=40.18 E-value=1.3e+02 Score=28.33 Aligned_cols=70 Identities=19% Similarity=0.314 Sum_probs=47.7
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-.+++..+.+..- ++++.+.. .....++.+|.+|++|+++..... ....+.+.+ .|+....+.++++++.
T Consensus 112 l~~~l~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~-~~~~~~l~~-~~l~~~~~~lv~~~~~ 181 (312)
T PRK10341 112 MSDMINKFKEVFP-KAQVSMYE-------AQLSSFLPAIRDGRLDFAIGTLSN-EMKLQDLHV-EPLFESEFVLVASKSR 181 (312)
T ss_pred HHHHHHHHHHhCC-CCEEEEEe-------CCHHHHHHHHHcCCCcEEEecCCc-ccccCCeeE-EEEecccEEEEEcCCC
Confidence 4577888877652 35576665 457899999999999999753211 112233433 7888889999987654
No 376
>PRK09701 D-allose transporter subunit; Provisional
Probab=40.14 E-value=2e+02 Score=26.99 Aligned_cols=83 Identities=6% Similarity=-0.045 Sum_probs=53.3
Q ss_pred cCCcEEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-HHHHHH
Q 011629 11 FGWRNVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-WGLEVL 87 (481)
Q Consensus 11 fgW~~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~~~~il 87 (481)
|-=..|+++..+ +.|.....+.+++++++.|+.+..... +...+.+.....++.+...+++.||+..... .....+
T Consensus 22 ~~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~v~~~~~-~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~~l 100 (311)
T PRK09701 22 FAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFAS-PSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPV 100 (311)
T ss_pred ccCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCeEEEecC-CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHH
Confidence 444588999854 556677888999999999988775421 2122222345667777777889888876443 233445
Q ss_pred HHHHHcC
Q 011629 88 NAAKHLR 94 (481)
Q Consensus 88 ~~a~~~g 94 (481)
.++.+.|
T Consensus 101 ~~~~~~g 107 (311)
T PRK09701 101 ARAWKKG 107 (311)
T ss_pred HHHHHCC
Confidence 5666655
No 377
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=40.13 E-value=2.3e+02 Score=24.03 Aligned_cols=84 Identities=10% Similarity=-0.048 Sum_probs=47.8
Q ss_pred cEEEEEEEeCCcccchHHHHHHHHHhc--CCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHH
Q 011629 14 RNVIALYVDDDHGRNGIAALGDKLAEK--RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAK 91 (481)
Q Consensus 14 ~~V~ii~~dd~~g~~~~~~l~~~l~~~--gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~ 91 (481)
.+|.++.+..+ .++.+.+.+++. |+.|+....-+. ..++-..+++.|+++++++|++......-..++.+..
T Consensus 47 ~~v~llG~~~~----~~~~~~~~l~~~yp~l~i~g~~~g~~--~~~~~~~i~~~I~~~~pdiv~vglG~PkQE~~~~~~~ 120 (171)
T cd06533 47 LRVFLLGAKPE----VLEKAAERLRARYPGLKIVGYHHGYF--GPEEEEEIIERINASGADILFVGLGAPKQELWIARHK 120 (171)
T ss_pred CeEEEECCCHH----HHHHHHHHHHHHCCCcEEEEecCCCC--ChhhHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHH
Confidence 45666765554 345555555554 666664322221 1223344788999999999988776655555555544
Q ss_pred HcCCccCCeEEEEec
Q 011629 92 HLRMMESGYVWIVTD 106 (481)
Q Consensus 92 ~~g~~~~~~~wI~~~ 106 (481)
+. + +.-++|..+
T Consensus 121 ~~-l--~~~v~~~vG 132 (171)
T cd06533 121 DR-L--PVPVAIGVG 132 (171)
T ss_pred HH-C--CCCEEEEec
Confidence 43 1 334666554
No 378
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=40.10 E-value=1.6e+02 Score=27.08 Aligned_cols=83 Identities=19% Similarity=0.137 Sum_probs=53.2
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF 397 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 397 (481)
+++++++.. .. ...+-.+++..+.++.. ++++.+.. +....++..|.+|++|+++...
T Consensus 89 g~l~i~~~~--~~------------~~~~~~~~l~~~~~~~P-~i~i~v~~-------~~~~~~~~~l~~g~~Di~i~~~ 146 (290)
T PRK10837 89 GALRIYASS--TI------------GNYILPAMIARYRRDYP-QLPLELSV-------GNSQDVINAVLDFRVDIGLIEG 146 (290)
T ss_pred CeEEEEecc--hh------------HhhhhHHHHHHHHHHCC-CceEEEEE-------CCHHHHHHHHHhCCceEEEecC
Confidence 578888874 11 11334577888887762 24466654 4577899999999999997532
Q ss_pred eeccccccceeeccceeecceEEEEecCC
Q 011629 398 AITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 398 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
+.....+.. .|+....+.++++++.
T Consensus 147 ---~~~~~~~~~-~~l~~~~~~lv~~~~h 171 (290)
T PRK10837 147 ---PCHSPELIS-EPWLEDELVVFAAPDS 171 (290)
T ss_pred ---CCCCCceeE-EEeecceEEEEEcCCC
Confidence 222223333 5677778888887654
No 379
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=40.08 E-value=98 Score=28.53 Aligned_cols=83 Identities=13% Similarity=0.099 Sum_probs=55.0
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF 397 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 397 (481)
++++||+.. . -...+-.+++..+.+..- .+++.+.. +....++..|.+|++|+++...
T Consensus 89 ~~l~Ig~~~--~------------~~~~~l~~~l~~f~~~~P-~v~v~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 146 (275)
T PRK03601 89 NELSIGASA--S------------LWECMLTPWLGRLYQNQE-ALQFEARI-------AQRQSLVKQLHERQLDLLITTE 146 (275)
T ss_pred ceEEEeccH--H------------HHHHHHHHHHHHHHHhCC-CcEEEEEE-------CChHHHHHHHHcCCCCEEEEcC
Confidence 578888863 1 112445677888876652 34566655 4577899999999999998643
Q ss_pred eeccccccceeeccceeecceEEEEecCC
Q 011629 398 AITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 398 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
. ... ..+ ...|+....+.++++++.
T Consensus 147 ~--~~~-~~l-~~~~l~~~~~~~v~~~~~ 171 (275)
T PRK03601 147 A--PKM-DEF-SSQLLGHFTLALYTSAPS 171 (275)
T ss_pred C--Ccc-CCc-cEEEecceeEEEEecCch
Confidence 2 222 234 346888888888887654
No 380
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=40.06 E-value=1.6e+02 Score=26.60 Aligned_cols=75 Identities=11% Similarity=-0.017 Sum_probs=47.8
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|++|.. ++.+.....+.+.+.+++.|+.+..... ..+.+.-...++.+...+++.||+.+..... ..+.++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~~~ 77 (268)
T cd06270 2 IGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITAG---HHSAEKEREAIEFLLERRCDALILHSKALSD-DELIELAAQ 77 (268)
T ss_pred EEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEeC---CCchHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhC
Confidence 455553 3566677888999999999998775422 2222334566777777789998887653222 225566555
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
|
T Consensus 78 ~ 78 (268)
T cd06270 78 V 78 (268)
T ss_pred C
Confidence 4
No 381
>PF09651 Cas_APE2256: CRISPR-associated protein (Cas_APE2256); InterPro: IPR013442 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 150 amino acids found in a family of Cas proteins in at least five archaeal and three bacterial species. In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus.; PDB: 3QYF_A.
Probab=39.67 E-value=1.2e+02 Score=24.72 Aligned_cols=45 Identities=20% Similarity=0.180 Sum_probs=34.0
Q ss_pred HhHHHHHHcCCc---EEEEEEEeCCcccchHHHHHHHHHhcCCEEEEE
Q 011629 3 AIADIVDYFGWR---NVIALYVDDDHGRNGIAALGDKLAEKRCRLSHK 47 (481)
Q Consensus 3 Ai~~ll~~fgW~---~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~ 47 (481)
++..+++...-. .+.++++|..-|...++.+++.+.+.|+.+...
T Consensus 9 sl~~~~~~~~~~~~~~~~Ll~SDT~~G~~~a~il~~~l~~~g~~v~~~ 56 (136)
T PF09651_consen 9 SLVRLLEKGKDDDKDEVVLLHSDTPDGRLCAEILKEYLEEKGINVEVV 56 (136)
T ss_dssp HHHHHHHHHT--GGGEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEE
T ss_pred HHHHHHHhCccccCcEEEEEeCCCHHHHHHHHHHHHHHHHcCCeEEEE
Confidence 455555554443 799999999999999999999999999886543
No 382
>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.
Probab=39.58 E-value=1.3e+02 Score=28.12 Aligned_cols=71 Identities=13% Similarity=0.121 Sum_probs=43.2
Q ss_pred hHHHHHHc--CCcEEEEEEEeCCc-ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 4 IADIVDYF--GWRNVIALYVDDDH-GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~f--gW~~V~ii~~dd~~-g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
-+++++.+ +-++|+++|++++- +....+.+++.+++.|+.+.... ++ +.+++...++.+... ..++++..+
T Consensus 120 ~l~l~~~l~P~~k~igvl~~~~~~~~~~~~~~~~~~a~~~g~~l~~~~-v~---~~~~~~~~~~~l~~~-~da~~~~~~ 193 (294)
T PF04392_consen 120 QLELIKKLFPDAKRIGVLYDPSEPNSVAQIEQLRKAAKKLGIELVEIP-VP---SSEDLEQALEALAEK-VDALYLLPD 193 (294)
T ss_dssp HHHHHHHHSTT--EEEEEEETT-HHHHHHHHHHHHHHHHTT-EEEEEE-ES---SGGGHHHHHHHHCTT--SEEEE-S-
T ss_pred HHHHHHHhCCCCCEEEEEecCCCccHHHHHHHHHHHHHHcCCEEEEEe-cC---cHhHHHHHHHHhhcc-CCEEEEECC
Confidence 34566664 46899999976654 44567888888889999876543 32 234677778877654 566666544
No 383
>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).
Probab=39.48 E-value=2.9e+02 Score=27.38 Aligned_cols=24 Identities=25% Similarity=0.592 Sum_probs=18.5
Q ss_pred hHhHHHH---HHcCCc----EEEEEEEeCCc
Q 011629 2 AAIADIV---DYFGWR----NVIALYVDDDH 25 (481)
Q Consensus 2 ~Ai~~ll---~~fgW~----~V~ii~~dd~~ 25 (481)
+||.+.+ +.-||+ ++.|+.+|..+
T Consensus 211 DAimQaaVC~~~IGWR~~a~rllv~~TDa~f 241 (423)
T smart00187 211 DAIMQAAVCTEQIGWREDARRLLVFSTDAGF 241 (423)
T ss_pred HHHHHHHhhccccccCCCceEEEEEEcCCCc
Confidence 5777777 789998 68888877765
No 384
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=39.44 E-value=1.5e+02 Score=26.68 Aligned_cols=75 Identities=16% Similarity=0.009 Sum_probs=46.2
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|++|..+ +.+.....+.+.+++++.|+.+..... ..+.++..+.++.+...+++.||+...... ...+..+.+.
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~-~~~~~~~~~~ 77 (268)
T cd01575 2 VAVLVPSLSNSVFADVLQGISDVLEAAGYQLLLGNT---GYSPEREEELLRTLLSRRPAGLILTGLEHT-ERTRQLLRAA 77 (268)
T ss_pred EEEEeCCCcchhHHHHHHHHHHHHHHcCCEEEEecC---CCCchhHHHHHHHHHHcCCCEEEEeCCCCC-HHHHHHHHhc
Confidence 5666643 445556678888999999988765321 222234556777887778898888764322 2334444444
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 78 ~ 78 (268)
T cd01575 78 G 78 (268)
T ss_pred C
Confidence 4
No 385
>PRK11425 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=39.41 E-value=2.2e+02 Score=23.86 Aligned_cols=76 Identities=13% Similarity=0.093 Sum_probs=49.3
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHH
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWG 83 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~ 83 (481)
+....++++-+.+.++- |..-.....+.+.+.+.-.|+.+... +.++....+++ +..+-++.|++-++.++
T Consensus 19 ~~~W~~~~~~~~IvVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~-------sv~~a~~~l~~-~~~~~~v~il~k~~~d~ 89 (157)
T PRK11425 19 GVQWVGFAGANLVLVAN-DEVAEDPVQQNLMEMVLAEGIAVRFW-------TLQKVIDNIHR-AADRQKILLVCKTPADF 89 (157)
T ss_pred hhhhhcccCCCEEEEEc-chhcCCHHHHHHHHhhCCCCCeEEEE-------EHHHHHHHHhc-cCCCceEEEEECCHHHH
Confidence 44556777777766554 44444456666666666678877643 22345566666 55667899999998888
Q ss_pred HHHHH
Q 011629 84 LEVLN 88 (481)
Q Consensus 84 ~~il~ 88 (481)
..+..
T Consensus 90 ~~l~~ 94 (157)
T PRK11425 90 LTLVK 94 (157)
T ss_pred HHHHH
Confidence 77755
No 386
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=39.25 E-value=1.6e+02 Score=26.64 Aligned_cols=75 Identities=11% Similarity=-0.074 Sum_probs=47.0
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++..+ +.|.....+.+++.+++.|..+..... ..+.+...+.++.+...+++.||+........ .+..+.+.
T Consensus 2 igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~-~~~~~~~~ 77 (264)
T cd06274 2 IGLIIPDLENRSFARIAKRLEALARERGYQLLIACS---DDDPETERETVETLIARQVDALIVAGSLPPDD-PYYLCQKA 77 (264)
T ss_pred EEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEcCCCCchH-HHHHHHhc
Confidence 4566643 556667788888999999998765422 22223345677778888899888875432222 24555554
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
|
T Consensus 78 ~ 78 (264)
T cd06274 78 G 78 (264)
T ss_pred C
Confidence 4
No 387
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=38.66 E-value=2.1e+02 Score=23.42 Aligned_cols=75 Identities=17% Similarity=0.093 Sum_probs=45.9
Q ss_pred EEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc-CCceEEEEEeCc-HHHHHHHHHHHHc
Q 011629 16 VIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS-MMSRILILHTYD-IWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~-s~~~vIvl~~~~-~~~~~il~~a~~~ 93 (481)
|++|.+... ....+.+.+...|+-+.....+-...+ -++.+.++-+.+ ..+++|+++... .+.+.++..+.+.
T Consensus 4 valisQSG~----~~~~~~~~~~~~g~g~s~~vs~Gn~~d-v~~~d~l~~~~~D~~t~~I~ly~E~~~d~~~f~~~~~~a 78 (138)
T PF13607_consen 4 VALISQSGA----LGTAILDWAQDRGIGFSYVVSVGNEAD-VDFADLLEYLAEDPDTRVIVLYLEGIGDGRRFLEAARRA 78 (138)
T ss_dssp EEEEES-HH----HHHHHHHHHHHTT-EESEEEE-TT-SS-S-HHHHHHHHCT-SS--EEEEEES--S-HHHHHHHHHHH
T ss_pred EEEEECCHH----HHHHHHHHHHHcCCCeeEEEEeCcccc-CCHHHHHHHHhcCCCCCEEEEEccCCCCHHHHHHHHHHH
Confidence 677775543 345567778888888877766654432 246677777654 689999999884 4678888888876
Q ss_pred CC
Q 011629 94 RM 95 (481)
Q Consensus 94 g~ 95 (481)
..
T Consensus 79 ~~ 80 (138)
T PF13607_consen 79 AR 80 (138)
T ss_dssp CC
T ss_pred hc
Confidence 53
No 388
>PRK15138 aldehyde reductase; Provisional
Probab=38.53 E-value=1.2e+02 Score=29.93 Aligned_cols=72 Identities=10% Similarity=0.077 Sum_probs=46.6
Q ss_pred hHHHHHHcCCcEEEEEEEeCCc-ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDDH-GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~-g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
+.++++. + +++-+|+.+... .......+.+.|. |+.+.....+..+.+.++.....+..++.++++||..+.
T Consensus 22 l~~~l~~-~-~~~livt~~~~~~~~g~~~~v~~~L~--~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGG 94 (387)
T PRK15138 22 LREQIPA-D-ARVLITYGGGSVKKTGVLDQVLDALK--GMDVLEFGGIEPNPTYETLMKAVKLVREEKITFLLAVGG 94 (387)
T ss_pred HHHHHhc-C-CeEEEECCCchHHhcCcHHHHHHHhc--CCeEEEECCccCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 3455665 4 788777643322 2334566777774 665544334555566667888888888889999997765
No 389
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=38.18 E-value=2.2e+02 Score=23.16 Aligned_cols=49 Identities=14% Similarity=0.045 Sum_probs=31.7
Q ss_pred HHHHHHHHHhcCCEEEEEE--e-cCC-CCChhHHHHHHHHhccCCceEEEEEe
Q 011629 30 IAALGDKLAEKRCRLSHKV--P-LSP-KGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 30 ~~~l~~~l~~~gi~v~~~~--~-~~~-~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
.+.+++.+.++|+.+.... . .+- ......+..+++.++....++||+.-
T Consensus 24 ~~~l~~~a~~~g~~i~~~~~D~~~SG~~~~Rp~l~~ll~~~~~g~vd~vvv~~ 76 (140)
T cd03770 24 KAILEEYAKENGLENIRHYIDDGFSGTTFDRPGFNRMIEDIEAGKIDIVIVKD 76 (140)
T ss_pred HHHHHHHHHHCCCEEEEEEEcCCCcCCcCCCHHHHHHHHHHHcCCCCEEEEec
Confidence 5566777888898875321 1 111 12345788888888887788887764
No 390
>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=38.04 E-value=42 Score=21.69 Aligned_cols=23 Identities=26% Similarity=0.648 Sum_probs=18.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcc
Q 011629 441 KMWCVTGIFFLVVGVVVWILEHR 463 (481)
Q Consensus 441 ~~W~~~~~~~~~~~~~~~~~~~~ 463 (481)
++|.++....+.+++++|.+...
T Consensus 12 ~~~~l~~~~~~Figiv~wa~~p~ 34 (48)
T cd01324 12 DSWGLLYLALFFLGVVVWAFRPG 34 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCC
Confidence 67888777788889999999433
No 391
>PRK13805 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional
Probab=37.91 E-value=1.5e+02 Score=32.91 Aligned_cols=69 Identities=10% Similarity=-0.000 Sum_probs=50.2
Q ss_pred CCcEEEEEEEeCCcccchHHHHHHHHH--hcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 12 GWRNVIALYVDDDHGRNGIAALGDKLA--EKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 12 gW~~V~ii~~dd~~g~~~~~~l~~~l~--~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+-+++-||++......+..+.+.+.++ +.|+.+.....+..+.+.+...+.+..+++.+++.||..+..
