Query 003093
Match_columns 848
No_of_seqs 528 out of 3938
Neff 9.6
Searched_HMMs 46136
Date Thu Mar 28 16:53:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003093.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003093hhsearch_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-87 2.9E-92 692.5 42.4 719 2-770 88-846 (897)
2 KOG4440 NMDA selective glutama 100.0 6.9E-79 1.5E-83 630.6 30.8 689 3-769 94-857 (993)
3 KOG1053 Glutamate-gated NMDA-t 100.0 3.3E-74 7.2E-79 617.6 50.0 706 3-765 99-852 (1258)
4 KOG1052 Glutamate-gated kainat 100.0 1.6E-66 3.4E-71 611.9 52.4 596 120-769 4-624 (656)
5 cd06390 PBP1_iGluR_AMPA_GluR1 100.0 1.4E-42 3E-47 376.2 31.7 308 1-331 53-363 (364)
6 cd06392 PBP1_iGluR_delta_1 N-t 100.0 1.7E-41 3.6E-46 367.1 30.5 308 1-332 59-399 (400)
7 cd06393 PBP1_iGluR_Kainate_Glu 100.0 8.1E-40 1.8E-44 361.2 31.3 307 2-332 70-382 (384)
8 cd06387 PBP1_iGluR_AMPA_GluR3 100.0 1.4E-39 3E-44 351.4 31.7 309 1-331 60-371 (372)
9 cd06389 PBP1_iGluR_AMPA_GluR2 100.0 1.4E-39 3.1E-44 355.4 31.6 313 1-332 54-369 (370)
10 cd06388 PBP1_iGluR_AMPA_GluR4 100.0 2.8E-39 6E-44 352.1 31.8 308 1-332 60-370 (371)
11 cd06365 PBP1_Pheromone_recepto 100.0 2.2E-39 4.7E-44 365.1 32.0 305 3-327 102-452 (469)
12 cd06380 PBP1_iGluR_AMPA N-term 100.0 3.6E-39 7.8E-44 357.0 33.1 320 1-331 59-381 (382)
13 cd06375 PBP1_mGluR_groupII Lig 100.0 6.4E-39 1.4E-43 359.8 33.6 304 3-327 104-454 (458)
14 cd06374 PBP1_mGluR_groupI Liga 100.0 6.4E-39 1.4E-43 363.1 32.1 311 2-332 115-468 (472)
15 cd06367 PBP1_iGluR_NMDA N-term 100.0 3.9E-39 8.5E-44 354.0 29.4 281 2-327 61-351 (362)
16 cd06376 PBP1_mGluR_groupIII Li 100.0 1.3E-38 2.8E-43 360.1 33.6 306 3-327 102-452 (463)
17 cd06362 PBP1_mGluR Ligand bind 100.0 2.3E-38 4.9E-43 358.4 33.3 310 3-331 102-450 (452)
18 cd06361 PBP1_GPC6A_like Ligand 100.0 2.2E-38 4.7E-43 349.5 32.1 285 3-330 102-396 (403)
19 cd06391 PBP1_iGluR_delta_2 N-t 100.0 2.8E-38 6.1E-43 346.1 32.2 312 1-331 59-398 (400)
20 cd06379 PBP1_iGluR_NMDA_NR1 N- 100.0 2.9E-38 6.3E-43 348.7 31.3 276 2-328 78-364 (377)
21 cd06364 PBP1_CaSR Ligand-bindi 100.0 4.9E-38 1.1E-42 356.2 33.4 309 3-328 117-494 (510)
22 cd06386 PBP1_NPR_C_like Ligand 100.0 1.9E-37 4.1E-42 342.2 29.4 297 2-328 65-379 (387)
23 cd06385 PBP1_NPR_A Ligand-bind 100.0 2.6E-36 5.6E-41 336.5 29.0 300 3-329 73-392 (405)
24 cd06363 PBP1_Taste_receptor Li 100.0 8.2E-36 1.8E-40 332.3 31.3 286 2-328 105-396 (410)
25 cd06378 PBP1_iGluR_NMDA_NR2 N- 100.0 3.7E-36 8.1E-41 325.2 26.5 285 3-332 61-354 (362)
26 cd06384 PBP1_NPR_B Ligand-bind 100.0 6.4E-36 1.4E-40 332.2 29.1 300 3-329 72-393 (399)
27 cd06371 PBP1_sensory_GC_DEF_li 100.0 1.5E-35 3.3E-40 326.1 29.6 292 2-325 64-369 (382)
28 cd06373 PBP1_NPR_like Ligand b 100.0 7.3E-36 1.6E-40 332.1 27.4 302 2-329 71-390 (396)
29 KOG1056 Glutamate-gated metabo 100.0 3.6E-35 7.8E-40 329.5 28.9 328 4-370 125-494 (878)
30 cd06366 PBP1_GABAb_receptor Li 100.0 4.6E-35 1E-39 320.6 27.7 282 2-333 64-348 (350)
31 cd06372 PBP1_GC_G_like Ligand- 100.0 1E-34 2.2E-39 322.3 30.4 301 2-329 66-387 (391)
32 cd06370 PBP1_Speract_GC_like L 100.0 1.2E-34 2.7E-39 322.3 28.1 294 2-323 67-390 (404)
33 cd06352 PBP1_NPR_GC_like Ligan 100.0 6.1E-34 1.3E-38 316.6 29.5 304 2-330 66-384 (389)
34 PF01094 ANF_receptor: Recepto 100.0 7.8E-34 1.7E-38 311.3 23.2 292 3-315 50-348 (348)
35 cd06394 PBP1_iGluR_Kainate_KA1 100.0 1.1E-33 2.4E-38 300.8 20.4 265 2-332 63-332 (333)
36 cd06382 PBP1_iGluR_Kainate N-t 100.0 5.4E-33 1.2E-37 301.1 23.8 262 2-331 61-326 (327)
37 cd06381 PBP1_iGluR_delta_like 100.0 3.2E-30 6.9E-35 279.5 28.6 277 2-331 60-362 (363)
38 cd06368 PBP1_iGluR_non_NMDA_li 100.0 1.5E-30 3.3E-35 281.9 23.4 263 2-331 60-323 (324)
39 cd06342 PBP1_ABC_LIVBP_like Ty 100.0 1.7E-29 3.7E-34 275.1 25.8 267 3-314 65-334 (334)
40 cd06383 PBP1_iGluR_AMPA_Like N 100.0 2.8E-30 6.1E-35 280.5 17.9 280 2-305 63-351 (368)
41 PRK15404 leucine ABC transport 100.0 5.6E-29 1.2E-33 272.7 26.0 274 2-320 90-365 (369)
42 cd06338 PBP1_ABC_ligand_bindin 100.0 7.2E-29 1.6E-33 271.3 25.1 267 3-314 70-345 (345)
43 cd06350 PBP1_GPCR_family_C_lik 100.0 8E-29 1.7E-33 271.3 24.8 246 3-328 90-340 (348)
44 cd06345 PBP1_ABC_ligand_bindin 100.0 2.6E-28 5.6E-33 266.5 25.9 259 3-305 66-337 (344)
45 cd06346 PBP1_ABC_ligand_bindin 100.0 3.9E-28 8.4E-33 261.0 22.9 243 2-310 65-309 (312)
46 cd06348 PBP1_ABC_ligand_bindin 100.0 3.4E-27 7.4E-32 257.8 25.8 273 3-311 66-343 (344)
47 cd06340 PBP1_ABC_ligand_bindin 100.0 2.3E-27 5E-32 258.9 23.1 262 3-307 69-342 (347)
48 cd06344 PBP1_ABC_ligand_bindin 100.0 4.5E-27 9.8E-32 255.2 22.8 260 2-307 64-327 (332)
49 cd06360 PBP1_alkylbenzenes_lik 99.9 1.9E-26 4E-31 251.4 25.7 265 3-308 64-331 (336)
50 cd06351 PBP1_iGluR_N_LIVBP_lik 99.9 1.3E-26 2.8E-31 251.8 24.4 259 2-327 61-322 (328)
51 cd06355 PBP1_FmdD_like Peripla 99.9 4E-26 8.7E-31 248.9 27.1 277 2-322 65-345 (348)
52 cd06327 PBP1_SBP_like_1 Peripl 99.9 2.2E-26 4.7E-31 250.2 23.0 261 3-307 65-330 (334)
53 cd06377 PBP1_iGluR_NMDA_NR3 N- 99.9 1.5E-25 3.2E-30 238.1 28.6 275 2-331 79-374 (382)
54 cd06359 PBP1_Nba_like Type I p 99.9 5.8E-26 1.3E-30 246.7 25.5 265 3-312 64-331 (333)
55 cd06329 PBP1_SBP_like_3 Peripl 99.9 4.9E-26 1.1E-30 248.1 23.6 259 2-305 64-336 (342)
56 COG0683 LivK ABC-type branched 99.9 1.5E-25 3.3E-30 245.0 25.8 275 2-318 76-356 (366)
57 cd06347 PBP1_ABC_ligand_bindin 99.9 1.5E-25 3.2E-30 244.1 25.3 260 3-308 66-330 (334)
58 cd06336 PBP1_ABC_ligand_bindin 99.9 7.8E-26 1.7E-30 246.9 23.0 262 3-309 70-344 (347)
59 cd06349 PBP1_ABC_ligand_bindin 99.9 2.3E-25 4.9E-30 242.9 26.6 270 2-318 65-339 (340)
60 TIGR03669 urea_ABC_arch urea A 99.9 3E-25 6.6E-30 242.5 27.2 278 2-326 66-349 (374)
61 cd06343 PBP1_ABC_ligand_bindin 99.9 2.7E-25 5.8E-30 244.7 26.3 277 2-319 72-362 (362)
62 cd06331 PBP1_AmiC_like Type I 99.9 2.6E-25 5.6E-30 241.7 25.5 259 3-305 66-326 (333)
63 cd06328 PBP1_SBP_like_2 Peripl 99.9 2.5E-25 5.4E-30 241.3 25.2 261 3-309 67-331 (333)
64 cd06330 PBP1_Arsenic_SBP_like 99.9 5.7E-25 1.2E-29 240.5 23.7 259 3-301 66-333 (346)
65 TIGR03407 urea_ABC_UrtA urea A 99.9 1.7E-24 3.8E-29 237.0 27.3 269 2-315 66-338 (359)
66 cd06357 PBP1_AmiC Periplasmic 99.9 3.1E-24 6.7E-29 235.1 28.6 280 2-323 65-347 (360)
67 cd06332 PBP1_aromatic_compound 99.9 1.4E-24 3.1E-29 236.3 25.2 261 3-307 64-327 (333)
68 cd06337 PBP1_ABC_ligand_bindin 99.9 1.4E-24 3E-29 237.7 21.9 271 2-319 67-357 (357)
69 cd06358 PBP1_NHase Type I peri 99.9 7.1E-24 1.5E-28 230.3 24.6 258 3-307 66-327 (333)
70 cd06335 PBP1_ABC_ligand_bindin 99.9 1.2E-23 2.5E-28 229.8 26.0 260 3-301 66-335 (347)
71 PF13458 Peripla_BP_6: Peripla 99.9 5.2E-24 1.1E-28 232.9 20.8 270 2-315 67-339 (343)
72 cd06356 PBP1_Amide_Urea_BP_lik 99.9 2.3E-23 4.9E-28 226.1 24.4 258 2-303 65-325 (334)
73 cd06334 PBP1_ABC_ligand_bindin 99.9 5.1E-23 1.1E-27 224.0 24.5 272 3-301 66-345 (351)
74 cd06339 PBP1_YraM_LppC_lipopro 99.9 2.6E-23 5.7E-28 225.3 20.1 249 2-304 57-329 (336)
75 KOG1055 GABA-B ion channel rec 99.9 3.5E-24 7.6E-29 232.9 11.2 304 5-329 114-431 (865)
76 cd06269 PBP1_glutamate_recepto 99.9 2.7E-22 5.8E-27 214.5 21.3 165 3-170 70-235 (298)
77 TIGR03863 PQQ_ABC_bind ABC tra 99.9 2.3E-22 5.1E-27 216.4 18.7 251 2-314 57-315 (347)
78 PRK09495 glnH glutamine ABC tr 99.9 2E-21 4.4E-26 201.3 20.7 218 375-718 24-243 (247)
79 PRK10797 glutamate and asparta 99.9 4.1E-21 8.8E-26 203.5 20.1 223 375-719 39-272 (302)
80 cd06369 PBP1_GC_C_enterotoxin_ 99.9 1.4E-20 3.1E-25 194.3 21.1 275 4-329 81-366 (380)
81 cd06326 PBP1_STKc_like Type I 99.9 3E-20 6.6E-25 202.4 24.7 255 3-300 67-326 (336)
82 PRK11260 cystine transporter s 99.9 1.7E-20 3.8E-25 196.5 19.9 221 374-718 39-261 (266)
83 PF13433 Peripla_BP_5: Peripla 99.9 3.7E-20 8.1E-25 192.2 20.3 253 2-301 66-324 (363)
84 PF00497 SBP_bac_3: Bacterial 99.9 5.2E-21 1.1E-25 195.4 13.9 221 378-718 1-224 (225)
85 PRK15010 ABC transporter lysin 99.8 4.2E-20 9E-25 192.9 20.7 222 374-718 24-254 (260)
86 PRK15007 putative ABC transpor 99.8 4.7E-20 1E-24 190.8 20.5 217 375-718 20-242 (243)
87 TIGR01096 3A0103s03R lysine-ar 99.8 6.3E-20 1.4E-24 190.8 19.9 218 376-717 24-250 (250)
88 PRK11917 bifunctional adhesin/ 99.8 1.5E-19 3.3E-24 187.7 21.2 217 374-716 36-257 (259)
89 PRK15437 histidine ABC transpo 99.8 2.9E-19 6.2E-24 186.4 20.3 222 374-718 24-254 (259)
90 TIGR02995 ectoine_ehuB ectoine 99.8 2.3E-19 5E-24 188.7 18.7 222 374-717 31-260 (275)
91 cd06341 PBP1_ABC_ligand_bindin 99.8 5.1E-19 1.1E-23 193.1 21.7 248 3-294 66-318 (341)
92 cd04509 PBP1_ABC_transporter_G 99.8 2.5E-19 5.4E-24 191.5 18.4 218 4-236 67-290 (299)
93 cd06333 PBP1_ABC-type_HAAT_lik 99.8 1.1E-18 2.4E-23 187.8 21.4 219 3-238 65-293 (312)
94 PRK10859 membrane-bound lytic 99.8 5.2E-18 1.1E-22 191.4 18.6 221 374-718 41-266 (482)
95 cd06268 PBP1_ABC_transporter_L 99.8 1.2E-17 2.6E-22 178.3 19.8 220 2-238 64-287 (298)
96 PRK09959 hybrid sensory histid 99.8 8.6E-18 1.9E-22 213.6 19.1 216 375-718 301-520 (1197)
97 TIGR03870 ABC_MoxJ methanol ox 99.7 4.8E-17 1E-21 167.9 16.1 208 377-716 1-241 (246)
98 TIGR02285 conserved hypothetic 99.7 7E-17 1.5E-21 169.3 15.9 228 375-718 17-261 (268)
99 PF00060 Lig_chan: Ligand-gate 99.7 6.1E-19 1.3E-23 167.1 -2.2 107 496-602 1-115 (148)
100 cd00134 PBPb Bacterial peripla 99.7 1.2E-15 2.5E-20 154.3 19.2 214 378-717 1-218 (218)
101 COG0834 HisJ ABC-type amino ac 99.7 1E-15 2.3E-20 161.6 18.9 224 374-718 32-264 (275)
102 smart00062 PBPb Bacterial peri 99.7 1.7E-15 3.6E-20 153.1 18.7 215 377-717 1-219 (219)
103 PRK09959 hybrid sensory histid 99.7 7.2E-16 1.6E-20 196.1 17.8 220 374-719 54-278 (1197)
104 TIGR03871 ABC_peri_MoxJ_2 quin 99.6 8.9E-15 1.9E-19 150.1 18.0 210 378-717 2-228 (232)
105 smart00079 PBPe Eukaryotic hom 99.4 3.9E-12 8.4E-17 118.1 11.8 123 591-718 1-133 (134)
106 COG4623 Predicted soluble lyti 99.3 5.6E-11 1.2E-15 120.1 13.0 220 375-718 22-247 (473)
107 cd01391 Periplasmic_Binding_Pr 99.2 2.1E-10 4.5E-15 119.9 16.8 163 3-169 57-221 (269)
108 TIGR01098 3A0109s03R phosphate 98.9 1.5E-08 3.3E-13 105.4 14.0 198 376-703 32-254 (254)
109 PRK00489 hisG ATP phosphoribos 98.8 1.8E-08 4E-13 105.8 10.6 163 434-718 52-219 (287)
110 PF04348 LppC: LppC putative l 98.8 4E-08 8.7E-13 111.4 13.4 253 2-314 276-533 (536)
111 PF10613 Lig_chan-Glu_bd: Liga 98.8 1.1E-09 2.4E-14 84.1 0.3 50 395-444 13-65 (65)
112 TIGR03431 PhnD phosphonate ABC 98.1 4.1E-05 8.8E-10 81.2 14.5 116 590-711 125-257 (288)
113 cd01537 PBP1_Repressors_Sugar_ 98.0 7.5E-05 1.6E-09 77.7 12.5 153 3-163 54-211 (264)
114 cd01536 PBP1_ABC_sugar_binding 97.9 0.00042 9.1E-09 72.3 16.3 154 3-165 54-215 (267)
115 cd06267 PBP1_LacI_sugar_bindin 97.8 0.00016 3.5E-09 75.2 12.8 154 2-163 53-210 (264)
116 COG3107 LppC Putative lipoprot 97.8 0.00042 9.2E-09 74.5 13.9 254 2-322 317-603 (604)
117 cd06300 PBP1_ABC_sugar_binding 97.6 0.0016 3.5E-08 68.3 15.4 145 3-157 59-211 (272)
118 cd06282 PBP1_GntR_like_2 Ligan 97.4 0.0017 3.8E-08 67.7 13.1 148 3-160 54-206 (266)
119 cd06320 PBP1_allose_binding Pe 97.3 0.0056 1.2E-07 64.3 15.5 154 3-165 56-216 (275)
120 cd06323 PBP1_ribose_binding Pe 97.2 0.0079 1.7E-07 62.7 15.6 153 3-165 54-214 (268)
121 cd06319 PBP1_ABC_sugar_binding 97.2 0.0092 2E-07 62.6 15.7 156 3-165 54-219 (277)
122 PF12974 Phosphonate-bd: ABC t 97.1 0.0031 6.8E-08 64.9 10.2 121 590-716 95-230 (243)
123 PRK11553 alkanesulfonate trans 97.0 0.0033 7.2E-08 67.5 10.4 71 590-666 119-193 (314)
124 cd06325 PBP1_ABC_uncharacteriz 97.0 0.0069 1.5E-07 63.8 12.6 144 2-154 58-208 (281)
125 cd06273 PBP1_GntR_like_1 This 97.0 0.0078 1.7E-07 62.8 12.4 148 3-160 54-208 (268)
126 cd06301 PBP1_rhizopine_binding 96.9 0.026 5.7E-07 59.0 15.8 156 3-165 55-218 (272)
127 cd06317 PBP1_ABC_sugar_binding 96.9 0.023 4.9E-07 59.6 15.0 158 3-165 55-221 (275)
128 cd01545 PBP1_SalR Ligand-bindi 96.9 0.013 2.7E-07 61.3 12.9 157 2-165 54-215 (270)
129 cd06312 PBP1_ABC_sugar_binding 96.7 0.038 8.2E-07 57.8 15.3 155 3-164 56-216 (271)
130 cd06305 PBP1_methylthioribose_ 96.7 0.032 7E-07 58.3 14.2 156 3-165 54-217 (273)
131 cd06309 PBP1_YtfQ_like Peripla 96.5 0.058 1.3E-06 56.4 15.2 158 3-165 54-221 (273)
132 cd06298 PBP1_CcpA_like Ligand- 96.5 0.029 6.3E-07 58.4 12.4 153 3-165 54-213 (268)
133 cd06271 PBP1_AglR_RafR_like Li 96.3 0.05 1.1E-06 56.7 13.1 152 3-162 58-213 (268)
134 cd06289 PBP1_MalI_like Ligand- 96.3 0.033 7.2E-07 58.0 11.7 157 2-165 53-214 (268)
135 TIGR01729 taurine_ABC_bnd taur 96.3 0.019 4.1E-07 61.2 10.0 70 590-666 90-164 (300)
136 cd06313 PBP1_ABC_sugar_binding 96.3 0.14 3.1E-06 53.5 16.4 155 3-165 54-216 (272)
137 PRK10653 D-ribose transporter 96.3 0.12 2.6E-06 54.8 16.0 154 3-165 81-240 (295)
138 cd06310 PBP1_ABC_sugar_binding 96.2 0.2 4.3E-06 52.3 16.7 156 3-166 56-218 (273)
139 TIGR01481 ccpA catabolite cont 96.2 0.064 1.4E-06 57.9 13.3 146 3-158 114-264 (329)
140 cd06284 PBP1_LacI_like_6 Ligan 95.8 0.12 2.6E-06 53.7 12.9 146 3-157 54-203 (267)
141 cd06295 PBP1_CelR Ligand bindi 95.7 0.13 2.9E-06 53.8 13.0 153 3-165 63-222 (275)
142 PF13407 Peripla_BP_4: Peripla 95.7 0.084 1.8E-06 54.6 11.2 149 3-156 54-208 (257)
143 cd06288 PBP1_sucrose_transcrip 95.7 0.1 2.2E-06 54.4 11.8 153 3-164 55-211 (269)
144 COG3221 PhnD ABC-type phosphat 95.6 0.31 6.7E-06 51.1 14.5 110 590-705 134-260 (299)
145 cd01575 PBP1_GntR Ligand-bindi 95.5 0.18 3.9E-06 52.4 13.1 150 3-160 54-207 (268)
146 cd06311 PBP1_ABC_sugar_binding 95.5 0.41 8.9E-06 50.0 15.8 156 3-166 59-220 (274)
147 cd01540 PBP1_arabinose_binding 95.5 0.39 8.5E-06 50.6 15.7 163 3-165 53-229 (289)
148 TIGR03427 ABC_peri_uca ABC tra 95.5 0.046 9.9E-07 58.5 8.2 68 592-666 98-170 (328)
149 cd06278 PBP1_LacI_like_2 Ligan 95.4 0.18 3.8E-06 52.4 12.5 141 3-153 53-197 (266)
150 cd06303 PBP1_LuxPQ_Quorum_Sens 95.4 0.49 1.1E-05 49.6 15.9 158 3-165 59-224 (280)
151 cd06322 PBP1_ABC_sugar_binding 95.4 0.5 1.1E-05 49.1 15.8 143 3-154 54-203 (267)
152 PF13379 NMT1_2: NMT1-like fam 95.4 0.073 1.6E-06 55.0 9.3 74 590-668 104-189 (252)
153 cd01542 PBP1_TreR_like Ligand- 95.3 0.2 4.3E-06 51.8 12.4 149 3-164 54-207 (259)
154 cd06281 PBP1_LacI_like_5 Ligan 95.3 0.19 4.1E-06 52.4 12.1 154 3-165 54-212 (269)
155 PRK10703 DNA-binding transcrip 95.2 0.22 4.7E-06 54.1 12.7 154 3-163 114-272 (341)
156 cd06283 PBP1_RegR_EndR_KdgR_li 95.2 0.32 6.9E-06 50.5 13.5 152 3-163 54-211 (267)
157 cd06274 PBP1_FruR Ligand bindi 95.2 0.31 6.7E-06 50.6 13.3 153 3-164 54-212 (264)
158 PRK10014 DNA-binding transcrip 95.1 0.3 6.4E-06 53.1 13.6 147 3-157 119-270 (342)
159 cd06299 PBP1_LacI_like_13 Liga 95.1 0.3 6.5E-06 50.7 13.1 153 3-163 54-208 (265)
160 cd06324 PBP1_ABC_sugar_binding 95.1 0.46 1E-05 50.6 14.8 158 4-165 58-238 (305)
161 cd05466 PBP2_LTTR_substrate Th 95.1 0.94 2E-05 43.4 16.0 70 402-483 13-82 (197)
162 cd01539 PBP1_GGBP Periplasmic 95.0 0.88 1.9E-05 48.4 16.3 162 3-165 56-240 (303)
163 cd06294 PBP1_ycjW_transcriptio 95.0 0.33 7.2E-06 50.5 12.9 155 4-165 60-219 (270)
164 cd06275 PBP1_PurR Ligand-bindi 94.9 0.34 7.3E-06 50.4 12.8 135 22-163 73-211 (269)
165 cd06293 PBP1_LacI_like_11 Liga 94.9 0.53 1.1E-05 49.0 14.2 153 3-163 54-210 (269)
166 cd06285 PBP1_LacI_like_7 Ligan 94.9 0.34 7.5E-06 50.3 12.7 152 3-165 54-211 (265)
167 cd06308 PBP1_sensor_kinase_lik 94.8 0.88 1.9E-05 47.3 15.7 155 3-166 55-217 (270)
168 cd06270 PBP1_GalS_like Ligand 94.8 0.44 9.4E-06 49.6 13.4 148 3-158 54-205 (268)
169 COG1609 PurR Transcriptional r 94.8 0.45 9.8E-06 51.4 13.6 147 2-158 112-265 (333)
170 cd06307 PBP1_uncharacterized_s 94.8 1.3 2.8E-05 46.2 17.0 154 4-165 58-219 (275)
171 cd06272 PBP1_hexuronate_repres 94.8 0.37 8E-06 49.9 12.6 149 3-160 50-202 (261)
172 cd01574 PBP1_LacI Ligand-bindi 94.7 0.51 1.1E-05 48.9 13.6 144 3-158 55-202 (264)
173 cd08418 PBP2_TdcA The C-termin 94.7 1.9 4.2E-05 41.8 17.0 72 402-483 13-84 (201)
174 cd08459 PBP2_DntR_NahR_LinR_li 94.7 1.2 2.7E-05 43.3 15.6 70 402-483 13-82 (201)
175 TIGR02990 ectoine_eutA ectoine 94.7 0.57 1.2E-05 47.5 13.0 135 17-154 60-207 (239)
176 cd08468 PBP2_Pa0477 The C-term 94.6 1.5 3.2E-05 43.0 15.9 73 402-483 13-85 (202)
177 TIGR02122 TRAP_TAXI TRAP trans 94.5 0.13 2.8E-06 55.3 8.7 60 590-656 131-197 (320)
178 cd08442 PBP2_YofA_SoxR_like Th 94.5 2 4.3E-05 41.3 16.5 70 402-483 13-82 (193)
179 cd06292 PBP1_LacI_like_10 Liga 94.5 0.55 1.2E-05 48.9 13.2 136 22-163 77-214 (273)
180 cd01538 PBP1_ABC_xylose_bindin 94.5 1.1 2.4E-05 47.2 15.5 147 3-156 54-216 (288)
181 cd06316 PBP1_ABC_sugar_binding 94.5 1.5 3.2E-05 46.4 16.5 158 3-165 55-219 (294)
182 cd06306 PBP1_TorT-like TorT-li 94.4 1.1 2.4E-05 46.6 15.3 150 3-163 56-215 (268)
183 PRK11303 DNA-binding transcrip 94.4 0.93 2E-05 48.8 15.0 150 3-162 116-270 (328)
184 cd06321 PBP1_ABC_sugar_binding 94.4 1.4 3E-05 45.8 15.9 152 4-166 57-215 (271)
185 cd08421 PBP2_LTTR_like_1 The C 94.3 2.3 4.9E-05 41.2 16.5 70 402-483 13-82 (198)
186 PF03466 LysR_substrate: LysR 94.3 1.1 2.3E-05 44.0 14.4 183 402-704 19-205 (209)
187 cd06296 PBP1_CatR_like Ligand- 94.3 0.55 1.2E-05 48.8 12.6 155 3-165 54-214 (270)
188 PRK11151 DNA-binding transcrip 94.3 1.9 4.2E-05 45.8 17.0 83 376-483 91-173 (305)
189 COG1879 RbsB ABC-type sugar tr 94.2 1.4 3.1E-05 47.3 16.0 150 3-156 90-245 (322)
190 cd06354 PBP1_BmpA_PnrA_like Pe 94.2 0.9 1.9E-05 47.3 14.0 144 3-153 56-206 (265)
191 cd08440 PBP2_LTTR_like_4 TThe 94.2 3.1 6.7E-05 40.0 17.1 70 402-483 13-82 (197)
192 cd06314 PBP1_tmGBP Periplasmic 94.1 2.1 4.5E-05 44.5 16.6 152 3-165 54-213 (271)
193 cd06290 PBP1_LacI_like_9 Ligan 94.0 0.74 1.6E-05 47.7 12.8 125 27-158 76-204 (265)
194 cd01544 PBP1_GalR Ligand-bindi 94.0 0.78 1.7E-05 47.8 13.0 149 3-162 51-211 (270)
195 cd06279 PBP1_LacI_like_3 Ligan 94.0 0.8 1.7E-05 48.1 13.1 155 2-165 54-231 (283)
196 PRK10936 TMAO reductase system 94.0 1.4 3E-05 47.9 15.2 142 3-154 103-254 (343)
197 cd06318 PBP1_ABC_sugar_binding 93.9 2.6 5.7E-05 44.0 17.1 155 3-163 54-222 (282)
198 cd08420 PBP2_CysL_like C-termi 93.9 3.2 6.9E-05 40.0 16.7 70 402-483 13-82 (201)
199 COG2984 ABC-type uncharacteriz 93.9 1.5 3.3E-05 45.5 14.1 143 4-154 88-240 (322)
200 PRK10423 transcriptional repre 93.9 1 2.2E-05 48.5 14.0 130 27-163 135-268 (327)
201 cd06297 PBP1_LacI_like_12 Liga 93.7 0.73 1.6E-05 48.0 12.2 135 19-163 69-213 (269)
202 cd06287 PBP1_LacI_like_8 Ligan 93.6 1.7 3.7E-05 45.2 14.7 152 3-163 55-211 (269)
203 cd08463 PBP2_DntR_like_4 The C 93.5 4.8 0.00011 39.4 17.2 71 402-483 13-83 (203)
204 cd08438 PBP2_CidR The C-termin 93.5 4.2 9E-05 39.1 16.6 70 402-483 13-82 (197)
205 PF00532 Peripla_BP_1: Peripla 93.5 0.42 9.2E-06 50.2 9.8 154 3-163 55-214 (279)
206 cd01543 PBP1_XylR Ligand-bindi 93.5 1.3 2.8E-05 46.0 13.5 153 3-165 49-207 (265)
207 cd08433 PBP2_Nac The C-teminal 93.4 4.9 0.00011 38.8 17.0 70 402-483 13-82 (198)
208 cd06291 PBP1_Qymf_like Ligand 93.4 1.1 2.5E-05 46.3 13.0 127 23-158 70-201 (265)
209 PRK12684 transcriptional regul 93.4 3 6.5E-05 44.6 16.5 116 593-718 184-305 (313)
210 cd01541 PBP1_AraR Ligand-bindi 93.4 0.96 2.1E-05 47.1 12.4 154 3-163 54-216 (273)
211 PRK10727 DNA-binding transcrip 93.3 0.92 2E-05 49.2 12.6 111 52-163 156-270 (343)
212 cd06302 PBP1_LsrB_Quorum_Sensi 93.3 4.2 9E-05 43.1 17.3 154 3-164 55-218 (298)
213 cd06277 PBP1_LacI_like_1 Ligan 93.2 1.1 2.5E-05 46.4 12.6 146 3-158 57-205 (268)
214 cd08466 PBP2_LeuO The C-termin 93.2 3.4 7.3E-05 40.1 15.5 70 402-483 13-82 (200)
215 TIGR02417 fruct_sucro_rep D-fr 93.2 1.3 2.8E-05 47.7 13.3 149 3-162 115-269 (327)
216 PRK09701 D-allose transporter 93.0 4.5 9.7E-05 43.2 17.1 158 3-165 81-250 (311)
217 CHL00180 rbcR LysR transcripti 93.0 4.6 9.9E-05 43.0 17.2 86 376-483 95-180 (305)
218 PRK15408 autoinducer 2-binding 92.9 3 6.5E-05 45.1 15.6 147 2-154 78-233 (336)
219 TIGR01728 SsuA_fam ABC transpo 92.9 0.81 1.8E-05 48.1 11.0 71 590-666 91-165 (288)