T Consensus 479 ~~~~~lvVtd~~~~~~g~~~~v~~~L~~~~~~i~~~~~~~v~~np~~~~v~~~~~~~~~~~~D~IIaiGGG 549 (862)
T PRK13805 479 GKKRAFIVTDRFMVELGYVDKVTDVLKKRENGVEYEVFSEVEPDPTLSTVRKGAELMRSFKPDTIIALGGG 549 (862)
T ss_pred CCCEEEEEECcchhhcchHHHHHHHHhcccCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 668888888544333346778888898 778877655455556666678888888999999999987653
No 392
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=37.79 E-value=2.1e+02 Score=22.79 Aligned_cols=65 Identities=17% Similarity=0.090 Sum_probs=38.9
Q ss_pred HHHHHHHHHhcCCEEEEEE--ecCC---CCChhHHHHHHHHhccCCceEEEEEeCc------HHHHHHHHHHHHcC
Q 011629 30 IAALGDKLAEKRCRLSHKV--PLSP---KGSRNQIIDTLLTVSSMMSRILILHTYD------IWGLEVLNAAKHLR 94 (481)
Q Consensus 30 ~~~l~~~l~~~gi~v~~~~--~~~~---~~~~~~~~~~l~~i~~s~~~vIvl~~~~------~~~~~il~~a~~~g 94 (481)
.+.+++.+..+|+.+.... .-.. ......+..+++.++....++||+.--. .....++..+...|
T Consensus 20 ~~~~~~~a~~~g~~i~~~~~d~~~s~~~~~~R~~~~~ll~~~~~~~~d~ivv~~~~Rl~R~~~~~~~~~~~l~~~g 95 (137)
T cd00338 20 REALREYAARNGLEVVGEYEDAGSSATSLVDRPGLQRLLADVKAGKIDVVLVEKLDRLSRNLVDLLELLELLEAHG 95 (137)
T ss_pred HHHHHHHHHHCCCEEEEEEEeCCCCcccccCCHHHHHHHHHHHcCCCCEEEEEecchhhCCHHHHHHHHHHHHHCC
Confidence 5666777777887654321 1111 1123468888888887677777776432 35556666666544
No 393
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=37.77 E-value=2e+02 Score=22.48 Aligned_cols=74 Identities=14% Similarity=0.075 Sum_probs=38.0
Q ss_pred HHHHcCCcEEEEEEEeCC-cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 7 IVDYFGWRNVIALYVDDD-HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 7 ll~~fgW~~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
-|...|.+.|.-+-.|++ -++.....+.+.+++.|+...+.-.-....+.+++....+.+...... |+++|.+.
T Consensus 22 ~la~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y~~iPv~~~~~~~~~v~~f~~~l~~~~~P-vl~hC~sG 96 (110)
T PF04273_consen 22 QLAAQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQYVHIPVDGGAITEEDVEAFADALESLPKP-VLAHCRSG 96 (110)
T ss_dssp HHHHCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EEEE----TTT--HHHHHHHHHHHHTTTTS-EEEE-SCS
T ss_pred HHHHCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeEEEeecCCCCCCHHHHHHHHHHHHhCCCC-EEEECCCC
Confidence 456689999888876654 345567778899999998866432222223445555555556555434 55555543
No 394
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=37.76 E-value=2e+02 Score=27.55 Aligned_cols=79 Identities=10% Similarity=-0.097 Sum_probs=49.5
Q ss_pred cEEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-HHHHHHHHH
Q 011629 14 RNVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-WGLEVLNAA 90 (481)
Q Consensus 14 ~~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~~~~il~~a 90 (481)
+.|++|..+ +.|.....+.+++.+++.|..+.....-. ..+.+.....++.+.+.+++.||+..... .....+ ++
T Consensus 47 ~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~-~~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l-~~ 124 (343)
T PRK10936 47 WKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGG-YYNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDL-EL 124 (343)
T ss_pred eEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCC-CCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHH-HH
Confidence 477888744 45666778888999999998877643211 11222344667777777889888865433 323444 56
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.|
T Consensus 125 ~~~g 128 (343)
T PRK10936 125 QAAN 128 (343)
T ss_pred HHCC
Confidence 5554
No 395
>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=37.70 E-value=1.6e+02 Score=26.88 Aligned_cols=69 Identities=16% Similarity=0.177 Sum_probs=45.9
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. .+++.+.. ++...++..|.+|++|+++..-.. ....+.+ .|+....+.++++++
T Consensus 98 ~~~~~l~~~~~~~p-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~~-~~l~~~~~~lv~s~~ 165 (279)
T TIGR03339 98 YVLDLVARFRQRYP-GIEVSVRI-------GNSQEVLQALQSYRVDVAVSSEVV---DDPRLDR-VVLGNDPLVAVVHRQ 165 (279)
T ss_pred HHHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEeccc---CCCceEE-EEcCCceEEEEECCC
Confidence 34577777777653 34466655 457789999999999999753222 2233433 677788888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 166 ~ 166 (279)
T TIGR03339 166 H 166 (279)
T ss_pred C
Confidence 4
No 396
>TIGR00035 asp_race aspartate racemase.
Probab=37.55 E-value=58 Score=29.28 Aligned_cols=40 Identities=10% Similarity=0.017 Sum_probs=27.7
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEE
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLS 45 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~ 45 (481)
+.++-++.-|-++|+++.+.... ....+++.+++.|+.+.
T Consensus 107 ~~~~~~~~~~~~~VgvLaT~~T~---~s~~y~~~l~~~g~~v~ 146 (229)
T TIGR00035 107 ETAEAVKEDGVKKAGLLGTKGTM---KDGVYEREMKKHGIEIV 146 (229)
T ss_pred HHHHHHHHcCCCEEEEEecHHHH---HhHHHHHHHHHCCCEEE
Confidence 44455566789999999865432 33457888888897654
No 397
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=37.46 E-value=1.9e+02 Score=26.08 Aligned_cols=75 Identities=11% Similarity=-0.037 Sum_probs=48.4
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++..+ +.+.....+.+.+.+++.|..+... ....+.......++.+...+++.||+....... ..+.++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (265)
T cd06285 2 IGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVA---NTGDNPDAQRRAIEMLLDRRVDGLILGDARSDD-HFLDELTRR 77 (265)
T ss_pred EEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE---eCCCCHHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHHHc
Confidence 5677753 5666777889999999999987532 222232344566777878889988886543222 345666554
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 78 ~ 78 (265)
T cd06285 78 G 78 (265)
T ss_pred C
Confidence 4
No 398
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=37.36 E-value=1e+02 Score=29.15 Aligned_cols=70 Identities=9% Similarity=0.101 Sum_probs=49.0
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
++-.+++..+.++.. ++++.+.. ++...++..|.+|++|+++... +.....+.+ .++....+.+++++
T Consensus 125 ~~l~~~l~~f~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Di~i~~~---~~~~~~l~~-~~l~~~~~~lv~~~ 192 (314)
T PRK09508 125 RLTSQIYNRIEQIAP-NIHVVFKS-------SLNQNIEHQLRYQETEFVISYE---EFDRPEFTS-VPLFKDELVLVASK 192 (314)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe-------CcchhHHHHHhcCCccEEEecC---CCCccccce-eeeecCceEEEEcC
Confidence 355788888888763 34566665 4567889999999999997643 222234544 57788888888876
Q ss_pred CC
Q 011629 425 KK 426 (481)
Q Consensus 425 ~~ 426 (481)
+.
T Consensus 193 ~h 194 (314)
T PRK09508 193 NH 194 (314)
T ss_pred CC
Confidence 54
No 399
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=37.18 E-value=1.9e+02 Score=26.15 Aligned_cols=76 Identities=9% Similarity=-0.147 Sum_probs=48.5
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-H---HHHHHHHH
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-I---WGLEVLNA 89 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~---~~~~il~~ 89 (481)
||+|.. ++.+.....+.+.+.+++.|..+... ....+.+...+.++.+...+++.||+.... . .....+.+
T Consensus 2 Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~---~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~i~~ 78 (273)
T cd06292 2 VGLLVPELSNPIFPAFAEAIEAALAQYGYTVLLC---NTYRGGVSEADYVEDLLARGVRGVVFISSLHADTHADHSHYER 78 (273)
T ss_pred EEEEeCCCcCchHHHHHHHHHHHHHHCCCEEEEE---eCCCChHHHHHHHHHHHHcCCCEEEEeCCCCCcccchhHHHHH
Confidence 566664 35566778899999999999887643 222233345577888888889988886432 1 12233555
Q ss_pred HHHcC
Q 011629 90 AKHLR 94 (481)
Q Consensus 90 a~~~g 94 (481)
+.+.|
T Consensus 79 ~~~~~ 83 (273)
T cd06292 79 LAERG 83 (273)
T ss_pred HHhCC
Confidence 55544
No 400
>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=37.07 E-value=1.3e+02 Score=25.19 Aligned_cols=70 Identities=14% Similarity=0.036 Sum_probs=43.5
Q ss_pred eeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEec
Q 011629 345 GYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPI 424 (481)
Q Consensus 345 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 424 (481)
.+-.+++..+.++.- ++++++.. .+...++.+|.+|++|+++..... .....+. +.+.....+.+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~~ 81 (195)
T cd08431 13 QPLYPLIAEFYQLNK-ATRIRLSE-------EVLGGTWDALASGRADLVIGATGE--LPPGGVK-TRPLGEVEFVFAVAP 81 (195)
T ss_pred HHHHHHHHHHHHHCC-CCceEEEE-------eccchHHHHHhCCCCCEEEEecCC--CCCCceE-EEecccceEEEEEcC
Confidence 345688888888863 24466665 346688999999999999753211 1112232 355566666666654
Q ss_pred C
Q 011629 425 K 425 (481)
Q Consensus 425 ~ 425 (481)
+
T Consensus 82 ~ 82 (195)
T cd08431 82 N 82 (195)
T ss_pred C
Confidence 4
No 401
>PRK01215 competence damage-inducible protein A; Provisional
Probab=36.77 E-value=2.9e+02 Score=25.52 Aligned_cols=63 Identities=6% Similarity=0.081 Sum_probs=43.3
Q ss_pred EEEEEEEeCC--ccc---chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 15 NVIALYVDDD--HGR---NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 15 ~V~ii~~dd~--~g~---~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+++||...|+ .|. .....+.+.+.+.|+.+.....++. +.+++...+++..+ .+++||+.+..
T Consensus 5 ~v~Ii~~GdEll~G~i~dtn~~~l~~~L~~~G~~v~~~~~v~D--d~~~I~~~l~~a~~-~~DlVIttGG~ 72 (264)
T PRK01215 5 FAWIITIGNELLIGRTVNTNASWIARRLTYLGYTVRRITVVMD--DIEEIVSAFREAID-RADVVVSTGGL 72 (264)
T ss_pred EEEEEEEChhccCCeEEEhhHHHHHHHHHHCCCeEEEEEEeCC--CHHHHHHHHHHHhc-CCCEEEEeCCC
Confidence 5777776654 333 3466888889999999988766654 33466777777665 36888887653
No 402
>cd08172 GlyDH-like1 Glycerol dehydrogenases-like. Glycerol dehydrogenases-like. The proteins in this family have not been characterized, but they show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=36.76 E-value=1.1e+02 Score=29.54 Aligned_cols=72 Identities=11% Similarity=0.083 Sum_probs=46.2
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.++ +++.+|++...+ ....+.+.+.+++.++.+. .+....+.+...+.+...++.++++||..+..
T Consensus 15 l~~~~~~~~-~~~liv~d~~~~-~~~~~~l~~~L~~~~~~~~---~~~~~p~~~~v~~~~~~~~~~~~D~iIavGGG 86 (347)
T cd08172 15 LGELLKRFG-KRPLIVTGPRSW-AAAKPYLPESLAAGEAFVL---RYDGECSEENIERLAAQAKENGADVIIGIGGG 86 (347)
T ss_pred HHHHHHHhC-CeEEEEECHHHH-HHHHHHHHHHHhcCeEEEE---EeCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 345666675 888888854433 3456666677755555432 23322455677888888888889999887653
No 403
>PRK10586 putative oxidoreductase; Provisional
Probab=36.57 E-value=1.8e+02 Score=28.38 Aligned_cols=72 Identities=7% Similarity=-0.027 Sum_probs=45.4
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+.++++.+|.+++.+|+....+ ......+.+.+++.|+.+. .+....+.+++.++.+..+ .++++||..+..
T Consensus 25 l~~~~~~~g~~~~lvv~g~~~~-~~~~~~~~~~l~~~~~~~~---~~~g~~~~~~v~~l~~~~~-~~~d~iiavGGG 96 (362)
T PRK10586 25 LHDFFTDEQLSRAVWIYGERAI-AAAQPYLPPAFELPGAKHI---LFRGHCSESDVAQLAAASG-DDRQVVIGVGGG 96 (362)
T ss_pred HHHHHHhcCCCeEEEEEChHHH-HHHHHHHHHHHHHcCCeEE---EeCCCCCHHHHHHHHHHhc-cCCCEEEEecCc
Confidence 5577888999999988844332 2223556777888887553 3433334455665544443 468999877654
No 404
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=36.48 E-value=1.7e+02 Score=26.31 Aligned_cols=61 Identities=15% Similarity=0.022 Sum_probs=37.9
Q ss_pred EEEEEEe------CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 16 VIALYVD------DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 16 V~ii~~d------d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
|++|..+ +.|.....+.+.+.+++.|+.+..... ....+......+.+...+++.||+.+.
T Consensus 2 igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~~~~~~vdgiii~~~ 68 (268)
T cd06271 2 IGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYDLVLLPV---DPDEDPLEVYRRLVESGLVDGVIISRT 68 (268)
T ss_pred eEEEeCCcccccCCccHHHHHHHHHHHHHHCCceEEEecC---CCcHHHHHHHHHHHHcCCCCEEEEecC
Confidence 5666644 567777888999999999998766532 111122233333345556888887653
No 405
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=36.41 E-value=2.4e+02 Score=26.56 Aligned_cols=79 Identities=9% Similarity=-0.058 Sum_probs=47.9
Q ss_pred CcEEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHH
Q 011629 13 WRNVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAA 90 (481)
Q Consensus 13 W~~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a 90 (481)
-..|+++..+ +.+.....+.+.+.+.+.|+.+..... ..+.+.-...++.+...+.+-||+..........+.++
T Consensus 61 ~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 137 (328)
T PRK11303 61 TRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACS---DDQPDNEMRCAEHLLQRQVDALIVSTSLPPEHPFYQRL 137 (328)
T ss_pred CceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEcCCCCCChHHHHHH
Confidence 3578888753 456666788888999999998765421 11222334566667667788888765322122344555
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.+
T Consensus 138 ~~~~ 141 (328)
T PRK11303 138 QNDG 141 (328)
T ss_pred HhcC
Confidence 4444
No 406
>PF12916 DUF3834: Protein of unknown function (DUF3834); InterPro: IPR024533 This family is likely to be related to solute-binding lipo-proteins.; PDB: 3MST_A.
Probab=36.11 E-value=55 Score=28.32 Aligned_cols=44 Identities=23% Similarity=0.274 Sum_probs=25.6
Q ss_pred eeeHHH-HHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 345 GYCIDV-FTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 345 G~~~dl-~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
|=.-|+ ++.+++..|.+.++.+. .+|..++.++.+|++|-++-+
T Consensus 77 GsaADvl~Ral~d~~~~~~EvVyt--------dD~~~i~~Ml~~g~vdsAVv~ 121 (201)
T PF12916_consen 77 GSAADVLTRALLDLKGIKAEVVYT--------DDMSEIVKMLNEGEVDSAVVG 121 (201)
T ss_dssp TSHHHHHHHHHHHHH--T-EEEE-----------HHHHHHHHHTT-E--EEEE
T ss_pred ccHHHHHHHHHHhhccccceeEEe--------cCHHHHHHHHhcCceeeeeec
Confidence 334554 46667777867556555 369999999999999988654
No 407
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=36.08 E-value=1.9e+02 Score=26.33 Aligned_cols=75 Identities=13% Similarity=0.037 Sum_probs=47.7
Q ss_pred EEEEEE-eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH-HHHHHHHHHHH
Q 011629 16 VIALYV-DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI-WGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~-dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~-~~~~il~~a~~ 92 (481)
|++|.. .+.|.......+.+++++.|+.+.... +...+.+.-...++.+...+.+.+|+..... .....+.++.+
T Consensus 2 i~~v~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~--~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~~l~~~~~ 78 (271)
T cd06314 2 IAVVTNGASPFWKIAEAGVKAAGKELGVDVEFVV--PQQGTVNAQLRMLEDLIAEGVDGIAISPIDPKAVIPALNKAAA 78 (271)
T ss_pred eEEEcCCCcHHHHHHHHHHHHHHHHcCCeEEEeC--CCCCCHHHHHHHHHHHHhcCCCEEEEecCChhHhHHHHHHHhc
Confidence 566653 345666778889999999998876541 1222333345667777778889888875433 23456666644
No 408
>COG0107 HisF Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]
Probab=35.82 E-value=56 Score=29.19 Aligned_cols=49 Identities=20% Similarity=0.190 Sum_probs=38.3
Q ss_pred CCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEe
Q 011629 340 TDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVG 395 (481)
Q Consensus 340 ~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~ 395 (481)
+|.-.||+++|++.+++..+.. +.-.- .-++-..+.+.+..+++|.+++
T Consensus 180 DGtk~GyDl~l~~~v~~~v~iP--vIASG-----GaG~~ehf~eaf~~~~adAaLA 228 (256)
T COG0107 180 DGTKAGYDLELTRAVREAVNIP--VIASG-----GAGKPEHFVEAFTEGKADAALA 228 (256)
T ss_pred cccccCcCHHHHHHHHHhCCCC--EEecC-----CCCcHHHHHHHHHhcCccHHHh
Confidence 7888899999999999999854 43221 1246788999999999997755
No 409
>TIGR01120 rpiB ribose 5-phosphate isomerase B. Involved in the non-oxidative branch of the pentose phospate pathway.
Probab=35.77 E-value=2.5e+02 Score=23.15 Aligned_cols=63 Identities=16% Similarity=-0.038 Sum_probs=37.4
Q ss_pred EEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCC-ChhHH-HHHHHHhccCCceEEEEEeCcHH
Q 011629 20 YVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKG-SRNQI-IDTLLTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 20 ~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~-~~~~~-~~~l~~i~~s~~~vIvl~~~~~~ 82 (481)
...|.-|....+.+.+.|++.|.+|...-..+... +..++ ....+.+.+..++.-|++|.+..
T Consensus 4 igsDhaG~~lK~~l~~~L~~~g~eV~D~G~~~~~~~dYpd~a~~va~~V~~~~~~~GIliCGtGi 68 (143)
T TIGR01120 4 IGSDHAGFILKEEIKAFLVERGVKVIDKGTWSSERTDYPHYAKQVALAVAGGEVDGGILICGTGI 68 (143)
T ss_pred EEeCcchHHHHHHHHHHHHHCCCEEEEeCCCCCCCCCHHHHHHHHHHHHHCCCCceEEEEcCCcH
Confidence 33566788999999999999999987654333221 22233 23345565544544444444443
No 410
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=35.74 E-value=1.8e+02 Score=26.89 Aligned_cols=80 Identities=10% Similarity=0.055 Sum_probs=0.0
Q ss_pred EEEEEE--EeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHHHHH
Q 011629 15 NVIALY--VDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLNAAK 91 (481)
Q Consensus 15 ~V~ii~--~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~~a~ 91 (481)
+|++|. .++.+.......+++++++.|+.+... .....+.......++.+...+++.||+...... ....+.++.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~--~~~~~~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~~~i~~~~ 78 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVAT--TDAQFDPAKQVADIETTISQKPDIIISIPVDPVSTAAAYKKVA 78 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHHcCCEEEEe--cCCCCCHHHHHHHHHHHHHhCCCEEEEcCCCchhhhHHHHHHH
Q ss_pred HcCCc
Q 011629 92 HLRMM 96 (481)
Q Consensus 92 ~~g~~ 96 (481)
+.|..
T Consensus 79 ~~~iP 83 (294)
T cd06316 79 EAGIK 83 (294)
T ss_pred HcCCc
No 411
>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=35.59 E-value=1.5e+02 Score=24.88 Aligned_cols=65 Identities=9% Similarity=0.052 Sum_probs=41.7
Q ss_pred HHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 348 IDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 348 ~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
..++..+.++. ++++++.. .+...+...+.+|++|+++.. .+.....+ .+.++......++++++
T Consensus 16 ~~~l~~f~~~~--~v~l~l~~-------~~~~~~~~~l~~~~~D~~i~~---~~~~~~~~-~~~~l~~~~~~~~~~~~ 80 (195)
T cd08428 16 LPALAPVLKRE--RILLDLIV-------DDEDRTHDLLRDGEVVGCIST---QAQPMQGC-RSDYLGSMDYLLVASPD 80 (195)
T ss_pred HHHHHHHHhCc--CeEEEEEe-------CCchhHHHHHHcCcceEEEEe---cCCCCCCc-eeEEeeeeeEEEEECCc
Confidence 45677777764 45576665 456788999999999987642 22222333 34566677777776543
No 412
>KOG1014 consensus 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism]
Probab=35.40 E-value=2.3e+02 Score=26.76 Aligned_cols=67 Identities=15% Similarity=0.167 Sum_probs=44.5
Q ss_pred HHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc---CCceEEEEEeCcHH
Q 011629 6 DIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS---MMSRILILHTYDIW 82 (481)
Q Consensus 6 ~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~---s~~~vIvl~~~~~~ 82 (481)
++.+.+| +|.++--..|.-| +...++|+++|+.|... . .+.+.+....++|.+ -..|++++.+...+
T Consensus 43 ~~~~~~g-~WAVVTGaTDGIG----KayA~eLAkrG~nvvLI---s--Rt~~KL~~v~kEI~~~~~vev~~i~~Dft~~~ 112 (312)
T KOG1014|consen 43 DLKEKLG-SWAVVTGATDGIG----KAYARELAKRGFNVVLI---S--RTQEKLEAVAKEIEEKYKVEVRIIAIDFTKGD 112 (312)
T ss_pred chHHhcC-CEEEEECCCCcch----HHHHHHHHHcCCEEEEE---e--CCHHHHHHHHHHHHHHhCcEEEEEEEecCCCc
Confidence 5778899 8877766666544 66677888899997654 2 234456666666654 34677777766544
No 413
>PF13155 Toprim_2: Toprim-like
Probab=35.07 E-value=69 Score=23.88 Aligned_cols=39 Identities=15% Similarity=0.338 Sum_probs=29.6
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcC
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKR 41 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~g 41 (481)
.+.++++..+=+.|.+..++|.-|....+.+.+.+...+
T Consensus 37 ~~~~~l~~~~~~~i~l~~DnD~aG~~~~~~~~~~l~~~~ 75 (96)
T PF13155_consen 37 QQIKFLKENPYKKIVLAFDNDEAGRKAAEKLQKELKEEG 75 (96)
T ss_pred HHHHHHHhCCCCcEEEEeCCCHHHHHHHHHHHHHHHhhC
Confidence 456667555547788778788888888888888888876
No 414
>PRK13054 lipid kinase; Reviewed
Probab=35.04 E-value=3e+02 Score=25.88 Aligned_cols=75 Identities=12% Similarity=0.007 Sum_probs=46.2
Q ss_pred cEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHH
Q 011629 14 RNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKH 92 (481)
Q Consensus 14 ~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~ 92 (481)
+++.+|+.....+......+.+.+.+.|+.+... ...... +...+.++....+.++||+.+-...+..++..+.+
T Consensus 4 ~~~~~i~N~~~~~~~~~~~~~~~l~~~g~~~~v~--~t~~~~--~a~~~a~~~~~~~~d~vvv~GGDGTl~evv~~l~~ 78 (300)
T PRK13054 4 PKSLLILNGKSAGNEELREAVGLLREEGHTLHVR--VTWEKG--DAARYVEEALALGVATVIAGGGDGTINEVATALAQ 78 (300)
T ss_pred ceEEEEECCCccchHHHHHHHHHHHHcCCEEEEE--EecCCC--cHHHHHHHHHHcCCCEEEEECCccHHHHHHHHHHh
Confidence 4667777433323444666677788889875542 222222 34556666655667888888877777777776654
No 415
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=35.03 E-value=3.4e+02 Score=24.42 Aligned_cols=87 Identities=14% Similarity=0.069 Sum_probs=48.9
Q ss_pred CCcEEEEEEEeCC-cccchHHHHHHHHHhc-CCEEEEEEecCCCCChhHHHHHHHHhccC--CceEEEEEeCcHHHHHHH
Q 011629 12 GWRNVIALYVDDD-HGRNGIAALGDKLAEK-RCRLSHKVPLSPKGSRNQIIDTLLTVSSM--MSRILILHTYDIWGLEVL 87 (481)
Q Consensus 12 gW~~V~ii~~dd~-~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~~~~~~l~~i~~s--~~~vIvl~~~~~~~~~il 87 (481)
|-.++++++..+. ......+.+++.+++. |+.+... ....+.+.....++++... +.++ |++.+...+..++
T Consensus 120 g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~ 195 (267)
T cd06322 120 GKGQVAIIDYPTVQSVVDRVRGFKEALADYPNIKIVAV---QPGITRAEALTAAQNILQANPDLDG-IFAFGDDAALGAV 195 (267)
T ss_pred CCceEEEEecCCCccHHHHHHHHHHHHHhCCCcEEEEe---cCCCChHHHHHHHHHHHHhCCCCCE-EEEcCCcHHHHHH
Confidence 7789999974322 2345677888888888 8875322 1111222233334443322 2443 4445556667788
Q ss_pred HHHHHcCCccCCeEEEEe
Q 011629 88 NAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 88 ~~a~~~g~~~~~~~wI~~ 105 (481)
..+.+.|. +.+.|.+
T Consensus 196 ~al~~~g~---~di~vvg 210 (267)
T cd06322 196 SAIKAAGR---DNVKVIG 210 (267)
T ss_pred HHHHHCCC---CCeEEEE
Confidence 88888875 3454443
No 416
>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=34.98 E-value=3.3e+02 Score=24.90 Aligned_cols=78 Identities=14% Similarity=0.023 Sum_probs=49.0
Q ss_pred cEEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHHHH
Q 011629 14 RNVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLNAA 90 (481)
Q Consensus 14 ~~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~~a 90 (481)
+.|++|..+ +.|.....+.+.+.+++.|..+.... ...+.++-...++.+...+.+.||+...... ....+..+
T Consensus 1 ~~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~~~~~~---~~~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~~~~~~~ 77 (280)
T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRILD---GRGSEAGQAAALNQAIALKPDGIVLGGVDAAELQAELELA 77 (280)
T ss_pred CeEEEEecccCCcHHHHHHHHHHHHHHHcCcEEEEEC---CCCCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHHHHHHH
Confidence 357877754 34555678888899999998876532 1223333456777788888898888754322 23444555
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.+
T Consensus 78 ~~~~ 81 (280)
T cd06315 78 QKAG 81 (280)
T ss_pred HHCC
Confidence 4544
No 417
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=34.95 E-value=1.7e+02 Score=27.45 Aligned_cols=85 Identities=19% Similarity=0.192 Sum_probs=54.1
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.+++++|+.. ... ..+-..+++.+.++.. ++++.+.. ++++++...|.+|++|+++..
T Consensus 92 ~g~l~Ig~~~--~~~------------~~~l~~~i~~f~~~~P-~i~l~~~~-------~~~~~~~~~L~~~~~D~~i~~ 149 (309)
T PRK12683 92 SGHLTVATTH--TQA------------RYALPKVVRQFKEVFP-KVHLALRQ-------GSPQEIAEMLLNGEADIGIAT 149 (309)
T ss_pred CceEEEEecc--chH------------HHHHHHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHcCCccEEEec
Confidence 3678888863 111 1223567777777652 34566665 568999999999999998752
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
... .....+.+ .|+....+.++++++.
T Consensus 150 ~~~--~~~~~l~~-~~l~~~~~~~v~~~~h 176 (309)
T PRK12683 150 EAL--DREPDLVS-FPYYSWHHVVVVPKGH 176 (309)
T ss_pred CCC--CCCCCceE-EEcccCeEEEEecCCC
Confidence 211 12233544 4677778888887654
No 418
>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=34.69 E-value=2.1e+02 Score=24.07 Aligned_cols=67 Identities=22% Similarity=0.170 Sum_probs=44.2
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
-.+++..+.++.. .+++++.. ++-.++...|.+|++|+++..... ....+. +.++......++++.+
T Consensus 15 l~~~l~~f~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~ 81 (196)
T cd08458 15 MSGVIQTFIADRP-DVSVYLDT-------VPSQTVLELVSLQHYDLGISILAG---DYPGLT-TEPVPSFRAVCLLPPG 81 (196)
T ss_pred hHHHHHHHHHHCC-CcEEEEec-------cChHHHHHHHHcCCCCEEEEeccC---CCCCce-EEEeccCceEEEecCC
Confidence 4677888887763 35566665 456678899999999998753221 122232 3577777878877653
No 419
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=34.66 E-value=2e+02 Score=26.57 Aligned_cols=86 Identities=16% Similarity=0.143 Sum_probs=54.5
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.+++++++.. .. ...+-.+++..+.++.. ++++.+.. .+-...+.+|.+|++|+++..
T Consensus 96 ~~~l~I~~~~--~~------------~~~~l~~~l~~f~~~~p-~i~l~i~~-------~~~~~~~~~l~~g~~D~~i~~ 153 (294)
T PRK09986 96 AGRIEIGIVG--TA------------LWGRLRPAMRHFLKENP-NVEWLLRE-------LSPSMQMAALERRELDAGIWR 153 (294)
T ss_pred cceEEEEEeh--HH------------hHHHHHHHHHHHHHhCC-CeEEEEEe-------CCHHHHHHHHHcCCCCEEEec
Confidence 3578888863 11 11233566777776653 34466654 345788999999999998742
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
. ..+.....+.+ .|.....+.+++++..
T Consensus 154 ~-~~~~~~~~l~~-~~l~~~~~~~v~~~~~ 181 (294)
T PRK09986 154 M-ADLEPNPGFTS-RRLHESAFAVAVPEEH 181 (294)
T ss_pred C-CccCCCCCeEE-EEeecccEEEEEcCCC
Confidence 1 11223344555 6788889999987654
No 420
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=34.46 E-value=2.2e+02 Score=25.60 Aligned_cols=74 Identities=9% Similarity=0.039 Sum_probs=46.6
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++..+ +.+.....+.+.+.+++.|+.+.+... ..+. +....++++...+++.||+....... ..+..+.+.
T Consensus 2 I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~-~~~~~i~~~~~~~vdgiii~~~~~~~-~~~~~~~~~ 76 (266)
T cd06278 2 IGVVVADLDNPFYSELLEALSRALQARGYQPLLINT---DDDE-DLDAALRQLLQYRVDGVIVTSGTLSS-ELAEECRRN 76 (266)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcC---CCCH-HHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhc
Confidence 4666643 456667788899999999998765421 2222 45566777777788888876543222 346666555
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
|
T Consensus 77 ~ 77 (266)
T cd06278 77 G 77 (266)
T ss_pred C
Confidence 4
No 421
>cd03522 MoeA_like MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is unknown.
Probab=34.30 E-value=1.8e+02 Score=27.70 Aligned_cols=78 Identities=19% Similarity=0.107 Sum_probs=50.5
Q ss_pred cCCcEEEEEEEeCCc--c---cchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHH
Q 011629 11 FGWRNVIALYVDDDH--G---RNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGL 84 (481)
Q Consensus 11 fgW~~V~ii~~dd~~--g---~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~ 84 (481)
|.=.+|++|.+.++- | ......+.+.+++.|..+.....++.+ .+.+...+++..+.++++||+.+.. ..-.
T Consensus 157 ~r~~rv~II~TG~Ev~~G~i~D~~~~~l~~~L~~~G~~v~~~~iv~Dd--~~~I~~ai~~~~~~g~DlIItTGGtsvg~~ 234 (312)
T cd03522 157 FRPLRVGLIVTGSEVYGGRIEDKFGPVLRARLAALGVELVEQVIVPHD--EAAIAAAIAEALEAGAELLILTGGASVDPD 234 (312)
T ss_pred cCCCEEEEEEcCCcCCCCcEEEhHHHHHHHHHHHCCCEEEEEEEcCCC--HHHHHHHHHHHhcCCCCEEEEeCCcccCCc
Confidence 334578888865532 2 244667888899999998887777543 3456777777665568898887654 2333
Q ss_pred HHHHHH
Q 011629 85 EVLNAA 90 (481)
Q Consensus 85 ~il~~a 90 (481)
.+..+|
T Consensus 235 D~tp~A 240 (312)
T cd03522 235 DVTPAA 240 (312)
T ss_pred chHHHH
Confidence 444444
No 422
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=34.29 E-value=1.9e+02 Score=26.98 Aligned_cols=70 Identities=9% Similarity=0.030 Sum_probs=47.8
Q ss_pred eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHHHHHcC
Q 011629 22 DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNAAKHLR 94 (481)
Q Consensus 22 dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~a~~~g 94 (481)
++++.....+.+++++++.|+.+... +...+.....+.++.+...+++.||+.... ......+..+.+.+
T Consensus 9 ~~~~~~~~~~~i~~~a~~~g~~v~~~---~~~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~~~ 79 (302)
T TIGR02634 9 RLERWQKDRDIFVAAAESLGAKVFVQ---SANGNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKDEG 79 (302)
T ss_pred chhhHHHHHHHHHHHHHhcCCEEEEE---eCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHHCC
Confidence 45677778889999999999988653 222233334567778888889998887643 33456677776655
No 423
>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents uroporphyrinogen III synthase (4.2.1.75 from EC) which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the inversion of the final pyrrole unit (ring D) of the linear tetrapyrrole molecule, linking it to the first pyrrole unit (ring A), thereby generating a large macrocyclic structure called uroporphyrinogen III []. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains []. Congenital erythropoietic porphyria (CEP) is an autosomal recessive inborn error of metabolism that results from the markedly deficient activity of uroporphyrinogen III synthase []. ; GO: 0004852 uroporphyrinogen-III synthase activity, 0033014 tetrapyrrole biosynthetic process; PDB: 1WD7_B 1WCX_A 1WCW_A 3D8R_A 3D8T_B 3D8S_A 3D8N_A 3RE1_A 3MW8_A 3P9Z_A ....
Probab=34.18 E-value=1.2e+02 Score=27.08 Aligned_cols=81 Identities=12% Similarity=0.085 Sum_probs=40.6
Q ss_pred HhHHHHHH-cCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 3 AIADIVDY-FGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 3 Ai~~ll~~-fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++++++.. ..=.+|.++..+. ....|.+.|++.|+.|.....+.. ...+......+.+......+ |++.++.
T Consensus 106 ~L~~~l~~~~~~~~vl~~~g~~-----~~~~l~~~L~~~g~~v~~~~vY~~-~~~~~~~~~~~~l~~~~~~~-v~ftS~~ 178 (231)
T PF02602_consen 106 GLAELLKEQLRGKRVLILRGEG-----GRPDLPEKLREAGIEVTEVIVYET-PPEELSPELKEALDRGEIDA-VVFTSPS 178 (231)
T ss_dssp HHHGGHHHCCTTEEEEEEESSS-----SCHHHHHHHHHTTEEEEEEECEEE-EEHHHHHHHHHHHHHTTTSE-EEESSHH
T ss_pred HHHHHHHhhCCCCeEEEEcCCC-----ccHHHHHHHHHCCCeEEEEEEeec-ccccchHHHHHHHHcCCCCE-EEECCHH
Confidence 44444442 2225555555333 245566777777777666555543 22222334444554444444 3445555
Q ss_pred HHHHHHHHH
Q 011629 82 WGLEVLNAA 90 (481)
Q Consensus 82 ~~~~il~~a 90 (481)
.+..++...
T Consensus 179 ~~~~~~~~~ 187 (231)
T PF02602_consen 179 AVRAFLELL 187 (231)
T ss_dssp HHHHHHHHS
T ss_pred HHHHHHHHh
Confidence 555555554
No 424
>COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane]
Probab=33.86 E-value=1.7e+02 Score=26.12 Aligned_cols=41 Identities=20% Similarity=0.071 Sum_probs=28.7
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLS 45 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~ 45 (481)
++-++=+++-|-++|+++.+.-.- ...-.++.|.++|+.+.
T Consensus 106 daTa~~ik~~g~kkvgLLgT~~Tm---~~~fY~~~l~~~gievv 146 (230)
T COG1794 106 DATAKAIKAAGAKKVGLLGTRFTM---EQGFYRKRLEEKGIEVV 146 (230)
T ss_pred HHHHHHHHhcCCceeEEeeccchH---HhHHHHHHHHHCCceEe
Confidence 455566778899999999975321 22333778999998764
No 425
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=33.57 E-value=98 Score=28.35 Aligned_cols=70 Identities=11% Similarity=0.063 Sum_probs=39.3
Q ss_pred HHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeee-cc-ccccceeeccceeecceEEEEecCC
Q 011629 349 DVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAI-TT-ERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 349 dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~-t~-~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
+.+....+..+.+.++... .+....+.+|.+|++|.++++-.. .. ..........++...++.+++++++
T Consensus 161 ~~l~~~~~~~~~~~~~~~~--------~~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~k~~ 232 (259)
T PRK11917 161 KAIGEAAKKIGIDVKFSEF--------PDYPSIKAALDAKRVDAFSVDKSILLGYVDDKSEILPDSFEPQSYGIVTKKDD 232 (259)
T ss_pred HHHHHhhHhcCCceeEEec--------CCHHHHHHHHHcCCCcEEEecHHHHHHhhhcCCeecCCcCCCCceEEEEeCCC
Confidence 3344555555544333333 357888999999999998776432 11 1111122234455566677776654
No 426
>PF02698 DUF218: DUF218 domain; InterPro: IPR003848 This domain of unknown function is found in several uncharacterised proteins.; PDB: 3CA8_A.
Probab=33.54 E-value=83 Score=26.02 Aligned_cols=90 Identities=14% Similarity=0.027 Sum_probs=44.1
Q ss_pred HHHHHHcCCcEEEEEEEeCCc--ccchHHHHHHHHHhcCCEEEEEEecC-CCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 5 ADIVDYFGWRNVIALYVDDDH--GRNGIAALGDKLAEKRCRLSHKVPLS-PKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~~--g~~~~~~l~~~l~~~gi~v~~~~~~~-~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++|.+. |.....++...... +....+.+++.+.+.|+.-.....-+ ...+.+++....+.+++.+.+-|++.++..
T Consensus 30 ~~L~~~-g~~~~il~SGg~~~~~~~~ea~~~~~~l~~~gvp~~~I~~e~~s~~T~ena~~~~~~~~~~~~~~iilVT~~~ 108 (155)
T PF02698_consen 30 ARLYKA-GYAPRILFSGGYGHGDGRSEAEAMRDYLIELGVPEERIILEPKSTNTYENARFSKRLLKERGWQSIILVTSPY 108 (155)
T ss_dssp HHHHH--HHT--EEEE--SSTTHTS-HHHHHHHHHHHT---GGGEEEE----SHHHHHHHHHHHHHT-SSS-EEEE--CC
T ss_pred HHHHhc-CCCCeEEECCCCCCCCCCCHHHHHHHHHHhcccchheeEccCCCCCHHHHHHHHHHHHHhhcCCeEEEECCHH
Confidence 445554 33334444432222 45678999999988887522111111 123455666666777777666777778777
Q ss_pred HHHHHHHHHHHcCC
Q 011629 82 WGLEVLNAAKHLRM 95 (481)
Q Consensus 82 ~~~~il~~a~~~g~ 95 (481)
++...+..+.+.+.
T Consensus 109 H~~Ra~~~~~~~~~ 122 (155)
T PF02698_consen 109 HMRRARMIFRKVGP 122 (155)
T ss_dssp CHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHhCC
Confidence 77777666666543
No 427
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=33.43 E-value=2.1e+02 Score=26.00 Aligned_cols=75 Identities=9% Similarity=-0.052 Sum_probs=40.9
Q ss_pred HHcCCcEEEEEEEeCCcccchHHHHHHHHHh-cCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHH
Q 011629 9 DYFGWRNVIALYVDDDHGRNGIAALGDKLAE-KRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVL 87 (481)
Q Consensus 9 ~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~-~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il 87 (481)
...| .+|.++-++.+. ++.+.+.+++ .|+.|+-.. ....+.++...+++.|.+++++++++......-..++
T Consensus 102 ~~~~-~~v~llG~~~~v----~~~a~~~l~~~y~l~i~g~~--~Gyf~~~e~~~i~~~I~~s~~dil~VglG~PkQE~~~ 174 (243)
T PRK03692 102 GKEG-TPVFLVGGKPEV----LAQTEAKLRTQWNVNIVGSQ--DGYFTPEQRQALFERIHASGAKIVTVAMGSPKQEIFM 174 (243)
T ss_pred HhcC-CeEEEECCCHHH----HHHHHHHHHHHhCCEEEEEe--CCCCCHHHHHHHHHHHHhcCCCEEEEECCCcHHHHHH
Confidence 3445 567777655543 3444444432 266665322 1111223445678889999999988876654444444
Q ss_pred HHH
Q 011629 88 NAA 90 (481)
Q Consensus 88 ~~a 90 (481)
...