220 cd08435 PBP2_GbpR The C-termin 92.8 7.7 0.00017 37.4 17.4 72 402-483 13-84 (201)
221 cd06286 PBP1_CcpB_like Ligand- 92.7 1.5 3.3E-05 45.2 12.7 145 3-158 54-203 (260)
222 PF09084 NMT1: NMT1/THI5 like; 92.7 0.33 7.2E-06 48.7 7.4 59 590-654 83-145 (216)
223 PRK09526 lacI lac repressor; R 92.7 2.1 4.6E-05 46.3 14.2 147 3-162 119-272 (342)
224 PRK11242 DNA-binding transcrip 92.5 5.1 0.00011 42.3 16.6 83 376-483 91-173 (296)
225 cd08417 PBP2_Nitroaromatics_li 92.4 4.4 9.5E-05 39.2 15.0 70 402-483 13-82 (200)
226 cd08412 PBP2_PAO1_like The C-t 92.3 5.3 0.00011 38.5 15.5 71 401-483 12-82 (198)
227 cd08411 PBP2_OxyR The C-termin 92.3 4.6 9.9E-05 39.1 15.0 70 402-483 14-83 (200)
228 PRK09492 treR trehalose repres 92.2 2 4.4E-05 45.8 13.2 137 3-154 117-256 (315)
229 PRK09791 putative DNA-binding 92.1 5 0.00011 42.6 15.9 86 375-483 94-179 (302)
230 PRK10401 DNA-binding transcrip 92.1 2.4 5.3E-05 46.0 13.8 111 52-163 156-270 (346)
231 cd08434 PBP2_GltC_like The sub 92.0 5.5 0.00012 38.2 15.1 70 402-483 13-82 (195)
232 PF07885 Ion_trans_2: Ion chan 92.0 0.18 3.8E-06 41.4 3.5 55 529-583 21-77 (79)
233 cd06304 PBP1_BmpA_like Peripla 91.8 4 8.8E-05 42.1 14.5 144 3-153 55-202 (260)
234 cd08415 PBP2_LysR_opines_like 91.7 8.5 0.00018 36.9 16.1 71 401-483 12-82 (196)
235 PRK12682 transcriptional regul 91.7 6 0.00013 42.1 16.1 84 376-483 93-176 (309)
236 PRK14987 gluconate operon tran 91.5 2.5 5.4E-05 45.5 13.0 152 3-163 118-272 (331)
237 cd08426 PBP2_LTTR_like_5 The C 91.4 12 0.00026 36.0 16.9 70 402-483 13-82 (199)
238 PRK15395 methyl-galactoside AB 91.3 8 0.00017 41.6 16.6 151 3-154 80-249 (330)
239 cd08462 PBP2_NodD The C-termin 91.3 7.1 0.00015 37.9 15.0 68 403-483 14-81 (200)
240 cd08419 PBP2_CbbR_RubisCO_like 91.3 13 0.00029 35.5 17.0 70 402-483 12-81 (197)
241 cd08444 PBP2_Cbl The C-termina 91.2 13 0.00028 36.0 16.9 71 402-483 13-83 (198)
242 TIGR02424 TF_pcaQ pca operon t 91.2 6.8 0.00015 41.4 15.8 86 375-483 92-177 (300)
243 COG3473 Maleate cis-trans isom 91.2 7.8 0.00017 37.4 13.7 135 16-154 55-205 (238)
244 cd08464 PBP2_DntR_like_2 The C 91.1 8.1 0.00018 37.3 15.3 70 402-483 13-82 (200)
245 PRK12679 cbl transcriptional r 90.9 12 0.00025 40.1 17.4 207 376-718 93-306 (316)
246 TIGR02634 xylF D-xylose ABC tr 90.8 7 0.00015 41.5 15.4 146 3-155 53-209 (302)
247 TIGR02955 TMAO_TorT TMAO reduc 90.8 6 0.00013 41.8 14.9 141 3-154 56-207 (295)
248 cd08413 PBP2_CysB_like The C-t 90.7 8.3 0.00018 37.4 14.9 71 402-483 13-83 (198)
249 PF13377 Peripla_BP_3: Peripla 90.7 0.65 1.4E-05 43.8 6.6 99 64-164 1-102 (160)
250 cd06280 PBP1_LacI_like_4 Ligan 90.6 3.4 7.3E-05 42.7 12.6 129 25-163 74-205 (263)
251 PRK12681 cysB transcriptional 90.6 6.9 0.00015 42.0 15.2 85 375-483 92-176 (324)
252 cd08461 PBP2_DntR_like_3 The C 90.6 11 0.00024 36.3 15.7 70 402-483 13-82 (198)
253 cd08460 PBP2_DntR_like_1 The C 90.6 4.4 9.5E-05 39.4 12.8 70 401-483 12-81 (200)
254 cd08436 PBP2_LTTR_like_3 The C 90.3 17 0.00036 34.7 16.6 71 402-483 13-83 (194)
255 cd08465 PBP2_ToxR The C-termin 90.3 7.9 0.00017 37.7 14.4 70 402-483 13-82 (200)
256 PRK10837 putative DNA-binding 90.3 18 0.00039 37.9 17.9 83 376-483 89-171 (290)
257 PRK12683 transcriptional regul 90.3 11 0.00024 40.1 16.3 105 593-706 184-294 (309)
258 cd08437 PBP2_MleR The substrat 90.1 12 0.00026 36.1 15.5 72 402-483 13-84 (198)
259 PRK11041 DNA-binding transcrip 89.8 5.3 0.00011 42.4 13.5 112 52-164 132-247 (309)
260 TIGR02637 RhaS rhamnose ABC tr 89.7 12 0.00025 39.6 16.0 145 3-155 55-210 (302)
261 PRK10339 DNA-binding transcrip 89.4 4.9 0.00011 43.1 13.0 146 4-160 114-264 (327)
262 TIGR02405 trehalos_R_Ecol treh 89.2 6.3 0.00014 42.0 13.6 118 25-154 133-253 (311)
263 cd08441 PBP2_MetR The C-termin 89.0 18 0.00038 34.8 15.7 69 403-483 14-82 (198)
264 cd08449 PBP2_XapR The C-termin 89.0 22 0.00047 34.0 16.3 72 402-483 13-84 (197)
265 cd08467 PBP2_SyrM The C-termin 88.9 21 0.00045 34.5 16.2 70 402-483 13-82 (200)
266 cd08458 PBP2_NocR The C-termin 88.9 21 0.00046 34.3 16.2 70 402-483 13-82 (196)
267 TIGR00787 dctP tripartite ATP- 88.8 2.6 5.7E-05 43.6 9.8 103 590-704 126-231 (257)
268 PRK11480 tauA taurine transpor 88.8 1.2 2.7E-05 47.8 7.6 68 590-664 112-184 (320)
269 cd08425 PBP2_CynR The C-termin 88.6 19 0.00042 34.4 15.7 70 402-483 14-83 (197)
270 PRK11482 putative DNA-binding 88.6 15 0.00032 39.3 15.9 82 375-483 116-197 (317)
271 cd08469 PBP2_PnbR The C-termin 88.6 14 0.0003 36.5 15.0 70 402-483 13-82 (221)
272 cd08429 PBP2_NhaR The C-termin 88.5 26 0.00055 34.3 16.5 72 402-482 13-84 (204)
273 cd08427 PBP2_LTTR_like_2 The C 88.3 18 0.00038 34.6 15.1 72 402-483 13-84 (195)
274 PRK09860 putative alcohol dehy 88.3 2 4.4E-05 47.2 9.0 87 61-147 20-108 (383)
275 PRK10355 xylF D-xylose transpo 88.2 13 0.00028 40.1 15.1 146 3-155 80-236 (330)
276 PF03808 Glyco_tran_WecB: Glyc 88.2 7.6 0.00016 37.3 11.8 102 57-168 34-137 (172)
277 cd08448 PBP2_LTTR_aromatics_li 88.1 25 0.00053 33.6 16.1 70 402-483 13-82 (197)
278 cd08414 PBP2_LTTR_aromatics_li 87.7 26 0.00056 33.4 16.3 70 402-483 13-82 (197)
279 cd08443 PBP2_CysB The C-termin 87.7 26 0.00056 33.9 16.0 72 401-483 12-83 (198)
280 cd08423 PBP2_LTTR_like_6 The C 87.3 20 0.00044 34.2 15.0 73 402-483 13-87 (200)
281 COG1454 EutG Alcohol dehydroge 86.9 3.6 7.8E-05 44.6 9.5 92 60-151 17-110 (377)
282 PRK11233 nitrogen assimilation 86.6 11 0.00024 40.0 13.3 69 402-482 105-173 (305)
283 PRK10341 DNA-binding transcrip 86.4 19 0.00041 38.3 15.1 71 403-483 111-181 (312)
284 PRK15454 ethanol dehydrogenase 86.4 2.7 5.9E-05 46.4 8.6 80 60-139 37-116 (395)
285 cd08457 PBP2_OccR The C-termin 86.3 32 0.0007 32.9 17.1 70 402-483 13-82 (196)
286 cd08190 HOT Hydroxyacid-oxoaci 86.2 3.3 7.2E-05 46.1 9.3 80 60-139 11-90 (414)
287 TIGR00363 lipoprotein, YaeC fa 86.2 21 0.00045 36.8 14.3 121 590-716 106-250 (258)
288 KOG3857 Alcohol dehydrogenase, 86.1 4.9 0.00011 41.7 9.4 96 45-140 39-138 (465)
289 cd08456 PBP2_LysR The C-termin 85.9 30 0.00064 33.0 15.2 70 402-483 13-82 (196)
290 PRK12680 transcriptional regul 85.8 28 0.0006 37.4 16.0 84 376-483 93-176 (327)
291 cd08192 Fe-ADH7 Iron-containin 85.5 3.8 8.1E-05 45.0 9.2 88 61-148 13-102 (370)
292 cd08486 PBP2_CbnR The C-termin 85.2 36 0.00077 32.9 15.4 70 402-483 14-83 (198)
293 PRK10624 L-1,2-propanediol oxi 84.6 4 8.7E-05 45.0 8.9 80 60-139 18-97 (382)
294 TIGR01256 modA molybdenum ABC 84.2 12 0.00026 37.4 11.6 70 629-703 133-203 (216)
295 cd08551 Fe-ADH iron-containing 84.2 4.9 0.00011 44.1 9.4 87 61-147 12-100 (370)
296 cd08189 Fe-ADH5 Iron-containin 84.1 4.7 0.0001 44.3 9.2 89 60-148 14-104 (374)
297 cd08430 PBP2_IlvY The C-termin 84.0 40 0.00087 32.1 16.9 71 402-483 13-83 (199)
298 PF03480 SBP_bac_7: Bacterial 84.0 2.2 4.8E-05 44.9 6.3 215 401-703 13-230 (286)
299 cd08193 HVD 5-hydroxyvalerate 84.0 4.5 9.7E-05 44.5 9.0 87 61-147 15-103 (376)
300 PF13407 Peripla_BP_4: Peripla 83.8 3.2 6.9E-05 42.7 7.4 78 75-154 1-81 (257)
301 PRK09508 leuO leucine transcri 83.3 17 0.00038 38.7 13.1 84 375-483 111-194 (314)
302 PRK11074 putative DNA-binding 83.3 33 0.00071 36.2 15.1 85 376-483 92-176 (300)
303 cd08194 Fe-ADH6 Iron-containin 83.1 5.4 0.00012 43.8 9.2 79 61-139 12-90 (375)
304 cd08445 PBP2_BenM_CatM_CatR Th 82.4 49 0.0011 31.9 16.2 70 402-483 14-83 (203)
305 PF12727 PBP_like: PBP superfa 82.0 25 0.00054 34.4 12.3 102 590-701 81-190 (193)
306 PRK10094 DNA-binding transcrip 81.9 53 0.0011 34.8 16.1 70 404-483 108-177 (308)
307 TIGR02638 lactal_redase lactal 81.8 6 0.00013 43.5 8.9 80 60-139 17-96 (379)
308 PRK11063 metQ DL-methionine tr 81.7 21 0.00046 37.1 12.4 120 590-715 119-262 (271)
309 cd08185 Fe-ADH1 Iron-containin 81.4 7.4 0.00016 42.9 9.4 85 61-146 15-102 (380)
310 cd06315 PBP1_ABC_sugar_binding 80.7 44 0.00096 34.7 14.8 133 22-158 75-217 (280)
311 PF00465 Fe-ADH: Iron-containi 80.5 4 8.7E-05 44.7 6.9 89 61-151 12-102 (366)
312 cd08188 Fe-ADH4 Iron-containin 80.4 7.9 0.00017 42.6 9.2 80 60-139 16-95 (377)
313 PRK11062 nhaR transcriptional 79.9 43 0.00093 35.3 14.4 86 376-483 93-178 (296)
314 PF04392 ABC_sub_bind: ABC tra 79.9 22 0.00048 37.5 12.2 127 4-139 59-194 (294)
315 PF13531 SBP_bac_11: Bacterial 79.8 11 0.00024 38.0 9.5 194 401-715 10-226 (230)
316 KOG1419 Voltage-gated K+ chann 79.8 2.8 6.1E-05 46.2 5.1 89 497-585 234-324 (654)
317 cd06533 Glyco_transf_WecG_TagA 79.4 26 0.00056 33.5 11.3 101 56-166 31-133 (171)
318 PRK15421 DNA-binding transcrip 79.4 54 0.0012 35.0 15.1 69 403-483 103-171 (317)
319 TIGR03339 phn_lysR aminoethylp 79.3 81 0.0018 32.5 16.3 69 403-483 98-166 (279)
320 cd08181 PPD-like 1,3-propanedi 78.9 9.2 0.0002 41.7 9.1 78 61-139 15-93 (357)
321 cd08451 PBP2_BudR The C-termin 78.6 62 0.0013 30.8 16.4 70 403-483 15-84 (199)
322 cd06353 PBP1_BmpA_Med_like Per 78.6 19 0.00041 37.2 10.9 144 2-154 55-201 (258)
323 PF13685 Fe-ADH_2: Iron-contai 78.2 9.4 0.0002 39.0 8.2 103 62-168 9-111 (250)
324 PRK11013 DNA-binding transcrip 77.9 78 0.0017 33.5 15.8 70 402-483 107-176 (309)
325 cd08176 LPO Lactadehyde:propan 77.6 8.7 0.00019 42.3 8.4 79 61-139 17-95 (377)
326 cd08170 GlyDH Glycerol dehydro 77.3 8.1 0.00018 42.0 8.1 76 61-139 12-87 (351)
327 cd08191 HHD 6-hydroxyhexanoate 77.3 11 0.00025 41.5 9.3 86 61-147 12-99 (386)
328 COG1638 DctP TRAP-type C4-dica 76.9 9.9 0.00021 40.8 8.3 65 405-472 47-112 (332)
329 cd08453 PBP2_IlvR The C-termin 76.8 71 0.0015 30.5 16.4 73 402-483 13-85 (200)
330 PRK03635 chromosome replicatio 76.5 60 0.0013 34.0 14.4 82 376-483 90-171 (294)
331 cd06276 PBP1_FucR_like Ligand- 76.2 22 0.00048 36.3 10.6 122 20-160 68-192 (247)
332 cd08182 HEPD Hydroxyethylphosp 75.5 13 0.00028 40.8 9.0 85 61-148 12-98 (367)
333 COG0715 TauA ABC-type nitrate/ 75.2 13 0.00029 40.0 9.1 72 590-668 126-203 (335)
334 PRK11716 DNA-binding transcrip 74.8 82 0.0018 32.2 14.7 83 376-482 67-149 (269)
335 cd08187 BDH Butanol dehydrogen 74.4 12 0.00027 41.2 8.5 78 61-139 18-96 (382)
336 cd08446 PBP2_Chlorocatechol Th 74.0 83 0.0018 29.9 16.0 70 402-483 14-83 (198)
337 cd08186 Fe-ADH8 Iron-containin 73.6 15 0.00033 40.5 9.0 87 61-147 12-104 (383)
338 TIGR00696 wecB_tagA_cpsF bacte 73.5 43 0.00093 32.2 10.9 99 57-166 34-134 (177)
339 cd01537 PBP1_Repressors_Sugar_ 73.3 14 0.00031 37.6 8.5 78 74-154 1-80 (264)
340 cd08171 GlyDH-like2 Glycerol d 72.9 14 0.00031 40.0 8.5 77 61-139 12-88 (345)
341 cd06305 PBP1_methylthioribose_ 72.8 15 0.00033 37.9 8.6 77 75-154 2-81 (273)
342 cd08450 PBP2_HcaR The C-termin 72.6 88 0.0019 29.6 15.4 70 402-483 13-82 (196)
343 cd06353 PBP1_BmpA_Med_like Per 72.5 24 0.00051 36.5 9.7 85 74-166 1-89 (258)
344 cd06267 PBP1_LacI_sugar_bindin 72.5 14 0.00031 37.6 8.2 76 75-154 2-79 (264)
345 cd07766 DHQ_Fe-ADH Dehydroquin 72.5 17 0.00037 39.1 9.0 86 61-148 12-99 (332)
346 cd08431 PBP2_HupR The C-termin 72.4 90 0.0019 29.6 14.0 71 402-483 13-83 (195)
347 PLN02245 ATP phosphoribosyl tr 72.4 26 0.00056 38.1 9.9 104 591-703 178-294 (403)
348 cd06301 PBP1_rhizopine_binding 72.4 14 0.0003 38.2 8.1 78 74-154 1-82 (272)
349 cd08428 PBP2_IciA_ArgP The C-t 72.2 91 0.002 29.6 15.1 66 404-482 15-80 (195)
350 cd08416 PBP2_MdcR The C-termin 72.1 92 0.002 29.6 16.1 72 402-483 13-84 (199)
351 PRK03692 putative UDP-N-acetyl 71.4 42 0.00092 34.1 10.8 90 56-152 90-180 (243)
352 PF03401 TctC: Tripartite tric 71.4 63 0.0014 33.7 12.6 121 590-715 88-241 (274)
353 PRK09906 DNA-binding transcrip 70.7 1.3E+02 0.0028 31.5 15.2 70 402-483 103-172 (296)
354 PF00625 Guanylate_kin: Guanyl 70.1 69 0.0015 30.9 11.9 131 3-153 2-136 (183)
355 cd06306 PBP1_TorT-like TorT-li 68.9 18 0.00039 37.4 8.1 80 74-154 1-82 (268)
356 PRK09423 gldA glycerol dehydro 68.8 18 0.0004 39.5 8.3 76 61-139 19-94 (366)
357 cd08183 Fe-ADH2 Iron-containin 68.5 22 0.00047 39.1 8.8 82 61-147 12-95 (374)
358 PRK13583 hisG ATP phosphoribos 68.3 54 0.0012 32.8 10.5 48 435-482 54-107 (228)
359 cd06282 PBP1_GntR_like_2 Ligan 67.6 28 0.0006 35.7 9.2 77 75-154 2-80 (266)
360 TIGR00035 asp_race aspartate r 67.3 26 0.00057 35.4 8.5 41 61-104 106-146 (229)
361 PRK09861 cytoplasmic membrane 67.1 74 0.0016 33.1 11.9 121 589-716 119-264 (272)
362 cd06289 PBP1_MalI_like Ligand- 66.6 29 0.00063 35.6 9.1 77 75-154 2-80 (268)
363 cd06303 PBP1_LuxPQ_Quorum_Sens 66.5 20 0.00044 37.3 7.9 81 74-154 1-85 (280)
364 PRK15408 autoinducer 2-binding 66.1 22 0.00048 38.3 8.2 82 71-154 22-106 (336)
365 PRK03601 transcriptional regul 65.3 1.3E+02 0.0027 31.3 13.6 84 375-483 88-171 (275)
366 cd08485 PBP2_ClcR The C-termin 65.3 1.3E+02 0.0028 28.7 15.8 70 402-483 14-83 (198)
367 PRK09986 DNA-binding transcrip 65.2 1.8E+02 0.0039 30.3 16.6 85 376-483 97-181 (294)
368 PF15179 Myc_target_1: Myc tar 65.1 20 0.00042 33.8 6.2 38 731-768 13-51 (197)
369 cd08452 PBP2_AlsR The C-termin 65.0 1.3E+02 0.0028 28.6 16.1 70 402-483 13-82 (197)
370 cd06277 PBP1_LacI_like_1 Ligan 64.7 38 0.00083 34.8 9.5 75 75-154 2-81 (268)
371 cd06299 PBP1_LacI_like_13 Liga 64.7 52 0.0011 33.7 10.5 76 75-154 2-79 (265)
372 cd08447 PBP2_LTTR_aromatics_li 64.4 1.3E+02 0.0028 28.4 15.8 70 402-483 13-82 (198)
373 cd08550 GlyDH-like Glycerol_de 64.3 26 0.00056 38.1 8.3 76 61-139 12-87 (349)
374 cd08432 PBP2_GcdR_TrpI_HvrB_Am 64.1 65 0.0014 30.5 10.5 65 403-482 14-78 (194)
375 PRK10537 voltage-gated potassi 63.8 5.9 0.00013 43.6 3.1 56 528-583 164-221 (393)
376 cd06312 PBP1_ABC_sugar_binding 63.7 24 0.00053 36.4 7.8 79 74-154 1-83 (271)
377 cd06310 PBP1_ABC_sugar_binding 63.6 27 0.00059 36.0 8.2 80 74-154 1-83 (273)
378 cd01538 PBP1_ABC_xylose_bindin 63.5 35 0.00076 35.7 9.0 77 75-154 2-81 (288)
379 PRK11119 proX glycine betaine 62.9 25 0.00054 37.8 7.7 62 372-455 25-87 (331)
380 PF06506 PrpR_N: Propionate ca 62.9 1.2E+02 0.0025 29.1 11.7 108 31-155 38-145 (176)
381 PF02608 Bmp: Basic membrane p 62.8 96 0.0021 32.9 12.2 147 3-154 60-212 (306)
382 cd06167 LabA_like LabA_like pr 62.5 1.3E+02 0.0028 27.7 12.0 92 62-154 28-124 (149)
383 cd01536 PBP1_ABC_sugar_binding 62.3 34 0.00074 34.9 8.6 78 74-154 1-81 (267)
384 cd06322 PBP1_ABC_sugar_binding 61.6 34 0.00074 35.1 8.4 77 75-154 2-81 (267)
385 cd08178 AAD_C C-terminal alcoh 61.6 30 0.00066 38.3 8.4 78 70-147 19-98 (398)
386 PRK13348 chromosome replicatio 61.6 2.1E+02 0.0045 29.8 14.6 47 433-483 125-171 (294)
387 TIGR03298 argP transcriptional 61.4 2.1E+02 0.0045 29.8 15.8 64 406-482 107-170 (292)
388 PF07302 AroM: AroM protein; 61.2 1.2E+02 0.0027 30.1 11.4 113 25-149 84-200 (221)
389 cd01391 Periplasmic_Binding_Pr 60.9 31 0.00066 34.9 7.9 78 74-154 1-83 (269)
390 PF14503 YhfZ_C: YhfZ C-termin 60.8 21 0.00046 35.7 6.1 78 397-483 23-107 (232)
391 cd02071 MM_CoA_mut_B12_BD meth 60.6 74 0.0016 28.4 9.2 71 78-154 5-79 (122)
392 COG1910 Periplasmic molybdate- 60.6 1.8E+02 0.0039 28.8 12.7 107 590-708 87-202 (223)
393 cd06281 PBP1_LacI_like_5 Ligan 60.5 49 0.0011 34.0 9.4 77 75-154 2-80 (269)
394 cd01545 PBP1_SalR Ligand-bindi 60.4 45 0.00098 34.2 9.1 78 75-154 2-81 (270)
395 COG0725 ModA ABC-type molybdat 60.3 1.2E+02 0.0026 31.3 11.7 69 406-483 46-120 (258)
396 cd08422 PBP2_CrgA_like The C-t 59.3 51 0.0011 31.2 8.8 65 628-698 126-192 (197)
397 cd06318 PBP1_ABC_sugar_binding 59.3 39 0.00084 35.0 8.5 77 75-154 2-81 (282)
398 PF04273 DUF442: Putative phos 58.5 1.3E+02 0.0028 26.4 10.3 81 67-147 23-104 (110)
399 PLN03192 Voltage-dependent pot 58.4 6.2 0.00013 48.5 2.4 53 533-585 251-305 (823)
400 cd08175 G1PDH Glycerol-1-phosp 57.9 38 0.00083 36.7 8.2 84 61-146 12-99 (348)
401 cd06273 PBP1_GntR_like_1 This 57.7 58 0.0013 33.3 9.4 76 75-154 2-79 (268)
402 KOG3713 Voltage-gated K+ chann 57.3 12 0.00025 41.3 3.9 61 509-573 358-420 (477)
403 PF02608 Bmp: Basic membrane p 57.0 43 0.00094 35.5 8.3 87 73-166 2-93 (306)
404 PRK11303 DNA-binding transcrip 56.9 73 0.0016 33.9 10.3 80 72-154 61-142 (328)
405 PRK11139 DNA-binding transcrip 56.7 1.7E+02 0.0037 30.6 12.9 101 592-700 180-285 (297)
406 cd06270 PBP1_GalS_like Ligand 56.5 64 0.0014 33.1 9.5 76 75-154 2-79 (268)
407 cd06316 PBP1_ABC_sugar_binding 56.5 36 0.00078 35.7 7.7 79 74-154 1-82 (294)
408 PRK10936 TMAO reductase system 56.4 49 0.0011 35.8 8.8 81 72-154 46-129 (343)
409 cd06295 PBP1_CelR Ligand bindi 56.1 69 0.0015 33.0 9.7 77 72-154 3-88 (275)
410 cd01540 PBP1_arabinose_binding 55.5 41 0.00088 35.1 7.9 76 75-154 2-80 (289)
411 TIGR00249 sixA phosphohistidin 55.2 74 0.0016 29.7 8.6 98 52-150 23-120 (152)
412 cd08197 DOIS 2-deoxy-scyllo-in 55.2 1.1E+02 0.0023 33.4 10.9 101 61-165 12-119 (355)
413 PRK10014 DNA-binding transcrip 55.1 76 0.0017 34.0 10.1 79 73-154 65-145 (342)
414 cd06296 PBP1_CatR_like Ligand- 54.9 62 0.0013 33.2 9.1 76 75-154 2-79 (270)
415 cd08179 NADPH_BDH NADPH-depend 54.8 27 0.00058 38.4 6.4 77 70-146 21-100 (375)
416 cd06302 PBP1_LsrB_Quorum_Sensi 54.8 42 0.00091 35.3 7.8 78 75-154 2-82 (298)
417 PF02310 B12-binding: B12 bind 53.9 1.3E+02 0.0029 26.4 9.8 46 86-137 14-59 (121)
418 cd06274 PBP1_FruR Ligand bindi 53.8 72 0.0016 32.6 9.3 76 75-154 2-79 (264)
419 PF06084 Cytomega_TRL10: Cytom 53.7 23 0.00049 30.2 4.2 79 738-820 52-130 (150)
420 cd01575 PBP1_GntR Ligand-bindi 53.3 64 0.0014 32.9 8.9 76 75-154 2-79 (268)
421 cd06317 PBP1_ABC_sugar_binding 53.3 61 0.0013 33.3 8.7 77 75-154 2-82 (275)
422 cd06300 PBP1_ABC_sugar_binding 52.9 59 0.0013 33.4 8.5 80 74-154 1-86 (272)
423 cd08180 PDD 1,3-propanediol de 52.9 30 0.00064 37.3 6.3 71 68-139 18-88 (332)
424 cd01324 cbb3_Oxidase_CcoQ Cyto 52.5 15 0.00032 26.7 2.6 27 497-523 11-37 (48)
425 cd06320 PBP1_allose_binding Pe 52.5 54 0.0012 33.8 8.1 80 74-154 1-83 (275)
426 PF13380 CoA_binding_2: CoA bi 52.4 12 0.00026 33.2 2.6 86 73-165 1-88 (116)
427 cd06315 PBP1_ABC_sugar_binding 52.1 69 0.0015 33.2 8.9 79 73-154 1-82 (280)
428 COG4213 XylF ABC-type xylose t 52.1 3.1E+02 0.0067 28.9 13.4 145 6-155 84-242 (341)
429 PRK00002 aroB 3-dehydroquinate 52.0 1.1E+02 0.0023 33.5 10.4 101 61-165 20-127 (358)
430 TIGR00070 hisG ATP phosphoribo 51.7 60 0.0013 31.3 7.3 74 591-676 100-173 (182)
431 TIGR02370 pyl_corrinoid methyl 51.5 1.1E+02 0.0025 29.9 9.6 88 73-166 85-176 (197)
432 PRK10355 xylF D-xylose transpo 51.3 70 0.0015 34.3 8.9 79 73-154 26-107 (330)
433 cd06309 PBP1_YtfQ_like Peripla 51.2 51 0.0011 34.0 7.7 72 80-154 9-81 (273)
434 cd08177 MAR Maleylacetate redu 51.1 43 0.00093 36.1 7.2 77 60-139 11-87 (337)
435 cd06324 PBP1_ABC_sugar_binding 51.0 58 0.0013 34.4 8.2 77 75-154 2-83 (305)
436 PRK13010 purU formyltetrahydro 51.0 3.2E+02 0.0069 28.7 14.7 90 4-99 10-117 (289)
437 cd06285 PBP1_LacI_like_7 Ligan 50.8 93 0.002 31.8 9.6 76 75-154 2-79 (265)
438 cd01539 PBP1_GGBP Periplasmic 50.6 65 0.0014 34.0 8.5 78 74-154 1-83 (303)
439 PRK10677 modA molybdate transp 50.3 85 0.0018 32.3 8.9 71 404-483 41-117 (257)
440 PF14981 FAM165: FAM165 family 50.2 36 0.00077 23.9 3.9 33 736-768 3-35 (51)
441 PF06679 DUF1180: Protein of u 50.2 17 0.00037 34.1 3.3 31 739-769 94-124 (163)
442 PRK05452 anaerobic nitric oxid 49.8 2E+02 0.0044 32.7 12.6 139 8-166 198-347 (479)
443 COG3340 PepE Peptidase E [Amin 49.7 1.7E+02 0.0037 28.9 9.9 96 61-166 22-126 (224)
444 cd06278 PBP1_LacI_like_2 Ligan 49.2 85 0.0018 32.0 9.0 75 75-154 2-78 (266)
445 PRK09701 D-allose transporter 49.2 1.4E+02 0.003 31.7 10.8 85 69-154 21-108 (311)
446 PRK10653 D-ribose transporter 49.2 90 0.002 32.7 9.3 80 72-154 26-108 (295)
447 COG2358 Imp TRAP-type uncharac 49.1 1E+02 0.0023 32.6 9.2 79 590-674 127-214 (321)
448 PF00072 Response_reg: Respons 49.0 1.3E+02 0.0027 25.7 8.8 58 87-153 9-69 (112)
449 cd06319 PBP1_ABC_sugar_binding 48.8 66 0.0014 33.1 8.1 77 75-154 2-81 (277)
450 PRK00945 acetyl-CoA decarbonyl 48.6 81 0.0018 30.1 7.6 114 3-126 35-168 (171)
451 cd08184 Fe-ADH3 Iron-containin 48.6 79 0.0017 34.2 8.7 75 61-139 12-91 (347)
452 cd08549 G1PDH_related Glycerol 48.2 71 0.0015 34.4 8.3 84 61-146 12-99 (332)
453 CHL00073 chlN photochlorophyll 48.0 63 0.0014 36.2 7.9 141 4-155 194-339 (457)
454 TIGR02417 fruct_sucro_rep D-fr 47.9 1.4E+02 0.003 31.8 10.6 80 72-154 60-141 (327)
455 cd06271 PBP1_AglR_RafR_like Li 47.6 91 0.002 31.8 8.9 76 75-154 2-83 (268)
456 PRK10481 hypothetical protein; 47.4 2E+02 0.0044 28.8 10.5 68 71-142 128-195 (224)
457 cd06283 PBP1_RegR_EndR_KdgR_li 47.4 1E+02 0.0022 31.4 9.2 76 75-154 2-79 (267)
458 PRK14498 putative molybdopteri 47.2 1.4E+02 0.0031 35.4 11.3 68 69-139 183-262 (633)
459 cd06307 PBP1_uncharacterized_s 47.2 69 0.0015 33.0 7.9 80 74-154 1-84 (275)
460 cd01542 PBP1_TreR_like Ligand- 47.0 1E+02 0.0022 31.3 9.1 76 75-154 2-79 (259)
461 cd06323 PBP1_ribose_binding Pe 46.9 74 0.0016 32.5 8.1 77 75-154 2-81 (268)
462 KOG0025 Zn2+-binding dehydroge 46.5 3.6E+02 0.0079 28.1 13.3 97 47-154 162-258 (354)
463 cd06292 PBP1_LacI_like_10 Liga 46.5 1.3E+02 0.0028 30.9 9.8 77 75-154 2-84 (273)
464 COG0563 Adk Adenylate kinase a 46.3 53 0.0011 31.7 6.2 28 6-33 3-30 (178)
465 TIGR02667 moaB_proteo molybden 46.2 1.1E+02 0.0023 29.1 8.2 66 72-139 4-73 (163)
466 cd08173 Gro1PDH Sn-glycerol-1- 46.1 81 0.0017 34.1 8.3 81 62-146 14-97 (339)
467 cd06321 PBP1_ABC_sugar_binding 45.8 75 0.0016 32.6 7.9 77 75-154 2-83 (271)
468 TIGR02634 xylF D-xylose ABC tr 45.7 75 0.0016 33.5 8.0 72 80-154 8-80 (302)
469 cd08472 PBP2_CrgA_like_3 The C 45.5 2.7E+02 0.0058 26.3 11.6 66 402-482 14-79 (202)
470 TIGR03414 ABC_choline_bnd chol 45.5 2.6E+02 0.0057 29.3 11.8 41 404-453 23-63 (290)
471 cd00886 MogA_MoaB MogA_MoaB fa 45.4 1E+02 0.0023 28.7 8.0 64 74-139 2-71 (152)
472 cd01574 PBP1_LacI Ligand-bindi 45.4 1.2E+02 0.0025 30.9 9.3 77 75-154 2-80 (264)
473 PRK10200 putative racemase; Pr 44.6 99 0.0021 31.2 8.2 40 62-104 107-147 (230)
474 PRK02261 methylaspartate mutas 44.1 2.1E+02 0.0046 26.1 9.5 85 74-165 5-93 (137)
475 cd08475 PBP2_CrgA_like_6 The C 43.9 2.2E+02 0.0048 26.7 10.6 67 628-700 128-196 (199)
476 TIGR02637 RhaS rhamnose ABC tr 43.9 74 0.0016 33.4 7.7 72 81-154 9-82 (302)
477 COG1922 WecG Teichoic acid bio 43.6 1.4E+02 0.0031 30.4 8.8 102 57-169 94-198 (253)
478 cd08169 DHQ-like Dehydroquinat 43.3 2E+02 0.0044 31.0 10.9 101 61-165 12-118 (344)
479 PF01177 Asp_Glu_race: Asp/Glu 43.2 2.3E+02 0.0051 27.9 10.8 84 64-151 100-198 (216)
480 cd06298 PBP1_CcpA_like Ligand- 43.1 1.2E+02 0.0025 31.0 8.9 76 75-154 2-79 (268)
481 cd06294 PBP1_ycjW_transcriptio 42.8 1.3E+02 0.0028 30.7 9.1 70 81-154 15-84 (270)
482 cd03364 TOPRIM_DnaG_primases T 42.6 56 0.0012 26.5 5.0 40 64-104 36-75 (79)
483 COG1794 RacX Aspartate racemas 42.6 92 0.002 30.9 7.1 42 60-104 105-146 (230)
484 PRK14987 gluconate operon tran 42.1 1.8E+02 0.0038 31.1 10.3 78 73-154 64-143 (331)
485 PRK00843 egsA NAD(P)-dependent 42.0 1E+02 0.0022 33.4 8.4 82 61-146 22-106 (350)
486 cd00758 MoCF_BD MoCF_BD: molyb 41.9 1E+02 0.0023 27.9 7.2 49 87-138 19-67 (133)
487 COG1879 RbsB ABC-type sugar tr 41.7 1E+02 0.0023 32.8 8.4 82 73-155 34-118 (322)
488 PF13671 AAA_33: AAA domain; P 41.7 30 0.00065 31.6 3.7 32 5-36 1-32 (143)
489 PF08374 Protocadherin: Protoc 41.6 40 0.00087 32.9 4.4 33 734-766 32-64 (221)
490 PRK09189 uroporphyrinogen-III 41.2 72 0.0016 32.4 6.7 88 58-151 102-191 (240)
491 TIGR00177 molyb_syn molybdenum 40.8 1.1E+02 0.0024 28.2 7.3 49 88-139 28-76 (144)
492 PF01102 Glycophorin_A: Glycop 40.5 43 0.00092 29.9 4.1 27 742-768 67-93 (122)
493 PF01745 IPT: Isopentenyl tran 40.4 19 0.00042 35.4 2.1 31 4-34 2-32 (233)
494 cd02067 B12-binding B12 bindin 40.1 2.4E+02 0.0052 24.7 9.2 68 80-153 7-78 (119)
495 PF01634 HisG: ATP phosphoribo 39.9 30 0.00064 32.7 3.2 101 591-703 57-159 (163)
496 cd06313 PBP1_ABC_sugar_binding 39.7 93 0.002 32.1 7.5 71 81-154 10-81 (272)
497 PF01936 NYN: NYN domain; Int 39.7 1.5E+02 0.0033 26.9 8.2 99 60-164 22-126 (146)
498 cd06308 PBP1_sensor_kinase_lik 39.6 1.3E+02 0.0028 30.8 8.6 77 75-154 2-82 (270)
499 cd06286 PBP1_CcpB_like Ligand- 39.0 1.6E+02 0.0034 29.9 9.0 74 75-152 2-77 (260)
500 cd00338 Ser_Recombinase Serine 38.8 2.9E+02 0.0063 24.7 11.1 87 49-135 2-101 (137)
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-87 Score=692.45 Aligned_cols=719 Identities=20% Similarity=0.349 Sum_probs=596.8
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+||.||+|-+.-.....+..++...++|+|+++. |. +...++.+++.|+-. .++++++.||+|.+++++| |
T Consensus 88 s~Gv~Aifg~yd~ks~~~ltsfc~aLh~~~vtpsf--p~--~~~~~Fviq~RP~l~---~al~s~i~hy~W~~fv~ly-D 159 (897)
T KOG1054|consen 88 SRGVYAIFGFYDKKSVNTLTSFCGALHVSFVTPSF--PT--DGDNQFVIQMRPALK---GALLSLIDHYKWEKFVYLY-D 159 (897)
T ss_pred hhhHhhheecccccchhhhhhhccceeeeeecccC--Cc--CCCceEEEEeCchHH---HHHHHHHHhcccceEEEEE-c
Confidence 46899999999999999999999999999998655 32 334578888888754 8999999999999999999 6
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
.+.|....+.+.+.+.+++..|.....-. ..+..+++.+++.+...+.+.|++.|..+....++.++-+.|-...+|++
T Consensus 160 ~~rg~s~Lqai~~~a~~~nw~VtA~~v~~-~~d~~~yr~~f~~l~~r~e~rv~iDce~~~~~~il~q~i~~~k~~~~YHY 238 (897)
T KOG1054|consen 160 TDRGLSILQAIMEAAAQNNWQVTAINVGN-INDVKEYRMLFEMLDRRQENRVLIDCESERRNRILLQVIELGKHVKGYHY 238 (897)
T ss_pred ccchHHHHHHHHHHHHhcCceEEEEEcCC-cccHHHHHHHHHHHhccccceEEEEcccHHHHHHHHHHHHHhhhccceEE
Confidence 67899999999999999999998764333 33556799999999999999999999999999999999999988899999
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhcc-CCCCCCCCCCCcchhhhhhHHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTD-AKTPNGYIGLNAYGFYAYDTVWLLARA 240 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~-~~~~~~~~~~~~~~~~~YDAv~~~a~A 240 (848)
|..+......+. +.......++.+++..+.+.|..++|.++|++... +.++.....+..-++.+|||+.++++|
T Consensus 239 vlaNl~f~d~dl-----~~f~~g~aNitgFqivn~~~~~~~k~~~~~~~l~~~~~~g~~~~~~k~tsAlthDailV~~ea 313 (897)
T KOG1054|consen 239 VLANLGFTDIDL-----ERFQHGGANITGFQIVNKNNPMVKKFIQRWKELDEREYPGASNDPIKYTSALTHDAILVMAEA 313 (897)
T ss_pred EEeeCCCchhhH-----HHHhcCCcceeEEEEecCCChHHHHHHHHHhhhcccccCCCCCCCcchhhhhhhhHHHHHHHH
Confidence 998855444333 33445566789999999999999999999997653 345555456777899999999999999
Q ss_pred HHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecccEE
Q 003093 241 INSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYR 320 (848)
Q Consensus 241 l~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~ 320 (848)
++.+.++..++.. +...|.|.-.++.+|.+|..+.++|+++.++|+||+|+||..|.|.+.+.+|+++..++.+
T Consensus 314 f~~~~~q~~~~~r------RG~~GD~~an~~~p~~qG~~I~ralk~v~~eGLTGniqFd~~G~R~Nyt~~i~elk~~~~r 387 (897)
T KOG1054|consen 314 FRSLRRQRIDISR------RGNAGDCLANPAVPWEQGIDIERALKQVQVEGLTGNIQFDKYGRRTNYTIDIVELKSNGSR 387 (897)
T ss_pred HHHHHHhhhchhc------cCCCccccCCCCCchhcchhHHHHHHheeecccccceeecccCccccceEEEEEeccCCcc
Confidence 9999877643321 2233444445688999999999999999999999999999999999999999999999999
Q ss_pred EEEEeeCCCCCceecCCcccCCCCCCCCCccccceeEeCCCccccCCceeecCCCceEEEEecCCCCccceEE----eCC
Q 003093 321 RIGYWSNYSGLSVVRPETLYSKPPNRSSSNQRLYSVIWPGQTTQKPRGWVFPNNGRHLRIGVPNRVSFREFVS----VKG 396 (848)
Q Consensus 321 ~Vg~w~~~~gl~~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~p~~~~~~~~g~~lrv~v~~~~~~~p~~~----~~~ 396 (848)
.||+|....|+.....+. ... +.+ -....++..|.+....||..+.. ..+
T Consensus 388 k~~~W~e~~~fv~~~t~a-~~~--~d~-----------------------~~~~n~tvvvttiL~spyvm~kkn~~~~eg 441 (897)
T KOG1054|consen 388 KVGYWNEGEGFVPGSTVA-QSR--NDQ-----------------------ASKENRTVVVTTILESPYVMLKKNHEQLEG 441 (897)
T ss_pred eeeeecccCceeeccccc-ccc--ccc-----------------------cccccceEEEEEecCCchhHHHhhHHHhcC
Confidence 999999998876432110 000 000 01122444455544334433332 257
Q ss_pred CcceeeeeHHHHHHHHHhCCCCcceEEeeCC---CCCCCCC-hhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccc
Q 003093 397 SEMTSGFCIDVFTAAINLLPYAVPYKLIPFG---DGHNNPS-CTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIE 472 (848)
Q Consensus 397 ~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~---~~~~n~s-~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~ 472 (848)
+.++.|||+||+.+|+++.+++|++..+..| .....++ |+||++.|..|++|++++++|||-+|++.+|||.|++.
T Consensus 442 n~ryEGyCvdLa~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REeviDFSKPfMs 521 (897)
T KOG1054|consen 442 NERYEGYCVDLAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMS 521 (897)
T ss_pred CcccceeHHHHHHHHHHhcCceEEEEEecCCcccccCCCcccccchhHHHhcCccceEEeeeeeehhhhhhhccccchhh
Confidence 8899999999999999999998777766533 3345666 99999999999999999999999999999999999999
Q ss_pred cceEEEEeccC-CCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCC-------------CCCCcchhhh
Q 003093 473 SGLVVVAPVRK-LDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGP-------------PKRQVVTIFW 538 (848)
Q Consensus 473 ~~~~~v~~~~~-~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~-------------~~~~~~~~~~ 538 (848)
.|+.++.++|+ ..++.++||.|+..+.|+|++..++-+++++++..|.++.||+-. +.+++.|++|
T Consensus 522 lGISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~rg~~t~~~~~NeFgifNsLW 601 (897)
T KOG1054|consen 522 LGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTPSDPPNEFGIFNSLW 601 (897)
T ss_pred cCeEEEEeCcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccCchheeccccccCCCCCCCCCccchhhHHHH
Confidence 99999999988 678999999999999999999999999999999999998876422 2356899999
Q ss_pred hHHHHhhhcCcc-ccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCC-eeEEeCchHHHH
Q 003093 539 FSFSTMFFAHKE-KTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYP-IGYQVNSFARNY 616 (848)
Q Consensus 539 ~~~~~l~~~~~~-~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~-i~~~~~s~~~~~ 616 (848)
|+++++++||.. .|++.++||+-.+||||++||+++|||||++|||+.++.+||+|.|||+++.+. +|+..+....++
T Consensus 602 FsLgAFMQQG~DI~PRslSGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeF 681 (897)
T KOG1054|consen 602 FSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEF 681 (897)
T ss_pred HHHHHHHhcCCCCCccccccceeccchhhhhhhhhhhhhhHHHHHHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHH
Confidence 999999999966 899999999999999999999999999999999999999999999999988764 778887778888
Q ss_pred HHhhhCCC-ccCc----------ccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhc-CCcEEEeCCccccCCcee
Q 003093 617 LVDELNID-ESRL----------VPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLST-RCEFSIVGQVFTKNGWGF 684 (848)
Q Consensus 617 l~~~~~~~-~~~~----------~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~~~ 684 (848)
|++. ..+ -.+| +-+.+..|.+..+++. ++.+||+.|....+|..++ .|+-..||..+.+.+||+
T Consensus 682 Fr~S-kiavy~kMW~yM~SaepsVFv~t~aeGv~rVRks---KGkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGi 757 (897)
T KOG1054|consen 682 FRRS-KIAVYEKMWTYMKSAEPSVFVRTTAEGVARVRKS---KGKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGI 757 (897)
T ss_pred Hhhh-hHHHHHHHHHHHhcCCcceeeehhhhHHHHHHhc---CCceEeehHhhhhhhhhccCCccceecccccCCcceee
Confidence 8542 111 0122 2235677788777763 7789999999999988775 699999999999999999
Q ss_pred eecCCCCchHHHHHHHHhhhccCchHHHHHhhcc-cCCCCCCCCCc--cccceecccchhHHHHHHHHHHHHHHHHHHHH
Q 003093 685 AFPRDSPLAVDISTAILKLSENGDLQRIHDKWLL-RSACSSQGAKL--DVDRLQLKSFSGLYLLCGLACLLALFIYLMQI 761 (848)
Q Consensus 685 ~~~k~spl~~~in~~i~~l~e~G~~~~~~~kw~~-~~~c~~~~~~~--~~~~l~l~~~~g~f~il~~g~~la~~vf~~e~ 761 (848)
|.||||.|+..+|.++++|.|.|+++++++|||. +++|.....+. ....|+|.+++|+||||..|+++|.++.++|+
T Consensus 758 ATp~Gsslr~~vNLAvLkL~E~G~LdKLkNKWWYDkGeC~sg~~ds~~ktsaLsLSnVAGvFYIL~gGl~laMlvALiEF 837 (897)
T KOG1054|consen 758 ATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEF 837 (897)
T ss_pred cCCCCcccccchhhhhhhhcccchHHHhhhhhcccccccCCCCCCCCcchhhcchhhccceeeeehhhHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999 89999876553 44689999999999999999999999999999
Q ss_pred HHHhhccCC
Q 003093 762 VHQFSRHYP 770 (848)
Q Consensus 762 ~~~~~~~~~ 770 (848)
+++.+...+
T Consensus 838 ~yksr~Eak 846 (897)
T KOG1054|consen 838 CYKSRAEAK 846 (897)
T ss_pred HHHhhHHHH
Confidence 988766543
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=6.9e-79 Score=630.64 Aligned_cols=689 Identities=23% Similarity=0.414 Sum_probs=570.8
Q ss_pred CCeEEEE-c-cCCchh---HHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEE
Q 003093 3 GQTVAII-G-PQDAVT---SHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVI 76 (848)
Q Consensus 3 ~~V~aiI-G-p~~S~~---~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~va 76 (848)
..|.||+ . |.+|+. -.+++-.+.-+++|++....-+..+++ .-++.|.|++|+.+.|+.+..+.+..|.|++|.
T Consensus 94 ~~vyav~vSh~~Ts~d~f~p~~vSYT~gFY~iPV~G~~~Rda~fSdKnIh~sFlRtvpPyshqa~VwleMl~~~~y~~vi 173 (993)
T KOG4440|consen 94 SQVYAVLVSHPPTSNDHFTPTPVSYTAGFYRIPVLGLTTRDAIFSDKNIHLSFLRTVPPYSHQASVWLEMLRVYSYNHVI 173 (993)
T ss_pred hheeEEEecCCCCCCcccccccceeeccceeeeeeeeeehhhhhccCceeeeEeecCCCccchhHHHHHHHHHhhcceEE
Confidence 4566655 2 233322 245566778899999998888888988 568999999999999999999999999999999
Q ss_pred EEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 77 AIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 77 ii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
++.+||.-|+.....++..+++...++.....+.++. .+++..|-++|..++||+++..+.++|..+++.|.+++|++
T Consensus 174 ~l~s~d~~gra~~~r~qt~~e~~~~~~e~v~~f~p~~--~~~t~~l~~~k~~~~rv~~~~as~dDA~~ifr~Ag~lnmTG 251 (993)
T KOG4440|consen 174 LLVSDDHEGRAAQKRLQTLLEERESKAEKVLQFDPGT--KNVTALLMEAKELEARVIILSASEDDAATIFRAAGMLNMTG 251 (993)
T ss_pred EEEcccccchhHHhHHHHHHHHHhhhhhhheecCccc--chHHHHHhhhhhhhheeEEeecccchHHHHHHhhhhhcccC
Confidence 9999999999888888888887766665555677665 78999999999999999999999999999999999999999
Q ss_pred CCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHH
Q 003093 157 TGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 157 ~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~ 236 (848)
.||+||+++..... .+..+|++|++.-...+ ..+..-|+|.+
T Consensus 252 ~G~VWiV~E~a~~~-----------nn~PdG~LGlqL~~~~~---------------------------~~~hirDsv~v 293 (993)
T KOG4440|consen 252 SGYVWIVGERAISG-----------NNLPDGILGLQLINGKN---------------------------ESAHIRDSVGV 293 (993)
T ss_pred ceEEEEEecccccc-----------CCCCCceeeeEeecCcc---------------------------ccceehhhHHH
Confidence 99999998743221 24478999987643211 12356699999
Q ss_pred HHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhcc-ccccccceEeccCCCCCCCcEEEEEe-
Q 003093 237 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQAN-MTGTAGPARFNSHGDLINPAYEIINV- 314 (848)
Q Consensus 237 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~-f~G~tG~v~Fd~~g~~~~~~~~I~~~- 314 (848)
+|.|++++++...-..+. ..+|++...|..|..|...+...+ .+|.||++.||++|||+...|+|+|+
T Consensus 294 lasAv~e~~~~e~I~~~P----------~~c~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~Fnd~gdRi~a~YdiiN~h 363 (993)
T KOG4440|consen 294 LASAVHELLEKENITDPP----------RGCVDNTNIWKTGPLLKRVLMSSKYADGVTGRVEFNDDGDRIFANYDIINLH 363 (993)
T ss_pred HHHHHHHHHhhccCCCCC----------CcccCccchhcccHHHHHHHhhhcccCCcceeEEEcCCCceeeccceeEehh
Confidence 999999998663321111 336788889998999998888755 58999999999999999999999999
Q ss_pred ecccEEEEEEeeCCCCCceecCCcccCCCCCCCCCccccceeEeCCCccccCCceeecCCCceEEEEecCCCCccceEE-
Q 003093 315 IGTGYRRIGYWSNYSGLSVVRPETLYSKPPNRSSSNQRLYSVIWPGQTTQKPRGWVFPNNGRHLRIGVPNRVSFREFVS- 393 (848)
Q Consensus 315 ~~~~~~~Vg~w~~~~gl~~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~p~~~~~~~~g~~lrv~v~~~~~~~p~~~- 393 (848)
++...+.+|.|+. +.+. .+-..|+|||+.+..|+++.+| ++|||.+.+.+||....-
T Consensus 364 q~rk~Vg~~~yd~---~r~~----------------~nd~~IiWpGg~~~KP~gi~~p---thLrivTi~~~PFVYv~p~ 421 (993)
T KOG4440|consen 364 QNRKLVGVGIYDG---TRVI----------------PNDRKIIWPGGETEKPRGIQMP---THLRIVTIHQEPFVYVKPT 421 (993)
T ss_pred hhhhhhhhccccc---eeec----------------cCCceeecCCCCcCCCcccccc---ceeEEEEeccCCeEEEecC
Confidence 5555566666643 2221 1236899999999999999998 568988886644432110
Q ss_pred --e---------C-----------------------CCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCC-C--------
Q 003093 394 --V---------K-----------------------GSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDG-H-------- 430 (848)
Q Consensus 394 --~---------~-----------------------~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~-~-------- 430 (848)
+ + ..-|+.||||||+-.+++.+||+++..+++.|.- .
T Consensus 422 ~sd~~c~eef~~~~d~~~k~~c~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnss 501 (993)
T KOG4440|consen 422 LSDGTCKEEFTVNGDPVKKVICTGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSS 501 (993)
T ss_pred CCCcchhhhccccCCcccceeecCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeeccc
Confidence 1 0 0237889999999999999999999998885531 1
Q ss_pred --CCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHH
Q 003093 431 --NNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFL 508 (848)
Q Consensus 431 --~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~ 508 (848)
...+|+|++++|.++++||+++++||++||.++++||.||...|+.++.+++.+.+.+.+||+||+..+|+++++++.
T Consensus 502 eT~~kew~G~iGEL~~~~ADMivaplTINpERa~yieFskPfkYqGitILeKk~~r~Stl~SFlQPfqstLW~lv~~SVh 581 (993)
T KOG4440|consen 502 ETNKKEWNGMIGELLSGQADMIVAPLTINPERAQYIEFSKPFKYQGITILEKKEIRRSTLDSFLQPFQSTLWLLVGLSVH 581 (993)
T ss_pred ccccceehhhhhhhhCCccceEeeceeeChhhhhheeccCcccccceEEEeeCCCCCchHHHHHhHHHHHHHHHHHHHHH
Confidence 123699999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhcccCCC-CCC-------CCCCCcchhhhhHHHHhhhcC--ccccccchhHHHHHHHHhhhhhhhccccce
Q 003093 509 AVGAVVWILEHRLNDE-FRG-------PPKRQVVTIFWFSFSTMFFAH--KEKTVSALGRLVLIIWLFVVLIINSSYTAS 578 (848)
Q Consensus 509 ~~~~v~~~~~~~~~~~-~~~-------~~~~~~~~~~~~~~~~l~~~~--~~~p~s~~~R~~~~~w~~~~lil~~~Yta~ 578 (848)
+++++++++.+.++.+ |.. .....++..+||+|+.++..| ...|+|.+.|++-++|.-|++||+++||||
T Consensus 582 vVal~lYlLDrfSPFgRFk~~ds~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTAN 661 (993)
T KOG4440|consen 582 VVALMLYLLDRFSPFGRFKVNDSEEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTAN 661 (993)
T ss_pred HHHHHHHHHHhcCcccceeeccCccchhhhcchhhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhh
Confidence 9999999999998763 221 234568999999999999887 348999999999999999999999999999
Q ss_pred eeeeeeeccccCCCCChHHhhcC----CCCeeEEeCchHHHHHHhhhCCCc--cCc--ccCCCHHHHHHHhhcCCCCCce
Q 003093 579 LTSILTVQKLSSPIKGIDSLRSS----NYPIGYQVNSFARNYLVDELNIDE--SRL--VPLNSPEEYAKALKDGPHKGGV 650 (848)
Q Consensus 579 L~s~Lt~~~~~~~i~sl~dL~~s----~~~i~~~~~s~~~~~l~~~~~~~~--~~~--~~~~~~~~~~~~l~~~~~~~~~ 650 (848)
|++||...+.+..+.++.|-.-. +...+...+|.+..||+++-.... .+| ..|.+.+|.++++.+ |..
T Consensus 662 LAAFLVLdrPe~~ltGinDpRLRNps~nf~~aTVk~SsVd~YFrRqVELS~MyR~ME~hNy~~A~eAiq~v~~----gkL 737 (993)
T KOG4440|consen 662 LAAFLVLDRPEERLTGINDPRLRNPSDNFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRD----GKL 737 (993)
T ss_pred hhhheeecCccccccCCCCccccCcccceeEEEecCccHHHHHHHHhHHHHHHHhhhhcchhhHHHHHHHHHc----Cce
Confidence 99999999999999999984322 235788899999999976433221 112 246788899999999 999
Q ss_pred EEEEccHHHHHHHHhcCCcEEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccCchHHHHHhhccc---CCCCCCCC
Q 003093 651 AAVVDDRAYAELFLSTRCEFSIVGQVFTKNGWGFAFPRDSPLAVDISTAILKLSENGDLQRIHDKWLLR---SACSSQGA 727 (848)
Q Consensus 651 ~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~G~~~~~~~kw~~~---~~c~~~~~ 727 (848)
+||+.|...++|..+++|.+...|+.|...+||++++|+||+.+.+..+|+++.|+|+++++.++|... ..|.....
T Consensus 738 ~AFIWDS~rLEfEAs~~CeLvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEkLDk~Wi~~Ggpq~c~~~~k 817 (993)
T KOG4440|consen 738 HAFIWDSARLEFEASQKCELVTTGELFGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEKLDKTWIRYGGPQECDSRSK 817 (993)
T ss_pred eEEEeecceeeehhhcccceEeccccccccccccccccCCCCcchhhHHHHHhhhcchHHHHHHHHHhcCCcchhhhhcc
Confidence 999999999999999999999999999999999999999999999999999999999999999999983 44544433
Q ss_pred CccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 003093 728 KLDVDRLQLKSFSGLYLLCGLACLLALFIYLMQIVHQFSRHY 769 (848)
Q Consensus 728 ~~~~~~l~l~~~~g~f~il~~g~~la~~vf~~e~~~~~~~~~ 769 (848)
.+..|++.++.|+|++.+.|++++++..++|+.|++++..