T Consensus 175 ~~~ 177 (243)
T PRK03692 175 RDC 177 (243)
T ss_pred HHH
Confidence 443
No 428
>cd08169 DHQ-like Dehydroquinate synthase-like which includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. Dehydroquinate synthase-like. This group contains dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. They exhibit the dehydroquinate synthase structural fold. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-Deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes ne
Probab=33.41 E-value=2.2e+02 Score=27.51 Aligned_cols=86 Identities=2% Similarity=-0.182 Sum_probs=49.9
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHh-cCCEEEEEEecCCCCChhHHHHHHHHhcc---CCceEEEEEeC
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAE-KRCRLSHKVPLSPKGSRNQIIDTLLTVSS---MMSRILILHTY 79 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~-~gi~v~~~~~~~~~~~~~~~~~~l~~i~~---s~~~vIvl~~~ 79 (481)
+.++++.++-+++.+|++.... ....+.+.+.+++ .++.+........+.+.+.+...++.+++ .+.+.||..+.
T Consensus 14 l~~~~~~~~~~k~livtd~~v~-~~~~~~v~~~L~~~~~~~~~~~~~~e~~k~~~~v~~~~~~~~~~~~~r~d~IIaiGG 92 (344)
T cd08169 14 VESYTTRDLFDQYFFISDSGVA-DLIAHYIAEYLSKILPVHILVIEGGEEYKTFETVTRILERAIALGANRRTAIVAVGG 92 (344)
T ss_pred HHHHHHhcCCCeEEEEECccHH-HHHHHHHHHHHHhhcCceEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEEECC
Confidence 3456677777888888754333 2466777788876 56654322222233455566666666664 44788887665
Q ss_pred c--HHHHHHHHHH
Q 011629 80 D--IWGLEVLNAA 90 (481)
Q Consensus 80 ~--~~~~~il~~a 90 (481)
. .++..++...
T Consensus 93 Gsv~D~ak~vA~~ 105 (344)
T cd08169 93 GATGDVAGFVAST 105 (344)
T ss_pred cHHHHHHHHHHHH
Confidence 3 3444444433
No 429
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=33.33 E-value=2.8e+02 Score=25.20 Aligned_cols=76 Identities=12% Similarity=-0.066 Sum_probs=45.8
Q ss_pred CcEEEEEEEe---------CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHH
Q 011629 13 WRNVIALYVD---------DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWG 83 (481)
Q Consensus 13 W~~V~ii~~d---------d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~ 83 (481)
.+.||+|..+ +.+.....+.+.+.+++.|+.+.... . ... +.....+.+.+.+++.||+......
T Consensus 3 s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~--~-~~~--~~~~~~~~l~~~~~dgiii~~~~~~- 76 (275)
T cd06295 3 TDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSF--V-SSP--DRDWLARYLASGRADGVILIGQHDQ- 76 (275)
T ss_pred ceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEe--C-Cch--hHHHHHHHHHhCCCCEEEEeCCCCC-
Confidence 4678888842 23555667778889999998876542 1 111 2334445566677888887654322
Q ss_pred HHHHHHHHHcC
Q 011629 84 LEVLNAAKHLR 94 (481)
Q Consensus 84 ~~il~~a~~~g 94 (481)
...+..+.+.|
T Consensus 77 ~~~~~~~~~~~ 87 (275)
T cd06295 77 DPLPERLAETG 87 (275)
T ss_pred hHHHHHHHhCC
Confidence 23456666554
No 430
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=33.11 E-value=1.6e+02 Score=27.68 Aligned_cols=69 Identities=12% Similarity=0.111 Sum_probs=45.1
Q ss_pred HHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 348 IDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 348 ~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
.+++..+.++.. .+++.+.. ++-..+...|.+|++|++++. ...+.....+.+ .+.....+.++++++.
T Consensus 109 ~~~l~~~~~~~P-~i~l~l~~-------~~~~~~~~~l~~g~~D~~i~~-~~~~~~~~~l~~-~~l~~~~~~~v~~~~h 177 (308)
T PRK10094 109 AQLLAWLNERYP-FTQFHISR-------QIYMGVWDSLLYEGFSLAIGV-TGTEALANTFSL-DPLGSVQWRFVMAADH 177 (308)
T ss_pred HHHHHHHHHhCC-CcEEEEEe-------ehhhhHHHHHhCCCccEEEec-ccCccccCCeeE-EEecceeEEEEECCCC
Confidence 578888887774 24566665 446788899999999998762 211122334444 5777777777776543
No 431
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=33.07 E-value=35 Score=24.70 Aligned_cols=32 Identities=22% Similarity=0.395 Sum_probs=19.2
Q ss_pred cEEEEEEEeCCcccchHHHHHHHHHhcCCEEE
Q 011629 14 RNVIALYVDDDHGRNGIAALGDKLAEKRCRLS 45 (481)
Q Consensus 14 ~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~ 45 (481)
+.|.+.+++|.-|+...+.+.+.+...|+.|.
T Consensus 47 ~~Vii~~D~D~~G~~~a~~i~~~l~~~gi~v~ 78 (81)
T PF13662_consen 47 KEVIIAFDNDKAGEKAAQKIAKKLLPLGIRVT 78 (81)
T ss_dssp SEEEEEEESSHHHHHHHHHHHHHHG-------
T ss_pred ceEEEEeCcCHHHHHHHHHHHHHHHhhccccc
Confidence 77777777777777777777777776666553
No 432
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=32.93 E-value=94 Score=28.44 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=39.4
Q ss_pred chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 28 NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 28 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
..++-|.+.|...|+.+.....++.+ .+++...++...+. +++||+.+-
T Consensus 21 tNa~~la~~L~~~G~~v~~~~~VgD~--~~~I~~~l~~a~~r-~D~vI~tGG 69 (255)
T COG1058 21 TNAAFLADELTELGVDLARITTVGDN--PDRIVEALREASER-ADVVITTGG 69 (255)
T ss_pred chHHHHHHHHHhcCceEEEEEecCCC--HHHHHHHHHHHHhC-CCEEEECCC
Confidence 56888999999999999998887643 44677888877777 999998653
No 433
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=32.93 E-value=4e+02 Score=24.60 Aligned_cols=88 Identities=14% Similarity=0.105 Sum_probs=49.1
Q ss_pred HHHHHcCCc-EEEEEEEeC--CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceE-EEEEeCcH
Q 011629 6 DIVDYFGWR-NVIALYVDD--DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI-LILHTYDI 81 (481)
Q Consensus 6 ~ll~~fgW~-~V~ii~~dd--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v-Ivl~~~~~ 81 (481)
.|++..|.+ +++++..+. .......+.+++.+++.|+.+... .....+..+....++++.++..++ .|++.+..
T Consensus 140 ~l~~~~~~~~~i~~~~~~~~~~~~~~R~~gf~~al~~~g~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~ 217 (295)
T PRK10653 140 FIAKKLGEGAKVIQLEGIAGTSAARERGEGFKQAVAAHKFNVLAS--QPADFDRTKGLNVMQNLLTAHPDVQAVFAQNDE 217 (295)
T ss_pred HHHHHhCCCceEEEEEccCCCccHHHHHHHHHHHHhhCCCEEEEe--cCCCCCHHHHHHHHHHHHHhCCCcCEEEECCCh
Confidence 355555653 566555332 234466788899999999876422 111222223334455554433333 34445556
Q ss_pred HHHHHHHHHHHcCC
Q 011629 82 WGLEVLNAAKHLRM 95 (481)
Q Consensus 82 ~~~~il~~a~~~g~ 95 (481)
.+..+++++.+.|+
T Consensus 218 ~A~g~l~al~~~G~ 231 (295)
T PRK10653 218 MALGALRALQTAGK 231 (295)
T ss_pred hHHHHHHHHHHcCC
Confidence 66678888888875
No 434
>PRK10481 hypothetical protein; Provisional
Probab=32.79 E-value=3.6e+02 Score=24.19 Aligned_cols=65 Identities=12% Similarity=0.089 Sum_probs=41.2
Q ss_pred cEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH
Q 011629 14 RNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 14 ~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~ 82 (481)
.++|++.-..+.. +...+.+...|..+.+...-|...+.+......++++..++++||+.|....
T Consensus 130 ~riGVitP~~~qi----~~~~~kw~~~G~~v~~~~aspy~~~~~~l~~aa~~L~~~gaD~Ivl~C~G~~ 194 (224)
T PRK10481 130 HQVGVIVPVEEQL----AQQAQKWQVLQKPPVFALASPYHGSEEELIDAGKELLDQGADVIVLDCLGYH 194 (224)
T ss_pred CeEEEEEeCHHHH----HHHHHHHHhcCCceeEeecCCCCCCHHHHHHHHHHhhcCCCCEEEEeCCCcC
Confidence 7889888665432 3333444444877665443222234445677788888889999999887544
No 435
>cd06578 HemD Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism also known as Gunther disease.
Probab=32.45 E-value=3.5e+02 Score=23.85 Aligned_cols=61 Identities=11% Similarity=-0.007 Sum_probs=27.6
Q ss_pred HHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHH
Q 011629 30 IAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKH 92 (481)
Q Consensus 30 ~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~ 92 (481)
...|.+.+.+.|..+.....+...... +.....+.+.+.... +|++.+...+..++....+
T Consensus 134 ~~~l~~~L~~~g~~v~~~~~Y~~~~~~-~~~~~~~~l~~~~~~-~iiftS~~~v~~f~~~~~~ 194 (239)
T cd06578 134 REDLAEALRERGAEVDEVEVYRTVPPD-LDAELLELLEEGAID-AVLFTSPSTVRNLLELLGK 194 (239)
T ss_pred hHHHHHHHHHCCCEEEEEEEEEEECCC-CcHHHHHHHHcCCCc-EEEEeCHHHHHHHHHHHhh
Confidence 356666666666665544444322110 011222333333222 4555555666666655543
No 436
>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=32.08 E-value=43 Score=29.25 Aligned_cols=74 Identities=19% Similarity=0.226 Sum_probs=47.9
Q ss_pred HHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 348 IDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 348 ~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
=+++..+-...|+.. .-++ ++...-.+...+...+..|++|++++ +....++-..++| .|.....+-+++++..
T Consensus 106 R~l~d~~l~~~gi~~--~~i~-gy~~~~~th~~vA~aVa~G~AD~G~g-~~~~A~~~~gL~F-vpl~~E~~dlv~~~~~ 179 (193)
T PF12727_consen 106 RILFDQLLAEEGIDP--EDIP-GYAQEANTHLAVAAAVASGKADAGIG-IRAAAEEFYGLDF-VPLAEERYDLVIRRED 179 (193)
T ss_pred HHHHHHHHHHcCCCh--hhCC-CccccccChHHHHHHHHcCCCCEEee-hHHHHHhhcCCCc-EEccccceEEEEEhhH
Confidence 456666666666442 1111 11111245678999999999999865 3222233368999 6889999999998876
No 437
>cd00757 ThiF_MoeB_HesA_family ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1).
Probab=31.81 E-value=3.8e+02 Score=23.97 Aligned_cols=82 Identities=11% Similarity=0.082 Sum_probs=49.7
Q ss_pred HhHHHHHHcCCcEEEEE---------------EEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhc
Q 011629 3 AIADIVDYFGWRNVIAL---------------YVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVS 67 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii---------------~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~ 67 (481)
.+++.|-..|-..+.++ +..++-|..-++.+.+.+.+.+-.+... .++...+.++....+ +
T Consensus 35 ~va~~La~~Gvg~i~lvD~D~ve~sNL~Rq~l~~~~diG~~Ka~~~~~~l~~~np~~~i~-~~~~~i~~~~~~~~~---~ 110 (228)
T cd00757 35 PAAEYLAAAGVGKLGLVDDDVVELSNLQRQILHTEADVGQPKAEAAAERLRAINPDVEIE-AYNERLDAENAEELI---A 110 (228)
T ss_pred HHHHHHHHcCCCEEEEEcCCEEcCcccccccccChhhCCChHHHHHHHHHHHhCCCCEEE-EecceeCHHHHHHHH---h
Confidence 35667777888888877 2334567778888888888875433221 122222222332222 2
Q ss_pred cCCceEEEEEeCcHHHHHHHHHH
Q 011629 68 SMMSRILILHTYDIWGLEVLNAA 90 (481)
Q Consensus 68 ~s~~~vIvl~~~~~~~~~il~~a 90 (481)
+.++||.+.+....+..+.++
T Consensus 111 --~~DvVi~~~d~~~~r~~l~~~ 131 (228)
T cd00757 111 --GYDLVLDCTDNFATRYLINDA 131 (228)
T ss_pred --CCCEEEEcCCCHHHHHHHHHH
Confidence 378988888877777666554
No 438
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=31.59 E-value=2.4e+02 Score=25.39 Aligned_cols=75 Identities=12% Similarity=0.008 Sum_probs=45.7
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|+++..+ +.+.....+.+++.+++.|..+.... . ..+.+.-...++++...+++.||+..... ...++..+.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~--~-~~~~~~~~~~i~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06298 2 VGVIIPDITNSYFAELARGIDDIATMYKYNIILSN--S-DNDKEKELKVLNNLLAKQVDGIIFMGGKI-SEEHREEFKRS 77 (268)
T ss_pred EEEEECCCcchHHHHHHHHHHHHHHHcCCeEEEEe--C-CCCHHHHHHHHHHHHHhcCCEEEEeCCCC-cHHHHHHHhcC
Confidence 5666643 45666778888999999998876553 1 22223345666777777788888765421 12344444443
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 78 ~ 78 (268)
T cd06298 78 P 78 (268)
T ss_pred C
Confidence 3
No 439
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=31.43 E-value=2.6e+02 Score=25.05 Aligned_cols=75 Identities=7% Similarity=-0.028 Sum_probs=46.2
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHc
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHL 93 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~ 93 (481)
|++|.. ++.|.....+.+++.+++.|+.+.... ...+.+.....++.+...+.+.||+....... ..+..+.+.
T Consensus 2 igvi~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~---~~~~~~~~~~~~~~l~~~~~dgiii~~~~~~~-~~l~~~~~~ 77 (267)
T cd06283 2 IGVIVADITNPFSSLVLKGIEDVCRAHGYQVLVCN---SDNDPEKEKEYLESLLAYQVDGLIVNPTGNNK-ELYQRLAKN 77 (267)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEc---CCCCHHHHHHHHHHHHHcCcCEEEEeCCCCCh-HHHHHHhcC
Confidence 455553 355666788899999999998875432 22222334566777777788888886543222 234555444
Q ss_pred C
Q 011629 94 R 94 (481)
Q Consensus 94 g 94 (481)
+
T Consensus 78 ~ 78 (267)
T cd06283 78 G 78 (267)
T ss_pred C
Confidence 3
No 440
>PRK09189 uroporphyrinogen-III synthase; Validated
Probab=31.26 E-value=1.4e+02 Score=26.85 Aligned_cols=60 Identities=7% Similarity=-0.077 Sum_probs=30.6
Q ss_pred HHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHH
Q 011629 30 IAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAA 90 (481)
Q Consensus 30 ~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a 90 (481)
...|.+.|++.|+.|.....+.......+.......+++.+.++|++ .++..+..++...
T Consensus 130 r~~l~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~l~~~~~d~i~f-~S~~~~~~f~~~~ 189 (240)
T PRK09189 130 APVFEDRLAAAGIPFRVAECYDMLPVMYSPATLSAILGGAPFDAVLL-YSRVAARRFFALM 189 (240)
T ss_pred cchhHHHHHhCCCeeEEEEEEEeecCCCChHHHHHHHhcCCCCEEEE-eCHHHHHHHHHHH
Confidence 35666777777877665554432211111223344455544555444 4455566666554
No 441
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=31.23 E-value=2.6e+02 Score=25.18 Aligned_cols=68 Identities=9% Similarity=-0.020 Sum_probs=39.0
Q ss_pred CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHcC
Q 011629 23 DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHLR 94 (481)
Q Consensus 23 d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~g 94 (481)
+.+.....+.+++.+++.|+++.... . ....+....+.+.+...+++.||+...... ...+..+.+.|
T Consensus 16 ~~~~~~~~~~~~~~~~~~g~~~~~~~--~-~~~~~~~~~~~~~~~~~~~dgiii~~~~~~-~~~~~~~~~~~ 83 (270)
T cd06294 16 NPFFIEVLRGISAVANENGYDISLAT--G-KNEEELLEEVKKMIQQKRVDGFILLYSRED-DPIIDYLKEEK 83 (270)
T ss_pred CCCHHHHHHHHHHHHHHCCCEEEEec--C-CCcHHHHHHHHHHHHHcCcCEEEEecCcCC-cHHHHHHHhcC
Confidence 45666778888999999999876532 1 112222233333345556888887653222 34455565554
No 442
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=31.20 E-value=2.9e+02 Score=22.40 Aligned_cols=66 Identities=15% Similarity=0.070 Sum_probs=40.7
Q ss_pred hHHHHHHHHHhcCCEEEEE--Ee-cCCC-CChhHHHHHHHHhccCCceEEEEEeCc------HHHHHHHHHHHHcC
Q 011629 29 GIAALGDKLAEKRCRLSHK--VP-LSPK-GSRNQIIDTLLTVSSMMSRILILHTYD------IWGLEVLNAAKHLR 94 (481)
Q Consensus 29 ~~~~l~~~l~~~gi~v~~~--~~-~~~~-~~~~~~~~~l~~i~~s~~~vIvl~~~~------~~~~~il~~a~~~g 94 (481)
-.+.+++.+.++|+.+... .. .+.. .....+..+++.++....++||+.--. .+...++..+...|
T Consensus 20 Q~~~~~~~a~~~g~~i~~~~~d~~~Sg~~~~Rp~l~~ll~~~~~g~~~~ivv~~~~Rl~R~~~~~~~~~~~l~~~g 95 (148)
T smart00857 20 QLEALRAYAKANGWEVVRIYEDEGVSGKKADRPGLQRLLADLRAGDIDVLVVYKLDRLGRSLRDLLALLELLEKKG 95 (148)
T ss_pred HHHHHHHHHHHCCCEEEEEEEeCCCcCCCCCCHHHHHHHHHHHcCCCCEEEEeccchhhCcHHHHHHHHHHHHHCC
Confidence 4566777888889886432 21 1211 123568888888888777787775432 34555666665554
No 443
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=31.13 E-value=2.1e+02 Score=25.82 Aligned_cols=69 Identities=23% Similarity=0.183 Sum_probs=45.2
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+-.+++..+.++.. ++++.+.. ++-.++...|.+|++|+++..... .....+.. .+.....+.++++++
T Consensus 81 ~~~~~l~~~~~~~p-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~~--~~~~~~~~-~~l~~~~~~~v~~~~ 149 (269)
T PRK11716 81 HLPPILDRFRAEHP-LVEIKLTT-------GDAADAVEKVQSGEADLAIAAKPE--TLPASVAF-SPIDEIPLVLIAPAL 149 (269)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEE-------CCHHHHHHHHHCCCccEEEEecCC--CCCcceEE-EEcccceEEEEEcCC
Confidence 44678888888763 34566665 456788999999999999753211 11222333 567777778777654
No 444
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=31.08 E-value=2.4e+02 Score=22.62 Aligned_cols=96 Identities=11% Similarity=0.039 Sum_probs=43.5
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecC---CCCChhHHH---HHHHHhccCCceEEEEE
Q 011629 4 IADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLS---PKGSRNQII---DTLLTVSSMMSRILILH 77 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~---~~~~~~~~~---~~l~~i~~s~~~vIvl~ 77 (481)
+.+.+...|--....+|.+ ........+.+.+...|+.+....... ......|.. .++....+.....+|+.