T Consensus 818 --~PatLgl~NMagvFiLV~~Gia~GifLifiEv~Ykrh~~~ 857 (993)
T KOG4440|consen 818 --APATLGLENMAGVFILVAGGIAAGIFLIFIEVAYKRHKDA 857 (993)
T ss_pred --CcccccccccccEEEEEecchhheeeEEEEeehhhhhhhh
Confidence 4778999999999999999999888888899998887764
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=3.3e-74 Score=617.63 Aligned_cols=706 Identities=20% Similarity=0.380 Sum_probs=537.9
Q ss_pred CCeEEEE-ccCCc--hhHHHHHHhhccCCccEEecccC-CCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEE
Q 003093 3 GQTVAII-GPQDA--VTSHVVSHVANELQVPLLSFSAT-DPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIA 77 (848)
Q Consensus 3 ~~V~aiI-Gp~~S--~~~~ava~i~~~~~vP~Is~~at-~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vai 77 (848)
.+|.+|| ++.+- +++..+--++...+||+|+..+. ++.+++ ...-.|++..|+-.+|++++.++++.|+|..+++
T Consensus 99 ~~V~glvf~d~s~~~avaq~LDfiSs~t~iPIisi~gg~a~~~~~kd~gs~flQlg~Sieqqa~Vml~iL~~ydW~~Fs~ 178 (1258)
T KOG1053|consen 99 ARVHGLVFEDDSDTEAVAQILDFISSQTHIPIISIHGGAAMVLTPKDLGSTFLQLGPSIEQQAQVMLKILEEYDWYNFSL 178 (1258)
T ss_pred cceeEEEeecCccchHHHHHHHHHHHhcCCcEEEEecCccceecCCCCcceEEEeCCcHHHHHHHHHHHHHHcCcceeEE
Confidence 4677776 44433 34444556778899999998765 444554 3335799999999999999999999999999999
Q ss_pred EEEcCCCccchHHHHHHHHhc--cCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 78 IYVDDDHGRNGIAALGDTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 78 i~~dd~~g~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
|...-+.-+.....++..... .|+++........+. ++.......+++..++.||+++|+.+++..||..|.++||+
T Consensus 179 vtt~~pg~~~f~~~ir~~~d~s~vgwe~i~v~~l~~s~-~d~~a~~q~qLkki~a~VillyC~~eea~~IF~~A~q~Gl~ 257 (1258)
T KOG1053|consen 179 VTTQFPGNRTFVSLIRQTNDNSHVGWEMINVLTLDPST-DDLLAKLQAQLKKIQAPVILLYCSREEAERIFEEAEQAGLT 257 (1258)
T ss_pred EEeecCchHHHHHHHHHhhhhccccceeeeeeecCCCC-CchHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHhcCCc
Confidence 998877767777777766665 366666555555543 23334444566666799999999999999999999999999
Q ss_pred CCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHH
Q 003093 156 GTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVW 235 (848)
Q Consensus 156 ~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~ 235 (848)
+++|+||++...... + ....+...|.+.+... .|+ ..+....-|+|-
T Consensus 258 g~~y~Wi~pqlv~g~-~------~~pa~~P~GLisv~~~------------~w~--------------~~l~~rVrdgva 304 (1258)
T KOG1053|consen 258 GPGYVWIVPQLVEGL-E------PRPAEFPLGLISVSYD------------TWR--------------YSLEARVRDGVA 304 (1258)
T ss_pred CCceEEEeehhccCC-C------CCCccCccceeeeecc------------chh--------------hhHHHHHhhhHH
Confidence 999999997644321 0 1112445666654321 122 223355679999
Q ss_pred HHHHHHHHHHhcCCCccccCCCccccccCccccCc--ccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEE
Q 003093 236 LLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDS--LRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIIN 313 (848)
Q Consensus 236 ~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~--~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~ 313 (848)
++|.|...+....+.+... ..+|.. ......++.+...|.|++|+| +.++|+++|..+.++..|+.
T Consensus 305 iva~aa~s~~~~~~~lp~~----------~~~C~~~~~~~~~~~~~l~r~l~NvT~~g--~~lsf~~~g~~v~p~lvvI~ 372 (1258)
T KOG1053|consen 305 IVARAASSMLRIHGFLPEP----------KMDCREQEETRLTSGETLHRFLANVTWDG--RDLSFNEDGYLVHPNLVVID 372 (1258)
T ss_pred HHHHHHHHHHhhcccCCCc----------ccccccccCccccchhhhhhhhheeeecc--cceeecCCceeeccceEEEe
Confidence 9999999998775543211 112321 112234899999999999999 78999999988888877776
Q ss_pred ee-cccEEEEEEeeCCCCCceecC-CcccCCCCCCCCCccccceeEeCCCccccCCcee---ecCCCceEEEEecCCCCc
Q 003093 314 VI-GTGYRRIGYWSNYSGLSVVRP-ETLYSKPPNRSSSNQRLYSVIWPGQTTQKPRGWV---FPNNGRHLRIGVPNRVSF 388 (848)
Q Consensus 314 ~~-~~~~~~Vg~w~~~~gl~~~~~-~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~p~~~~---~~~~g~~lrv~v~~~~~~ 388 (848)
.. +..|.+||.|.+.. |.|..+ +..|.+......++.+|+.++-. +.|--++ -|..|.+++-.+++....
T Consensus 373 l~~~r~We~VG~We~~~-L~M~y~vWPr~~~~~q~~~d~~HL~VvTLe----E~PFVive~vDP~t~~C~~ntvpc~s~~ 447 (1258)
T KOG1053|consen 373 LNRDRTWERVGSWENGT-LVMKYPVWPRYHKFLQPVPDKLHLTVVTLE----ERPFVIVEDVDPLTQTCVRNTVPCRSQL 447 (1258)
T ss_pred cCCCcchheeceecCCe-EEEeccccccccCccCCCCCcceeEEEEec----cCCeEEEecCCCCcCcCCCCCCcchhhh
Confidence 64 46799999998753 554322 11122222222222233322210 1111000 023333333333322100
Q ss_pred cceEE---e----CCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCC-C-CCCCChhHHHHHHhcCeeeEEeeceeeecC
Q 003093 389 REFVS---V----KGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGD-G-HNNPSCTELVRLITAGVYDAAVGDIAIITN 459 (848)
Q Consensus 389 ~p~~~---~----~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~-~-~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~ 459 (848)
...+ . +-+.|++|||||||+.|++.+||+|+++.+..|. | +.||.|+|||++|..+++||++++++|+++
T Consensus 448 -~~t~ss~~~~~~tvKkCCkGfCIDiLkKlA~~v~FtYDLYlVtnGKhGkk~ng~WnGmIGev~~~rA~MAVgSltINee 526 (1258)
T KOG1053|consen 448 -NSTFSSGDEANRTVKKCCKGFCIDILKKLARDVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEE 526 (1258)
T ss_pred -hhccCCCccCCchHHhhhhhhhHHHHHHHHhhcCcceEEEEecCCcccceecCcchhhHHHHHhhhhheeeeeeEechh
Confidence 0000 0 0145899999999999999999998877776554 3 378999999999999999999999999999
Q ss_pred ceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHH-hhhhhcccCCCCC---------CCC
Q 003093 460 RTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAV-VWILEHRLNDEFR---------GPP 529 (848)
Q Consensus 460 R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v-~~~~~~~~~~~~~---------~~~ 529 (848)
|.+.+|||.||.++++.++|.+.+...+..+||.||++.+|+++++++++++.+ ++++|+.++-.+. +.+
T Consensus 527 RSevVDFSvPFveTgIsVmV~rsngtvspsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp 606 (1258)
T KOG1053|consen 527 RSEVVDFSVPFVETGISVMVARSNGTVSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGP 606 (1258)
T ss_pred hhccccccccccccceEEEEEecCCccCchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcCcccccccccCCCCCCCc
Confidence 999999999999999999999999999999999999999999999998877665 5688998765432 224
Q ss_pred CCCcchhhhhHHHHhhhcC--ccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcC------
Q 003093 530 KRQVVTIFWFSFSTMFFAH--KEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSS------ 601 (848)
Q Consensus 530 ~~~~~~~~~~~~~~l~~~~--~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s------ 601 (848)
.++++.++|..|+.+|... .++|+++.+||++.+|.||++|+.++|||||++||...++..++.++.|=.-+
T Consensus 607 ~FtigkaiwllwaLvFnnsVpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~vSGlsD~KfqrP~dq~ 686 (1258)
T KOG1053|consen 607 SFTIGKAIWLLWALVFNNSVPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDTVSGLSDPKFQRPHDQY 686 (1258)
T ss_pred ceehhhHHHHHHHHHhCCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccccCccccC
Confidence 6789999999999999885 56999999999999999999999999999999999999999999999985532
Q ss_pred -CCCeeEEeCchHHHHHHhhhCCCccCcccC--CCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhc--CCcEEEeC--
Q 003093 602 -NYPIGYQVNSFARNYLVDELNIDESRLVPL--NSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLST--RCEFSIVG-- 674 (848)
Q Consensus 602 -~~~i~~~~~s~~~~~l~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~--~~~l~~~~-- 674 (848)
..++|+..++..++++++........|+.| ...+++++.|++ |+.||||.|...++|...+ .|+|..+|
T Consensus 687 PpFRFGTVpngSTE~niR~Nyp~MHeYM~kyNq~~v~dal~sLK~----gKLDAFIyDaAVLnY~agkDegCKLvTIGsg 762 (1258)
T KOG1053|consen 687 PPFRFGTVPNGSTERNIRSNYPEMHEYMVKYNQPGVEDALESLKN----GKLDAFIYDAAVLNYMAGKDEGCKLVTIGSG 762 (1258)
T ss_pred CCcccccCCCCchhhhHHhccHHHHHHHHHhccCchHHHHHHHhc----ccchhHHHHHHHHHHhhccCCCceEEEecCC
Confidence 346888888778888866433333455555 578999999999 9999999999999999987 69999999
Q ss_pred CccccCCceeeecCCCCchHHHHHHHHhhhccCchHHHHHhhcccCCCCCCCCCccccceecccchhHHHHHHHHHHHHH
Q 003093 675 QVFTKNGWGFAFPRDSPLAVDISTAILKLSENGDLQRIHDKWLLRSACSSQGAKLDVDRLQLKSFSGLYLLCGLACLLAL 754 (848)
Q Consensus 675 ~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~G~~~~~~~kw~~~~~c~~~~~~~~~~~l~l~~~~g~f~il~~g~~la~ 754 (848)
+.|...+||+++|||||++..||.+|+++...|.++.+++.|+. +.|.++..+..+.+|++++|.|+|++|++|+++++
T Consensus 763 KvFAttGYGIal~k~Spwkr~IdlallQy~gdGeme~Le~~Wlt-gic~n~k~evmSsqLdIdnmaGvFymL~~amgLSl 841 (1258)
T KOG1053|consen 763 KVFATTGYGIALPKNSPWKRQIDLALLQYLGDGEMEMLETLWLT-GICHNSKNEVMSSQLDIDNMAGVFYMLAVAMGLSL 841 (1258)
T ss_pred ceeeecceeeecCCCCcchhhHHHHHHHHhccchHHHHHHHHhh-cccccchhhhhhcccChhhhhhHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999998 67777767778899999999999999999999999
Q ss_pred HHHHHHHHHHh
Q 003093 755 FIYLMQIVHQF 765 (848)
Q Consensus 755 ~vf~~e~~~~~ 765 (848)
++|++|-+.++
T Consensus 842 lvfi~EHlvYw 852 (1258)
T KOG1053|consen 842 LVFIWEHLVYW 852 (1258)
T ss_pred HHHHHHHHHHH
Confidence 99999977544
No 4
>KOG1052 consensus Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.6e-66 Score=611.92 Aligned_cols=596 Identities=37% Similarity=0.634 Sum_probs=507.8
Q ss_pred HHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCch
Q 003093 120 DLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSV 199 (848)
Q Consensus 120 ~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~ 199 (848)
..+.+++....+++++++.+..+..++.+|.++||+..+|+|+.+.......+.... ....+..+|.++...+.+.+.
T Consensus 4 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~a~~~~~~~~~~~~i~t~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~s~ 81 (656)
T KOG1052|consen 4 KLLLKLKAMRTRVFVLHMFPILALAIFSQAEELGMMQFGYVWILTNLLTDALDLDEL--YSLIDVMNGVLGLRGHIPRSE 81 (656)
T ss_pred hHHHHhhccCceEEEEeCCHHHHHHHHHHHHHhCccccCeEEEEEecchhhhccccc--ccchhheeeEEeeccCCCccH
Confidence 345566678899999999988999999999999999999999999987766655432 345567889999999999999
Q ss_pred hHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHH
Q 003093 200 LKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNL 279 (848)
Q Consensus 200 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~ 279 (848)
..+.|..+|+.. . .....++.++||+++++|.|++.+.. .... .+.|+..+.|.++..
T Consensus 82 ~~~~~~~~~~~~-~-------~~~~~~~~~~~D~~~~~a~~~~~~~~-~~~~-------------~~~~~~~~~~~~~~~ 139 (656)
T KOG1052|consen 82 LLQNFVTRWQTS-N-------VELLVYALWAYDAIQALARAVESLLN-IGNL-------------SLSCGRNNSWLDALG 139 (656)
T ss_pred HHHHHHHHHhhc-c-------ccccchhhHHHHHHHHHHHHHHHhhc-CCCC-------------ceecCCCCcccchhH
Confidence 999999999866 2 34677899999999999999999764 1111 344554455666888
Q ss_pred HHHHHHhcccc---ccccceEeccCCCCCCCcEEEEEeecccEEEEEEeeCCCCCceecCCcccCCCCCCCCCcccccee
Q 003093 280 LRDSILQANMT---GTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGLSVVRPETLYSKPPNRSSSNQRLYSV 356 (848)
Q Consensus 280 l~~~l~~~~f~---G~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~Vg~w~~~~gl~~~~~~~~~~~~~~~~~~~~~l~~i 356 (848)
+.+.+...... |.+|.+.++.++.+....|+|+|+.+.+.+.||.|++..| ..|
T Consensus 140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~n~~~~~~~~ig~W~~~~~-----------------------~~i 196 (656)
T KOG1052|consen 140 VFNFGKKLLVVNLSGVTGQFQFFRGGLLEYFKYEILNLNGSGERRIGYWYPRGG-----------------------ENI 196 (656)
T ss_pred HHHHHHhhhhhccccceeEEEecCCCccccceEEEEEecCcCceeEEEecCCCC-----------------------cee
Confidence 88888876644 4567888888888889999999999999999999998764 368
Q ss_pred EeCCCccccCCceeecCCCceEEEEecCCCCccceEEe----CCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCC--
Q 003093 357 IWPGQTTQKPRGWVFPNNGRHLRIGVPNRVSFREFVSV----KGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGH-- 430 (848)
Q Consensus 357 ~Wpg~~~~~p~~~~~~~~g~~lrv~v~~~~~~~p~~~~----~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~-- 430 (848)
.||+.....|+++.+|.+|+++||+++..+||..++.. .++..+.|+|+||++++++.|||+++++.++.+.|.
T Consensus 197 ~~~~~~~~~~~~~~~~~~~~~l~v~~~~~~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~ 276 (656)
T KOG1052|consen 197 SWPGKDYFVPKGWFFPTNGKPLRVGVVTEPPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRD 276 (656)
T ss_pred eccCCcccCcCCccccCCCceEEEEEeccCCceeeeecccccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCCCCCC
Confidence 89999999999999999999999999988776666553 256799999999999999999999999999876644
Q ss_pred CCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHH
Q 003093 431 NNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAV 510 (848)
Q Consensus 431 ~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~ 510 (848)
++|+|+|++++|.+|++|++ ++++++++|.+++|||.||++.++++++++++.....|.|++||++++|++++++++++
T Consensus 277 ~~g~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~~~~fl~Pf~~~vW~~i~~~~l~~ 355 (656)
T KOG1052|consen 277 PNGNWDGLVGQLVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSKLWNFLAPFSPEVWLLILASLLLV 355 (656)
T ss_pred CCCChhHHHHHHhcCccccc-cceEEeecccccEEeccceEeccEEEEEEecCCcccceEEecCCcHHHHHHHHHHHHHH
Confidence 45899999999999999999 99999999999999999999999999999998665599999999999999999999999
Q ss_pred HHHhhhhhcccCCCCCCCC-----CCCcchhhhhHHHHhhhcC-ccccccchhHHHHHHHHhhhhhhhccccceeeeeee
Q 003093 511 GAVVWILEHRLNDEFRGPP-----KRQVVTIFWFSFSTMFFAH-KEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILT 584 (848)
Q Consensus 511 ~~v~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~l~~~~-~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt 584 (848)
++++|+++|+.+.++ ..+ .....+++|+++++++.|+ .+.|++.++|+++++||++++||+++|||+|+|+||
T Consensus 356 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt 434 (656)
T KOG1052|consen 356 GLLLWILERLSPYEL-PPRQIVTSLFSLLNCLWLTVGSLLQQGSDEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLT 434 (656)
T ss_pred HHHHHHHhccccccC-CccccceeEeecccchhhhhHHHhccCCCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999888 211 1224668899999999887 569999999999999999999999999999999999
Q ss_pred eccccCCCCChHHhhc-CCCCeeEEeCchHHHHHHhh---hCCCcc-CcccCCCHHHHHHHhhcCCCCCceEEEEccHHH
Q 003093 585 VQKLSSPIKGIDSLRS-SNYPIGYQVNSFARNYLVDE---LNIDES-RLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAY 659 (848)
Q Consensus 585 ~~~~~~~i~sl~dL~~-s~~~i~~~~~s~~~~~l~~~---~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~ 659 (848)
++++.++|++++||.+ ++..+|...+++...++.+. ...... +.+.+.+.+++.+++.+|.. +++.++.++.++
T Consensus 435 ~~~~~~~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~-~~~~~~~~~~~~ 513 (656)
T KOG1052|consen 435 VPRLRSPIDSLDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLASPEEGVERVRKGPS-GGYAFASDELYL 513 (656)
T ss_pred ccccCCcccCHHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCCCccCCCHHHHHHHHHcCCC-CceEEEeccHHH
Confidence 9999999999999995 77889999999999999665 333334 77889999999999999544 345445444444
Q ss_pred HHHHHhcC-CcEEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccCchHHHHHhhcccC----CCCCCCCCccccce
Q 003093 660 AELFLSTR-CEFSIVGQVFTKNGWGFAFPRDSPLAVDISTAILKLSENGDLQRIHDKWLLRS----ACSSQGAKLDVDRL 734 (848)
Q Consensus 660 ~~~~~~~~-~~l~~~~~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~G~~~~~~~kw~~~~----~c~~~~~~~~~~~l 734 (848)
..+..+++ |+++++++.+...+++ ++||||||++.++++|+++.|.|+++++++||+... .|.... +...|
T Consensus 514 ~~~~~~~~~c~~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g~l~~~~~kw~~~~~~~~~~~~~~---~~~~l 589 (656)
T KOG1052|consen 514 AYLFLRDEICDLTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQETGILQKLKRKWFSKKPCLPKCSQTE---KTKAL 589 (656)
T ss_pred HHHHhhcCCCceEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhccccHHHHHHHHhccCCCCCCCCCCcc---ccccc
Confidence 44444433 9999999999999999 999999999999999999999999999999999954 444333 46789
Q ss_pred ecccchhHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 003093 735 QLKSFSGLYLLCGLACLLALFIYLMQIVHQFSRHY 769 (848)
Q Consensus 735 ~l~~~~g~f~il~~g~~la~~vf~~e~~~~~~~~~ 769 (848)
++++++|+|+++++|+++|+++|++|++|++++..
T Consensus 590 ~~~~~~g~F~i~~~g~~lal~vfi~E~~~~~~~~~ 624 (656)
T KOG1052|consen 590 DLESFWGLFLILLVGYLLALLVFILELLYSRRRTL 624 (656)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999988875
No 5
>cd06390 PBP1_iGluR_AMPA_GluR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=1.4e-42 Score=376.15 Aligned_cols=308 Identities=20% Similarity=0.312 Sum_probs=261.6
Q ss_pred CCCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 1 MEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 1 ~~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
|++||+|||||.++..+..++.+|+..+||+|+++. |..+ ..+|++++.|+ +++|+++++++|||++|++||+
T Consensus 53 ~~~gV~AI~Gp~s~~~a~~v~sic~~~~vP~i~~~~--~~~~--~~~~~i~~~P~---~~~Ai~diI~~~~W~~v~iIYd 125 (364)
T cd06390 53 FSKGVYAIFGFYDRKTVNMLTSFCGALHVCFITPSF--PVDT--SNQFVLQLRPE---LQDALISVIEHYKWQKFVYIYD 125 (364)
T ss_pred hhcCceEEEccCChhHHHHHHHhhcCCCCCceecCC--CCCC--CCceEEEeChh---HHHHHHHHHHHcCCcEEEEEEe
Confidence 468999999999999999999999999999999754 4333 34579999997 8999999999999999999996
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
+| ||...++.|.+++++.|++|.+...++. +..+++.+|++|+.+++|+||++|+.+.+..+++++.+.+|+..+|+
T Consensus 126 ~d-~g~~~lq~l~~~~~~~~~~I~~~~~~~~--~~~d~~~~L~~ik~~~~rvIVl~~~~~~~~~~L~~a~~~~~~~~gy~ 202 (364)
T cd06390 126 AD-RGLSVLQKVLDTAAEKNWQVTAVNILTT--TEEGYRKLFQDLDKKKERLIVVDCESERLNAILNQIIKLEKNGIGYH 202 (364)
T ss_pred CC-ccHHHHHHHHHhhhccCceeeEEEeecC--ChHHHHHHHHhccccCCeEEEEECCHHHHHHHHHHHHHhhccCCceE
Confidence 55 9999999999999999999998777664 34799999999999999999999999999999999999999999999
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccC-CCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
||.|+......+. +......+|+++++++.|+++..++|.++|++.... .+..+...++.+++++|||||++|+
T Consensus 203 wI~t~l~~~~~~~-----~~~~~~~~nitg~r~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~l~yDaV~~~A~ 277 (364)
T cd06390 203 YILANLGFMDIDL-----TKFRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRVDWKRPKYTSALTYDGVRVMAE 277 (364)
T ss_pred EEecCCCcccccH-----HHHhcCCcCceEEEEecCCCHHHHHHHHHHHhhccccCCCCCcCCcchHHHHHHHHHHHHHH
Confidence 9999843322222 345567899999999999999999999999887642 2334444678899999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccC--cccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecc
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLD--SLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGT 317 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~--~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~ 317 (848)
|++++...+...++... ...|. ...+|+.|..|+++|++++|+|+||+++||++|+|....|+|+|+.+.
T Consensus 278 A~~~l~~~~~~~~~~~~--------~~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~i~F~~~G~r~~~~~~I~~~~~~ 349 (364)
T cd06390 278 AFQNLRKQRIDISRRGN--------AGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHD 349 (364)
T ss_pred HHHHHHHcCCCcccCCC--------CCCCCCCCCCCCccHHHHHHHHHhhcccccccceeeCCCCCcccceEEEEEecCC
Confidence 99998665443321111 12343 345789999999999999999999999999999999999999999999
Q ss_pred cEEEEEEeeCCCCC
Q 003093 318 GYRRIGYWSNYSGL 331 (848)
Q Consensus 318 ~~~~Vg~w~~~~gl 331 (848)
|+++||+|++..||
T Consensus 350 g~~~vG~W~~~~g~ 363 (364)
T cd06390 350 GIRKIGYWNEDEKL 363 (364)
T ss_pred cceEEEEECCCCCc
Confidence 99999999998876
No 6
>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=1.7e-41 Score=367.07 Aligned_cols=308 Identities=17% Similarity=0.273 Sum_probs=244.7
Q ss_pred CCCCeEEEEccCCchhHHHHHHhhccCCccEEeccc-----------CCCCCCCCCCCceEeccCChHHHHHHHHHHHHH
Q 003093 1 MEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSA-----------TDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH 69 (848)
Q Consensus 1 ~~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~a-----------t~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~ 69 (848)
|++||+|||||.++..+..++.+|+.++||+|++++ ++|.++..+||++.|+. ..+.+|+++++++
T Consensus 59 ~~~gV~AI~Gp~s~~~a~~v~sic~~l~VP~is~~~~~~~~~~~~~~~~p~~~~~~~~~~lrp~---~~~~~Ai~dlV~~ 135 (400)
T cd06392 59 MTQGILALVTSTGCASANALQSLTDAMHIPHLFVQRNSGGSPRTACHLNPSPEGEEYTLAARPP---VRLNDVMLKLVTE 135 (400)
T ss_pred HhcCeEEEECCCchhHHHHHHHHhccCcCCcEeecccccccccccccCCCCcCcCceeEEecCc---hHHHHHHHHHHHh
Confidence 468999999999999999999999999999999866 45666667777777763 4677899999999
Q ss_pred cCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeee-------cCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcH
Q 003093 70 YGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAP-------LSVEATEDEITDLLVKVALTESRIIVVHTHYNRG 142 (848)
Q Consensus 70 ~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~-------~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~ 142 (848)
|+|++|++|| |++||...++.+.+++.+.+.+|.+... +++.. .+.....|.+++..+ ++||++|+++.+
T Consensus 136 ~~W~~v~~iY-D~d~gl~~lq~L~~~~~~~~~~I~~~~v~~~~~~~~~~~l-~~~~~~~L~~~~~~~-r~iVv~~s~~~~ 212 (400)
T cd06392 136 LRWQKFIVFY-DSEYDIRGLQSFLDQASRLGLDVSLQKVDRNISRVFTNLF-TTMKTEELNRYRDTL-RRAILLLSPRGA 212 (400)
T ss_pred CCCcEEEEEE-ECcccHHHHHHHHHHHhhcCceEEEEEcccCcchhhhhHH-HHHHHhhhhhccccc-eEEEEEcCcHHH
Confidence 9999999999 8999999999999999999999987652 22111 222344455555555 899999999999
Q ss_pred HHHHHHHHHcCCCCCCeEEEecCccccccCCCCCCCccccccccee----EEEEEecCCchhHHHHH----HHHHhhccC
Q 003093 143 PVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGV----LTLRTYTPDSVLKRKFI----SRWRNLTDA 214 (848)
Q Consensus 143 ~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~----~~~~~~~~~~~~~~~f~----~~~~~~~~~ 214 (848)
..++++|+++||+..+|+||++++.....+. .+..+|. .+++.+.|.++...+|. .+|++....
T Consensus 213 ~~il~qA~~lgM~~~~y~wI~t~~~~~~~dl--------~~~~~g~~~niT~~r~~~~~~~~~~~~~~~~~~r~~~~~~~ 284 (400)
T cd06392 213 QTFINEAVETNLASKDSHWVFVNEEISDTEI--------LELVHSALGRMTVIRQIFPLSKDNNQRCIRNNHRISSLLCD 284 (400)
T ss_pred HHHHHHHHHhCcccCCeEEEEecCCcccccH--------HHHhcccccceeeEEEecCCcHHHHHHHHHHHHHHHhhhcc
Confidence 9999999999999999999999987765443 3344444 44888888777565554 677655432
Q ss_pred CCCCCCCCCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCcccc--CcccccCChHHHHHHHHhcccccc
Q 003093 215 KTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRL--DSLRIFNGGNLLRDSILQANMTGT 292 (848)
Q Consensus 215 ~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~--~~~~~~~~g~~l~~~l~~~~f~G~ 292 (848)
........+..+++++|||||++|+|+++++........ . .++| ++..+|+.|..|+++|++++|+|+
T Consensus 285 ~~~~~~~~l~~~aalayDaV~~~A~Al~~ll~~~~~~~~---------~-~l~C~~~~~~~w~~G~~ll~~ik~v~f~GL 354 (400)
T cd06392 285 PQEGYLQMLQVSNLYLYDSVLMLANAFHRKLEDRKWHSM---------A-SLNCIRKSTKPWNGGRSMLETIKKGHITGL 354 (400)
T ss_pred cccccccccchhHHHHHHHHHHHHHHHHHHhhccccCCC---------C-CCccCCCCCCCCCChHHHHHHHHhCCCccC
Confidence 111111247889999999999999999987643222211 1 3456 568899999999999999999999
Q ss_pred ccceEeccCCCCCCCcEEEEEe-----ecccEEEEEEeeCCCCCc
Q 003093 293 AGPARFNSHGDLINPAYEIINV-----IGTGYRRIGYWSNYSGLS 332 (848)
Q Consensus 293 tG~v~Fd~~g~~~~~~~~I~~~-----~~~~~~~Vg~w~~~~gl~ 332 (848)
||+|+||++|+|.++.|+|+|+ .|.|.++||+|++.+||.
T Consensus 355 TG~I~F~~~G~r~~~~ldIi~l~~~~~~g~g~~~iG~W~~~~gl~ 399 (400)
T cd06392 355 TGVMEFKEDGANPHVQFEILGTSYSETFGKDVRRLATWDSEKGLN 399 (400)
T ss_pred ccceeECCCCCCcCCceEEEeccccccCCCCceEeEEecCCCCCC
Confidence 9999999999999999999995 467799999999999864
No 7
>cd06393 PBP1_iGluR_Kainate_GluR5_7 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated
Probab=100.00 E-value=8.1e-40 Score=361.24 Aligned_cols=307 Identities=19% Similarity=0.254 Sum_probs=254.3
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.++|+|||||.+|..+.++++++++++||+|++++++|.+++. .+||+|+.|++..++.++++++++|+|++|++||++
T Consensus 70 ~~~V~AiiGp~~S~~~~av~~i~~~~~iP~Is~~~t~~~lt~~-~~~~~~~~~~~~~~~~a~~~~~~~~~wk~vaily~~ 148 (384)
T cd06393 70 ALGVVAIFGPSQGSCTNAVQSICNALEVPHIQLRWKHHPLDNK-DTFYVNLYPDYASLSHAILDLVQYLKWRSATVVYDD 148 (384)
T ss_pred ccCcEEEECCCChHHHHHHHHHHhccCCCeEeccCCCcccCcc-ceeEEEeccCHHHHHHHHHHHHHHcCCcEEEEEEeC
Confidence 3689999999999999999999999999999999999999864 367888889998999999999999999999999976
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++ |....+.|.+.+++.|++|+. +.++.+ +.|++.+|++|++.++++||++++.+++..+++||+++||+.+.|+|
T Consensus 149 ~~-g~~~l~~~~~~~~~~g~~v~~-~~~~~~--~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~~~~ 224 (384)
T cd06393 149 ST-GLIRLQELIMAPSRYNIRLKI-RQLPTD--SDDARPLLKEMKRGREFRIIFDCSHQMAAQILKQAMAMGMMTEYYHF 224 (384)
T ss_pred ch-hHHHHHHHHHhhhccCceEEE-EECCCC--chHHHHHHHHHhhcCceEEEEECCHHHHHHHHHHHHHhccccCceEE
Confidence 64 666667888889999999986 346543 48999999999999999999999999999999999999999999999
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhh-ccCCCCCC----CCCCCcchhhhhhHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNL-TDAKTPNG----YIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~-~~~~~~~~----~~~~~~~~~~~YDAv~~ 236 (848)
+.++......+. +........++++....++.+..++|.++|+++ ++..+..+ ...+..+++++||||++
T Consensus 225 ~~~~~~~~~~~~-----~~~~~~~~~it~~~~~~~~~~~~~~f~~~~~~~~~~~~p~~~~~~~~~~~~~~aal~yDav~~ 299 (384)
T cd06393 225 IFTTLDLYALDL-----EPYRYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQAAPKPETGLLDGVMMTDAALLYDAVHM 299 (384)
T ss_pred EEccCccccccc-----hhhhcCcceEEEEEecCCCcHHHHHHHHHHHhhhhccccccccccccccccchhHHhhhhHHH
Confidence 988754433222 111111222577778888899999999999854 55322111 11236789999999999
Q ss_pred HHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEecc-CCCCCCCcEEEEEee
Q 003093 237 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNS-HGDLINPAYEIINVI 315 (848)
Q Consensus 237 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~-~g~~~~~~~~I~~~~ 315 (848)
+|+|++++.+... ..++|+...+|+.|.+|+++|++++|+|+||+++||+ +|+|.+..++|+|+.