T Consensus 25 l~~~i~~~~~~~~~~~y~~--~~~~~~~~~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ivLv 102 (146)
T PF01936_consen 25 LLEEIRKYGPLVRIRAYGN--WDDPNQKSFQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTIVLV 102 (146)
T ss_dssp HHHHHTTTEEEEEEEEEE------HHHHHHHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEEEEE
T ss_pred HHHHHHhcCCeEEEEEEee--ccccchhhHHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEEEEE
Confidence 3444444333223444544 222346778889999999775543321 111111222 22333323334777777
Q ss_pred eCcHHHHHHHHHHHHcCCccCCeEEEEe
Q 011629 78 TYDIWGLEVLNAAKHLRMMESGYVWIVT 105 (481)
Q Consensus 78 ~~~~~~~~il~~a~~~g~~~~~~~wI~~ 105 (481)
+...+...++..+.+.|. .++++.
T Consensus 103 SgD~Df~~~v~~l~~~g~----~V~v~~ 126 (146)
T PF01936_consen 103 SGDSDFAPLVRKLRERGK----RVIVVG 126 (146)
T ss_dssp ---GGGHHHHHHHHHH------EEEEEE
T ss_pred ECcHHHHHHHHHHHHcCC----EEEEEE
Confidence 776788888888887652 466665
No 445
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=30.61 E-value=1.6e+02 Score=26.86 Aligned_cols=71 Identities=13% Similarity=0.084 Sum_probs=47.3
Q ss_pred eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH-HHHHHHHHHHcCC
Q 011629 22 DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW-GLEVLNAAKHLRM 95 (481)
Q Consensus 22 dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~-~~~il~~a~~~g~ 95 (481)
++.|.....+.+.+.++++|+.+.... ...+.+...+.++.+...+++.||+...... ....+.++.+.+.
T Consensus 10 ~~~~~~~~~~~~~~~a~~~g~~~~~~~---~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~i~~~~~~~i 81 (273)
T cd06309 10 ESPWRTAETKSIKDAAEKRGFDLKFAD---AQQKQENQISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAAGI 81 (273)
T ss_pred CCHHHHHHHHHHHHHHHhcCCEEEEeC---CCCCHHHHHHHHHHHHHcCCCEEEEcCCccccchHHHHHHHHCCC
Confidence 456667789999999999999987642 1223334456777777778888887654322 2456677766553
No 446
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=30.60 E-value=2.3e+02 Score=26.47 Aligned_cols=69 Identities=17% Similarity=0.159 Sum_probs=46.0
Q ss_pred eeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecC
Q 011629 346 YCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIK 425 (481)
Q Consensus 346 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 425 (481)
+..+++..+.++.. ++++.+.. +....+...|.+|++|+++.. .+.....+. +.|+....+.++++++
T Consensus 106 ~~~~~l~~~~~~~p-~i~l~~~~-------~~~~~~~~~l~~g~~Di~i~~---~~~~~~~~~-~~~l~~~~~~lv~~~~ 173 (305)
T PRK11233 106 LTMPLLQAVRAEFP-GIVLYLHE-------NSGATLNEKLMNGQLDMAVIY---EHSPVAGLS-SQPLLKEDLFLVGTQD 173 (305)
T ss_pred HHHHHHHHHHHHCC-CcEEEEEE-------CCcHHHHHHHHCCCCCEEEEc---CCcCCCCcE-EEEEeeeeEEEEEcCc
Confidence 34567888887762 34466655 345688899999999999753 222223343 3688888888888765
Q ss_pred C
Q 011629 426 K 426 (481)
Q Consensus 426 ~ 426 (481)
.
T Consensus 174 ~ 174 (305)
T PRK11233 174 C 174 (305)
T ss_pred c
Confidence 3
No 447
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=30.50 E-value=2.7e+02 Score=25.00 Aligned_cols=61 Identities=7% Similarity=-0.027 Sum_probs=41.5
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
|+++..+ +.|.....+.+++.+++.|..+..... ..+.+.-...++.+...+++.||+...
T Consensus 2 i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~ 64 (260)
T cd06286 2 IGVVLPYINHPYFSQLVDGIEKAALKHGYKVVLLQT---NYDKEKELEYLELLKTKQVDGLILCSR 64 (260)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeC---CCChHHHHHHHHHHHHcCCCEEEEeCC
Confidence 5677753 556677788999999999998865422 222223446677777778888887654
No 448
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=30.36 E-value=3.2e+02 Score=24.47 Aligned_cols=63 Identities=6% Similarity=0.000 Sum_probs=41.1
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
|++|.. ++.+.....+.+++.+++.|+.+.... ....+.......++.+.+.+++-||+....
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~vdgiii~~~~ 66 (264)
T cd01574 2 IGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSM--LAEADEEALRAAVRRLLAQRVDGVIVNAPL 66 (264)
T ss_pred EEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEe--CCCCchHHHHHHHHHHHhcCCCEEEEeCCC
Confidence 566664 334556778889999999998876542 111122344566777777778888876543
No 449
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=30.22 E-value=4.2e+02 Score=23.99 Aligned_cols=89 Identities=12% Similarity=0.128 Sum_probs=48.9
Q ss_pred HHHH-HHc-CCcEEEEEEEeCC-cccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHh-cc-CCceEEEEEeC
Q 011629 5 ADIV-DYF-GWRNVIALYVDDD-HGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTV-SS-MMSRILILHTY 79 (481)
Q Consensus 5 ~~ll-~~f-gW~~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i-~~-s~~~vIvl~~~ 79 (481)
++.| +++ |-.+|+++..... ......+.+++.+++.++.+... .....+.+.....++.+ ++ .+.+.| ++.+
T Consensus 117 a~~l~~~~~g~~~i~~~~g~~~~~~~~R~~gf~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~ 193 (274)
T cd06311 117 GEYIATKLGGNGNIVVLRGIPTPIDNERVDAFDAAIAKYPIKILDR--QYANWNRDDAFSVMQDLLTKFPKIDAV-WAHD 193 (274)
T ss_pred HHHHHHHhCCCCeEEEEECCCCcchhHHHHHHHHHHhhCCcEEEec--cCCCCcHHHHHHHHHHHHHhCCCcCEE-EECC
Confidence 3444 433 7889999975432 22345677888898888665432 22122222223334443 22 234443 3444
Q ss_pred cHHHHHHHHHHHHcCCc
Q 011629 80 DIWGLEVLNAAKHLRMM 96 (481)
Q Consensus 80 ~~~~~~il~~a~~~g~~ 96 (481)
...+..++..+.+.|..
T Consensus 194 d~~a~g~~~al~~~g~~ 210 (274)
T cd06311 194 DDMAVGVLAAIKQAGRT 210 (274)
T ss_pred CcHHHHHHHHHHHcCCC
Confidence 55667788888887753
No 450
>PRK11914 diacylglycerol kinase; Reviewed
Probab=30.01 E-value=2.9e+02 Score=26.02 Aligned_cols=76 Identities=9% Similarity=-0.001 Sum_probs=48.3
Q ss_pred HcCCcEEEEEEEeCCccc----chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHH
Q 011629 10 YFGWRNVIALYVDDDHGR----NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLE 85 (481)
Q Consensus 10 ~fgW~~V~ii~~dd~~g~----~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~ 85 (481)
...-+++.+|+ +...|. ...+.+.+.+++.|+.+... .+. ...+...+.++....+.++||+.+-...+..
T Consensus 5 ~~~~~~~~iI~-NP~sG~g~~~~~~~~~~~~l~~~g~~~~~~--~t~--~~~~~~~~a~~~~~~~~d~vvv~GGDGTi~e 79 (306)
T PRK11914 5 RHEIGKVTVLT-NPLSGHGAAPHAAERAIARLHHRGVDVVEI--VGT--DAHDARHLVAAALAKGTDALVVVGGDGVISN 79 (306)
T ss_pred cCCCceEEEEE-CCCCCCCcHHHHHHHHHHHHHHcCCeEEEE--EeC--CHHHHHHHHHHHHhcCCCEEEEECCchHHHH
Confidence 34557888888 433332 33556777888899875532 221 2335666666666666788888887777777
Q ss_pred HHHHH
Q 011629 86 VLNAA 90 (481)
Q Consensus 86 il~~a 90 (481)
++..+
T Consensus 80 vv~~l 84 (306)
T PRK11914 80 ALQVL 84 (306)
T ss_pred HhHHh
Confidence 77655
No 451
>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=29.86 E-value=3.1e+02 Score=24.89 Aligned_cols=78 Identities=10% Similarity=-0.078 Sum_probs=43.9
Q ss_pred EEEEEEe----CCcccchHHHHHHHHHh-------cCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHH
Q 011629 16 VIALYVD----DDHGRNGIAALGDKLAE-------KRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGL 84 (481)
Q Consensus 16 V~ii~~d----d~~g~~~~~~l~~~l~~-------~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~ 84 (481)
||++... ..+|......++..+.. .|..+.....- ...+.+.....++++.+.++.+||.........
T Consensus 2 ig~~~p~sg~~~~~~~~~~~g~~~a~~~~n~~gg~~g~~v~~~~~d-~~~~~~~~~~~~~~l~~~~v~~iig~~~~~~~~ 80 (298)
T cd06268 2 IGVLLPLSGPLAALGEPVRNGAELAVEEINAAGGILGRKIELVVED-TQGDPEAAAAAARELVDDGVDAVIGPLSSGVAL 80 (298)
T ss_pred eeeeecCcCchhhcChhHHHHHHHHHHHHHhcCCCCCeEEEEEEec-CCCCHHHHHHHHHHHHhCCceEEEcCCcchhHH
Confidence 5666644 34666666666666655 35566555432 222333455666667666777776655454455
Q ss_pred HHHHHHHHcC
Q 011629 85 EVLNAAKHLR 94 (481)
Q Consensus 85 ~il~~a~~~g 94 (481)
.+...+.+.+
T Consensus 81 ~~~~~~~~~~ 90 (298)
T cd06268 81 AAAPVAEEAG 90 (298)
T ss_pred hhHHHHHhCC
Confidence 5566665554
No 452
>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes t
Probab=29.75 E-value=2.8e+02 Score=24.90 Aligned_cols=86 Identities=6% Similarity=-0.010 Sum_probs=54.4
Q ss_pred HHHHHH--cCCcEEEEEEEeC-CcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcH
Q 011629 5 ADIVDY--FGWRNVIALYVDD-DHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDI 81 (481)
Q Consensus 5 ~~ll~~--fgW~~V~ii~~dd-~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~ 81 (481)
++-|.. -|-+++++|.... ..+....+.+++.++++|+.... .. ... . . .+. ..+ .|++.+..
T Consensus 107 ~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l~~~g~~~~~---~~-~~~--~--~---~~~--~~~-ai~~~~d~ 172 (247)
T cd06276 107 LQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFCKDYNIETEI---IN-DYE--N--R---EIE--KGD-LYIILSDT 172 (247)
T ss_pred HHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHHHHcCCCccc---cc-ccc--h--h---hcc--CCc-EEEEeCHH
Confidence 344444 6999999997543 34556688889999999985432 11 101 0 0 011 123 46677778
Q ss_pred HHHHHHHHHHHcCCccCCeEEEE
Q 011629 82 WGLEVLNAAKHLRMMESGYVWIV 104 (481)
Q Consensus 82 ~~~~il~~a~~~g~~~~~~~wI~ 104 (481)
.+..+++.+.+.|+..++-+=|+
T Consensus 173 ~A~g~~~~l~~~g~~iP~disvi 195 (247)
T cd06276 173 DLVFLIKKARESGLLLGKDIGII 195 (247)
T ss_pred HHHHHHHHHHHcCCcCCceeEEE
Confidence 88899999999998766554444
No 453
>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein. This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source.
Probab=29.62 E-value=3.2e+02 Score=25.38 Aligned_cols=76 Identities=7% Similarity=-0.079 Sum_probs=46.1
Q ss_pred EEEEEe--CCcccchHHHHHHHHHhcCCE-EEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHHHHH
Q 011629 17 IALYVD--DDHGRNGIAALGDKLAEKRCR-LSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNAAKH 92 (481)
Q Consensus 17 ~ii~~d--d~~g~~~~~~l~~~l~~~gi~-v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~a~~ 92 (481)
++|..+ +.|.....+.+++.+++.|.. +.+. .+...+.......++.+...+++.||+.... ......+.++.+
T Consensus 2 gvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~i~~--~~~~~d~~~q~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~~~~ 79 (302)
T TIGR02637 2 GLVVKSLGNPFFEAANKGAEEAAKELGSVYIIYT--GPTGTTAEGQIEVVNSLIAQKVDAIAISANDPDALVPALKKAMK 79 (302)
T ss_pred EEEeccCCCHHHHHHHHHHHHHHHHhCCeeEEEE--CCCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHH
Confidence 455533 456666788888999999953 3321 1112233334566777777788888886543 334566777766
Q ss_pred cC
Q 011629 93 LR 94 (481)
Q Consensus 93 ~g 94 (481)
.|
T Consensus 80 ~g 81 (302)
T TIGR02637 80 RG 81 (302)
T ss_pred CC
Confidence 55
No 454
>PHA02650 hypothetical protein; Provisional
Probab=29.51 E-value=1e+02 Score=22.12 Aligned_cols=25 Identities=8% Similarity=0.204 Sum_probs=14.7
Q ss_pred cCcchhHHHHHHHHHHHHHHHHHhh
Q 011629 436 NPFTPKMWCVTGIFFLVVGVVVWIL 460 (481)
Q Consensus 436 ~pf~~~~W~~~~~~~~~~~~~~~~~ 460 (481)
.++.+..|+.++++.+++.++++++
T Consensus 45 ~~~~~~~~ii~i~~v~i~~l~~flY 69 (81)
T PHA02650 45 SWFNGQNFIFLIFSLIIVALFSFFV 69 (81)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHH
Confidence 5666677766655555555555443
No 455
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=29.44 E-value=4.1e+02 Score=24.97 Aligned_cols=79 Identities=10% Similarity=-0.062 Sum_probs=48.4
Q ss_pred CcEEEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHH
Q 011629 13 WRNVIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAA 90 (481)
Q Consensus 13 W~~V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a 90 (481)
=+.|+++..+ +.+.....+.+.+.+.+.|..+..... ..+.+.....++.+...+.+-||+..........+.++
T Consensus 60 ~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~---~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 136 (327)
T TIGR02417 60 SRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACS---DDNPDQEKVVIENLLARQVDALIVASCMPPEDAYYQKL 136 (327)
T ss_pred CceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEeCCCCCChHHHHHH
Confidence 3578888753 456667788899999999998765422 11222334566677777788887765332122344455
Q ss_pred HHcC
Q 011629 91 KHLR 94 (481)
Q Consensus 91 ~~~g 94 (481)
.+.+
T Consensus 137 ~~~~ 140 (327)
T TIGR02417 137 QNEG 140 (327)
T ss_pred HhcC
Confidence 4443
No 456
>PLN02617 imidazole glycerol phosphate synthase hisHF
Probab=29.16 E-value=1e+02 Score=31.88 Aligned_cols=51 Identities=12% Similarity=0.088 Sum_probs=38.7
Q ss_pred CCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 339 GTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 339 ~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.+|...||+++|++.+++..+.. +...- .-++-+.+...+..+.+|.++++
T Consensus 462 ~DGt~~G~d~~l~~~v~~~~~ip--viasG-----G~g~~~d~~~~~~~~~~~a~~aa 512 (538)
T PLN02617 462 CDGQGKGFDIELVKLVSDAVTIP--VIASS-----GAGTPEHFSDVFSKTNASAALAA 512 (538)
T ss_pred ccccccCcCHHHHHHHHhhCCCC--EEEEC-----CCCCHHHHHHHHhcCCccEEEEE
Confidence 37899999999999999998844 44332 11478888888888888877654
No 457
>PF03853 YjeF_N: YjeF-related protein N-terminus; InterPro: IPR004443 The YjeF N-terminal domains occur either as single proteins or fusions with other domains and are commonly associated with enzymes. In bacteria and archaea, YjeF N-terminal domains are often fused to a YjeF C-terminal domain with high structural homology to the members of a ribokinase-like superfamily (see PDOC00806 from PROSITEDOC)and/or belong to operons that encode enzymes of diverse functions: pyridoxal phosphate biosynthetic protein PdxJ; phosphopanteine-protein transferase; ATP/GTP hydrolase; and pyruvate-formate lyase 1-activating enzyme. In plants, the YjeF N-terminal domain is fused to a C-terminal putative pyridoxamine 5'-phosphate oxidase. In eukaryotes, proteins that consist of (Sm)-FDF-YjeF N-terminal domains may be involved in RNA processing [, ]. The YjeF N-terminal domains represent a novel version of the Rossmann fold, one of the most common protein folds in nature observed in numerous enzyme families, that has acquired a set of catalytic residues and structural features that distinguish them from the conventional dehydrogenases. The YjeF N-terminal domain is comprised of a three-layer alpha-beta-alpha sandwich with a central beta-sheet surrounded by helices. The conservation of the acidic residues in the predicted active site of the YjeF N-terminal domains is reminiscent of the presence of such residues in the active sites of diverse hydrolases [, ].; PDB: 3K5W_A 2O8N_A 2DG2_F 3RNO_A 1JZT_B 3D3K_A 3D3J_A 3RSG_A 3RT9_A 3RRF_A ....
Probab=28.74 E-value=2.8e+02 Score=23.48 Aligned_cols=70 Identities=21% Similarity=0.302 Sum_probs=35.8
Q ss_pred HhHHHH-HHc---CCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceE
Q 011629 3 AIADIV-DYF---GWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRI 73 (481)
Q Consensus 3 Ai~~ll-~~f---gW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~v 73 (481)
++++++ +.+ ....|.++.-....|-.++..-+ .|.+.|++|.....-+.....++....++.+++.+.++
T Consensus 11 ~~a~~i~~~~~~~~~~~v~il~G~GnNGgDgl~~AR-~L~~~G~~V~v~~~~~~~~~~~~~~~~~~~~~~~g~~~ 84 (169)
T PF03853_consen 11 AIAELIRKLFGSPKGPRVLILCGPGNNGGDGLVAAR-HLANRGYNVTVYLVGPPEKLSEDAKQQLEILKKMGIKI 84 (169)
T ss_dssp HHHHHHHHHSTCCTT-EEEEEE-SSHHHHHHHHHHH-HHHHTTCEEEEEEEESSSSTSHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHhcccCCCeEEEEECCCCChHHHHHHHH-HHHHCCCeEEEEEEeccccCCHHHHHHHHHHHhcCCcE
Confidence 455544 334 46777777766655544444333 45777777766333333333345556666666554443
No 458
>TIGR00646 MG010 DNA primase-related protein. The DNA primase DnaG of E. coli and its apparent orthologs in other eubacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein modelled by this alignment, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown.
Probab=28.72 E-value=1.9e+02 Score=25.81 Aligned_cols=47 Identities=13% Similarity=0.120 Sum_probs=34.4
Q ss_pred HHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCC
Q 011629 5 ADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSP 52 (481)
Q Consensus 5 ~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~ 52 (481)
+++|+++.=+.|.+.+++|.-|+.......+.+.+.|..+... .+|.
T Consensus 146 ~~lLkr~~~~~Iil~~D~D~AG~~Aa~r~~~~L~~~G~~v~vv-~lP~ 192 (218)
T TIGR00646 146 MKFFKQKKIEKIFICFDNDFAGKNAAANLEEILKKAGFITKVI-EIKA 192 (218)
T ss_pred HHHHhccCCCEEEEEeCCCHHHHHHHHHHHHHHHHCCCeEEEE-eCCC
Confidence 3456665557888888888889988888888888888775432 3443
No 459
>PF00763 THF_DHG_CYH: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; InterPro: IPR020630 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the N-terminal catalytic domain of these enzymes. ; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 2C2X_B 2C2Y_A 1EDZ_A 1EE9_A 4A26_B 3NGL_C 3NGX_A 1B0A_A 1DIA_A 1A4I_B ....