T Consensus 300 ~a~A~~~~~~~~~--------------~~~~c~~~~~w~~G~~i~~~l~~~~~~GltG~i~Fd~~~g~r~~~~~~i~~~~ 365 (384)
T cd06393 300 VSVCYQRAPQMTV--------------NSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLK 365 (384)
T ss_pred HHHHHhhhhhcCC--------------CCCCCCCCCCCcccHHHHHHHhheeecccccceEecCCCCeeeeeEEEEEEec
Confidence 9999997532210 1456888889999999999999999999999999996 678899999999999
Q ss_pred cccEEEEEEeeCCCCCc
Q 003093 316 GTGYRRIGYWSNYSGLS 332 (848)
Q Consensus 316 ~~~~~~Vg~w~~~~gl~ 332 (848)
++++++||+|++..||+
T Consensus 366 ~~g~~~vg~W~~~~g~~ 382 (384)
T cd06393 366 EDGLEKVGVWNPNTGLN 382 (384)
T ss_pred CCcceeeEEEcCCCCcC
Confidence 99999999999999875
No 8
>cd06387 PBP1_iGluR_AMPA_GluR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=1.4e-39 Score=351.36 Aligned_cols=309 Identities=15% Similarity=0.292 Sum_probs=257.2
Q ss_pred CCCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 1 MEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 1 ~~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
|++||.||+||.++..+.++..+|+..+||+|.+.-. .+...+|.+++.|+ +..|+++++++|+|++|++||
T Consensus 60 ~~~GV~AIfGp~~~~s~~~v~s~c~~~~iP~i~~~~~----~~~~~~~~l~l~P~---l~~Ai~diI~~~~Wr~~~~iY- 131 (372)
T cd06387 60 FSRGVYAIFGFYDQMSMNTLTSFCGALHTSFITPSFP----TDADVQFVIQMRPA---LKGAILSLLAHYKWEKFVYLY- 131 (372)
T ss_pred hhcccEEEEecCCHhHHHHHHHhhccccCCeeeeCCC----CCCCCceEEEEChh---HHHHHHHHHHhcCCCEEEEEe-
Confidence 4689999999999999999999999999999986332 12345788899998 689999999999999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
|+++|...++.+.+.++..+..|.+....+.. ...+++.+|++|+.++.++||++|+++.+..++++|+++||++.+|+
T Consensus 132 d~d~gl~~Lq~L~~~~~~~~~~V~~~~v~~~~-~~~~~~~~l~el~~~~~r~iIld~s~~~~~~il~~a~e~gM~~~~y~ 210 (372)
T cd06387 132 DTERGFSILQAIMEAAVQNNWQVTARSVGNIK-DVQEFRRIIEEMDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYH 210 (372)
T ss_pred cCchhHHHHHHHHHhhccCCceEEEEEeccCC-chHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHcCccccceE
Confidence 77899999999999999999998877544433 34689999999999999999999999999999999999999999999
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhcc-CCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTD-AKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~-~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
||.++......+. .+......++++++++.++.+..++|.++|+++.. ..++.....+..+++++|||||++|+
T Consensus 211 ~ilt~ld~~~~dl-----~~~~~g~~NItg~rl~~~~~~~~~~f~~~w~~~~~~~~~~~~~~~l~~~~al~yDaV~~~A~ 285 (372)
T cd06387 211 YMLANLGFTDISL-----ERVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEAKNSPLKYTSALTHDAILVIAE 285 (372)
T ss_pred EEEecCCcccccH-----HHhccCCcceeEEEEecCCCchHHHHHHHHHhCCcccCCCCCCCCcchHHHHHHHHHHHHHH
Confidence 9999854444333 12222333399999999999999999999987764 23343444577899999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccC--cccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecc
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLD--SLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGT 317 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~--~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~ 317 (848)
|++++...+...... +. +..|. ...+|..|..|+++|++++|+|+||+++||++|+|.+..|+|+|+.+.
T Consensus 286 A~~~l~~~~~~~~~~------~~--~~~C~~~~~~~W~~G~~l~~~ik~v~~~GLTG~i~F~~~G~R~~~~ldIinl~~~ 357 (372)
T cd06387 286 AFRYLRRQRVDVSRR------GS--AGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDVYEMKPS 357 (372)
T ss_pred HHHHHHhcCCCcccC------CC--CCCcCCCCCCCccchHHHHHHHHhcccCCCccceeeCCCCCcccceEEEEEecCC
Confidence 999986543332110 01 22443 356889999999999999999999999999999999999999999999
Q ss_pred cEEEEEEeeCCCCC
Q 003093 318 GYRRIGYWSNYSGL 331 (848)
Q Consensus 318 ~~~~Vg~w~~~~gl 331 (848)
|+++||+|++..|+
T Consensus 358 g~~kIG~W~~~~g~ 371 (372)
T cd06387 358 GSRKAGYWNEYERF 371 (372)
T ss_pred CceeEEEECCCCCc
Confidence 99999999999886
No 9
>cd06389 PBP1_iGluR_AMPA_GluR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=1.4e-39 Score=355.44 Aligned_cols=313 Identities=19% Similarity=0.308 Sum_probs=252.7
Q ss_pred CCCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 1 MEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 1 ~~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
|++||+||+||++|..+.+++++|++++||+|+++++. +..++|.+++.|+ ...++++++++|+|++|++||+
T Consensus 54 ~~~GV~AI~Gp~ss~~~~~v~~i~~~~~IP~I~~~~~~----~~~~~f~~~~~p~---~~~ai~d~i~~~~wk~vailYd 126 (370)
T cd06389 54 FSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPT----DGTHPFVIQMRPD---LKGALLSLIEYYQWDKFAYLYD 126 (370)
T ss_pred hhcCcEEEEecCCHHHHHHHHHhhccCCCCeeeecCCC----CCCCceEEEecch---hhhHHHHHHHhcCCcEEEEEec
Confidence 46899999999999999999999999999999876552 3467888899888 5799999999999999999997
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeee--cCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAP--LSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~--~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
++||...++.|.+.+++.|++|+.... +.......|++.+|++|++.++|+||+.|+.+++..+++||+++||+.++
T Consensus 127 -sd~gl~~lq~l~~~~~~~g~~V~~~~~~~i~~~~~~~d~~~~L~~ik~~~~~~Iil~~~~~~~~~il~qa~~~gm~~~~ 205 (370)
T cd06389 127 -SDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDRKDEAYRSLFQDLENKKERRVILDCERDKVNDIVDQVITIGKHVKG 205 (370)
T ss_pred -CchHHHHHHHHHHhhccCCceEEEEEeecCCCccchHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHhCccccc
Confidence 569999999999999999988775442 22223457999999999999999999999999999999999999999999
Q ss_pred eEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhcc-CCCCCCCCCCCcchhhhhhHHHHH
Q 003093 159 YVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTD-AKTPNGYIGLNAYGFYAYDTVWLL 237 (848)
Q Consensus 159 ~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~-~~~~~~~~~~~~~~~~~YDAv~~~ 237 (848)
|+||+++......+.. .....-.++.+++...++.+..++|.++|++... .+++.....|..+++++||||+++
T Consensus 206 y~~il~~~~~~~~~l~-----~~~~~~~nitg~~~~~~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~aAl~yDAV~v~ 280 (370)
T cd06389 206 YHYIIANLGFTDGDLS-----KIQFGGANVSGFQIVDYDDPLVSKFIQRWSTLEEKEYPGAHTKTIKYTSALTYDAVQVM 280 (370)
T ss_pred eEEEEccCCccccchh-----hhccCCcceEEEEEecCCCchHHHHHHHHHhcCccccCCCCCcCcchHHHHHHHHHHHH
Confidence 9999987533332221 1111233577777888888999999999987322 122323346788999999999999
Q ss_pred HHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecc
Q 003093 238 ARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGT 317 (848)
Q Consensus 238 a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~ 317 (848)
|+|++++.......... ...++|..++..+|.+|..|.++|++++|+|+||+++||++|+|.+..++|++++++
T Consensus 281 a~A~~~l~~~~~~~~~~------~~~~~C~~~~~~~w~~G~~i~~~l~~~~~~GlTG~i~Fd~~G~r~~~~~~ii~l~~~ 354 (370)
T cd06389 281 TEAFRNLRKQRIEISRR------GNAGDCLANPAVPWGQGVEIERALKQVQVEGLTGNIKFDQNGKRINYTINVMELKSN 354 (370)
T ss_pred HHHHHHHHHcCCCcccC------CCCCCcCCCCCCCCCCcHHHHHHHHhcccCccccceEeCCCCccccceEEEEEecCC
Confidence 99999985543222110 001122223467899999999999999999999999999999998889999999999
Q ss_pred cEEEEEEeeCCCCCc
Q 003093 318 GYRRIGYWSNYSGLS 332 (848)
Q Consensus 318 ~~~~Vg~w~~~~gl~ 332 (848)
|+++||+|++..||.
T Consensus 355 g~~kvG~W~~~~~~~ 369 (370)
T cd06389 355 GPRKIGYWSEVDKMV 369 (370)
T ss_pred cceEEEEEcCCCCcc
Confidence 999999999988864
No 10
>cd06388 PBP1_iGluR_AMPA_GluR4 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=2.8e-39 Score=352.14 Aligned_cols=308 Identities=18% Similarity=0.296 Sum_probs=245.9
Q ss_pred CCCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 1 MEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 1 ~~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
|++||+|||||.+|..+.+++++|++++||+|+++++ +...+.|.+++.|+ +..++++++++|+|++|++||+
T Consensus 60 ~~~gV~AI~Gp~ss~~~~~v~~i~~~~~IP~I~~~~~----~~~~~~f~i~~~p~---~~~a~~~~i~~~~wk~vaiiYd 132 (371)
T cd06388 60 YSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFP----TEGESQFVLQLRPS---LRGALLSLLDHYEWNRFVFLYD 132 (371)
T ss_pred HhCCceEEEecCCHHHHHHHHHHhhCCCCCeeecCcc----ccCCCceEEEeChh---hhhHHHHHHHhcCceEEEEEec
Confidence 4689999999999999999999999999999997654 22334444455555 4578888999999999999994
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
+++|....+.|.+.+++.|++|+.....+.+ +.|++.+|++|+..++|+||++|+++.+..+++||+++||+.++|+
T Consensus 133 -~~~~~~~lq~l~~~~~~~g~~v~~~~~~~~~--~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~y~ 209 (371)
T cd06388 133 -TDRGYSILQAIMEKAGQNGWQVSAICVENFN--DASYRRLLEDLDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYH 209 (371)
T ss_pred -CCccHHHHHHHHHhhHhcCCeeeeEEeccCC--cHHHHHHHHHhcccccEEEEEECCHHHHHHHHHHHHhcCccccceE
Confidence 4456677999999999999999876655433 4699999999999999999999999999999999999999999999
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCC-CCCCCCCCCcchhhhhhHHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAK-TPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~-~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
||.++......+. .+......++.++...+++.+..++|.++|++.+... ++.. ..|..+++++||||+++|+
T Consensus 210 ~il~~~~~~~~~l-----~~~~~g~~nitg~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~-~~~~~~aAl~YDaV~l~a~ 283 (371)
T cd06388 210 YIIANLGFKDISL-----ERFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSE-SPPKYTSALTYDGVLVMAE 283 (371)
T ss_pred EEEccCccccccH-----HHHhccCCceEEEEeecCCChhHHHHHHHHHhcCccccCCCC-CCccchHHHHHHHHHHHHH
Confidence 9998753322221 1111223337888888888899999999998876432 2221 2578899999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCcccc--CcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecc
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRL--DSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGT 317 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~--~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~ 317 (848)
|++++......... . ..+..| +...+|..|..|.++|++++|+|+||+++||++|+|.+..++|+++++.
T Consensus 284 A~~~l~~~~~~~~~-----~---~~~~~C~~~~~~~w~~G~~i~~~lk~~~~~GlTG~i~Fd~~G~r~~~~l~Ii~l~~~ 355 (371)
T cd06388 284 AFRNLRRQKIDISR-----R---GNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNIQFDHYGRRVNYTMDVFELKSN 355 (371)
T ss_pred HHHHHHhcCCCccc-----C---CCCCCcCCCCCCCCcccHHHHHHHHhcCcCCCccceeECCCCCcccceEEEEEccCC
Confidence 99997543222110 0 002245 4467899999999999999999999999999999998889999999999
Q ss_pred cEEEEEEeeCCCCCc
Q 003093 318 GYRRIGYWSNYSGLS 332 (848)
Q Consensus 318 ~~~~Vg~w~~~~gl~ 332 (848)
|+++||+|++..||.
T Consensus 356 g~~kvG~W~~~~g~~ 370 (371)
T cd06388 356 GPRKIGYWNDMDKLV 370 (371)
T ss_pred CceEEEEEcCCCCcc
Confidence 999999999998864
No 11
>cd06365 PBP1_Pheromone_receptor Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptor, the GABAb receptor, the calcium-sensing receptor (CaSR), the T1R taste receptor, and a small group of uncharacterized orphan receptors.
Probab=100.00 E-value=2.2e-39 Score=365.14 Aligned_cols=305 Identities=18% Similarity=0.286 Sum_probs=248.8
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|+|||||.+|..+.+++++++.++||+||++++++.+++ .+||||||+.|+|..|+.++++++++|+|++|++|+.|
T Consensus 102 ~~vvavIG~~~S~~s~~va~i~~~~~IP~Is~~sts~~lsd~~~yp~ffRt~psd~~q~~ai~~li~~f~W~~Vaiv~~d 181 (469)
T cd06365 102 RKSVAVIGGPSWALSATIATLLGLYKFPQLTYGPFDPLLSDRVQFPSLYQMAPKDTSLPLGMVSLMLHFSWTWVGLVISD 181 (469)
T ss_pred CceEEEEcCCccHHHHHHHHHhhhhcccceeeccCCccccchhhCCcceEecCCchhHHHHHHHHHHhcCCeEEEEEEec
Confidence 57999999999999999999999999999999999999997 67999999999999999999999999999999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCCh--HHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATE--DEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~--~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
++||+...+.|.+++++.|+||++.+.++....+ .++..+|++|+.+++|+||++++.+.+..++.++.+.+. .++
T Consensus 182 ~~yg~~~~~~~~~~~~~~gi~I~~~~~i~~~~~~~~~~~~~~l~~i~~~~arvIvl~~~~~~~~~l~~~~~~~~~--~~~ 259 (469)
T cd06365 182 DDRGEQFLSDLREEMQRNGICLAFVEKIPVNMQLYLTRAEKYYNQIMTSSAKVIIIYGDTDSLLEVSFRLWQYLL--IGK 259 (469)
T ss_pred ChhHHHHHHHHHHHHHHCCeEEEEEEEecCCchhhHHHHHHHHHHhhcCCCeEEEEEcCcHHHHHHHHHHHHhcc--Cce
Confidence 9999999999999999999999999988876532 488999999999999999999998888666555554443 479
Q ss_pred EEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHH---------------HHhhcc-----------
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISR---------------WRNLTD----------- 213 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~---------------~~~~~~----------- 213 (848)
+||++++|....... ....+.++|++++.++.+..+.+++|.++ |+..|+
T Consensus 260 ~wi~s~~w~~~~~~~----~~~~~~~~G~lg~~~~~~~~~~f~~fl~~l~~~~~~~npw~~efwe~~f~c~~~~~~~~~~ 335 (469)
T cd06365 260 VWITTSQWDVTTSPK----DFTLNSFHGTLIFSHHHSEIPGFKDFLQTVNPSKYPEDIFLEKLWWIYFNCSLSKSSCKTL 335 (469)
T ss_pred EEEeecccccccccc----ccccceeeEEEEEEeccCcCcchHHHhhccCcccCCCccHHHhhHhHhcCcccCcCCcccc
Confidence 999998876543221 34557899999999999888888877654 555553
Q ss_pred -CCCCCCCCC----------CCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHH
Q 003093 214 -AKTPNGYIG----------LNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRD 282 (848)
Q Consensus 214 -~~~~~~~~~----------~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~ 282 (848)
.|+...... ...++.+.||||+++|+||++++++++.... ..+|. ....+ +.+|++
T Consensus 336 ~~c~~~~~~~~~~~~~~~~~~~~~~~~v~dAVya~AhALh~~l~c~~~~~~-----------~~~~~-~~~~~-~~~l~~ 402 (469)
T cd06365 336 KNCLSNASLEWLPLHYFDMAMSEESYNVYNAVYAVAHALHEMLLQQVETQS-----------ENNGK-RLIFL-PWQLHS 402 (469)
T ss_pred CCCCCCccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHhhccCCC-----------cCCCC-CCCcc-HHHHHH
Confidence 122221111 2335788999999999999999987543110 11222 23343 889999
Q ss_pred HHHhccccccccc-eEeccCCCCCCCcEEEEEeec--c---cEEEEEEeeC
Q 003093 283 SILQANMTGTAGP-ARFNSHGDLINPAYEIINVIG--T---GYRRIGYWSN 327 (848)
Q Consensus 283 ~l~~~~f~G~tG~-v~Fd~~g~~~~~~~~I~~~~~--~---~~~~Vg~w~~ 327 (848)
.|++++|+|.+|. |+||+||++ ...|+|+|++. + .++.||+|++
T Consensus 403 ~l~~v~F~~~~g~~v~Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~VG~~~~ 452 (469)
T cd06365 403 FLKNIQFKNPAGDEVNLNQKRKL-DTEYDILNYWNFPQGLGLKVKVGEFSP 452 (469)
T ss_pred HHHhccccCCCCCEEEecCCCCc-CceeeEEEEEECCCCCEEEEEEEEEeC
Confidence 9999999999995 999999995 67999999983 2 3699999975
No 12
>cd06380 PBP1_iGluR_AMPA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excita
Probab=100.00 E-value=3.6e-39 Score=357.03 Aligned_cols=320 Identities=20% Similarity=0.343 Sum_probs=251.8
Q ss_pred CCCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 1 MEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 1 ~~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
|+++|+|||||.+|..+.++++++++++||+|+++++.|.++ ..+||+||+.|+. ..++++++++++|++|++||+
T Consensus 59 l~~~V~aiiGp~~s~~~~~~~~~~~~~~iP~i~~~~~~~~l~-~~~~~~fr~~p~~---~~a~~~~~~~~~wk~vaii~~ 134 (382)
T cd06380 59 LSRGVFAIFGSYDKSSVNTLTSYSDALHVPFITPSFPTNDLD-DGNQFVLQMRPSL---IQALVDLIEHYGWRKVVYLYD 134 (382)
T ss_pred HhcCcEEEEecCcHHHHHHHHHHHhcCCCCeEecCCCcccCC-CCCcEEEEeccch---hHHHHHHHHhcCCeEEEEEEC
Confidence 357899999999999999999999999999999999988885 4679999998863 458889999999999999997
Q ss_pred cCCCccchHHHHHHHHhccC--cEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 81 DDDHGRNGIAALGDTLAAKR--CRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g--~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
+++ |....+.+.+.+++.| ++|.... +....+..|++.+|++|++.++|+||+.++.+++..+++||+++||+.++
T Consensus 135 ~~~-~~~~~~~~~~~~~~~g~~i~v~~~~-~~~~~~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~i~~qa~~~gm~~~~ 212 (382)
T cd06380 135 SDR-GLLRLQQLLDYLREKDNKWQVTARR-VDNVTDEEEFLRLLEDLDRRKEKRIVLDCESERLNKILEQIVDVGKNRKG 212 (382)
T ss_pred CCc-chHHHHHHHHHHhccCCceEEEEEE-ecCCCcHHHHHHHHHHhhcccceEEEEECCHHHHHHHHHHHHHhhhcccc
Confidence 665 6677788889999988 6665432 33222347999999999999999999999999999999999999999999
Q ss_pred eEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccC-CCCCCCCCCCcchhhhhhHHHHH
Q 003093 159 YVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLL 237 (848)
Q Consensus 159 ~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~ 237 (848)
|+||.+++.....+.. .......++.++....+..+..++|.++|+++++. .+......+..+++++||||+++
T Consensus 213 y~~i~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~aYDav~~~ 287 (382)
T cd06380 213 YHYILANLGFDDIDLS-----KFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPGAGTSPIKYTAALAHDAVLVM 287 (382)
T ss_pred eEEEEccCCcccccHH-----HhccCceeeEEEeccCCCCHHHHHHHHHHHhcCccccCcCCcCCcchHHHHHHHHHHHH
Confidence 9999987654443321 11122334666666676788999999999998852 12222234678999999999999
Q ss_pred HHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecc
Q 003093 238 ARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGT 317 (848)
Q Consensus 238 a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~ 317 (848)
|+|++++.+.++...+............|.-+...+|.+|++|.++|++++|+|++|+++||++|++....++|++++++
T Consensus 288 a~Al~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG~i~Fd~~G~~~~~~~~i~~~~~~ 367 (382)
T cd06380 288 AEAFRSLRRQRGSGRHRIDISRRGNGGDCLANPAVPWEHGIDIERALKKVQFEGLTGNVQFDEFGQRTNYTLDVVELKTR 367 (382)
T ss_pred HHHHHHHHHhccccccccccccCCCCCcCCCCCCCCccchHHHHHHHHhcccCCcccceEECCCCCcccccEEEEEecCC
Confidence 99999987654321100000000001123323456788899999999999999999999999999988889999999999
Q ss_pred cEEEEEEeeCCCCC
Q 003093 318 GYRRIGYWSNYSGL 331 (848)
Q Consensus 318 ~~~~Vg~w~~~~gl 331 (848)
+.+.||+|++..||
T Consensus 368 ~~~~vg~w~~~~g~ 381 (382)
T cd06380 368 GLRKVGYWNEDDGL 381 (382)
T ss_pred CceEEEEECCCcCc
Confidence 99999999998875
No 13
>cd06375 PBP1_mGluR_groupII Ligand binding domain of the group II metabotropic glutamate receptor. Ligand binding domain of the group II metabotropic glutamate receptor, a family that contains mGlu2R and mGlu3R, all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes
Probab=100.00 E-value=6.4e-39 Score=359.78 Aligned_cols=304 Identities=20% Similarity=0.351 Sum_probs=253.8
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|+|||||.+|.++.+++++++.++||+||+++++|.|++ .+||||||+.|+|..|++++++++++|||++|++||+|
T Consensus 104 ~~V~aVIG~~~S~~s~ava~~~~~~~IP~Is~~sts~~Ls~~~~~~~ffRt~psd~~qa~ai~~ll~~~~W~~Vaii~~~ 183 (458)
T cd06375 104 LAIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASE 183 (458)
T ss_pred CCeEEEEcCCCchHHHHHHHHhhhccccceeeccCChhhcccccCCCeEEecCCcHHHHHHHHHHHHHCCCeEEEEEEeC
Confidence 47999999999999999999999999999999999999997 67999999999999999999999999999999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc-CCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~-~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
++||+...+.|.+++++.|+||+..+.++...+..|+..++++|+. .++||||+++...++..++++|+++|+. +.
T Consensus 184 ~~yG~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~l~~~~~a~vVvl~~~~~~~~~ll~~a~~~g~~---~~ 260 (458)
T cd06375 184 GDYGETGIEAFEQEARLRNICIATSEKVGRSADRKSYDSVIRKLLQKPNARVVVLFTRSEDARELLAAAKRLNAS---FT 260 (458)
T ss_pred chHHHHHHHHHHHHHHHCCeeEEEEEEecCCCCHHHHHHHHHHHhccCCCEEEEEecChHHHHHHHHHHHHcCCc---EE
Confidence 9999999999999999999999998888776666899999999875 6999999999999999999999999984 89
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHH---------------HHhhccC-----------
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISR---------------WRNLTDA----------- 214 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~---------------~~~~~~~----------- 214 (848)
||++++|....... ....+.++|++++.+.....+.+++|++. |+..|+.
T Consensus 261 wigs~~~~~~~~~~----~~~~~~~~G~i~~~~~~~~i~~f~~yl~~l~p~~~~~n~w~~e~w~~~f~c~~~~~~~~~~~ 336 (458)
T cd06375 261 WVASDGWGAQESIV----KGSEDVAEGAITIELASHPIPDFDRYFQSLTPETNTRNPWFKDFWEQKFQCSLQNRDCANTT 336 (458)
T ss_pred EEEeccccccchhh----hccchhhceEEEEEeccccchhHHHHHHhCCcCcCCCCcHHHHHHHHHcCCCCCCCCccCCC
Confidence 99999886432221 22446789999999988887877776644 6666641
Q ss_pred CCCCCC------CCCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHH-HHHHhc
Q 003093 215 KTPNGY------IGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLR-DSILQA 287 (848)
Q Consensus 215 ~~~~~~------~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~-~~l~~~ 287 (848)
|.+.+. .....++.+.||||+++|+||++++++.+... .-.|.....++ +.+|+ +.|+++
T Consensus 337 C~~~~~~~~~~~~~~~~~~~~v~~AVyA~AhaLh~~l~~~c~~~------------~~~c~~~~~~~-~~~l~~~~L~~v 403 (458)
T cd06375 337 TNDKERLLDKVNYEQESKIMFVVNAVYAMAHALHNMQRDLCPNT------------TKLCDAMKPLD-GKKLYKEYLLNV 403 (458)
T ss_pred CCchhcccccCcccccchHHHHHHHHHHHHHHHHHHHHhcCCCC------------CCCCCCCCCCC-HHHHHHHHHHhc
Confidence 211111 12245788999999999999999997654321 11355545565 89999 599999
Q ss_pred ccc-----cccc-ceEeccCCCCCCCcEEEEEeec--cc----EEEEEEeeC
Q 003093 288 NMT-----GTAG-PARFNSHGDLINPAYEIINVIG--TG----YRRIGYWSN 327 (848)
Q Consensus 288 ~f~-----G~tG-~v~Fd~~g~~~~~~~~I~~~~~--~~----~~~Vg~w~~ 327 (848)
+|. |.+| +|.||++|+. ...|+|+|++. ++ ++.||.|++
T Consensus 404 ~F~~~~~~~~~g~~v~Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 404 SFTAPFRPDLADSEVKFDSQGDG-LGRYNIFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred cccccccCCCCCCeeEECCCCCC-CcceEEEEEEEcCCCCcEEEEEEEEEec
Confidence 999 9988 5999999995 68999999993 32 589999964
No 14
>cd06374 PBP1_mGluR_groupI Ligand binding domain of the group I metabotropic glutamate receptor. Ligand binding domain of the group I metabotropic glutamate receptor, a family containing mGlu1R and mGlu5R, all of which stimulate phospholipase C (PLC) hydrolysis. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes.
Probab=100.00 E-value=6.4e-39 Score=363.14 Aligned_cols=311 Identities=21% Similarity=0.339 Sum_probs=251.8
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|+|||||.+|.++.+++++++.++||+|+++++++.+++ .+||||||+.|+|..|+.++++++++|+|++|++||+
T Consensus 115 ~~~V~aiiGp~~S~~~~ava~~~~~~~iP~Is~~ats~~ls~~~~~p~~fRt~p~d~~~~~al~~l~~~~~W~~Vaii~~ 194 (472)
T cd06374 115 KKPIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSIDLSDKTLFKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHT 194 (472)
T ss_pred CCCeEEEECCCcchHHHHHHHHhhhhcccccccccCchhhcccccCCceEEcCCChHHHHHHHHHHHHHCCCcEEEEEEe
Confidence 358999999999999999999999999999999999999998 5799999999999999999999999999999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCC--CeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~--~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
|++||+...+.|.+.+++.|+||++.+.++...+..|+..+|++|++.+ ++||++++....+..++++|+++||. .+
T Consensus 195 ~~~yg~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~lk~~~~da~vvv~~~~~~~~~~~l~~a~~~g~~-~~ 273 (472)
T cd06374 195 EGNYGESGMEAFKELAAHEGLCIAHSDKIYSNAGEQSFDRLLRKLRSRLPKARVVVCFCEGMTVRGLLMAMRRLGVG-GE 273 (472)
T ss_pred cchHHHHHHHHHHHHHHHCCeeEEEEEEecCCCchHHHHHHHHHHHhcCCCcEEEEEEechHHHHHHHHHHHHhcCC-Cc
Confidence 9999999999999999999999999888865556689999999999764 55666667777889999999999995 56
Q ss_pred eEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHH---------------HHHHhhccC---------
Q 003093 159 YVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFI---------------SRWRNLTDA--------- 214 (848)
Q Consensus 159 ~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~---------------~~~~~~~~~--------- 214 (848)
++||++++|....... ....+.++|++++.+..+..+.+++|. +.|++.|..
T Consensus 274 ~~wi~s~~~~~~~~~~----~~~~~~~~G~l~~~~~~~~~~~F~~~l~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~ 349 (472)
T cd06374 274 FQLIGSDGWADRDDVV----EGYEEEAEGGITIKLQSPEVPSFDDYYLKLRPETNTRNPWFREFWQHRFQCRLPGHPQEN 349 (472)
T ss_pred eEEEEecccccchHhh----hcchhhhheeEEEEecCCCCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCcCCccCcC
Confidence 8999999876532221 234567899999999888777777654 456665541
Q ss_pred ------CCCCCCC----CCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHH
Q 003093 215 ------KTPNGYI----GLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSI 284 (848)
Q Consensus 215 ------~~~~~~~----~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l 284 (848)
|.+.... ....+++++|||||++|+||++++.+.+... ...|...... +|.+|+++|
T Consensus 350 ~~~~~~c~~~~~~~~~~~~~~~~~~vyDAVyaiA~ALh~~~~~~~~~~------------~~~c~~~~~~-~~~~l~~~l 416 (472)
T cd06374 350 PNYIKICTGNESLDEQYVQDSKMGFVINAIYAMAHGLHNMHQDLCPGH------------VGLCDAMKPI-DGRKLLEYL 416 (472)
T ss_pred CccCCCCCCcccccccccccceeHHHHHHHHHHHHHHHHHHHhhCCCC------------CCCCcCCCCC-CHHHHHHHH
Confidence 1111101 1125667999999999999999986543211 1124333334 499999999
Q ss_pred Hhcccccccc-ceEeccCCCCCCCcEEEEEeec-----ccEEEEEEeeCCCCCc
Q 003093 285 LQANMTGTAG-PARFNSHGDLINPAYEIINVIG-----TGYRRIGYWSNYSGLS 332 (848)
Q Consensus 285 ~~~~f~G~tG-~v~Fd~~g~~~~~~~~I~~~~~-----~~~~~Vg~w~~~~gl~ 332 (848)
++++|+|++| +|.||++|++. ..|+|+|++. .+++.||.|++ .+|.
T Consensus 417 ~~v~F~g~tG~~v~Fd~~G~~~-~~ydI~n~~~~~~~~~~~~~VG~w~~-~~l~ 468 (472)
T cd06374 417 LKTSFSGVSGEEVYFDENGDSP-GRYDIMNLQYTEDLRFDYINVGSWHE-GDLG 468 (472)
T ss_pred HhCcccCCCCCeEEEcCCCCCC-CceEEEEEEECCCCCEEEEEEEEEeC-Cccc
Confidence 9999999999 69999999974 6899999994 35799999974 3554
No 15
>cd06367 PBP1_iGluR_NMDA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits
Probab=100.00 E-value=3.9e-39 Score=354.01 Aligned_cols=281 Identities=22% Similarity=0.329 Sum_probs=242.2
Q ss_pred CCCeEEEEccCCchh---HHHHHHhhccCCccEEecccCCCCC-CC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEE
Q 003093 2 EGQTVAIIGPQDAVT---SHVVSHVANELQVPLLSFSATDPTL-SS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVI 76 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~---~~ava~i~~~~~vP~Is~~at~p~l-s~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~va 76 (848)
+++|.+||||.+|.. +.+++++++.++||+|+++++++.+ ++ .+||||||+.|++..|++++++++++|+|++|+
T Consensus 61 ~~~v~~iig~~~s~~~~~~~~~~~v~~~~~iP~Is~~~~~~~~~s~~~~~~~~~R~~p~~~~~~~ai~~ll~~~~w~~va 140 (362)
T cd06367 61 VQVVAGVVFSDPTDEEAVAQILDFTSAQTRIPVVGISGRESIFMSDKNIHSLFLQTGPSLEQQADVMLEILEEYDWHQFS 140 (362)
T ss_pred ccceEEEEecCCCCccchhhhhhhhhhhhcCcEEEeeccccccccCCCcccceEeecCcHHHHHHHHHHHHHHcCCeEEE
Confidence 357999999999998 9999999999999999999999998 76 689999999999999999999999999999999
Q ss_pred EEEEcCCCccchHHHHHHHHhccCcE--EEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 77 AIYVDDDHGRNGIAALGDTLAAKRCR--ISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 77 ii~~dd~~g~~~~~~l~~~l~~~g~~--v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
+||++++||++..+.+++.+++.|++ ++....++... ..++..++.++++.++|+||++++.+++..++++|+++||
T Consensus 141 ii~~~~~~g~~~~~~l~~~l~~~g~~~~i~~~~~~~~~~-~~~~~~~l~~l~~~~~~vivl~~~~~~~~~il~~a~~~g~ 219 (362)
T cd06367 141 VVTSRDPGYRDFLDRVETTLEESFVGWEFQLVLTLDLSD-DDGDARLLRQLKKLESRVILLYCSKEEAERIFEAAASLGL 219 (362)
T ss_pred EEEEcCcccHHHHHHHHHHHHhcccceeeeeeEEeccCC-CcchHHHHHHHHhcCCcEEEEeCCHHHHHHHHHHHHHcCC
Confidence 99999999999999999999999999 77666666543 2378999999999999999999999999999999999999
Q ss_pred CCCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHH
Q 003093 155 LGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTV 234 (848)
Q Consensus 155 ~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv 234 (848)
++++|+||+++.+.... ....+...|++++++... ..+++++||||
T Consensus 220 ~~~~~~wI~~~~~~~~~-------~~~~~~~~G~~g~~~~~~---------------------------~~~~~~~~Dav 265 (362)
T cd06367 220 TGPGYVWIVGELALGSG-------LAPEGLPVGLLGVGLDTW---------------------------YSLEARVRDAV 265 (362)
T ss_pred CCCCcEEEECccccccc-------CCccCCCCeeEEEEeccc---------------------------ccHHHHHHHHH
Confidence 99999999999876421 123356789999876532 23578899999
Q ss_pred HHHHHHHHHHHhcCCCccccCCCccccccCccccCccc--ccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEE
Q 003093 235 WLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLR--IFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEII 312 (848)
Q Consensus 235 ~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~--~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~ 312 (848)
+++|+|+++++++...... +..+|.... .|..|..|.++|++++|.|++|+|+||++|++..+.|+|+
T Consensus 266 ~~~a~Al~~~~~~~~~~~~----------~~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg~v~F~~~G~~~~~~~~I~ 335 (362)
T cd06367 266 AIVARAAESLLRDKGALPE----------PPVNCYDTANKRESSGQYLARFLMNVTFDGETGDVSFNEDGYLSNPKLVII 335 (362)
T ss_pred HHHHHHHHHHHHhcCCCCC----------CCCCcCCCCCCCCCchHHHHHHHhcccccCCCCceeECCCcccccceEEEE
Confidence 9999999999876433211 123455442 2677999999999999999999999999999888899999
Q ss_pred Eee-cccEEEEEEeeC
Q 003093 313 NVI-GTGYRRIGYWSN 327 (848)
Q Consensus 313 ~~~-~~~~~~Vg~w~~ 327 (848)
|++ +.+|++||.|++
T Consensus 336 ~l~~~~~~~~VG~W~~ 351 (362)
T cd06367 336 NLRRNRKWERVGSWEN 351 (362)
T ss_pred EecCCCcceEEEEEcC
Confidence 999 889999999975
No 16
>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=1.3e-38 Score=360.14 Aligned_cols=306 Identities=21% Similarity=0.371 Sum_probs=250.7
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|+|||||.+|.++.+++++++.++||+|++++++|.+++ .+||||||+.|+|..|++++++++++|+|++|++||.|
T Consensus 102 ~~V~aviG~~~S~~t~ava~i~~~~~iP~Is~~ats~~ls~~~~~~~ffR~~p~d~~~~~ai~~~i~~~~w~~Vaii~~~ 181 (463)
T cd06376 102 EKVVGVIGASASSVSIMVANILRLFQIPQISYASTAPELSDDRRYDFFSRVVPPDSFQAQAMVDIVKALGWNYVSTLASE 181 (463)
T ss_pred CCeEEEECCCCchHHHHHHHHhccccCcccccccCChhhcccccCCceEEccCCHHHHHHHHHHHHHHcCCeEEEEEEeC
Confidence 58999999999999999999999999999999999999987 67999999999999999999999999999999999999
Q ss_pred CCCccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhc-CCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 82 DDHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~-~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
++||....+.|.+.+++. |++|...+.++...++.|+..+|++|++ .++|+||+.++..++..++++|+++|+.+ .|
T Consensus 182 ~~yg~~~~~~~~~~~~~~g~~~v~~~~~i~~~~~~~d~~~~l~~ik~~~~~~vIvl~~~~~~~~~ll~~a~~~~~~g-~~ 260 (463)
T cd06376 182 GNYGESGVEAFTQISREAGGVCIAQSIKIPREPRPGEFDKIIKRLLETPNARAVIIFANEDDIRRVLEAAKRANQVG-HF 260 (463)
T ss_pred ChHHHHHHHHHHHHHHHcCCceEEEEEecCCCCCHHHHHHHHHHHhccCCCeEEEEecChHHHHHHHHHHHhcCCcC-ce
Confidence 999999999999999997 4788776666655567899999999986 69999999999999999999999999864 59
Q ss_pred EEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHH---------------HHHhhccC----------
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFIS---------------RWRNLTDA---------- 214 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~---------------~~~~~~~~---------- 214 (848)
+||++++|....... ....+.++|++++.+.....+.+++|.. .|+..|+.
T Consensus 261 ~wig~d~~~~~~~~~----~~~~~~~~G~~~~~~~~~~~~~F~~~~~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~~ 336 (463)
T cd06376 261 LWVGSDSWGAKISPI----LQQEDVAEGAITILPKRASIEGFDAYFTSRTLENNRRNVWFAEFWEENFNCKLTISGSKKE 336 (463)
T ss_pred EEEEecccccccccc----ccCcceeeeEEEEEeccccchhHHHHHHhCCcccCCCCcHHHHHHHHhCCCcccCCCCccc
Confidence 999999886543322 1223568999999888777777766554 57665531
Q ss_pred -----CCCCCCC------CCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHH
Q 003093 215 -----KTPNGYI------GLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDS 283 (848)
Q Consensus 215 -----~~~~~~~------~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~ 283 (848)
|.+.+.. .....++++||||+++|+||++++++.+... ...|...... +|.+|+++
T Consensus 337 ~~~~~C~~~~~~~~~~~~~~~~~~~~v~dAVyaiA~ALh~l~~~~c~~~------------~~~C~~~~~~-~~~~l~~~ 403 (463)
T cd06376 337 DTDRKCTGQERIGRDSTYEQEGKVQFVIDAVYAMAHALHSMHKDLCPGY------------TGVCPEMEPA-DGKKLLKY 403 (463)
T ss_pred cccCcCcchhhccccCcccccchhHHHHHHHHHHHHHHHHHHHhhCCCC------------CCCCccCCCC-CHHHHHHH
Confidence 1111111 1123688999999999999999986544211 1134433334 49999999
Q ss_pred HHhcccccccc-ceEeccCCCCCCCcEEEEEeec-----ccEEEEEEeeC
Q 003093 284 ILQANMTGTAG-PARFNSHGDLINPAYEIINVIG-----TGYRRIGYWSN 327 (848)
Q Consensus 284 l~~~~f~G~tG-~v~Fd~~g~~~~~~~~I~~~~~-----~~~~~Vg~w~~ 327 (848)
|++++|+|++| +|+||++|++ .+.|+|++++. .+++.||.|++
T Consensus 404 L~~v~F~g~tg~~v~Fd~~G~~-~~~Ydi~n~q~~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 404 IRAVNFNGSAGTPVMFNENGDA-PGRYDIFQYQITNTSSPGYRLIGQWTD 452 (463)
T ss_pred HHhCCccCCCCCeEEeCCCCCC-CCceEEEEEEecCCCceeEEEEEEECC
Confidence 99999999999 6999999996 46899999983 35799999975
No 17
>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-38 Score=358.41 Aligned_cols=310 Identities=21% Similarity=0.361 Sum_probs=254.5
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|+|||||.+|.++.+++++++.++||+|+++++++.+++ .+||||||+.|++..|+.++++++++|+|++|++||+|
T Consensus 102 ~~v~aviG~~~S~~~~av~~~~~~~~ip~Is~~sts~~ls~~~~~~~~fR~~p~d~~~~~a~~~~l~~~~w~~vaii~~~ 181 (452)
T cd06362 102 KPVAGVIGASYSSVSIQVANLLRLFKIPQISYASTSPELSDKTRYDYFSRTVPPDSFQAQAMVDIVKAFNWTYVSTVASE 181 (452)
T ss_pred CCeEEEECCCCCchHHHHHHHhccccCcccccccCchhhccccccCCEEEecCChHHHHHHHHHHHHHCCCcEEEEEEeC
Confidence 58999999999999999999999999999999999999987 68999999999999999999999999999999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc-CCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~-~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
++||+...+.|.+.+++.|+||+..+.++...+..|+..++++|++ .++|+||+.+...++..++++|+++|+. ..++
T Consensus 182 ~~~G~~~~~~~~~~~~~~gi~i~~~~~~~~~~~~~d~~~~l~~l~~~~~a~viil~~~~~~~~~~~~~a~~~g~~-~~~~ 260 (452)
T cd06362 182 GNYGEKGIEAFEKLAAERGICIAGSEKIPSSATEEEFDNIIRKLLSKPNARVVVLFCREDDIRGLLAAAKRLNAE-GHFQ 260 (452)
T ss_pred CHHHHHHHHHHHHHHHHCCeeEEEEEEcCCCCCHHHHHHHHHHHhhcCCCeEEEEEcChHHHHHHHHHHHHcCCc-CceE
Confidence 9999999999999999999999998888765566899999999987 5799999999999999999999999997 5689
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHH---------------HHHHhhccC-----------
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFI---------------SRWRNLTDA----------- 214 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~---------------~~~~~~~~~----------- 214 (848)
||++++|....... ....++.+|++++.+.....+.+++|+ +.|+..+..
T Consensus 261 ~i~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~i~~f~~~l~~l~~~~~~~~~~~~~~w~~~~~c~~~~~~~~~~~ 336 (452)
T cd06362 261 WIASDGWGARNSVV----EGLEDVAEGAITIELQSAEVPGFDEYFLSLTPENNSRNPWFREFWEQKFNCKLTGNGSTKDN 336 (452)
T ss_pred EEEeccccccchhh----cccccccceEEEEEecccccccHHHHhhhCCcCcCCCChHHHHHHHHhcCCCcCCCCccccC
Confidence 99998876542221 334577899999888766655554433 334444431
Q ss_pred --CCCCCC----CCCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhcc
Q 003093 215 --KTPNGY----IGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQAN 288 (848)
Q Consensus 215 --~~~~~~----~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~ 288 (848)
|+.... .....+++++|||||++|+||+++++++.... .-.|.....+ ++.+|.++|++++
T Consensus 337 ~~c~~~~~~~~~~~~~~~~~~vyDAV~a~A~AL~~~l~~~~~~~------------~~~c~~~~~~-~~~~l~~~l~~v~ 403 (452)
T cd06362 337 TCCTERILLLSNYEQESKVQFVIDAVYAMAHALHNMHRDLCPGT------------TGLCDAMKPI-DGRKLLFYLRNVS 403 (452)
T ss_pred CCCccccccccccccccchhHHHHHHHHHHHHHHHHHHhhCCCC------------CCCCcCccCC-CHHHHHHHHHhCC
Confidence 111110 12345889999999999999999987643211 1124333334 4999999999999
Q ss_pred cccccc-ceEeccCCCCCCCcEEEEEeec----ccEEEEEEeeCCCCC
Q 003093 289 MTGTAG-PARFNSHGDLINPAYEIINVIG----TGYRRIGYWSNYSGL 331 (848)
Q Consensus 289 f~G~tG-~v~Fd~~g~~~~~~~~I~~~~~----~~~~~Vg~w~~~~gl 331 (848)
|.|++| +|+||++|++ ...|+|+|++. .++++||+|++..|+
T Consensus 404 f~g~tg~~v~Fd~~G~~-~~~y~I~~~~~~~~~~~~~~VG~w~~~~~~ 450 (452)
T cd06362 404 FSGLAGGPVRFDANGDG-PGRYDIFNYQRTNGKYDYVKVGSWKGELSL 450 (452)
T ss_pred cCCCCCceEEECCCCCC-CCceEEEEEEEcCCceEEEEEEEEeccccc
Confidence 999998 7999999997 56999999984 358999999877664
No 18
>cd06361 PBP1_GPC6A_like Ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor. This family includes the ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor, and its fish homolog, the 5.24 chemoreceptor. GPRC6A is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses.
Probab=100.00 E-value=2.2e-38 Score=349.47 Aligned_cols=285 Identities=24% Similarity=0.294 Sum_probs=240.0
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|.|||||.+|.++.+++++++.++||+||+++++|.|++ .+||||||++|+|..|++++++++++|||++|++|++|
T Consensus 102 ~~V~aVIG~~~S~~s~ava~v~~~~~IP~IS~~ats~~Ls~~~~~~~ffRt~p~D~~qa~ai~~li~~~~w~~Vaii~~~ 181 (403)
T cd06361 102 PRIKAVIGAGYSEISMAVSRMLNLQLIPQVSYASTAEILSDKIRFPSFLRTVPSDFYQTKAMAHLIKKSGWNWVGIIITD 181 (403)
T ss_pred CCeEEEECCCcchHHHHHHHHhccCCcceEecCcCCcccCCcccCCCeeECCCchHhHHHHHHHHHHHcCCcEEEEEEec
Confidence 58999999999999999999999999999999999999997 68999999999999999999999999999999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCCh-----HHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATE-----DEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~-----~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
++||+...+.|.+++++.|+||+..+.++...++ .++..+++.+++.++||||+++..+++..++++|+++|+
T Consensus 182 d~yG~~~~~~f~~~~~~~GicIa~~e~~~~~~~~~~~~~~~~~~~~~~ik~~~a~vVvv~~~~~~~~~l~~~a~~~g~-- 259 (403)
T cd06361 182 DDYGRSALETFIIQAEANGVCIAFKEILPASLSDNTKLNRIIRTTEKIIEENKVNVIVVFARQFHVFLLFNKAIERNI-- 259 (403)
T ss_pred CchHHHHHHHHHHHHHHCCeEEEEEEEecCccCcchhHHHHHHHHHHHHhcCCCeEEEEEeChHHHHHHHHHHHHhCC--
Confidence 9999999999999999999999999988775322 466677777899999999999999999999999999998
Q ss_pred CCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHH
Q 003093 157 TGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 157 ~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~ 236 (848)
+++||++++|........ ....+...|++++.+..+..+. |.+.|++++ ..++||||++
T Consensus 260 -~~~wigs~~w~~~~~~~~---~~~~~~~~g~ig~~~~~~~~~~---F~~~~~~~~--------------~~~v~~AVya 318 (403)
T cd06361 260 -NKVWIASDNWSTAKKILT---DPNVKKIGKVVGFTFKSGNISS---FHQFLKNLL--------------IHSIQLAVFA 318 (403)
T ss_pred -CeEEEEECcccCcccccc---CCcccccceEEEEEecCCccch---HHHHHHHhh--------------HHHHHHHHHH
Confidence 689999998875433221 2223567889998886655554 445555443 2358999999
Q ss_pred HHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeec
Q 003093 237 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIG 316 (848)
Q Consensus 237 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~ 316 (848)
+|+||+++..+. .|....+++ +++|+++|++++|+|++|++.||++|+. ...|+|+++++
T Consensus 319 iA~Al~~~~~~~------------------~c~~~~~~~-~~~l~~~L~~~~f~g~~~~v~Fd~~gd~-~~~y~I~~~~~ 378 (403)
T cd06361 319 LAHAIRDLCQER------------------QCQNPNAFQ-PWELLGQLKNVTFEDGGNMYHFDANGDL-NLGYDVVLWKE 378 (403)
T ss_pred HHHHHHHhccCC------------------CCCCCCCcC-HHHHHHHHheeEEecCCceEEECCCCCC-CcceEEEEeEe
Confidence 999999964321 133333444 9999999999999999889999999995 68999999986
Q ss_pred cc----EEEEEEeeCCCC
Q 003093 317 TG----YRRIGYWSNYSG 330 (848)
Q Consensus 317 ~~----~~~Vg~w~~~~g 330 (848)
++ +++||.|++...
T Consensus 379 ~~~~~~~~~vg~~~~~~~ 396 (403)
T cd06361 379 DNGHMTVTIMAEYDPQND 396 (403)
T ss_pred cCCcEEEEEEEEEeCCCC
Confidence 43 699999988653
No 19
>cd06391 PBP1_iGluR_delta_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related to non-NMDA receptors. GluRdelta2 was shown to function as a
Probab=100.00 E-value=2.8e-38 Score=346.11 Aligned_cols=312 Identities=19% Similarity=0.301 Sum_probs=248.9
Q ss_pred CCCCeEEEEccCCchhHHHHHHhhccCCccEEec----ccCC-----CCCCC--CCCCceEeccCChHHHHHHHHHHHHH
Q 003093 1 MEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSF----SATD-----PTLSS--LQFPYFVRTTQSDQYQMAAIAEIVDH 69 (848)
Q Consensus 1 ~~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~----~at~-----p~ls~--~~~p~f~r~~p~d~~q~~ai~~~~~~ 69 (848)
++++|.|||||.++..+..++.+|+.++||+|++ ++++ |.+++ .+||+++| |+ ..+++++++++++
T Consensus 59 ~~~gv~ai~Gp~~~~~~~~v~~~~~~~~vP~i~~~~~~~~t~~~~~~~~~~~~~~~y~~~~r--p~-~~~~~ai~~li~~ 135 (400)
T cd06391 59 MNQGILALVSSIGCTSAGSLQSLADAMHIPHLFIQRSTAGTPRSSCGLTRSNRNDDYTLSVR--PP-VYLNDVILRVVTE 135 (400)
T ss_pred HhCCeEEEECCCcchHHHHHHHHhccCcCCeEEeecccccCccccCCCCCCCCcccceEEec--Ch-HHHHHHHHHHHHH
Confidence 3578999999988889999999999999999985 5543 44443 56888888 43 6789999999999
Q ss_pred cCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCCh---HHHHH-HHHHHhc--CCCeEEEEEccCCcHH
Q 003093 70 YGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATE---DEITD-LLVKVAL--TESRIIVVHTHYNRGP 143 (848)
Q Consensus 70 ~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~---~d~~~-~l~~i~~--~~~~viv~~~~~~~~~ 143 (848)
|+|++|+++| |++||...++.+.+++++.|+||..... ....++ ..+.. .+++|+. .+.++||++++.+.+.
T Consensus 136 f~W~~v~i~~-d~~~~~~~l~~l~~~~~~~~i~I~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~rviVl~~~~~~~~ 213 (400)
T cd06391 136 YAWQKFIIFY-DTDYDIRGIQEFLDKVSQQGMDVALQKV-ENNINKMITGLFRTMRIEELNRYRDTLRRAILVMNPATAK 213 (400)
T ss_pred cCCcEEEEEE-eCCccHHHHHHHHHHHHHcCCeEEEEec-CcchhhhhHHHHHHHHHHHHHhhcccccEEEEECCcHHHH
Confidence 9999999765 6778999999999999999999997442 221110 12322 4456665 5679999999999999
Q ss_pred HHHHHHHHcCCCCCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccC--C-CCCC-
Q 003093 144 VVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA--K-TPNG- 219 (848)
Q Consensus 144 ~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~--~-~~~~- 219 (848)
.+|++|+++||++.+|+||.+++....++.. +...+.+.|+.+++++.|.+....+|..+|+.++.. + +...
T Consensus 214 ~ll~~a~~~gm~~~~y~wi~t~~~~~~~dl~----~~~~~~~~~v~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~ 289 (400)
T cd06391 214 SFITEVVETNLVAFDCHWIIINEEISDMDVQ----ELVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSLCDPKDPF 289 (400)
T ss_pred HHHHHHHHcCCCCCCeEEEEeCccccccccc----hHHhcccceEEEeccCCchHHHHHHHHHHHhhhccccccCccccc
Confidence 9999999999999999999999988877653 223345678888999998888889999999887632 1 1111
Q ss_pred CCCCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCcccc--CcccccCChHHHHHHHHhccccccccceE
Q 003093 220 YIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRL--DSLRIFNGGNLLRDSILQANMTGTAGPAR 297 (848)
Q Consensus 220 ~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~--~~~~~~~~g~~l~~~l~~~~f~G~tG~v~ 297 (848)
...++.+++++|||||++|+|++++...+...... .++| ++..+|+.|..|+++|++++|+|+||+++
T Consensus 290 ~~~~~~~~alayDaV~~~A~A~~~l~~~~~~~~~~----------~~~c~~~~~~~w~~G~~ll~~i~~~~f~GlTG~i~ 359 (400)
T cd06391 290 AQMMEISNLYIYDTVLLLANAFHKKLEDRKWHSMA----------SLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELE 359 (400)
T ss_pred cccccchhhHHHHHHHHHHHHHHHHHhhccccCCC----------CcccccCCCCCCCChHHHHHHHHhcCcccceeceE
Confidence 12367899999999999999999875332221110 2334 34668999999999999999999999999
Q ss_pred eccCCCCCCCcEEEEEee-----cccEEEEEEeeCCCCC
Q 003093 298 FNSHGDLINPAYEIINVI-----GTGYRRIGYWSNYSGL 331 (848)
Q Consensus 298 Fd~~g~~~~~~~~I~~~~-----~~~~~~Vg~w~~~~gl 331 (848)
||++|+|.+..|+|+|+. +.|.++||+|++..||
T Consensus 360 f~~~g~r~~~~~dIin~~~~~~~~~g~rkiG~Ws~~~gl 398 (400)
T cd06391 360 FNENGGNPNVHFEILGTNYGEDLGRGVRKLGCWNPITGL 398 (400)
T ss_pred ECCCCCccCCceEEEEeeccccCCCcceEEEEEcCCcCC
Confidence 999999999999999996 8899999999999886
No 20
>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=2.9e-38 Score=348.72 Aligned_cols=276 Identities=24% Similarity=0.372 Sum_probs=235.1
Q ss_pred CCCeEEEEc-cC-Cch---hHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEE
Q 003093 2 EGQTVAIIG-PQ-DAV---TSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREV 75 (848)
Q Consensus 2 ~~~V~aiIG-p~-~S~---~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~v 75 (848)
+++|+|||| +. +|. .+.+++.+++.++||+|+++++++.+++ ..||||||+.|++..|+.++++++++|+|++|
T Consensus 78 ~~~V~aii~~~~~ss~~~~~~~~v~~~~~~~~iP~Is~~a~~~~ls~~~~~~~~~R~~psd~~~~~a~~~~l~~~~w~~v 157 (377)
T cd06379 78 SNQVYAVIVSHPPTSNDHLTPTSVSYTAGFYRIPVVGISTRDSIFSDKNIHLSFLRTVPPYSHQADVWLEMLRSFKWNKV 157 (377)
T ss_pred hcceEEEEEeCCCCCcccccHHHHHHHhhCCCCcEEecccCCccccCccccccEEEecCCHHHHHHHHHHHHHHcCCeEE
Confidence 568999973 33 443 4777888999999999999999999987 46999999999999999999999999999999
Q ss_pred EEEEEcCCCccchHHHHHHHHhccCc----EEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHH
Q 003093 76 IAIYVDDDHGRNGIAALGDTLAAKRC----RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQY 151 (848)
Q Consensus 76 aii~~dd~~g~~~~~~l~~~l~~~g~----~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~ 151 (848)
++||++++||....+.|++.+++.|+ +|+..+.++.+ ..|+..+|++|++.++|+|+++++.+++..++++|++
T Consensus 158 aii~~~~~~g~~~~~~~~~~~~~~g~~~~~~v~~~~~~~~~--~~d~~~~l~~ik~~~~~vIvl~~~~~~~~~l~~qa~~ 235 (377)
T cd06379 158 ILLVSDDHEGRAAQKRFETLLEEREIEFKIKVEKVVEFEPG--EKNVTSLLQEAKELTSRVILLSASEDDAAVIYRNAGM 235 (377)
T ss_pred EEEEEcCcchhHHHHHHHHHHHhcCCccceeeeEEEecCCc--hhhHHHHHHHHhhcCCeEEEEEcCHHHHHHHHHHHHH
Confidence 99999999999999999999999999 88888778654 4799999999999999999999999999999999999
Q ss_pred cCCCCCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhh
Q 003093 152 LGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAY 231 (848)
Q Consensus 152 ~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~Y 231 (848)
+||++.+|+||.++.+... .+...|++++++..+ ..+++++|
T Consensus 236 ~g~~~~~~~wi~t~~~~~~-----------~~~~~g~~g~~~~~~---------------------------~~~~~~~y 277 (377)
T cd06379 236 LNMTGEGYVWIVSEQAGAA-----------RNAPDGVLGLQLING---------------------------KNESSHIR 277 (377)
T ss_pred cCCCCCCEEEEEecccccc-----------ccCCCceEEEEECCC---------------------------CCHHHHHH
Confidence 9999989999999986321 244578888876532 12467899
Q ss_pred hHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcc-cccCChHHHHHHHHhccccccccceEeccCCCCCCCcEE
Q 003093 232 DTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSL-RIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYE 310 (848)
Q Consensus 232 DAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~ 310 (848)
|||+++|+|++++.+... .+. . ...|... .+|..|..|+++|++++|+|++|+++||++|++....|+
T Consensus 278 DAV~~~A~Al~~~~~~~~-~~~--------~--~~~c~~~~~~~~~g~~l~~~l~~v~f~G~tg~i~Fd~~Gd~~~~~~~ 346 (377)
T cd06379 278 DAVAVLASAIQELFEKEN-ITE--------P--PRECVGNTVIWETGPLFKRALMSSKYPGETGRVEFNDDGDRKFANYD 346 (377)
T ss_pred HHHHHHHHHHHHHHcCCC-CCC--------C--CccccCCCCCCcchHHHHHHHHhCCcCCccCceEECCCCCccCccEE
Confidence 999999999999875321 110 0 1234432 257789999999999999999999999999998778999
Q ss_pred EEEeecccEEEEEEeeCC
Q 003093 311 IINVIGTGYRRIGYWSNY 328 (848)
Q Consensus 311 I~~~~~~~~~~Vg~w~~~ 328 (848)
|+|+++.+++.||+|++.
T Consensus 347 I~~~~~~~~~~VG~w~~~ 364 (377)
T cd06379 347 IMNIQNRKLVQVGLYNGD 364 (377)
T ss_pred EEEecCCCceEeeEEcCc
Confidence 999999999999999863
No 21
>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=4.9e-38 Score=356.21 Aligned_cols=309 Identities=22% Similarity=0.357 Sum_probs=251.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|+|||||.+|.++.+++++++.++||+|+++++++.+++ .+||||||+.|+|..|++++++++++|||++|++|+.|
T Consensus 117 ~~v~aVIG~~sS~~s~ava~~~~~~~IP~IS~~sss~~ls~~~~yp~ffRt~psd~~q~~Ai~~l~~~f~wk~VaiI~~d 196 (510)
T cd06364 117 PSTIAVVGATGSGVSTAVANLLGLFYIPQVSYASSSRLLSNKNQFKSFLRTIPNDEHQATAMADIIEYFRWNWVGTIAAD 196 (510)
T ss_pred CceEEEECCCchhHHHHHHHHhccccccccccccCCcccCCccccCCeeEcCCChHHHHHHHHHHHHHcCCeEEEEEEec
Confidence 35889999999999999999999999999999999999998 68999999999999999999999999999999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++||+...+.|.+.+++.|+||+..+.++...+..|+..++.+|+++++||||+.+...++..++++|+++|+. +.+|
T Consensus 197 d~yG~~~~~~~~~~~~~~Gi~I~~~~~i~~~~~~~d~~~~l~klk~~~a~vVvl~~~~~~~~~ll~qa~~~g~~--~~iw 274 (510)
T cd06364 197 DDYGRPGIEKFREEAEERDICIDFSELISQYSDEEEIQRVVEVIQNSTAKVIVVFSSGPDLEPLIKEIVRRNIT--GKIW 274 (510)
T ss_pred CcchHHHHHHHHHHHHHCCcEEEEEEEeCCCCCHHHHHHHHHHHHhcCCeEEEEEeCcHHHHHHHHHHHHhCCC--CcEE
Confidence 99999999999999999999999988777644668999999999999999999999999999999999999985 5799
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHH---------------HHHhhccC------------
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFIS---------------RWRNLTDA------------ 214 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~---------------~~~~~~~~------------ 214 (848)
|++++|........ ....+.+.|++++.+.....+.+++|+. .|++.|+.