Probab=28.69 E-value=2.1e+02 Score=22.57 Aligned_cols=65 Identities=8% Similarity=0.062 Sum_probs=40.5
Q ss_pred EEEEEEEeCCcc-cchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhcc-CCceEEEEEeCc
Q 011629 15 NVIALYVDDDHG-RNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSS-MMSRILILHTYD 80 (481)
Q Consensus 15 ~V~ii~~dd~~g-~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~-s~~~vIvl~~~~ 80 (481)
..++|..+++.+ ....+...+.+++.||.+... .++.+.+.+++...++++.+ .+.+-|++..+.
T Consensus 31 ~Laii~vg~d~~S~~Y~~~k~k~~~~~Gi~~~~~-~l~~~~~~~el~~~i~~lN~D~~V~GIlvq~PL 97 (117)
T PF00763_consen 31 KLAIILVGDDPASISYVRSKQKAAEKLGIEFELI-ELPEDISEEELLELIEKLNEDPSVHGILVQLPL 97 (117)
T ss_dssp EEEEEEES--HHHHHHHHHHHHHHHHHT-EEEEE-EE-TTSSHHHHHHHHHHHHH-TT-SEEEEESSS
T ss_pred EEEEEecCCChhHHHHHHHHHHHHHHcCCceEEE-ECCCCcCHHHHHHHHHHHhCCCCCCEEEEcCCC
Confidence 455555554443 345667777888889987765 46666666777777777754 567778887654
No 460
>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.
Probab=28.62 E-value=1.3e+02 Score=27.35 Aligned_cols=60 Identities=8% Similarity=0.024 Sum_probs=41.0
Q ss_pred EEEEEEEe----CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEe
Q 011629 15 NVIALYVD----DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 15 ~V~ii~~d----d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
+|++|..+ +.|.....+.+++.+++.|..+.+... . +.++....++.+...+++.||+..
T Consensus 1 ~Igvi~~~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~~~---~-~~~~~~~~~~~l~~~~vdgiii~~ 64 (260)
T cd06304 1 KVALVYDGGGGDKSFNQSAYEGLEKAEKELGVEVKYVES---V-EDADYEPNLRQLAAQGYDLIFGVG 64 (260)
T ss_pred CEEEEecCCCCcchHHHHHHHHHHHHHHhcCceEEEEec---C-CHHHHHHHHHHHHHcCCCEEEECC
Confidence 47777754 456667778888899999988776432 1 223455777778777788777754
No 461
>PF00070 Pyr_redox: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR001327 FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase [, , ]. Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently []. Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases [] and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) []. Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase [], thioredoxin reductase [], mercuric reductase [], lipoamide dehydrogenase [], trypanothione reductase [] and NADH peroxidase [] have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication []. This entry describes a small NADH binding domain within a larger FAD binding domain described by IPR023753 from INTERPRO. It is found in both class I and class II oxidoreductases. ; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZKQ_A 3DGZ_A 1ZDL_A 2R9Z_B 2RAB_A 2A87_B 1M6I_A 2YVG_A 2GR1_A 2GQW_A ....
Probab=28.58 E-value=1.7e+02 Score=20.81 Aligned_cols=45 Identities=13% Similarity=0.211 Sum_probs=26.9
Q ss_pred hHHHHHHcCCcEEEEEEEeCCcc----cchHHHHHHHHHhcCCEEEEEEe
Q 011629 4 IADIVDYFGWRNVIALYVDDDHG----RNGIAALGDKLAEKRCRLSHKVP 49 (481)
Q Consensus 4 i~~ll~~fgW~~V~ii~~dd~~g----~~~~~~l~~~l~~~gi~v~~~~~ 49 (481)
++..+.++| ..|.++...+... ....+.+++.+++.|+.+.....
T Consensus 14 ~A~~l~~~g-~~vtli~~~~~~~~~~~~~~~~~~~~~l~~~gV~v~~~~~ 62 (80)
T PF00070_consen 14 LAEALAELG-KEVTLIERSDRLLPGFDPDAAKILEEYLRKRGVEVHTNTK 62 (80)
T ss_dssp HHHHHHHTT-SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEEESEE
T ss_pred HHHHHHHhC-cEEEEEeccchhhhhcCHHHHHHHHHHHHHCCCEEEeCCE
Confidence 344556656 5666666555433 34566667777777777665443
No 462
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=28.54 E-value=2.3e+02 Score=26.62 Aligned_cols=85 Identities=16% Similarity=0.139 Sum_probs=54.4
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.+++++|+.. ... ..+-.+++..+.++.. ++++.+.. ++...++..|.+|++|+++..
T Consensus 92 ~g~l~Ig~~~--~~~------------~~~l~~~l~~~~~~~p-~i~l~~~~-------~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 92 QGNLTIATTH--TQA------------RYALPAAIKEFKKRYP-KVRLSILQ-------GSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred CCeEEEEech--HHH------------HHHhHHHHHHHHHHCC-CceEEEEe-------CChHHHHHHHHCCCcCEEEee
Confidence 4678888864 111 1234678888877653 34566665 457899999999999999753
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-... . ...+. +.|+......+++++..
T Consensus 150 ~~~~-~-~~~l~-~~~l~~~~~~~v~~~~~ 176 (313)
T PRK12684 150 EAIA-D-YKELV-SLPCYQWNHCVVVPPDH 176 (313)
T ss_pred cCCC-C-CCCce-EEEeccceEEEEeCCCC
Confidence 1111 1 12233 36777888888877654
No 463
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=28.53 E-value=2e+02 Score=24.48 Aligned_cols=48 Identities=19% Similarity=0.188 Sum_probs=28.7
Q ss_pred hHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 29 GIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 29 ~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
....|.+.+.+.|+.+.....++. +.+.+...++...+ .+++||..+.
T Consensus 20 n~~~l~~~L~~~G~~v~~~~~v~D--d~~~I~~~l~~~~~-~~dlVIttGG 67 (170)
T cd00885 20 NAAFLAKELAELGIEVYRVTVVGD--DEDRIAEALRRASE-RADLVITTGG 67 (170)
T ss_pred HHHHHHHHHHHCCCEEEEEEEeCC--CHHHHHHHHHHHHh-CCCEEEECCC
Confidence 455677777788887776655543 23345555555443 3667666543
No 464
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=28.50 E-value=1.3e+02 Score=28.44 Aligned_cols=70 Identities=11% Similarity=0.147 Sum_probs=42.6
Q ss_pred CCcEEEEEEEeCCcc-------------cchHHHHHHHHHh---cCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEE
Q 011629 12 GWRNVIALYVDDDHG-------------RNGIAALGDKLAE---KRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILI 75 (481)
Q Consensus 12 gW~~V~ii~~dd~~g-------------~~~~~~l~~~l~~---~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIv 75 (481)
|+|++.+-..+++.| ....+.|.+.+.+ ..-+|+..-.+|.....+.|.++++.+++.+++|+
T Consensus 85 g~TRinvki~~~~~~~~Tein~~Gp~is~~~~~~~l~~~~~~l~~~d~VvlsGSlP~g~~~d~y~~li~~~~~~g~~vi- 163 (310)
T COG1105 85 GDTRINVKILDEEDGEETEINFPGPEISEAELEQFLEQLKALLESDDIVVLSGSLPPGVPPDAYAELIRILRQQGAKVI- 163 (310)
T ss_pred CCCeeeEEEEecCCCcEEEecCCCCCCCHHHHHHHHHHHHHhcccCCEEEEeCCCCCCCCHHHHHHHHHHHHhcCCeEE-
Confidence 667777766555321 1224444444433 23347778888887776678888888888877764
Q ss_pred EEeCcHH
Q 011629 76 LHTYDIW 82 (481)
Q Consensus 76 l~~~~~~ 82 (481)
+.++...
T Consensus 164 lD~Sg~~ 170 (310)
T COG1105 164 LDTSGEA 170 (310)
T ss_pred EECChHH
Confidence 4444433
No 465
>TIGR00147 lipid kinase, YegS/Rv2252/BmrU family. The E. coli member of this family, YegS has been purified and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized.
Probab=28.46 E-value=3.9e+02 Score=24.90 Aligned_cols=74 Identities=15% Similarity=0.045 Sum_probs=44.1
Q ss_pred cEEEEEEEeCCcc----cchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHH
Q 011629 14 RNVIALYVDDDHG----RNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNA 89 (481)
Q Consensus 14 ~~V~ii~~dd~~g----~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~ 89 (481)
+++.+|+ +...| ....+.+.+.+.+.|+.+.....-.. . +....+++..+...++||+.+-......++..
T Consensus 2 ~~~~ii~-Np~sg~~~~~~~~~~i~~~l~~~~~~~~~~~t~~~--~--~~~~~~~~~~~~~~d~ivv~GGDGTl~~v~~~ 76 (293)
T TIGR00147 2 AEAPAIL-NPTAGKSNDNKPLREVIMLLREEGMEIHVRVTWEK--G--DAARYVEEARKFGVDTVIAGGGDGTINEVVNA 76 (293)
T ss_pred ceEEEEE-CCCccchhhHHHHHHHHHHHHHCCCEEEEEEecCc--c--cHHHHHHHHHhcCCCEEEEECCCChHHHHHHH
Confidence 4677777 33223 24456778888899987654432221 1 22333444444557788888777777777776
Q ss_pred HHH
Q 011629 90 AKH 92 (481)
Q Consensus 90 a~~ 92 (481)
+..
T Consensus 77 l~~ 79 (293)
T TIGR00147 77 LIQ 79 (293)
T ss_pred Hhc
Confidence 643
No 466
>KOG4132 consensus Uroporphyrinogen III synthase UROS/HEM4 [Coenzyme transport and metabolism]
Probab=28.11 E-value=4.4e+02 Score=23.63 Aligned_cols=69 Identities=12% Similarity=-0.051 Sum_probs=36.4
Q ss_pred ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHHcC
Q 011629 26 GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKHLR 94 (481)
Q Consensus 26 g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~~g 94 (481)
|...-+.|.+.|...||.|..-+.+....-.+-..++...++..+.---|++.++......++.....+
T Consensus 141 Gn~~rdil~kkL~~~G~~Vds~~VY~T~~hp~~~~~~~~alk~~~~~d~ivfFSPsgv~~~lq~f~~~~ 209 (260)
T KOG4132|consen 141 GNLRRDILPKKLHDKGIRVDSCEVYETREHPDGFKQFIHALKECGFIDWIVFFSPSGVKSSLQYFGDSN 209 (260)
T ss_pred ccchhHHHHHHHHhCCceeeEEEEEeeeecccHHHHHHHHHHhcCCcceEEEECcchHHHHHHHHHHhc
Confidence 455567777788888887777666643321112334444455543222234444555556665555443
No 467
>TIGR01118 lacA galactose-6-phosphate isomerase, LacA subunit. This family contains members from low GC gram-positive bacteria. Galactose-6-phosphate isomerase is involved in lactose catabolism by the tagatose-6-phosphate pathway.
Probab=27.90 E-value=3.4e+02 Score=22.29 Aligned_cols=60 Identities=8% Similarity=0.057 Sum_probs=36.6
Q ss_pred EEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHH-HHHHHHhccCCc-eEEEEEeCc
Q 011629 20 YVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQI-IDTLLTVSSMMS-RILILHTYD 80 (481)
Q Consensus 20 ~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~-~~~l~~i~~s~~-~vIvl~~~~ 80 (481)
...|.-|....+.+.+.|++.|..|..... ....+..++ ..+.+.+.+..+ +-|++|++.
T Consensus 5 IgsDh~G~~lK~~i~~~L~~~G~eV~D~G~-~~~~dYpd~a~~va~~V~~~e~~~GIliCGtG 66 (141)
T TIGR01118 5 IGSDLAGKRLKDVIKNFLVDNGFEVIDVTE-GDGQDFVDVTLAVASEVQKDEQNLGIVIDAYG 66 (141)
T ss_pred EEeCcchHHHHHHHHHHHHHCCCEEEEcCC-CCCCCcHHHHHHHHHHHHcCCCceEEEEcCCC
Confidence 345667889999999999999998865432 111122233 344455655444 555555553
No 468
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=27.85 E-value=2.5e+02 Score=26.32 Aligned_cols=84 Identities=15% Similarity=0.093 Sum_probs=54.5
Q ss_pred ceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeee
Q 011629 318 RHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDF 397 (481)
Q Consensus 318 ~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 397 (481)
+.++||+.. .+ ...+-.++++.+.++.. ++++.+.. ++-+.+...|.+|++|+++..-
T Consensus 93 g~l~Ig~~~--~~------------~~~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~ 150 (309)
T PRK12682 93 GTLTIATTH--TQ------------ARYVLPRVVAAFRKRYP-KVNLSLHQ-------GSPDEIARMVISGEADIGIATE 150 (309)
T ss_pred CeEEEeeCc--hH------------HHHHHHHHHHHHHHhCC-CeEEEEec-------CCHHHHHHHHHcCCccEEEecC
Confidence 578888863 11 11344678888887763 34566654 4467899999999999997532
Q ss_pred eeccccccceeeccceeecceEEEEecCC
Q 011629 398 AITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 398 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
. ......++. .|+......++++++.
T Consensus 151 ~--~~~~~~l~~-~~l~~~~~~~~~~~~~ 176 (309)
T PRK12682 151 S--LADDPDLAT-LPCYDWQHAVIVPPDH 176 (309)
T ss_pred c--ccCCCcceE-EEeeeeeEEEEecCCC
Confidence 1 112233443 5788888888887654
No 469
>TIGR00975 3a0107s03 phosphate ABC transporter, phosphate-binding protein. This family represents one type of (periplasmic, in Gram-negative bacteria) phosphate-binding protein found in phosphate ABC (ATP-binding cassette) transporters. This protein is accompanied, generally in the same operon, by an ATP binding protein and (usually) two permease proteins.
Probab=27.46 E-value=1.4e+02 Score=28.46 Aligned_cols=71 Identities=10% Similarity=0.044 Sum_probs=43.8
Q ss_pred HHHHHHHHHC---CCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccce---eeccceeecceEEEE
Q 011629 349 DVFTAVLELL---PYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMV---DFTQPYIESGLVVVA 422 (481)
Q Consensus 349 dl~~~ia~~l---~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~---~fs~p~~~~~~~~~~ 422 (481)
-+++++++.+ +-.+++.+... ++- +-+.++.+|++|++.++-.++++..+.. -...|+...++++++
T Consensus 11 pl~~~~~~~y~~~~~~v~v~v~~~------GSg-~Gi~~l~~g~~dia~ssr~l~~~E~~~~~~~~~~~pva~dai~viv 83 (314)
T TIGR00975 11 PLYTKWFPDYQKSNPGVTINYQGI------GSG-AGIAQFAAGTVDFGASDAPLSEADLASRGSGLLQFPTVIGAIVVTY 83 (314)
T ss_pred HHHHHHHHHHHHhCCCceEEEecC------CCH-HHHHHHHcCCCCEEecCCCCCHHHHHhhcCCcEEeeEEeeeEEEEE
Confidence 3455555443 21244555542 344 4468889999999998877776432211 123478888999999
Q ss_pred ecCC
Q 011629 423 PIKK 426 (481)
Q Consensus 423 ~~~~ 426 (481)
+.+.
T Consensus 84 n~~~ 87 (314)
T TIGR00975 84 NLPG 87 (314)
T ss_pred eCCC
Confidence 8643
No 470
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=27.44 E-value=2.7e+02 Score=26.28 Aligned_cols=82 Identities=12% Similarity=0.143 Sum_probs=53.2
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.++++||+.. ... ..+-..++..+.+..- ++++.... ++..+..|.+|++|+++..
T Consensus 116 ~~~l~Ig~~~--~~~------------~~~l~~~l~~f~~~~P-~i~i~~~~---------~~~~~~~l~~g~~Dl~i~~ 171 (317)
T PRK11482 116 QRTITIATTP--SVG------------ALVMPVIYQAIKTHYP-QLLLRNIP---------ISDAENQLSQFQTDLIIDT 171 (317)
T ss_pred CceEEEEecH--HHH------------HHHHHHHHHHHHHHCC-CCEEEEec---------chhHHHHHHCCCcCEEEec
Confidence 3578888874 111 1234567777777653 34454333 5688999999999999753
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
. +...+.+.+ .|.....+.++++++.
T Consensus 172 ~---~~~~~~~~~-~~l~~~~~~lv~~~~h 197 (317)
T PRK11482 172 H---SCSNRTIQH-HVLFTDNVVLVCRQGH 197 (317)
T ss_pred c---CCCCCceEE-EEEecCcEEEEEeCCC
Confidence 2 333444554 6888888888887654
No 471
>cd00858 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=27.33 E-value=2.3e+02 Score=22.32 Aligned_cols=45 Identities=9% Similarity=0.062 Sum_probs=24.0
Q ss_pred hHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 29 GIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 29 ~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
.+..+.+.+++.|+.+..... ..+...++.....+++.+++.+..
T Consensus 43 ~a~~la~~LR~~gi~v~~d~~-------~sl~kqlk~A~k~g~~~~iiiG~~ 87 (121)
T cd00858 43 IAKEISEELRELGFSVKYDDS-------GSIGRRYARQDEIGTPFCVTVDFD 87 (121)
T ss_pred HHHHHHHHHHHCCCEEEEeCC-------CCHHHHHHHhHhcCCCEEEEECcC
Confidence 344555566666666654321 134455555555566666666543
No 472
>PF13396 PLDc_N: Phospholipase_D-nuclease N-terminal
Probab=27.33 E-value=60 Score=20.47 Aligned_cols=28 Identities=18% Similarity=0.610 Sum_probs=22.9
Q ss_pred ccCcchhHHHHHHHHHHHHHHHHHhhhc
Q 011629 435 LNPFTPKMWCVTGIFFLVVGVVVWILEH 462 (481)
Q Consensus 435 l~pf~~~~W~~~~~~~~~~~~~~~~~~~ 462 (481)
.+|-+.-.|+.+++.+-++|.++|++-+
T Consensus 17 ~~~~~k~~W~~~i~~~P~iG~i~Yl~~g 44 (46)
T PF13396_consen 17 RSPSSKILWLIVILFFPIIGPILYLIFG 44 (46)
T ss_pred CCCchhhHHHHHHHHHHHHHHhheEEEe
Confidence 4666778999999999999999997743
No 473
>TIGR01162 purE phosphoribosylaminoimidazole carboxylase, PurE protein. Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, an N5-CAIR mutase.