T Consensus 275 I~s~~w~~~~~~~~---~~~~~~~gg~lg~~~~~~~i~~f~~~l~~l~p~~~~~~~~~~~~we~~f~c~~~~~~~~~~~~ 351 (510)
T cd06364 275 LASEAWASSSLIAM---PEYFDVMGGTIGFALKAGQIPGFREFLQKVHPKKSSHNGFAKEFWEETFNCYLEDSPKNALPV 351 (510)
T ss_pred EEEchhhccccccc---CCccceeeEEEEEEECCCcCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCCCCCccccccc
Confidence 99988865332221 2345778999999888766666555553 35655541
Q ss_pred -----------------------CCCCCCCC----------CCcchhhhhhHHHHHHHHHHHHHhcCCCc-cccCCCccc
Q 003093 215 -----------------------KTPNGYIG----------LNAYGFYAYDTVWLLARAINSFFKQGGNL-SFSKDSRLS 260 (848)
Q Consensus 215 -----------------------~~~~~~~~----------~~~~~~~~YDAv~~~a~Al~~~~~~~~~~-~~~~~~~~~ 260 (848)
|.+..... ...++.+.|||||++|+||++++.+.... .++
T Consensus 352 ~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~AVyAvAhaLh~~~~c~~~~~~~~------ 425 (510)
T cd06364 352 DTFLGHEESGDDSENGSTAFRPLCTGDENIASVETPYLDYTHLRISYNVYLAVYSIAHALQDIYTCTPGKGLFT------ 425 (510)
T ss_pred ccccccccccccccccccccCCCCCChhhhcccCCccccccchhhHHHHHHHHHHHHHHHHHHhcCCCCCCCcc------
Confidence 11111100 12346789999999999999998764221 110
Q ss_pred cccCccccCcccccCChHHHHHHHHhcccccccc-ceEeccCCCCCCCcEEEEEeec---c---cEEEEEEeeCC
Q 003093 261 DIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAG-PARFNSHGDLINPAYEIINVIG---T---GYRRIGYWSNY 328 (848)
Q Consensus 261 ~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG-~v~Fd~~g~~~~~~~~I~~~~~---~---~~~~Vg~w~~~ 328 (848)
+-.|.....++ +.+|++.|++++|+|.+| +|.||++|+. ...|+|+|++. + .++.||.|++.
T Consensus 426 ----~~~c~~~~~~~-~~~l~~~L~~v~F~~~~g~~v~Fd~~Gd~-~~~YdI~n~q~~~~~~~~~~v~VG~~~~~ 494 (510)
T cd06364 426 ----NGSCADIKKVE-AWQVLKHLRHLNFTDNMGEQVRFDEGGDL-VGNYSIINWHLSPEDGSVVFKEVGYYNVY 494 (510)
T ss_pred ----CCCCCCCCCCC-HHHHHHHHHhcEEecCCCCEEEEecCCCC-ccceeEEEeeecCCCCcEEEEEEEEEcCC
Confidence 11355544554 899999999999999988 5999999995 68999999993 2 25899999753
No 22
>cd06386 PBP1_NPR_C_like Ligand-binding domain of type C natriuretic peptide receptor. Ligand-binding domain of type C natriuretic peptide receptor (NPR-C). NPR-C is found in atrial, mesentery, placenta, lung, kidney, venous tissue, aortic smooth muscle, and aortic endothelial cells. The affinity of NPR-C for natriuretic peptides is ANPCNPBNP. The extracellular domain of NPR-C is about 30% identical to NPR-A and NPR-B. However, unlike the cyclase-linked receptors, it contains only 37 intracellular amino acids and no guanylyl cyclase activity. Major function of NPR-C is to clear natriuretic peptides from the circulation or extracellular surroundings through constitutive receptor-mediated internalization and degradation.
Probab=100.00 E-value=1.9e-37 Score=342.21 Aligned_cols=297 Identities=15% Similarity=0.269 Sum_probs=243.5
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS--LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIY 79 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~--~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~ 79 (848)
+++|.|||||.||.++.+++++++.++||+|+++++++.+++ ..|||+||+.|++..++.++++++++|+|++|++||
T Consensus 65 ~~~v~aiiGp~~s~~~~~va~ia~~~~iP~Is~~a~~~~~s~~~~~yp~~~R~~p~~~~~~~a~~~ll~~~~W~~vaiiy 144 (387)
T cd06386 65 ARKPDLILGPVCEYAAAPVARLASHWNIPMISAGALAAGFSHKKSEYSHLTRVAPSYVKMGETFSALFERFHWRSALLVY 144 (387)
T ss_pred hhCCCEEECCCCccHHHHHHHHHHhCCCcEEccccCchhhccCcccCCeeEEecCchHHHHHHHHHHHHhCCCeEEEEEE
Confidence 358999999999999999999999999999999999999976 368999999999999999999999999999999999
Q ss_pred EcCCCccch---HHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 80 VDDDHGRNG---IAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 80 ~dd~~g~~~---~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
++++||++. .+.|.+.+++.|++|+..+.++.. +.|+..+|+++++.+ |+||++++.+.+..++++|+++||+.
T Consensus 145 ~~~~~~~~~~~~~~~l~~~~~~~gi~v~~~~~~~~~--~~d~~~~l~~ik~~~-rvii~~~~~~~~~~ll~~A~~~gm~~ 221 (387)
T cd06386 145 EDDKQERNCYFTLEGVHHVFQEEGYHMSIYPFDETK--DLDLDEIIRAIQASE-RVVIMCAGADTIRSIMLAAHRRGLTS 221 (387)
T ss_pred EcCCCCccceehHHHHHHHHHhcCceEEEEecCCCC--cccHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCC
Confidence 999999876 899999999999999876655433 378999999999887 99999999999999999999999999
Q ss_pred CCeEEEecCccccccCC------CCCCC---cccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCC-CCCCCcc
Q 003093 157 TGYVWIATSWLSTALDT------NSPFP---SDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNG-YIGLNAY 226 (848)
Q Consensus 157 ~~~~wi~~~~~~~~~~~------~~~~~---~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~-~~~~~~~ 226 (848)
.+|+||..+...+.... .+..+ ..+.++++|+.++.+ ..+.+++|.++|++++...+... ...++.+
T Consensus 222 ~~yv~i~~d~~~~~~~~~~~w~~~~~~~~~~~~a~~~~~~v~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~ 298 (387)
T cd06386 222 GDYIFFNIELFNSSSYGDGSWKRGDKHDFEAKQAYSSLNTVTLLRT---VKPEFEKFSMEVKSSVEKAGDLNDCDYVNMF 298 (387)
T ss_pred CCEEEEEEecccccccCCCCCccCCCcCHHHHHHHHhheEEeccCC---CChHHHHHHHHHHHHHHhCCCCcccccchHH
Confidence 99999999866311000 00011 123345566655444 45778899999985554221111 1246689
Q ss_pred hhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCC
Q 003093 227 GFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLIN 306 (848)
Q Consensus 227 ~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~ 306 (848)
++++||||+++|+|++++++.+.. +.+|.+|.++|++++|+|++|+++||++|++ .
T Consensus 299 aa~~yDav~l~A~Al~~~~~~g~~-----------------------~~~g~~l~~~l~~~~f~G~tG~v~~d~~g~r-~ 354 (387)
T cd06386 299 VEGFHDAILLYALALHEVLKNGYS-----------------------KKDGTKITQRMWNRTFEGIAGQVSIDANGDR-Y 354 (387)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCC-----------------------CCCHHHHHHHHhCCceeeccccEEECCCCCc-c
Confidence 999999999999999998755321 1259999999999999999999999999998 5
Q ss_pred CcEEEEEee---cccEEEEEEeeCC
Q 003093 307 PAYEIINVI---GTGYRRIGYWSNY 328 (848)
Q Consensus 307 ~~~~I~~~~---~~~~~~Vg~w~~~ 328 (848)
..|.|+.++ .++++.||.|...
T Consensus 355 ~~~~v~~~~~~~~~~~~~~~~~~~~ 379 (387)
T cd06386 355 GDFSVIAMTDVEAGTYEVVGNYFGK 379 (387)
T ss_pred ccEEEEEccCCCCccEEEEeEEccc
Confidence 699999996 3678999999753
No 23
>cd06385 PBP1_NPR_A Ligand-binding domain of type A natriuretic peptide receptor. Ligand-binding domain of type A natriuretic peptide receptor (NPR-A). NPR-A is one of three known single membrane-spanning natriuretic peptide receptors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In mammals there are three natriuretic peptides: ANP, BNP, and CNP. NPR-A is highly expressed in kidney, adrenal, terminal ileum, adipose, aortic, and lung tissues. The rank order of NPR-A activation by natriuretic peptides is ANPBNPCNP. Single allele-inactivating mutations in the promoter of human NPR-A are associated with hypertension and heart failure.
Probab=100.00 E-value=2.6e-36 Score=336.54 Aligned_cols=300 Identities=18% Similarity=0.224 Sum_probs=243.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEE-EEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVI-AIYV 80 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~va-ii~~ 80 (848)
++|+|||||.||.++.+++++++.++||+|+++++++.+++ ..|||+||+.|++..++.++++++++|+|++++ ++|.
T Consensus 73 ~~v~aiiGp~~S~~~~~va~~a~~~~iP~Is~~a~~~~l~~~~~~~~~~R~~p~~~~~~~a~~~~~~~~~w~~va~ii~~ 152 (405)
T cd06385 73 HNPWAFIGPGCDYTASPVARFTTHWDVPLVTAGAPALGFGVKDEYATITRTGPTHKKLGEFVLHIHQHFGWRSHAMLIYS 152 (405)
T ss_pred cCCcEEECCCccchHHHHHHHHhccCCcEEccccChhhcCCcccCcceEEecCchHHHHHHHHHHHHhCCCeEEEEEEEe
Confidence 58999999999999999999999999999999999999987 679999999999999999999999999999998 4565
Q ss_pred cCCC-ccc---hHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 81 DDDH-GRN---GIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 81 dd~~-g~~---~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
++.+ ++. ..+.+.+.+++.|++|+..+..+. +..|+..+|++|++.. |+||++++...+..++++|+++||+.
T Consensus 153 ~~~~~~~~~~~~~~~l~~~~~~~gi~v~~~~~~~~--~~~d~~~~l~~ik~~~-~iii~~~~~~~~~~i~~~a~~~g~~~ 229 (405)
T cd06385 153 DNKVDDRPCYFAMEGLYMELKKNNITVVDLVFEED--DLINYTTLLQDIKQKG-RVIYVCCSPDIFRRLMLQFWREGLPS 229 (405)
T ss_pred cCcccccchHHHHHHHHHHHHhCCeEEEEeeccCC--chhhHHHHHHHHhhcc-eEEEEeCCHHHHHHHHHHHHHcCCCC
Confidence 5443 333 468899999999999998763322 3579999999998754 99999999999999999999999999
Q ss_pred CCeEEEecCccccccCC---------CCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCC--CCCCCc
Q 003093 157 TGYVWIATSWLSTALDT---------NSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNG--YIGLNA 225 (848)
Q Consensus 157 ~~~~wi~~~~~~~~~~~---------~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~--~~~~~~ 225 (848)
++|+||+++++...+.. .+..+....+++++++....+.+.++.+++|.++|+++....-+.. ...++.
T Consensus 230 ~~y~~i~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~ 309 (405)
T cd06385 230 EDYVFFYIDLFGASLQGPDPKRPWYRGDADDAAAREAFQSVKILTYKEPQNPEYKEFLSDLKTDAKEMFNFTVEDSLMNI 309 (405)
T ss_pred CcEEEEEeecchhhccCCCCCCCCCCCCcccHHHHHhhheeEEEeCCCCCChhHHHHHHHHHHHhhccCCCccchhhHHH
Confidence 99999998765432221 0111123456789998887777778889999999998632100011 112678
Q ss_pred chhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCC
Q 003093 226 YGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLI 305 (848)
Q Consensus 226 ~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~ 305 (848)
+++++|||||++|+|++++++.++ ++.+|++|.++|++++|+|++|++.||++|+|
T Consensus 310 ~aa~~YDav~l~a~Al~~~~~~~~-----------------------~~~~g~~i~~~l~~~~f~G~tG~v~fd~~G~r- 365 (405)
T cd06385 310 IAGGFYDGVMLYAHALNETMAKGG-----------------------TRPPGTAITQRMWNRTFYGVTGFVKIDDNGDR- 365 (405)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCC-----------------------CCCCHHHHHHHhhCceEeeceeEEEEcCCCCE-
Confidence 999999999999999999865532 22259999999999999999999999999997
Q ss_pred CCcEEEEEe---ecccEEEEEEeeCCC
Q 003093 306 NPAYEIINV---IGTGYRRIGYWSNYS 329 (848)
Q Consensus 306 ~~~~~I~~~---~~~~~~~Vg~w~~~~ 329 (848)
.+.|.|+++ ++++++.||+|+..+
T Consensus 366 ~~~~~~~~~~~~~~g~~~~v~~~~~~~ 392 (405)
T cd06385 366 ETDFALWDMTDTESGDFQVVSVYNGTQ 392 (405)
T ss_pred eceeEEEEccCCCCCcEEEEEEEcccC
Confidence 478877754 678999999998643
No 24
>cd06363 PBP1_Taste_receptor Ligand-binding domain of the T1R taste receptor. Ligand-binding domain of the T1R taste receptor. The T1R is a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptors, GABAb receptors, the calcium-sensing receptor (CaSR), the V2R pheromone receptors, and a small group of uncharacterized orphan receptors.
Probab=100.00 E-value=8.2e-36 Score=332.33 Aligned_cols=286 Identities=24% Similarity=0.391 Sum_probs=241.4
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|+|||||.+|..+.++++++++++||+|+++++++.+++ ..|||+||+.|++..++.++++++++++|++|++|++
T Consensus 105 ~~~V~aIiGp~~S~~~~av~~i~~~~~vp~is~~~~~~~lt~~~~~~~~fr~~~~~~~~~~al~~~l~~~~~k~vaii~~ 184 (410)
T cd06363 105 QPRVVAVIGPDSSTLALTVAPLFSFFLIPQISYGASSEVLSNKELYPSFLRTVPSDKDQIEAMVQLLQEFGWNWVAFLGS 184 (410)
T ss_pred CCCeEEEECCCccHHHHHHHHHhcccccccccccccCccccccccCCCeeEecCCcHHHHHHHHHHHHHCCCcEEEEEEe
Confidence 378999999999999999999999999999999999999987 6789999999999999999999999999999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCC-CChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVE-ATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~-~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
|++||....+.+.+.+++.|++|+..+.++.. .++.|+..+|++|++.++|+|++++..+++..++++|+++||. +.
T Consensus 185 ~~~~g~~~~~~~~~~l~~~gi~i~~~~~~~~~~~~~~d~~~~l~~i~~~~~dvIil~~~~~~~~~il~qa~~~g~~--~~ 262 (410)
T cd06363 185 DDEYGRDGLQLFSELIANTGICIAYQGLIPLDTDPETDYQQILKQINQTKVNVIVVFASRQPAEAFFNSVIQQNLT--GK 262 (410)
T ss_pred CChhHHHHHHHHHHHHHHCCeEEEEEEEecCCCchHHHHHHHHHHHhcCCCeEEEEEcChHHHHHHHHHHHhcCCC--CC
Confidence 99999999999999999999999998888753 2458999999999999999999999999999999999999995 44
Q ss_pred EEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
.||+++++........ ....+...+++++....+..+.+++|.++ +++.+||||+++|+
T Consensus 263 ~~i~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~f~~~------------------~~~~~YDaV~~~a~ 321 (410)
T cd06363 263 VWIASEAWSLNDELPS---LPGIRNIGTVLGVAQQTVTIPGFSDFIYS------------------FAFSVYAAVYAVAH 321 (410)
T ss_pred EEEEeCcccccccccC---CccceeeccEEEEEeCCCCCccHHHHHHH------------------HHHHHHHHHHHHHH
Confidence 8999876643221111 11223455677777777778888888876 45679999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecc--
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGT-- 317 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~-- 317 (848)
|++++++++.. .|...++.+ +++|.++|++++|+|++|++.||++|++ ...+.|++++..
T Consensus 322 Al~~a~~~~~~----------------~~~~~~~~~-~~~l~~~L~~~~~~g~~g~i~fd~~G~~-~~~~~i~~~~~~~~ 383 (410)
T cd06363 322 ALHNVLQCGSG----------------GCPKRVPVY-PWQLLEELKKVNFTLLGQTVRFDENGDP-NFGYDIVVWWWDNS 383 (410)
T ss_pred HHHHHhCCCCC----------------CCCCCCCCC-HHHHHHHHhccEEecCCcEEEeCCCCCC-ccceEEEEEEEcCC
Confidence 99998765332 232223343 8899999999999999999999999995 567999999543
Q ss_pred --cEEEEEEeeCC
Q 003093 318 --GYRRIGYWSNY 328 (848)
Q Consensus 318 --~~~~Vg~w~~~ 328 (848)
++++||+|++.
T Consensus 384 ~~~~~~vG~~~~~ 396 (410)
T cd06363 384 SGTFEEVGSYSFY 396 (410)
T ss_pred ceeEEEEEEEECC
Confidence 58999999874
No 25
>cd06378 PBP1_iGluR_NMDA_NR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=100.00 E-value=3.7e-36 Score=325.24 Aligned_cols=285 Identities=17% Similarity=0.275 Sum_probs=226.7
Q ss_pred CCeEEEE-ccCCch--hHHHHHHhhccCCccEEecccCCC-CCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEE
Q 003093 3 GQTVAII-GPQDAV--TSHVVSHVANELQVPLLSFSATDP-TLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIA 77 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~--~~~ava~i~~~~~vP~Is~~at~p-~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vai 77 (848)
.+|.|+| ||.++. .+..++.++++++||+|+++++++ .+++ ..+|||+|+.|++..|++|+++++++|+|++|++
T Consensus 61 ~~V~aiIfgp~~~~~~~a~~~s~~~~~~~vP~is~~~~s~~~ls~~~~~p~flr~~Psd~~q~~Ai~~Ii~~f~W~~v~i 140 (362)
T cd06378 61 TKVHGVVFEDDTDQEAVAQILDFISAQTFLPILGIHGGSSMIMAAKDSGSTFLQFGPSIEQQAAVMLKIMEEYDWHAFSV 140 (362)
T ss_pred cceEEEEecCCCCccccchhhhhhhhceeccEEEecccccccccCCCCCceEEEeCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence 3699866 999997 567899999999999999987765 5566 6899999999999999999999999999999999
Q ss_pred EEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCC-ChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 78 IYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEA-TEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 78 i~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~-~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
||++++.+..+.+.+++.+.+.++|+.....++... .+.++..++.+++..++++||++|+.+.+..++++|+++||++
T Consensus 141 V~~~~~g~~~~~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~lk~~~arViVl~~s~~~a~~if~~A~~~gm~g 220 (362)
T cd06378 141 VTSRFPGYDDFVSAVRTTVDNSFVGWELQSVLTLDMSDDDGDARTQRQLKKLESQVILLYCSKEEAEYIFRAARSAGLTG 220 (362)
T ss_pred EEEcCCCHHHHHHHHHHHHhhcccceeEEEEEeeccCCCcchHHHHHHHHhcCCCEEEEECCHHHHHHHHHHHHHcCCcC
Confidence 999998888888888888777666654433333322 2234788999999999999999999999999999999999999
Q ss_pred CCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHH
Q 003093 157 TGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 157 ~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~ 236 (848)
.+|+||++++.....+. ...+...|++++.. ++|+.. +.+..||||++
T Consensus 221 ~~yvWI~t~~~~~~~~~------~~~~~~~G~i~v~~------------~~w~~~--------------~~a~~~DaV~v 268 (362)
T cd06378 221 PGYVWIVPSLVLGNTDL------GPSEFPVGLISVSY------------DGWRYS--------------LRARVRDGVAI 268 (362)
T ss_pred CCeEEEecccccCCCcc------ccccCCcceEeecc------------cccccc--------------HHHHHHHHHHH
Confidence 99999999987655321 11234577776542 233211 24578999999
Q ss_pred HHHHHHHHHhcCCCccccCCCccccccCccccCc-cc-ccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEe
Q 003093 237 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDS-LR-IFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV 314 (848)
Q Consensus 237 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~-~~-~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~ 314 (848)
+|+|++.++++++.++. ...+|.. .. +|..|..|+++|++++|+|+ +++||++|++.++.|+|+|+
T Consensus 269 va~Al~~l~~~~~~~~~----------~~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~--~i~F~~~G~r~~~~ldIinl 336 (362)
T cd06378 269 IATGASAMLRQHGFIPE----------AKGSCYGQAEKRDLPPNTLHRYMMNVTWEGR--DLSFTEDGYLVNPKLVVISL 336 (362)
T ss_pred HHHHHHHHHhccCCCCC----------CCCCcCCCCCCCCCchHHHHHHhhcceECCC--ceeECCCCeEccceEEEEEe
Confidence 99999998765444321 1234532 33 47789999999999999996 99999999999999999999
Q ss_pred ec-ccEEEEEEeeCCCCCc
Q 003093 315 IG-TGYRRIGYWSNYSGLS 332 (848)
Q Consensus 315 ~~-~~~~~Vg~w~~~~gl~ 332 (848)
++ .+|++||+|+++ +|.
T Consensus 337 ~~~~g~~kVG~W~~~-~L~ 354 (362)
T cd06378 337 NKERVWEEVGKWENG-SLR 354 (362)
T ss_pred cCCCCceEEEEEcCC-eEE
Confidence 97 599999999854 454
No 26
>cd06384 PBP1_NPR_B Ligand-binding domain of type B natriuretic peptide receptor. Ligand-binding domain of type B natriuretic peptide receptor (NPR-B). NPR-B is one of three known single membrane-spanning natriuretic peptide receptors that have been identified. Natriuretic peptides are family of structurally related but genetically distinct hormones/paracrine factors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In mammals there are three natriuretic peptides: ANP, BNP, and CNP. Like NPR-A (or GC-A), NPR-B (or GC-B) is a transmembrane guanylyl cyclase, an enzyme that catalyzes the synthesis of cGMP. NPR-B is the predominant natriuretic peptide receptor in the brain. The rank of order activation of NPR-B by natriuretic peptides is CNPANPBNP. Homozygous inactivating mutations in human NPR-B cause a form of short-limbed dwarfism known as acromesomelic dysplasia type Maroteaux.
Probab=100.00 E-value=6.4e-36 Score=332.20 Aligned_cols=300 Identities=15% Similarity=0.202 Sum_probs=242.8
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEeccCChHHHHHHHHHHHHHcCcE-EEEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS--LQFPYFVRTTQSDQYQMAAIAEIVDHYGWR-EVIAIY 79 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~--~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~-~vaii~ 79 (848)
++|.+||||.||.++.+++++++.++||+|++++++|.+++ ..|||+||+.|++..++.++..++++|+|+ ++++||
T Consensus 72 ~~v~aviGp~~S~~~~av~~i~~~~~iP~Is~~at~~~ls~~~~~y~~~fR~~p~~~~~~~~~~~i~~~~~w~~~vaiiy 151 (399)
T cd06384 72 SDPDVFFGPGCVYPTASVARFATHWRLPLITAGAPAFGFSNKTDEYRTTVRTGPSTTKLGEFVNHLHEHFNWTSRAALLY 151 (399)
T ss_pred cCCCEEECCCCchHHHHHHHHHhhcCCcEEeeccchhhhccccccCCceEEecCcHHHHHHHHHHHHHhCCCcEEEEEEE
Confidence 56889999999999999999999999999999999999986 378999999999999999988889999999 688999
Q ss_pred EcCCCcc----chHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 80 VDDDHGR----NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 80 ~dd~~g~----~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
.++..+. ...+.+.+.+++.|++|+....+.. +..|+..+|++++. ++|+|+++++..++..+++||+++||+
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~gi~v~~~~~~~~--~~~d~~~~l~~ik~-~~~vIi~~~~~~~~~~i~~qa~~~g~~ 228 (399)
T cd06384 152 LDLKTDDRPHYFISEGVFLALQEENANVSAHPYHIE--KNSDIIEIIQFIKQ-NGRIVYICGPLETFLEIMLQAQREGLT 228 (399)
T ss_pred ecCCccCCcceEehHHHHHHHHhcCceEEEEEEecc--chhhHHHHHHHHhh-cccEEEEeCCchHHHHHHHHHHHcCCC
Confidence 6543221 1356788888999999998655543 34899999999997 899999999999999999999999999
Q ss_pred CCCeEEEecCccccccCCCC----------CCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCC--CCCC
Q 003093 156 GTGYVWIATSWLSTALDTNS----------PFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNG--YIGL 223 (848)
Q Consensus 156 ~~~~~wi~~~~~~~~~~~~~----------~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~--~~~~ 223 (848)
.++|+||..++....+.... ...+...+++++++++..+.+..+.+++|.++|++++....+.. +...
T Consensus 229 ~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~p~~~ 308 (399)
T cd06384 229 PGDYVFFYLDVFGESLRVKSPRESYKQMNHSSWTVLKEAFKSVFVITYREPENPEYKEFQRELHARAKEDFGVELEPSLM 308 (399)
T ss_pred CCcEEEEEehhcccccccCCCCccccCCCCcccHHHHHHHhheEEeecCCCCCchHHHHHHHHHHHHhhhcCCCcCcchH
Confidence 99999998876543221000 00133445789999998888888889999999998643111111 1123
Q ss_pred CcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCC
Q 003093 224 NAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGD 303 (848)
Q Consensus 224 ~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~ 303 (848)
+.+++++||||+++|.|++++++.++ ++.+|.+|.++|++++|+|++|++.||++|+
T Consensus 309 ~~~aa~~YDav~l~a~Al~~~~~~~~-----------------------~~~~g~~i~~~l~~~~f~GvtG~v~fd~~G~ 365 (399)
T cd06384 309 NFIAGCFYDGVMLYAMALNETLAEGG-----------------------SQKDGLNITRKMQDRRFWGVTGLVSIDKNND 365 (399)
T ss_pred hhhhhhhHHHHHHHHHHHHHHHhcCC-----------------------CCCCcHhHHHHHhCceeecceeEEEECCCCC
Confidence 67799999999999999999865432 2335899999999999999999999999999
Q ss_pred CCCCcEEE---EEeecccEEEEEEeeCCC
Q 003093 304 LINPAYEI---INVIGTGYRRIGYWSNYS 329 (848)
Q Consensus 304 ~~~~~~~I---~~~~~~~~~~Vg~w~~~~ 329 (848)
+ ...|.+ .++++++++.||+|+..+
T Consensus 366 r-~~~~~~~~~~~~~~g~~~~v~~~~~~~ 393 (399)
T cd06384 366 R-DIDFDLWAMTDHETGKYEVVAHYNGIT 393 (399)
T ss_pred c-ccceEEEEeecCCCCeEEEEEEEcCCC
Confidence 7 466777 466899999999998644
No 27
>cd06371 PBP1_sensory_GC_DEF_like Ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. This group includes the ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. They share a similar topology with an N-terminal extracellular ligand-binding domain, a single transmembrane domain, and a C-terminal cytosolic region that contains kinase-like and catalytic domains. GC-D is specifically expressed in a subpopulation of olfactory sensory neurons. GC-E and GC-F are colocalized within the same photoreceptor cells of the retina and have important roles in phototransduction. Unlike the other family members, GC-E and GC-F have no known extracellular ligands. Instead, they are activated under low calcium conditions by guanylyl cyclase activating proteins called GCAPs. GC-D expressing neurons have been implicated in pheromone detection and GC-D is phyloge
Probab=100.00 E-value=1.5e-35 Score=326.15 Aligned_cols=292 Identities=19% Similarity=0.277 Sum_probs=237.0
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|+|||||.||.++.++++++++++||+|++++++|.+++ .+||+|+|+.|++ +.++++++++|+|++|++||+
T Consensus 64 ~~~V~aviGp~~S~~~~a~a~va~~~~iP~Is~~a~~~~lt~~~~y~~f~r~~~~~---~~~~~~~~~~~~w~~vaii~~ 140 (382)
T cd06371 64 EGYASAFVGPVNPGYCEAAALLAKEWDKALFSWGCVNYELDDVRSYPTFARTLPSP---SRVLFTVLRYFRWAHVAIVSS 140 (382)
T ss_pred cCCceEEECCCCchHHHHHHHHHHhcCceEEecccCchhhcCcccCCCceecCCCc---HHHHHHHHHHCCCeEEEEEEe
Confidence 468999999999999999999999999999999999999997 6799999999987 466888999999999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCC-CeEEEEEccC-----CcHHHHHHHHHHcCC
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTE-SRIIVVHTHY-----NRGPVVFHVAQYLGM 154 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~-~~viv~~~~~-----~~~~~~~~~a~~~g~ 154 (848)
+++||....+.+.+.+++.|++|+..+.++.+ ..|++.+|++|++.+ +|+||++++. .++..+++||+++||
T Consensus 141 ~~~~~~~~~~~l~~~l~~~gi~v~~~~~~~~~--~~d~~~~L~~lk~~~~~~viv~~~~~~~~~~~~~~~i~~qa~~~Gm 218 (382)
T cd06371 141 PQDIWVETAQKLASALRAHGLPVGLVTSMGPD--EKGAREALKKVRSADRVRVVIMCMHSVLIGGEEQRLLLETALEMGM 218 (382)
T ss_pred cccchHHHHHHHHHHHHHCCCcEEEEEEecCC--HHHHHHHHHHHhcCCCcEEEEEEeeccccCcHHHHHHHHHHHHcCC
Confidence 99999999999999999999999988888754 489999999999987 6999998876 677899999999999
Q ss_pred CCCCeEEEecCccccccC----CCCC--CCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCC-CCCCCCcch
Q 003093 155 LGTGYVWIATSWLSTALD----TNSP--FPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPN-GYIGLNAYG 227 (848)
Q Consensus 155 ~~~~~~wi~~~~~~~~~~----~~~~--~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~-~~~~~~~~~ 227 (848)
+..+|+||.+++...... .... .++...++.+|++++....+..+..++|.++|+... .+.. .+..++.|+
T Consensus 219 ~~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~f~~~~~~~~--~~~~~~~~~~~~~~ 296 (382)
T cd06371 219 TDGRYVFIPYDTLLYSLPYRNVSYPALRNNSKLRRAYDAVLTITMDSGEQSFYEAFRAAQERGE--IPSDLEPEQVSPLF 296 (382)
T ss_pred cCCcEEEEEeccccccCCCCCccccCCCCCHHHHHHhHhhEEEEecCCCCcHHHHHHHHHhcCC--CCCCCCccccchhH
Confidence 999999999985431110 0000 012233578888888776555555566666553211 1111 112345677
Q ss_pred hhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCC
Q 003093 228 FYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINP 307 (848)
Q Consensus 228 ~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~ 307 (848)
+++|||++++|+|++++++.++. . ++++++++|++++|+|++|+++||++|++ .+
T Consensus 297 ~~~YDav~~~a~Al~~a~~~g~~-----------------------~-d~~~l~~~l~~~~f~GvtG~v~fd~~g~~-~~ 351 (382)
T cd06371 297 GTIYNSIYLLAHAVENARAAGGG-----------------------V-SGANLAQHTRNLEFQGFNQRLRTDSGGGG-QA 351 (382)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCC-----------------------c-cHHHHHHHHhCccccccceEEEecCCCCc-cc
Confidence 78999999999999998765332 1 48999999999999999999999999996 69
Q ss_pred cEEEEEeecccEEEEEEe
Q 003093 308 AYEIINVIGTGYRRIGYW 325 (848)
Q Consensus 308 ~~~I~~~~~~~~~~Vg~w 325 (848)
.|.|+++++.+++-+-++
T Consensus 352 ~~~v~~~~~~~~~~~~~~ 369 (382)
T cd06371 352 PYVVLDTDGKGDQLYPTY 369 (382)
T ss_pred ceEEEecCCCCCeeeeeE
Confidence 999999999888777665
No 28
>cd06373 PBP1_NPR_like Ligand binding domain of natriuretic peptide receptor (NPR) family. Ligand binding domain of natriuretic peptide receptor (NPR) family which consists of three different subtypes: type A natriuretic peptide receptor (NPR-A, or GC-A), type B natriuretic peptide receptors (NPR-B, or GC-B), and type C natriuretic peptide receptor (NPR-C). There are three types of natriuretic peptide (NP) ligands specific to the receptors: atrial NP (ANP), brain or B-type NP (BNP), and C-type NP (CNP). The NP family is thought to have arisen through gene duplication during evolution and plays an essential role in cardiovascular and body fluid homeostasis. ANP and BNP bind mainly to NPR-A, while CNP binds specifically to NPR-B. Both NPR-A and NPR-B have guanylyl cyclase catalytic activity and produces intracellular secondary messenger cGMP in response to peptide-ligand binding. Consequently, the NPR-A activation results in vasodilation and inhibition of vascular smooth muscle cell proli
Probab=100.00 E-value=7.3e-36 Score=332.09 Aligned_cols=302 Identities=18% Similarity=0.297 Sum_probs=246.2
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|+|||||.||.++.+++++++.++||+|++++++|.+++ ..|||+||+.|++..++.++++++++++|++|++||+
T Consensus 71 ~~~v~aiiGp~~S~~~~av~~~~~~~~ip~Is~~as~~~lt~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vaii~~ 150 (396)
T cd06373 71 QHKPDAFLGPGCEYAAAPVARFAAHWNVPVLTAGAPAAGFSDKSEYSTLTRTGPSYTKLGEFVLALHEHFNWSRAALLYH 150 (396)
T ss_pred ccCCeEEECCCccchhHHHHHHHhcCCCceECccCCccccccchhcCceeeccccHHHHHHHHHHHHHHcCCeEEEEEEE
Confidence 568999999999999999999999999999999999999987 6799999999999999999999999999999999999
Q ss_pred cCCCc----cchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 81 DDDHG----RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 81 dd~~g----~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
+++++ ....+.+.+.+++.|++|+.. .+.......|+..+|++|++.. |+||++++..++..++++|+++||..