Probab=27.21 E-value=2.6e+02 Score=23.40 Aligned_cols=54 Identities=11% Similarity=0.062 Sum_probs=37.4
Q ss_pred chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHH
Q 011629 28 NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIW 82 (481)
Q Consensus 28 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~ 82 (481)
...+...+.|++.|+...... .+...+.+...+.+++.++.+.+|||..+.-.-
T Consensus 12 ~~~~~a~~~L~~~gi~~dv~V-~SaHRtp~~~~~~~~~a~~~g~~viIa~AG~aa 65 (156)
T TIGR01162 12 PTMKKAADILEEFGIPYELRV-VSAHRTPELMLEYAKEAEERGIKVIIAGAGGAA 65 (156)
T ss_pred HHHHHHHHHHHHcCCCeEEEE-ECcccCHHHHHHHHHHHHHCCCeEEEEeCCccc
Confidence 467777788888898865543 333445556777777777778899888766543
No 474
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=27.14 E-value=2.9e+02 Score=21.33 Aligned_cols=70 Identities=14% Similarity=0.030 Sum_probs=0.0
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEe
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHT 78 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~ 78 (481)
..++..++..|| .|.++-.+... +.+.+.+.+.+-.+... ............++++.+|+..+++.++.+
T Consensus 18 ~~la~~l~~~G~-~v~~~d~~~~~-----~~l~~~~~~~~pd~V~i-S~~~~~~~~~~~~l~~~~k~~~p~~~iv~G 87 (121)
T PF02310_consen 18 LYLAAYLRKAGH-EVDILDANVPP-----EELVEALRAERPDVVGI-SVSMTPNLPEAKRLARAIKERNPNIPIVVG 87 (121)
T ss_dssp HHHHHHHHHTTB-EEEEEESSB-H-----HHHHHHHHHTTCSEEEE-EESSSTHHHHHHHHHHHHHTTCTTSEEEEE
T ss_pred HHHHHHHHHCCC-eEEEECCCCCH-----HHHHHHHhcCCCcEEEE-EccCcCcHHHHHHHHHHHHhcCCCCEEEEE
No 475
>PRK11070 ssDNA exonuclease RecJ; Provisional
Probab=27.13 E-value=2.9e+02 Score=28.90 Aligned_cols=81 Identities=11% Similarity=0.048 Sum_probs=54.7
Q ss_pred cEEEEEEEeCCcccchHHHHHHHHHhcCC-EEEEEEecCCCCC-hhHH-HHHHHHhccCCceEEEEEeCcHHHHHHHHHH
Q 011629 14 RNVIALYVDDDHGRNGIAALGDKLAEKRC-RLSHKVPLSPKGS-RNQI-IDTLLTVSSMMSRILILHTYDIWGLEVLNAA 90 (481)
Q Consensus 14 ~~V~ii~~dd~~g~~~~~~l~~~l~~~gi-~v~~~~~~~~~~~-~~~~-~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a 90 (481)
.+|.|..+-|..|......|.+.|.+.|+ .+.+. +|.... ...+ ...++++.+.+++.||.+-........+..|
T Consensus 70 e~I~I~gDyD~DGitstail~~~L~~~g~~~~~~~--IP~R~~eGYGl~~~~i~~~~~~~~~LiItvD~Gi~~~e~i~~a 147 (575)
T PRK11070 70 TRIIVVGDFDADGATSTALSVLALRSLGCSNVDYL--VPNRFEDGYGLSPEVVDQAHARGAQLIVTVDNGISSHAGVAHA 147 (575)
T ss_pred CEEEEEEecCccHHHHHHHHHHHHHHcCCCceEEE--eCCCCcCCCCCCHHHHHHHHhcCCCEEEEEcCCcCCHHHHHHH
Confidence 57777777788899999999999999998 56553 453211 0011 2456677666778877765555566677778
Q ss_pred HHcCCc
Q 011629 91 KHLRMM 96 (481)
Q Consensus 91 ~~~g~~ 96 (481)
.++|+.
T Consensus 148 ~~~gid 153 (575)
T PRK11070 148 HALGIP 153 (575)
T ss_pred HHCCCC
Confidence 887763
No 476
>PF10853 DUF2650: Protein of unknown function (DUF2650); InterPro: IPR022559 This region is found in proteins with unknown function in metazoa.
Probab=26.70 E-value=45 Score=20.36 Aligned_cols=15 Identities=20% Similarity=0.505 Sum_probs=10.6
Q ss_pred cchhHHHHHHHHHHH
Q 011629 438 FTPKMWCVTGIFFLV 452 (481)
Q Consensus 438 f~~~~W~~~~~~~~~ 452 (481)
|..+.|+.+++++++
T Consensus 22 f~lq~Wv~v~l~v~~ 36 (38)
T PF10853_consen 22 FRLQIWVIVLLAVLG 36 (38)
T ss_pred HHHHHHHHHHHHHHh
Confidence 567889887776654
No 477
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=26.68 E-value=4.7e+02 Score=24.81 Aligned_cols=78 Identities=10% Similarity=0.014 Sum_probs=47.4
Q ss_pred cEEEEEEEe--CCcccchHHHHHHHHHhcC-CEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC-cHHHHHHHHH
Q 011629 14 RNVIALYVD--DDHGRNGIAALGDKLAEKR-CRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY-DIWGLEVLNA 89 (481)
Q Consensus 14 ~~V~ii~~d--d~~g~~~~~~l~~~l~~~g-i~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~-~~~~~~il~~ 89 (481)
+.|+++..+ +.|.....+.+++.+++.| ..+... .+ ..+.+.-...++.+...+++.||++.. .......+.+
T Consensus 25 ~~Igvv~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~--~~-~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~ 101 (330)
T PRK15395 25 TRIGVTIYKYDDNFMSVVRKAIEKDAKAAPDVQLLMN--DS-QNDQSKQNDQIDVLLAKGVKALAINLVDPAAAPTVIEK 101 (330)
T ss_pred ceEEEEEecCcchHHHHHHHHHHHHHHhcCCeEEEEe--cC-CCCHHHHHHHHHHHHHcCCCEEEEeccCHHHHHHHHHH
Confidence 568888754 3455667788888888885 454432 11 222222335667777778898888753 3334456666
Q ss_pred HHHcC
Q 011629 90 AKHLR 94 (481)
Q Consensus 90 a~~~g 94 (481)
+.+.|
T Consensus 102 l~~~g 106 (330)
T PRK15395 102 ARGQD 106 (330)
T ss_pred HHHCC
Confidence 66654
No 478
>TIGR03405 Phn_Fe-ADH phosphonate metabolism-associated iron-containing alcohol dehydrogenase. 2-hydroxyethylphosphonate (2-HEP), the presumed product of the reaction of Pald with an alcohol dehydrogenase, is a biologically novel but reasonable analog of 2-AEP and may be a constituent of as-yet undescribed natural products. In the case of Azoarcus, downstream of the dehydrogenase is a CDP-glycerol:glycerophosphate transferase homolog that may indicate the existence of a pathway for 2-HEP-derived phosphonolipid biosynthesis.
Probab=26.66 E-value=3e+02 Score=26.65 Aligned_cols=73 Identities=10% Similarity=-0.018 Sum_probs=44.0
Q ss_pred HHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCC--ceEEEEEeCc
Q 011629 6 DIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMM--SRILILHTYD 80 (481)
Q Consensus 6 ~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~--~~vIvl~~~~ 80 (481)
+|-...+.+++-+|++.........+.+.+.++... +.....+..+.+.++..+..+.+++.+ ++.||..+..
T Consensus 16 ~l~~~~~~~r~lvVtd~~~~~~g~~~~v~~~L~~~~--~~~~~~v~~~pt~~~v~~~~~~~~~~~~~~D~IIaiGGG 90 (355)
T TIGR03405 16 LAPQLLHGRRVVVVTFPEARALGLARRLEALLGGRL--AALIDDVAPNPDVAQLDGLYARLWGDEGACDLVIALGGG 90 (355)
T ss_pred HHHHHhCCCeEEEEECcchhhcchHHHHHHHhccCc--EEEeCCCCCCcCHHHHHHHHHHHHhcCCCCCEEEEeCCc
Confidence 333334458888888444333455677777776543 222223444555566777777777655 8899887653
No 479
>PF08854 DUF1824: Domain of unknown function (DUF1824); InterPro: IPR014953 This uncharacterised group of proteins are principally found in cyanobacteria. ; PDB: 2Q22_B.
Probab=26.62 E-value=68 Score=25.68 Aligned_cols=40 Identities=15% Similarity=0.060 Sum_probs=30.0
Q ss_pred hHhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEE
Q 011629 2 AAIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRL 44 (481)
Q Consensus 2 ~Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v 44 (481)
+++..++....|..+||++.+.+ .+..+|+...++.|+..
T Consensus 26 ~~L~~~~~~sd~~~lGIcA~s~~---~ai~ALr~~~~alg~~~ 65 (125)
T PF08854_consen 26 QALRLLASNSDWFTLGICAPSAE---EAIAALRSYEQALGYPP 65 (125)
T ss_dssp HHHHHHHHTSSEEEEEEEESSHH---HHHHHHHHHHHHTT---
T ss_pred HHHHHHHhccCceEEEeecCCHH---HHHHHHHHHHHHcCCCc
Confidence 36777888899999999996654 46788888888888765
No 480
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=26.52 E-value=2.9e+02 Score=25.17 Aligned_cols=76 Identities=7% Similarity=-0.115 Sum_probs=48.4
Q ss_pred EEEEEEe--CCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc-HHHHHHHHHHHH
Q 011629 16 VIALYVD--DDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD-IWGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~d--d~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~-~~~~~il~~a~~ 92 (481)
+|+...+ +.|.....+.+.+.+++.|+.+..... ..+.+.....++.+...+++.||+.... ......+.++.+
T Consensus 2 ~~~~~~~~~~~f~~~~~~gi~~~~~~~G~~~~~~~~---~~d~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~i~~~~~ 78 (272)
T cd06313 2 AAFSNIGLQATWCAQGKQAADEAGKLLGVDVTWYGG---ALDAVKQVAAIENMASQGWDFIAVDPLGIGTLTEAVQKAIA 78 (272)
T ss_pred cceeecccCChHHHHHHHHHHHHHHHcCCEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEEcCCChHHhHHHHHHHHH
Confidence 3444432 345666778888999999998876532 2233344566777777788888886543 334566777766
Q ss_pred cC
Q 011629 93 LR 94 (481)
Q Consensus 93 ~g 94 (481)
.+
T Consensus 79 ~~ 80 (272)
T cd06313 79 RG 80 (272)
T ss_pred CC
Confidence 55
No 481
>PLN00125 Succinyl-CoA ligase [GDP-forming] subunit alpha
Probab=26.41 E-value=4.8e+02 Score=24.65 Aligned_cols=72 Identities=8% Similarity=-0.084 Sum_probs=49.6
Q ss_pred EEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCC--CChhHHHHHHHHhc-cCCceEEEEEeCc-----HHHHHH
Q 011629 15 NVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPK--GSRNQIIDTLLTVS-SMMSRILILHTYD-----IWGLEV 86 (481)
Q Consensus 15 ~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~--~~~~~~~~~l~~i~-~s~~~vIvl~~~~-----~~~~~i 86 (481)
.|++|.+.... ...+...+..+|+-+.....+-.. .+ -++.+.++-+. +..+++|+++... .+.+.+
T Consensus 152 ~ValiSQSG~l----~~~l~~~~~~~giG~S~~VS~Gn~~~ad-v~~~d~L~yl~~Dp~T~~I~ly~E~~G~~~~d~~~f 226 (300)
T PLN00125 152 RIGIVSRSGTL----TYEAVFQTTAVGLGQSTCVGIGGDPFNG-TNFVDCLEKFVKDPQTEGIILIGEIGGTAEEDAAAF 226 (300)
T ss_pred cEEEEeCCccH----HHHHHHHHHHcCCCeEEEEEeCCCCCCC-CCHHHHHHHHhhCCCCcEEEEEeccCCchHHHHHHH
Confidence 36777755543 455667778888877766655443 22 25677788775 4789999999984 578888
Q ss_pred HHHHH
Q 011629 87 LNAAK 91 (481)
Q Consensus 87 l~~a~ 91 (481)
+..+.
T Consensus 227 ~~aa~ 231 (300)
T PLN00125 227 IKESG 231 (300)
T ss_pred HHHhc
Confidence 87765
No 482
>PF00107 ADH_zinc_N: Zinc-binding dehydrogenase; InterPro: IPR013149 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of alcohols to their corresponding acetaldehyde or ketone with the concomitant reduction of NAD: alcohol + NAD = aldehyde or ketone + NADH Currently three structurally and catalytically different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Zinc-containing ADH's [, ] are dimeric or tetrameric enzymes that bind two atoms of zinc per subunit. One of the zinc atom is essential for catalytic activity while the other is not. Both zinc atoms are coordinated by either cysteine or histidine residues; the catalytic zinc is coordinated by two cysteines and one histidine. Zinc-containing ADH's are found in bacteria, mammals, plants, and in fungi. In many species there is more than one isozyme (for example, humans have at least six isozymes, yeast have three, etc.). A number of other zinc-dependent dehydrogenases are closely related to zinc ADH [] and are included in this family. Sorbitol dehydrogenase (1.1.1.14 from EC) L-threonine 3-dehydrogenase (1.1.1.103 from EC) Glutathione-dependent formaldehyde dehydrogenase (1.1.1.284 from EC) Mannitol dehydrogenase (1.1.1.255 from EC) In addition, this family includes NADP-dependent quinone oxidoreductase (1.6.5.5 from EC), an enzyme found in bacteria (gene qor), in yeast and in mammals where, in some species such as rodents, it has been recruited as an eye lens protein and is known as zeta-crystallin []. The sequence of quinone oxidoreductase is distantly related to that other zinc-containing alcohol dehydrogenases and it lacks the zinc-ligand residues. The torpedo fish and mammalian synaptic vesicle membrane protein vat-1 is related to qor. This entry represents the cofactor-binding domain of these enzymes, which is normally found towards the C terminus. Structural studies indicate that it forms a classical Rossman fold that reversibly binds NAD(H) [, , ].; GO: 0008270 zinc ion binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3PI7_A 3COS_D 1VJ1_A 2ZB3_A 1PIW_B 1Q1N_A 1PS0_A 2EER_B 3KRT_A 1ZSY_A ....
Probab=26.38 E-value=2.6e+02 Score=21.85 Aligned_cols=66 Identities=9% Similarity=0.012 Sum_probs=39.2
Q ss_pred HhHHHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccC-CceEEEEEeCcH
Q 011629 3 AIADIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSM-MSRILILHTYDI 81 (481)
Q Consensus 3 Ai~~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s-~~~vIvl~~~~~ 81 (481)
+.+++++++| ..|.++..++. -.+.+++.|.... +..... ++...++++... +.++|+-+....
T Consensus 5 ~a~q~ak~~G-~~vi~~~~~~~--------k~~~~~~~Ga~~~----~~~~~~--~~~~~i~~~~~~~~~d~vid~~g~~ 69 (130)
T PF00107_consen 5 MAIQLAKAMG-AKVIATDRSEE--------KLELAKELGADHV----IDYSDD--DFVEQIRELTGGRGVDVVIDCVGSG 69 (130)
T ss_dssp HHHHHHHHTT-SEEEEEESSHH--------HHHHHHHTTESEE----EETTTS--SHHHHHHHHTTTSSEEEEEESSSSH
T ss_pred HHHHHHHHcC-CEEEEEECCHH--------HHHHHHhhccccc----cccccc--ccccccccccccccceEEEEecCcH
Confidence 5678999999 55555553321 1455667773322 222222 466777777664 788888776644
Q ss_pred HH
Q 011629 82 WG 83 (481)
Q Consensus 82 ~~ 83 (481)
..
T Consensus 70 ~~ 71 (130)
T PF00107_consen 70 DT 71 (130)
T ss_dssp HH
T ss_pred HH
Confidence 33
No 483
>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.
Probab=26.29 E-value=1.7e+02 Score=27.37 Aligned_cols=65 Identities=11% Similarity=0.042 Sum_probs=39.9
Q ss_pred EEEEEEEeCC-cccchHHHHHHHHHhcCCEE---EEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 15 NVIALYVDDD-HGRNGIAALGDKLAEKRCRL---SHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 15 ~V~ii~~dd~-~g~~~~~~l~~~l~~~gi~v---~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+|||+..-+. .-....+.|++.|++.|+.. .+... ....+.+.....++++++.++++|+..+..
T Consensus 1 ~v~i~~~~~~~~~~~~~~gf~~~L~~~g~~~~~~~~~~~-~a~~d~~~~~~~~~~l~~~~~DlIi~~gt~ 69 (294)
T PF04392_consen 1 KVGILQFISHPALDDIVRGFKDGLKELGYDEKNVEIEYK-NAEGDPEKLRQIARKLKAQKPDLIIAIGTP 69 (294)
T ss_dssp EEEEEESS--HHHHHHHHHHHHHHHHTT--CCCEEEEEE-E-TT-HHHHHHHHHHHCCTS-SEEEEESHH
T ss_pred CeEEEEEeccHHHHHHHHHHHHHHHHcCCccccEEEEEe-cCCCCHHHHHHHHHHHhcCCCCEEEEeCcH
Confidence 4666664332 22356888999999988764 43322 223455667888889999999998887654
No 484
>PF06057 VirJ: Bacterial virulence protein (VirJ); InterPro: IPR010333 This entry contains several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localised to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium [].
Probab=26.28 E-value=1.9e+02 Score=25.16 Aligned_cols=67 Identities=10% Similarity=0.154 Sum_probs=43.3
Q ss_pred EEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecC---CCCCh----hHHHHHHHHhcc-CCceEEEEEeCcH
Q 011629 15 NVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLS---PKGSR----NQIIDTLLTVSS-MMSRILILHTYDI 81 (481)
Q Consensus 15 ~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~---~~~~~----~~~~~~l~~i~~-s~~~vIvl~~~~~ 81 (481)
.+++++|.|.-....-+.+-+.|++.|+.|.-..... ...+. .|+.++++...+ -+.+-++|.+++.
T Consensus 3 t~~v~~SGDgGw~~~d~~~a~~l~~~G~~VvGvdsl~Yfw~~rtP~~~a~Dl~~~i~~y~~~w~~~~vvLiGYSF 77 (192)
T PF06057_consen 3 TLAVFFSGDGGWRDLDKQIAEALAKQGVPVVGVDSLRYFWSERTPEQTAADLARIIRHYRARWGRKRVVLIGYSF 77 (192)
T ss_pred EEEEEEeCCCCchhhhHHHHHHHHHCCCeEEEechHHHHhhhCCHHHHHHHHHHHHHHHHHHhCCceEEEEeecC
Confidence 5788888776666788899999999999987544332 11222 244555555443 3566667777654
No 485
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=26.16 E-value=2.3e+02 Score=25.55 Aligned_cols=61 Identities=11% Similarity=-0.028 Sum_probs=41.9
Q ss_pred EEEEEE--eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 16 VIALYV--DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 16 V~ii~~--dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
|+++.. ++.+.....+.+.+.+++.|+++..... ..+.+.-...++.+...+.+-||+...
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~gy~~~~~~~---~~~~~~~~~~i~~l~~~~~dgiii~~~ 64 (265)
T cd06290 2 IGVLTQDFASPFYGRILKGMERGLNGSGYSPIIATG---HWNQSRELEALELLKSRRVDALILLGG 64 (265)
T ss_pred EEEEECCCCCchHHHHHHHHHHHHHHCCCEEEEEeC---CCCHHHHHHHHHHHHHCCCCEEEEeCC
Confidence 567764 4566677788899999999998765422 223334456677787777888887653
No 486
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=26.03 E-value=4.2e+02 Score=22.70 Aligned_cols=72 Identities=8% Similarity=-0.097 Sum_probs=41.9
Q ss_pred HcCCcEEEEEEEeCCcccchHHHHHHHHHhc--CCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHH
Q 011629 10 YFGWRNVIALYVDDDHGRNGIAALGDKLAEK--RCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVL 87 (481)
Q Consensus 10 ~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~--gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il 87 (481)
.-+ .+|.++-...+ .++.+.+.+++. |+.|+.. ....+.++-..+++.|.+++++++++......-..++
T Consensus 46 ~~~-~~vfllG~~~~----v~~~~~~~l~~~yP~l~i~g~---~g~f~~~~~~~i~~~I~~s~~dil~VglG~PkQE~~~ 117 (177)
T TIGR00696 46 KEK-LPIFLYGGKPD----VLQQLKVKLIKEYPKLKIVGA---FGPLEPEERKAALAKIARSGAGIVFVGLGCPKQEIWM 117 (177)
T ss_pred HcC-CeEEEECCCHH----HHHHHHHHHHHHCCCCEEEEE---CCCCChHHHHHHHHHHHHcCCCEEEEEcCCcHhHHHH
Confidence 345 36666665543 455555555554 6776643 1112223345678889999999988876554444444
Q ss_pred HH
Q 011629 88 NA 89 (481)
Q Consensus 88 ~~ 89 (481)
.+
T Consensus 118 ~~ 119 (177)
T TIGR00696 118 RN 119 (177)
T ss_pred HH
Confidence 43
No 487
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=25.54 E-value=3.1e+02 Score=26.04 Aligned_cols=85 Identities=14% Similarity=0.065 Sum_probs=54.7
Q ss_pred CceEEEeecCCCCCcCcEEecCCCCeEEeeeHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEee
Q 011629 317 GRHLRIGVPSQVIYPEFVAQGKGTDKFSGYCIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGD 396 (481)
Q Consensus 317 ~~~l~v~~~~~~~~~p~~~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 396 (481)
.+++++|+.. ... ..+-.+++..+.+... ++++.+.. ++...+...|.+|++|+++..
T Consensus 92 ~g~l~Ig~~~--~~~------------~~~l~~~l~~f~~~~P-~i~i~i~~-------~~~~~~~~~L~~g~iDl~i~~ 149 (324)
T PRK12681 92 KGSLYIATTH--TQA------------RYALPPVIKGFIERYP-RVSLHMHQ-------GSPTQIAEAAAKGNADFAIAT 149 (324)
T ss_pred CCeEEEEech--hHH------------HHhhHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCCCEEEec
Confidence 4678988864 211 1234677777777763 45566665 568899999999999999753
Q ss_pred eeeccccccceeeccceeecceEEEEecCC
Q 011629 397 FAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 397 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
- ...+...+.+ .|+......++++++.
T Consensus 150 ~--~~~~~~~l~~-~~l~~~~~~~v~~~~h 176 (324)
T PRK12681 150 E--ALHLYDDLIM-LPCYHWNRSVVVPPDH 176 (324)
T ss_pred C--cccCCCCeEE-EEeccceeEEEeCCCC
Confidence 1 1122233433 5777777788876543
No 488
>cd08195 DHQS Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway, which involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds, is found in bacteria, microbial eukaryotes, and plants, but not in mammals. Therefore, enzymes of this pathway are attractive targets for the development of non-toxic antimicrobial compounds, herbicides and anti-parasitic agents. The activity of DHQS requires nicotinamide adenine dinucleotide (NAD) as cofactor. A single active site in DHQS catalyzes five sequential reactions involving alcohol oxidation, phosphate elimination, carbonyl reduction, ring opening, and intramolecular aldol
Probab=25.41 E-value=2.8e+02 Score=26.67 Aligned_cols=82 Identities=6% Similarity=-0.135 Sum_probs=50.8
Q ss_pred cCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCC---CCChhHHHHHHHHhccCCc---eEEEEEeCc--HH
Q 011629 11 FGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSP---KGSRNQIIDTLLTVSSMMS---RILILHTYD--IW 82 (481)
Q Consensus 11 fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~---~~~~~~~~~~l~~i~~s~~---~vIvl~~~~--~~ 82 (481)
.+.+++.+|++...+ ....+.+.+.+++.|+.+... .++. +.+.+.+.+.++.+++.+. +.||..+.. .+
T Consensus 22 ~~~~~~livtd~~~~-~~~~~~l~~~L~~~g~~~~~~-~~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~IIaiGGGsv~D 99 (345)
T cd08195 22 PKGSKILIVTDENVA-PLYLEKLKAALEAAGFEVEVI-VIPAGEASKSLETLEKLYDALLEAGLDRKSLIIALGGGVVGD 99 (345)
T ss_pred cCCCeEEEEECCchH-HHHHHHHHHHHHhcCCceEEE-EeCCCCCcCCHHHHHHHHHHHHHcCCCCCCeEEEECChHHHh
Confidence 456888888844433 356788888999988766533 2332 3445567777777776544 777776653 45
Q ss_pred HHHHHHHHHHcC
Q 011629 83 GLEVLNAAKHLR 94 (481)
Q Consensus 83 ~~~il~~a~~~g 94 (481)
+..++...+..|
T Consensus 100 ~ak~vA~~~~rg 111 (345)
T cd08195 100 LAGFVAATYMRG 111 (345)
T ss_pred HHHHHHHHHhcC
Confidence 555554434433
No 489
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=25.40 E-value=2.7e+02 Score=26.36 Aligned_cols=68 Identities=10% Similarity=0.121 Sum_probs=46.0
Q ss_pred eHHHHHHHHHHCCCcccEEEEeCCCCCCCCCHHHHHHHHHcccccEEEeeeeeccccccceeeccceeecceEEEEecCC
Q 011629 347 CIDVFTAVLELLPYAVPYKLVPFGDGHNSPKRFDLLRLVSEEVYDAAVGDFAITTERTKMVDFTQPYIESGLVVVAPIKK 426 (481)
Q Consensus 347 ~~dl~~~ia~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~ 426 (481)
-.+++..+.+... ++++++.. ..-..+...|.+|++|+++.. .+.....+.+ .++....+.++++++.
T Consensus 104 l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~L~~g~~Dl~i~~---~~~~~~~~~~-~~l~~~~~~lv~~~~h 171 (317)
T PRK15421 104 LTPALENFHKNWP-QVEMDFKS-------GVTFDPQPALQQGELDLVMTS---DILPRSGLHY-SPMFDYEVRLVLAPDH 171 (317)
T ss_pred HHHHHHHHHHHCC-CceEEEEe-------CccHHHHHHHHCCCcCEEEec---CcccCCCceE-EEeccceEEEEEcCCC
Confidence 3567777776652 34566654 335678899999999999753 2333344554 7788888888887654
No 490
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=25.37 E-value=2.4e+02 Score=25.70 Aligned_cols=59 Identities=12% Similarity=-0.070 Sum_probs=27.6
Q ss_pred hHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHH
Q 011629 29 GIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLN 88 (481)
Q Consensus 29 ~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~ 88 (481)
+...|.+.|++.|+.|.....+.............+.+.....++|+ +.+...+..++.
T Consensus 141 ~r~~L~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~~~~~~~d~v~-ftS~~~~~~~~~ 199 (255)
T PRK05752 141 GRELLAERLREQGASVDYLELYRRCLPDYPAGTLLQRVEAERLNGLV-VSSGQGFEHLQQ 199 (255)
T ss_pred cHHHHHHHHHHCCCEEeEEEEEeecCCCCCHHHHHHHHHhCCCCEEE-ECCHHHHHHHHH
Confidence 34566777777777766555443221111122333444444344433 344444544443
No 491
>smart00852 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=25.02 E-value=3.6e+02 Score=21.60 Aligned_cols=49 Identities=16% Similarity=0.165 Sum_probs=35.0
Q ss_pred chHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 28 NGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 28 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
.....+.+.+++.|..+.....++ ++.+.+.+.+++..+ .+++||..+.
T Consensus 18 ~~~~~l~~~l~~~G~~~~~~~~v~--Dd~~~I~~~l~~~~~-~~dliittGG 66 (135)
T smart00852 18 SNGPALAELLTELGIEVTRYVIVP--DDKEAIKEALREALE-RADLVITTGG 66 (135)
T ss_pred CcHHHHHHHHHHCCCeEEEEEEeC--CCHHHHHHHHHHHHh-CCCEEEEcCC
Confidence 446778889999999988777665 344466677766654 4788887664
No 492
>TIGR03702 lip_kinase_YegS lipid kinase YegS. Members of this protein family are designated YegS, an apparent lipid kinase family in the Proteobacteria. Bakali, et al. report phosphatidylglycerol kinase activity for the member from Escherichia coli, but refrain from calling that activity synonymous with its biological role. Note that a broader, subfamily-type model (TIGR00147), includes this family but also multiple paralogs in some species and varied functions.
Probab=24.91 E-value=5.4e+02 Score=24.00 Aligned_cols=73 Identities=10% Similarity=0.014 Sum_probs=42.7
Q ss_pred EEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCcHHHHHHHHHHHH
Q 011629 16 VIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYDIWGLEVLNAAKH 92 (481)
Q Consensus 16 V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~~~~~~il~~a~~ 92 (481)
+.+|+.....+......+.+.+++.|+.+... ...... +...+.+++...+.++||+.+-...+..++..+.+
T Consensus 2 ~~~I~N~~~~~~~~~~~~~~~l~~~g~~~~v~--~t~~~~--~a~~~a~~~~~~~~d~vv~~GGDGTi~ev~ngl~~ 74 (293)
T TIGR03702 2 ALLILNGKQADNEDVREAVGDLRDEGIQLHVR--VTWEKG--DAQRYVAEALALGVSTVIAGGGDGTLREVATALAQ 74 (293)
T ss_pred EEEEEeCCccchhHHHHHHHHHHHCCCeEEEE--EecCCC--CHHHHHHHHHHcCCCEEEEEcCChHHHHHHHHHHh
Confidence 34555322223234566677888888875433 221112 34555666655567788888777777777766654
No 493
>PF10717 ODV-E18: Occlusion-derived virus envelope protein ODV-E18; InterPro: IPR019655 Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. Occlusion-derived viral envelope proteins that are detected in viral-induced intranuclear microvesicles, but not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. This entry represents ODV-E18 protein which is encoded by baculovirus late genes with transcription initiating from a TAAG motif. ODV-E18 exists as a dimer in the ODV envelope, which contains a hydrophobic domain that putatively acts as a target or retention signal for intranuclear microvesicles []. ; GO: 0019031 viral envelope
Probab=24.90 E-value=1.3e+02 Score=21.93 Aligned_cols=34 Identities=15% Similarity=0.317 Sum_probs=27.4
Q ss_pred cccCcchhHHHHHHHHHHHHHHHHHhhhcccCCC
Q 011629 434 FLNPFTPKMWCVTGIFFLVVGVVVWILEHRLNDD 467 (481)
Q Consensus 434 ~l~pf~~~~W~~~~~~~~~~~~~~~~~~~~~~~~ 467 (481)
-+.-++...-+.|++.++++.+++.+|+.-++..
T Consensus 18 ~~~~l~pn~lMtILivLVIIiLlImlfqsSS~~~ 51 (85)
T PF10717_consen 18 NLNGLNPNTLMTILIVLVIIILLIMLFQSSSNGN 51 (85)
T ss_pred cccccChhHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 4667888888999999999999999997665543
No 494
>PRK03670 competence damage-inducible protein A; Provisional
Probab=24.77 E-value=3.3e+02 Score=24.94 Aligned_cols=49 Identities=18% Similarity=0.232 Sum_probs=30.9
Q ss_pred hHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeC
Q 011629 29 GIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTY 79 (481)
Q Consensus 29 ~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~ 79 (481)
....|.+.+...|+.+.....++. +.+.+...++.......++||+.+.
T Consensus 21 N~~~la~~L~~~G~~v~~~~iV~D--d~~~I~~~l~~a~~~~~DlVIttGG 69 (252)
T PRK03670 21 NSAFIAQKLTEKGYWVRRITTVGD--DVEEIKSVVLEILSRKPEVLVISGG 69 (252)
T ss_pred hHHHHHHHHHHCCCEEEEEEEcCC--CHHHHHHHHHHHhhCCCCEEEECCC
Confidence 456777788888888877666643 2335556665554444577776654
No 495
>COG3439 Uncharacterized conserved protein [Function unknown]
Probab=24.59 E-value=3.9e+02 Score=21.83 Aligned_cols=71 Identities=11% Similarity=0.132 Sum_probs=51.0
Q ss_pred ccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHH-h-ccCCceEEEEEeCcHHHHHHHHHHHHcCCccCCeEEE
Q 011629 26 GRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLT-V-SSMMSRILILHTYDIWGLEVLNAAKHLRMMESGYVWI 103 (481)
Q Consensus 26 g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~-i-~~s~~~vIvl~~~~~~~~~il~~a~~~g~~~~~~~wI 103 (481)
..+..+.+.+.++++|..|.... |..+.+++ . .+..+-.|+.+|++..+..+|.+-.+.|+..|=++.+
T Consensus 21 ~~E~i~~l~~~lk~~G~~V~~~i---------d~~e~l~~~g~~~~~p~~Il~~cnP~~g~~ll~~~p~~gl~lPcrv~V 91 (137)
T COG3439 21 FDETIERLEEKLKKNGFKVFTEI---------DHAEALKNAGVLDIPPYTILVFCNPKAGTPLLSKNPEFGLLLPCRVLV 91 (137)
T ss_pred HHHHHHHHHHHHHhCCCeEEEEe---------cHHHHHHhcCcCCCCCeEEEEEcCCcccchhhccChhhhccCCeEEEE
Confidence 34678999999999999876442 23444543 3 4456777888899999999998888888766655554
Q ss_pred Ee
Q 011629 104 VT 105 (481)
Q Consensus 104 ~~ 105 (481)
-.
T Consensus 92 ~e 93 (137)
T COG3439 92 YE 93 (137)
T ss_pred EE
Confidence 43
No 496
>COG1587 HemD Uroporphyrinogen-III synthase [Coenzyme metabolism]
Probab=24.58 E-value=4.4e+02 Score=23.91 Aligned_cols=86 Identities=12% Similarity=0.018 Sum_probs=52.2
Q ss_pred HhHHHHHHcC--CcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc
Q 011629 3 AIADIVDYFG--WRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD 80 (481)
Q Consensus 3 Ai~~ll~~fg--W~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~ 80 (481)
+++..+.... =++|-++.++. ....|.+.|...|+.|.....+.......+.......++....++| ++.++
T Consensus 111 ~l~~~l~~~~~~~~~vl~~~~~~-----~r~~l~~~L~~~G~~v~~~~~Y~~~~~~~~~~~~~~~~~~~~~d~v-~ftS~ 184 (248)
T COG1587 111 GLLEELPELLKGGKRVLILRGNG-----GREVLEEKLEERGAEVREVEVYRTEPPPLDEATLIELLKLGEVDAV-VFTSS 184 (248)
T ss_pred HHHHHhhhhccCCCeEEEEcCCC-----chHHHHHHHHhCCCEEEEEeeeeecCCCccHHHHHHHHHhCCCCEE-EEeCH
Confidence 4444444443 24666665443 2378899999999998887777654333333334455565555554 45666
Q ss_pred HHHHHHHHHHHHcC
Q 011629 81 IWGLEVLNAAKHLR 94 (481)
Q Consensus 81 ~~~~~il~~a~~~g 94 (481)
..+..++..+...+
T Consensus 185 ~~v~~~~~~~~~~~ 198 (248)
T COG1587 185 SAVRALLALAPESG 198 (248)
T ss_pred HHHHHHHHHccccc
Confidence 77888887765543
No 497
>TIGR01357 aroB 3-dehydroquinate synthase. This model represents 3-dehydroquinate synthase, the enzyme catalyzing the second of seven steps in the shikimate pathway of chorismate biosynthesis. Chorismate is the last common intermediate in the biosynthesis of all three aromatic amino acids.
Probab=24.55 E-value=3.2e+02 Score=26.28 Aligned_cols=83 Identities=6% Similarity=-0.153 Sum_probs=49.1
Q ss_pred HHHHHcCCcEEEEEEEeCCcccchHHHHHHHHHhcCCEEEEEEecC---CCCChhHHHHHHHHhccCCc---eEEEEEeC
Q 011629 6 DIVDYFGWRNVIALYVDDDHGRNGIAALGDKLAEKRCRLSHKVPLS---PKGSRNQIIDTLLTVSSMMS---RILILHTY 79 (481)
Q Consensus 6 ~ll~~fgW~~V~ii~~dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~---~~~~~~~~~~~l~~i~~s~~---~vIvl~~~ 79 (481)
+.++. .+++.+|++...+ ....+.+.+.+++.|+.+.... ++ .+.+.+.....++.+++.+. +.||..+.
T Consensus 15 ~~l~~--~~~~livtd~~~~-~~~~~~v~~~L~~~g~~~~~~~-~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~IIavGG 90 (344)
T TIGR01357 15 EELAE--PSKLVIITDETVA-DLYADKLLEALQALGYNVLKLT-VPDGEESKSLETVQRLYDQLLEAGLDRSSTIIALGG 90 (344)
T ss_pred HHhhc--CCeEEEEECCchH-HHHHHHHHHHHHhcCCceeEEE-eCCCCCCCCHHHHHHHHHHHHHcCCCCCCEEEEEcC
Confidence 44544 3888888844433 3467778888888888654322 32 23344567777777776543 77877665
Q ss_pred c--HHHHHHHHHHHH
Q 011629 80 D--IWGLEVLNAAKH 92 (481)
Q Consensus 80 ~--~~~~~il~~a~~ 92 (481)
. -++..++.....
T Consensus 91 Gsv~D~aK~iA~~~~ 105 (344)
T TIGR01357 91 GVVGDLAGFVAATYM 105 (344)
T ss_pred hHHHHHHHHHHHHHc
Confidence 3 344444443333
No 498
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=24.53 E-value=5.5e+02 Score=23.52 Aligned_cols=85 Identities=8% Similarity=-0.064 Sum_probs=46.3
Q ss_pred CCcEEEEEEEeCC--cccchHHHHHHHHHhcC----CEEEEEEecCCCCChhHHHHHHHHhccCCc-eE-EEEEeCcHHH
Q 011629 12 GWRNVIALYVDDD--HGRNGIAALGDKLAEKR----CRLSHKVPLSPKGSRNQIIDTLLTVSSMMS-RI-LILHTYDIWG 83 (481)
Q Consensus 12 gW~~V~ii~~dd~--~g~~~~~~l~~~l~~~g----i~v~~~~~~~~~~~~~~~~~~l~~i~~s~~-~v-Ivl~~~~~~~ 83 (481)
|=.+++++..+.. ......+.|++.+++++ +.+... ......+.+.....++.+-++.. +. .|++.+...+
T Consensus 124 g~~~i~~l~g~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~I~~~~d~~a 202 (288)
T cd01538 124 PPGNIELIAGSPTDNNAKLFFNGAMSVLKPLIDSGKITIVGE-VATPDWDPETAQKRMENALTANYNKVDGVLAANDGTA 202 (288)
T ss_pred CCceEEEEECCCCCchHHHHHHHHHHHHHhccccCCeeEEec-cccCCCCHHHHHHHHHHHHHhCCCCccEEEeCCcHHH
Confidence 7889999875432 23345677788888887 433221 11112222222334444433222 22 3444456677
Q ss_pred HHHHHHHHHcCCcc
Q 011629 84 LEVLNAAKHLRMME 97 (481)
Q Consensus 84 ~~il~~a~~~g~~~ 97 (481)
..++..+.+.|+..
T Consensus 203 ~g~~~al~~~g~~~ 216 (288)
T cd01538 203 GGAIAALKAAGLAG 216 (288)
T ss_pred HHHHHHHHHcCCCC
Confidence 78888888887654
No 499
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=24.50 E-value=80 Score=26.10 Aligned_cols=28 Identities=14% Similarity=0.401 Sum_probs=21.4
Q ss_pred cCcchhHHHHHHHHHHHHHHHHHhhhcc
Q 011629 436 NPFTPKMWCVTGIFFLVVGVVVWILEHR 463 (481)
Q Consensus 436 ~pf~~~~W~~~~~~~~~~~~~~~~~~~~ 463 (481)
.|.++.+++.|++++++++.++|.+-|.
T Consensus 115 ~~~~~~i~~~i~g~ll~i~~giy~~~r~ 142 (145)
T PF10661_consen 115 KPISPTILLSIGGILLAICGGIYVVLRK 142 (145)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5777888887877888878888877664
No 500
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=24.22 E-value=3.4e+02 Score=21.05 Aligned_cols=67 Identities=10% Similarity=-0.038 Sum_probs=43.9
Q ss_pred eCCcccchHHHHHHHHHhcCCEEEEEEecCCCCChhHHHHHHHHhccCCceEEEEEeCc----HHHHHHHHHHHHcC
Q 011629 22 DDDHGRNGIAALGDKLAEKRCRLSHKVPLSPKGSRNQIIDTLLTVSSMMSRILILHTYD----IWGLEVLNAAKHLR 94 (481)
Q Consensus 22 dd~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~~~~~~l~~i~~s~~~vIvl~~~~----~~~~~il~~a~~~g 94 (481)
.++.-.-+...+...++..|+.|.+.. ...+ ....++.+.+.++++|.+.+.. ..+..+..+..+.+
T Consensus 8 ~~e~H~lG~~~~~~~l~~~G~~V~~lg---~~~~---~~~l~~~~~~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~ 78 (119)
T cd02067 8 GGDGHDIGKNIVARALRDAGFEVIDLG---VDVP---PEEIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELKEAG 78 (119)
T ss_pred CCchhhHHHHHHHHHHHHCCCEEEECC---CCCC---HHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHHcC
Confidence 344445567788889999999985432 2223 3456667778889999988762 34556666666653
Done!