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~-~~~~~~~~~d~~~~l~~ik~~~-~vii~~~~~~~~~~~~~qa~~~g~~~ 228 (396)
T cd06373 151 DDKNDDRPCYFTLEGVYTVLKEENITVSDF-PFDEDKELDDYKELLRDISKKG-RVVIMCASPDTVREIMLAAHRLGLTS 228 (396)
T ss_pred CCCCCcchHHHHHHHHHHHHhhcCceeeEE-eecCCccccCHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCC
Confidence 88774 557889999999999998754 3443211378999999999865 99999999999999999999999999
Q ss_pred CCeEEEecCccccccCC--------CCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCC--CCCCCCCCCcc
Q 003093 157 TGYVWIATSWLSTALDT--------NSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAK--TPNGYIGLNAY 226 (848)
Q Consensus 157 ~~~~wi~~~~~~~~~~~--------~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~--~~~~~~~~~~~ 226 (848)
.+|+||..+........ .....+...++.+|++++..+.++.+.+++|.++|+++.... ...+...++.+
T Consensus 229 ~~yv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~ 308 (396)
T cd06373 229 GEYVFFNIDLFGSSLYGGGPWWWERGDEDDEKAKEAYQALMTITLREPDNPEYKEFSLEVKERAKKKFNTTSDDSLVNFF 308 (396)
T ss_pred CcEEEEEEccchhhhccCCCCcCCCCCcccHHHHHHHHHheEEecCCCCChHHHHHHHHHHHHhhhcCCCCcchhHHHHH
Confidence 99999997654321100 000112334567788888888888889999999999763210 01112246789
Q ss_pred hhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCC
Q 003093 227 GFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLIN 306 (848)
Q Consensus 227 ~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~ 306 (848)
++++||||+++++|++++.++++. ..++++|.++|++++|+|++|+++||++|++ .
T Consensus 309 a~~~YDav~~~a~Al~~~~~~~~~-----------------------~~~~~~i~~~l~~~~f~G~tG~v~fd~~G~~-~ 364 (396)
T cd06373 309 AGAFYDAVLLYALALNETLAEGGD-----------------------PRDGTNITRRMWNRTFEGITGNVSIDENGDR-E 364 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCC-----------------------CCChHHHHHHhcCCceecccCceEeecCCcc-c
Confidence 999999999999999998654321 1148999999999999999999999999996 4
Q ss_pred CcEEEEEe---ecccEEEEEEeeCCC
Q 003093 307 PAYEIINV---IGTGYRRIGYWSNYS 329 (848)
Q Consensus 307 ~~~~I~~~---~~~~~~~Vg~w~~~~ 329 (848)
..|.|+.+ ++++++.||.++..+
T Consensus 365 ~~~~v~~~~~~~~g~~~~~~~~~~~~ 390 (396)
T cd06373 365 SDFSLWDMTDTETGTFEVVANYNGSN 390 (396)
T ss_pred ceeeeeeccCCCCceEEEEeeccccc
Confidence 77888665 678899999998754
No 29
>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=3.6e-35 Score=329.53 Aligned_cols=328 Identities=23% Similarity=0.436 Sum_probs=277.7
Q ss_pred CeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 4 QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 4 ~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.|+|||||..|+++.+++.+..-++||+|||++|+|.|++ .+|+||.|+.|+|.+|++|+++++++|+|++|..+++++
T Consensus 125 ~v~~VIG~s~Ssvsi~vanlLrlf~ipQisyaSts~~LSdk~ry~~F~RtVP~D~~Qa~Am~~il~~f~W~yVstv~s~~ 204 (878)
T KOG1056|consen 125 PVVAVIGPSYSSVSIAVANLLRLFLIPQISYASTSPDLSDKTRYDYFLRTVPSDVFQAQAMVDILKKFNWNYVSTVASEG 204 (878)
T ss_pred ceeEEeCCCCchHHHHHHHHHHhhcCceeccccCCcccccchhhhceeeecCChHHHHHHHHHHHHHhCeeEeeehhcCc
Confidence 5899999999999999999999999999999999999999 799999999999999999999999999999999999999
Q ss_pred CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc-CCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 83 DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~-~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
+||+.++++|.+..+++|+||...+.++....+..|+.+++++.. .++++||+++..++++.++++|+++++.+ .++|
T Consensus 205 dYGE~Gieaf~~~a~~~~iCIa~s~ki~~~~~~~~~~~~l~kl~~~~~a~vvV~F~~~~~~r~~~~aa~~~n~~g-~~~w 283 (878)
T KOG1056|consen 205 DYGESGIEAFKEEAAERGICIAFSEKIYQLSIEQEFDCVLRKLLETPNARVVVVFCRGEDARRLLKAARRANLTG-EFLW 283 (878)
T ss_pred cchhhhHHHHHHhHHhcCceEEehhhcccccchhHHHHHHHHHhhcCCCeEEEEecCcchHHHHHHHHHHhCCCc-ceEE
Confidence 999999999999999999999999888877777899999999988 79999999999999999999999999864 6999
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHH---------------HHhhccC------------
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISR---------------WRNLTDA------------ 214 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~---------------~~~~~~~------------ 214 (848)
|++|+|...-+.. ......++|++++.+..+..+.+++|.+. |+++|..
T Consensus 284 iaSd~W~~~~~~~----~~~e~~a~g~i~i~l~~~~v~~F~~y~~s~~p~nn~~n~w~~e~w~~~f~C~l~~~~~~~~~~ 359 (878)
T KOG1056|consen 284 IASDGWASQNSPT----EAPEREAEGAITIKLASPQVPGFDRYFQSLHPENNRRNPWFAEFWEDKFNCSLPNSAFKNENL 359 (878)
T ss_pred EecchhhccCChh----hhhhhhhceeEEEEecCCcchhHHHHHHhcCccccccCcccchhhhhcccCCCCcccccchhh
Confidence 9999998754443 23345799999999998888888777654 5555431
Q ss_pred ---CCCCCC-C-----CCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHH
Q 003093 215 ---KTPNGY-I-----GLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSIL 285 (848)
Q Consensus 215 ---~~~~~~-~-----~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~ 285 (848)
|++.+. . .-..-....+|||+++|+||+.+.++..... .-.|......+ |..|.+.++
T Consensus 360 ~~~Ct~~e~~~~~~~~~q~~k~~~Vi~aVya~A~aLh~m~~~lc~~~------------~~~C~~m~~~d-g~~L~~~l~ 426 (878)
T KOG1056|consen 360 IRLCTAVERITLDSAYEQDSKVQFVIDAVYAMAHALHNMHQDLCPGT------------SGLCSAMKAID-GSLLLKYLL 426 (878)
T ss_pred hhhcccchhhccccchhhhcccccHHHHHHHHHHHHHHHHHhhcCCc------------cccCcCccccC-HHHHHhhhh
Confidence 222210 0 1112356799999999999999987644321 23566677766 999999999
Q ss_pred hccccccccceEeccCCCCCCCcEEEEEeecc----cEEEEEEeeCCCCCceecCCcccCCCCCCCCCccccceeEeCCC
Q 003093 286 QANMTGTAGPARFNSHGDLINPAYEIINVIGT----GYRRIGYWSNYSGLSVVRPETLYSKPPNRSSSNQRLYSVIWPGQ 361 (848)
Q Consensus 286 ~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~----~~~~Vg~w~~~~gl~~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~ 361 (848)
+++|.|..|.+.||++||. ...|+|++++.. .++.||+|++... .+...+.|.++
T Consensus 427 ~vnF~~~~~~v~Fd~~gD~-~~~y~I~~~~~~~~~~~y~~vg~w~~~~~--------------------l~i~~~~w~~~ 485 (878)
T KOG1056|consen 427 NVNFTGPAGSVRFDENGDG-PGRYDILNYQLTNGSYTYKEVGYWSEGLS--------------------LNIEDLDWTTK 485 (878)
T ss_pred eeEEecCCCceeecCCCCC-ccceeEEEeeccCCCccceeeeeeccccc--------------------ccceeeeeccC
Confidence 9999999999999999994 799999999853 4799999987542 23457889999
Q ss_pred ccccCCcee
Q 003093 362 TTQKPRGWV 370 (848)
Q Consensus 362 ~~~~p~~~~ 370 (848)
..+.|++.|
T Consensus 486 ~~~v~~S~C 494 (878)
T KOG1056|consen 486 PSGVPKSVC 494 (878)
T ss_pred CCCCccccc
Confidence 888999988
No 30
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=100.00 E-value=4.6e-35 Score=320.62 Aligned_cols=282 Identities=46% Similarity=0.807 Sum_probs=246.3
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|++||||.+|..+.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.++++++++++|++|++||.
T Consensus 64 ~~~v~~viG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~~~r~~p~~~~~~~a~~~~~~~~~~~~v~ii~~ 143 (350)
T cd06366 64 NKPVVAIIGPQCSSVAEFVAEVANEWNVPVLSFAATSPSLSSRLQYPYFFRTTPSDSSQNPAIAALLKKFGWRRVATIYE 143 (350)
T ss_pred cCCceEEECCCcHHHHHHHHHHhhcCCeeEEeccCCCccccccccCCceEEcccchHhHHHHHHHHHHHCCCcEEEEEEE
Confidence 358999999999999999999999999999999999999965 6789999999999999999999999999999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
|++||....+.+.+.+++.|++|+..+.++.+.+..|+..++++|++.++|+|++++...++..++++|+++||..++|+
T Consensus 144 ~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~dvvi~~~~~~~~~~~~~~a~~~g~~~~~~~ 223 (350)
T cd06366 144 DDDYGSGGLPDLVDALQEAGIEISYRAAFPPSANDDDITDALKKLKEKDSRVIVVHFSPDLARRVFCEAYKLGMMGKGYV 223 (350)
T ss_pred cCcccchhHHHHHHHHHHcCCEEEEEeccCCCCChhHHHHHHHHHhcCCCeEEEEECChHHHHHHHHHHHHcCCcCCCEE
Confidence 99999999999999999999999999888876445899999999999999999999999999999999999999888899
Q ss_pred EEecCccccccCC-CCCCCcccccccceeEEEEEecCC-chhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 161 WIATSWLSTALDT-NSPFPSDVMDDIQGVLTLRTYTPD-SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 161 wi~~~~~~~~~~~-~~~~~~~~~~~~~G~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
||.++++...++. .....+...+..+|++++.++.+. .+.+++|.++|+++++..+.. ...|+.+++++|||+++
T Consensus 224 ~i~~~~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~-~~~p~~~a~~~YDav~~-- 300 (350)
T cd06366 224 WILTDWLSSNWWSSSDCTDEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWRKRFGNENPE-LTEPSIYALYAYDAVWA-- 300 (350)
T ss_pred EEECcchhhhhccCCCCChHHHHHhhceEEEEeecccccCccHHHHHHHHHHHhcccCcC-cCCCCcccchhhhheee--
Confidence 9999876543311 001113455778999999998887 888999999999998631111 12578899999999997
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeeccc
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTG 318 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~~ 318 (848)
+.+|+|++|+++||++|++....|+++++.+++
T Consensus 301 -----------------------------------------------~~~~~G~~G~v~fd~~~~~~~~~~~~~~~~~~~ 333 (350)
T cd06366 301 -----------------------------------------------STNFNGLSGPVQFDGGRRLASPAFEIINIIGKG 333 (350)
T ss_pred -----------------------------------------------eceEEeeeeeEEEcCCCccCCcceEEEEecCCc
Confidence 126889999999999999888999999999999
Q ss_pred EEEEEEeeCCCCCce
Q 003093 319 YRRIGYWSNYSGLSV 333 (848)
Q Consensus 319 ~~~Vg~w~~~~gl~~ 333 (848)
++.||+|++.+|+++
T Consensus 334 ~~~vg~~~~~~~~~~ 348 (350)
T cd06366 334 YRKIGFWSSESGLSV 348 (350)
T ss_pred eEEEEEEeCCCCccc
Confidence 999999999888764
No 31
>cd06372 PBP1_GC_G_like Ligand-binding domain of membrane guanylyl cyclase G. This group includes the ligand-binding domain of membrane guanylyl cyclase G (GC-G) which is a sperm surface receptor and might function, similar to its sea urchin counterpart, in the early signaling event that regulates the Ca2+ influx/efflux and subsequent motility response in sperm. GC-G appears to be a pseudogene in human. Furthermore, in contrast to the other orphan receptor GCs, GC-G has a broad tissue distribution in rat, including lung, intestine, kidney, and skeletal muscle.
Probab=100.00 E-value=1e-34 Score=322.28 Aligned_cols=301 Identities=14% Similarity=0.234 Sum_probs=236.0
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|.|||||.||.++.+++++++.++||+|++++++|.+++ ..||+++|+.|++..++.++++++++|||++|++||.
T Consensus 66 ~~~v~aiiGp~~S~~~~av~~va~~~~iP~is~~s~s~~ls~~~~~~~~~r~~p~~~~~~~a~~~l~~~~~w~~vaii~~ 145 (391)
T cd06372 66 KEHISALFGPACPEAAEVTGLLASQWNIPMFGFVGQTAKLDNRFLYDTYVKLVPPKQKIGEVLQKSLQHFGWKHIGLFGG 145 (391)
T ss_pred hcCceEEECCCCCcHHHHHHHHHhccCccEEEeecCCccccccccCCceEEecCchhhHHHHHHHHHHHCCCeEEEEEEe
Confidence 358999999999999999999999999999999999999987 6799999999999999999999999999999999985
Q ss_pred cC---CCc--cchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 81 DD---DHG--RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 81 dd---~~g--~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
++ .|+ ....+.+.+.++ .+++++..+.++.+. .++...+.+.+..++|+||++++..++..++++|+++||+
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~~~~~~~~~--~d~~~~~l~~~~~~~~vii~~~~~~~~~~i~~~a~~~g~~ 222 (391)
T cd06372 146 SSRDSSWDEVDELWKAVENQLK-FHFNITATVRYSSSN--PDLLQEKLRYISSVARVIILICSSEDAKAILQAAEKLGLM 222 (391)
T ss_pred ccccchhhhHHHHHHHHHHHHh-hCEEEEEEEecCCCC--hHHHHHHHHhhhccceEEEEEcChHHHHHHHHHHHHcCCC
Confidence 43 343 223445555554 678988888776543 6777777666678999999999999999999999999998
Q ss_pred CCCeEEEecCccccccCCCCCC---CcccccccceeEEEEEecCC-chhHHHHHHHHHhhccCCCC----CCCCCCCcch
Q 003093 156 GTGYVWIATSWLSTALDTNSPF---PSDVMDDIQGVLTLRTYTPD-SVLKRKFISRWRNLTDAKTP----NGYIGLNAYG 227 (848)
Q Consensus 156 ~~~~~wi~~~~~~~~~~~~~~~---~~~~~~~~~G~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~----~~~~~~~~~~ 227 (848)
.++|+||.+++....+...... .....++.+|++++.+..+. .+..++|.++|+++++..|. .....++.++
T Consensus 223 ~~~y~~i~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~f~~~~~~~~~~~p~~~~~~~~~~~~~~a 302 (391)
T cd06372 223 KGKFVFFLLQQFEDNFWKEVLTDDQVQHLPKVYESVFLIAPSSYGGYSGGYEFRKQVYQKLKRPPFQSSLSSEEQVSPYS 302 (391)
T ss_pred CCCEEEEEehhhcCccccccCCCcchHHHHHHHhhEEEEecCCCCCCcchhHHHHHHHHHHhcCCccccccccccchHHH
Confidence 8789999964322211110000 01233567888888776543 35577888888877753221 1112456889
Q ss_pred hhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHH---hccccccccceEeccCCCC
Q 003093 228 FYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSIL---QANMTGTAGPARFNSHGDL 304 (848)
Q Consensus 228 ~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~---~~~f~G~tG~v~Fd~~g~~ 304 (848)
+++|||||++|+|++++++++.. +.+|..|.++|+ +++|+|++|+|.||++|++
T Consensus 303 ~~~yDav~~~A~Al~~~~~~g~~-----------------------~~~g~~l~~~l~~~~~~~f~G~tG~v~fd~~G~r 359 (391)
T cd06372 303 AYLHDAVLLYALAVKEMLKAGKD-----------------------FRNGRQLVSTLRGANQVELQGITGLVLLDEQGKR 359 (391)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCC-----------------------CCCHHHHHHHHhhccCceEeccceeEEECCCCCc
Confidence 99999999999999998765321 224889999999 6899999999999999997
Q ss_pred CCCcEEEEEeec----ccEEEEEEeeCCC
Q 003093 305 INPAYEIINVIG----TGYRRIGYWSNYS 329 (848)
Q Consensus 305 ~~~~~~I~~~~~----~~~~~Vg~w~~~~ 329 (848)
.+.|.|+++++ ..++.||+|+..+
T Consensus 360 -~~~y~i~~~~~~~~~~~~~~vg~~~~~~ 387 (391)
T cd06372 360 -QMDYSVYALQKSGNSSLFLPFLHYDSHQ 387 (391)
T ss_pred -ceeEEEEeccccCCccceeeEEEecchh
Confidence 68999999985 2479999998643
No 32
>cd06370 PBP1_Speract_GC_like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model.
Probab=100.00 E-value=1.2e-34 Score=322.25 Aligned_cols=294 Identities=18% Similarity=0.286 Sum_probs=238.2
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|+|||||.+|.. +++.++++++||+|+++++++.+++ ..||+|||+.|++..++.++++++++++|++|++||+
T Consensus 67 ~~~v~aiiGp~~S~~--~~a~i~~~~~iP~Is~~a~~~~l~~~~~~~~f~r~~~~~~~~~~a~~~~~~~~~w~~vaii~~ 144 (404)
T cd06370 67 KRGVVAFIGPECTCT--TEARLAAAWNLPMISYKCDEEPVSDKSKYPTFARTVPPSIQVVKSVIALLKHFNWNKFSVVYE 144 (404)
T ss_pred hcCceEEECCCchhH--HHHHHHhhcCCcEEecccCCccccccccCCCeEEcCCCHHHHHHHHHHHHHHCCCcEEEEEEe
Confidence 458999999999854 4568999999999999999999987 5799999999999999999999999999999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCC-----ChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEA-----TEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~-----~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
+++||+...+.|.+.+++.|++|+..+.++... ...++..+|++++.. ++++|++++..++..+++||+++||+
T Consensus 145 ~~~~g~~~~~~~~~~~~~~g~~iv~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~v~~~~~~~~~~~l~qa~~~g~~ 223 (404)
T cd06370 145 NDSKYSSVFETLKEEAELRNITISHVEYYADFYPPDPIMDNPFEDIIQRTKET-TRIYVFIGEANELRQFLMSMLDEGLL 223 (404)
T ss_pred cCcccHHHHHHHHHHHHHcCCEEEEEEEECCCCCchhhhHHHHHHHHHhccCC-CEEEEEEcCHHHHHHHHHHHHHcCCC
Confidence 999999999999999999999999988887652 247899999998864 67888877778899999999999998
Q ss_pred -CCCeEEEecCcccccc---------------CCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCC-
Q 003093 156 -GTGYVWIATSWLSTAL---------------DTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPN- 218 (848)
Q Consensus 156 -~~~~~wi~~~~~~~~~---------------~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~- 218 (848)
..+|+||+++...... ...........++++|++.+.+..+ .+..++|.++|+++....+..
T Consensus 224 ~~~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~ 302 (404)
T cd06370 224 ESGDYMVLGVDIEYYDRDSQDYYSLHRGFQSREYNRSDDEKALEAMKSVLIIVPTPV-SPDYDSFSIFVRKYNLEPPFNG 302 (404)
T ss_pred CCCcEEEEEEchhhccccchhhhhhhhhhccccccccccHHHHHHhHheEEEecCCC-CchHHHHHHHHHHhccCCCCcc
Confidence 5789999876321100 0000011244567899988876555 777889999999875421111
Q ss_pred ------CCCCCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhcccccc
Q 003093 219 ------GYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGT 292 (848)
Q Consensus 219 ------~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~ 292 (848)
....++.+++++||||+++|+|++++++++... .+|++|.++|++++|+|+
T Consensus 303 ~~~~~~~~~~~~~~aa~~yDAv~~~a~Al~~~~~~~~~~-----------------------~~g~~i~~~l~~~~f~Gv 359 (404)
T cd06370 303 DLGESELVLEIDIEAAYLYDAVMLYAKALDETLLEGGDI-----------------------YNGTAIVSHILNRTYRSI 359 (404)
T ss_pred cccccccccccceeeehhHHHHHHHHHHHHHHHHhcCCC-----------------------CCHHHHHHHHhCcccccc
Confidence 123577899999999999999999987653321 148999999999999999
Q ss_pred cc-ceEeccCCCCCCCcEEEEEeecccEEEEE
Q 003093 293 AG-PARFNSHGDLINPAYEIINVIGTGYRRIG 323 (848)
Q Consensus 293 tG-~v~Fd~~g~~~~~~~~I~~~~~~~~~~Vg 323 (848)
+| ++.||++|++ ...|.|++++++.|-.-|
T Consensus 360 tG~~v~fd~~G~~-~~~y~v~~~~~~~~~~~~ 390 (404)
T cd06370 360 TGFDMYIDENGDA-EGNYSVLALQPIPPGDNG 390 (404)
T ss_pred cCceEEEcCCCCc-ccceEEEEeccccccCCC
Confidence 99 8999999997 589999999887664433
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=100.00 E-value=6.1e-34 Score=316.58 Aligned_cols=304 Identities=21% Similarity=0.363 Sum_probs=257.9
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|+|||||.+|..+.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.++++++++++|++++++++
T Consensus 66 ~~~v~aiiG~~~s~~~~a~~~~~~~~~ip~Is~~~~~~~~~~~~~~~~~fr~~~~~~~~~~a~~~~l~~~~~~~v~ii~~ 145 (389)
T cd06352 66 EHNVDAFIGPGCPYACAPVARLAAHWNIPMISWGCVALSLSDKSEYPTLTRTLPPARKLGEAVLALLRWFNWHVAVVVYS 145 (389)
T ss_pred hcCCcEEECCCChhHHHHHHHHHhcCCCCEecccccccccCccccCCceeecCCcHHHHHHHHHHHHHHcCceEEEEEEe
Confidence 468999999999999999999999999999999999999986 5789999999999999999999999999999999998
Q ss_pred cCC-CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 81 DDD-HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 81 dd~-~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
++. ||....+.+.+++++.|++|+....++...+..|+..+|+++++.+ |+|++++...++..++++++++|+...++
T Consensus 146 ~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~d~~~~l~~i~~~~-~vii~~~~~~~~~~~l~q~~~~g~~~~~~ 224 (389)
T cd06352 146 DDSENCFFTLEALEAALREFNLTVSHVVFMEDNSGAEDLLEILQDIKRRS-RIIIMCGSSEDVRELLLAAHDLGLTSGDY 224 (389)
T ss_pred cCCccHHHHHHHHHHHHHhcCCeEEEEEEecCCccchhHHHHHHHhhhcc-eEEEEECCHHHHHHHHHHHHHcCCCCCcE
Confidence 888 9999999999999999999999888876522478999999999887 99999999999999999999999987889
Q ss_pred EEEecCccccccCC--------CCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCC---CCCCCCcchh
Q 003093 160 VWIATSWLSTALDT--------NSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPN---GYIGLNAYGF 228 (848)
Q Consensus 160 ~wi~~~~~~~~~~~--------~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~---~~~~~~~~~~ 228 (848)
+||.++.+...... .....+...++++|++++.+..+..+.+++|.++|+++++..+.+ ....++.+++
T Consensus 225 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~a~ 304 (389)
T cd06352 225 VFILIDLFNYSLPYQNSYPWERGDGDDEKAKEAYDAVLTITLRPPDNPEYEEFSEEVKEAAKRPPFNTDAEPEQVSPYAG 304 (389)
T ss_pred EEEEEehhccccccCCCCCcccCCcccHHHHHHHHhheEEEecCCCCchHHHHHHHHHHHHhcccCccCCCccccchhhh
Confidence 99998876554211 011113345678999998888888889999999999998632211 1235678999
Q ss_pred hhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCc
Q 003093 229 YAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPA 308 (848)
Q Consensus 229 ~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~ 308 (848)
++||||+++++|++++.++++. +.++.++.++|++++|.|++|++.||++|++ .+.
T Consensus 305 ~~YDav~~~a~Al~~~~~~~~~-----------------------~~~~~~v~~~l~~~~f~g~~G~v~fd~~G~~-~~~ 360 (389)
T cd06352 305 YLYDAVLLYAHALNETLAEGGD-----------------------YNGGLIITRRMWNRTFSGITGPVTIDENGDR-EGD 360 (389)
T ss_pred hHHHHHHHHHHHHHHHHHhCCC-----------------------CCchHHHHHHhcCcEEEeeeeeEEEcCCCCe-eee
Confidence 9999999999999998765321 1248899999999999999999999999997 478
Q ss_pred EEEEEeec--ccEEEEEEeeCCCC
Q 003093 309 YEIINVIG--TGYRRIGYWSNYSG 330 (848)
Q Consensus 309 ~~I~~~~~--~~~~~Vg~w~~~~g 330 (848)
|.|+++++ +....++.+...+|
T Consensus 361 ~~v~~~~~~~~~~~~~~~~~~~~~ 384 (389)
T cd06352 361 YSLLDLDSTGGQLEVVYLYDTSSG 384 (389)
T ss_pred EEEEEecCCCceEEEEEeccccce
Confidence 99999996 56788888766553
No 34
>PF01094 ANF_receptor: Receptor family ligand binding region The Prosite family is a sub-family of the Pfam family; InterPro: IPR001828 This describes a ligand binding domain and includes extracellular ligand binding domains of a wide range of receptors, as well as the bacterial amino acid binding proteins of known structure [].; PDB: 3SAJ_D 3Q41_B 3QEM_C 3QEK_A 3QEL_C 3MQ4_A 3QLV_G 3OM1_A 3QLU_A 3OM0_A ....
Probab=100.00 E-value=7.8e-34 Score=311.32 Aligned_cols=292 Identities=28% Similarity=0.482 Sum_probs=243.7
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS--LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~--~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
++|+|||||.|+..+.+++.+++.++||+|+++++++.+++ .+||+|+|+.|++..+++++++++++|+|++|++||+
T Consensus 50 ~~v~aviGp~~~~~~~~~~~~~~~~~ip~is~~~~~~~ls~~~~~~~~~~r~~p~~~~~~~a~~~~l~~~~w~~v~vv~~ 129 (348)
T PF01094_consen 50 QGVVAVIGPSCSSSAEAVASLASEWNIPQISPGSTSPSLSDRKTRYPTFFRTVPSDSSQARALVDLLKHFGWTRVSVVYS 129 (348)
T ss_dssp HTECEEEETSSHHHHHHHHHHHHHTT-EEEESSGGSGGGGSTTTTTTTEEESSB-HHHHHHHHHHHHHHTTSSEEEEEEE
T ss_pred CCcEEEECCCcccccchhheeecccccceeeccccccccccchhhccccccccccHHHHHHHHHHhhhcCCCceeeeecc
Confidence 57999999999999999999999999999999999999988 4799999999999999999999999999999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEe-eecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFK-APLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~-~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
++++|......+.+.+++.++.+... ...+.. ..++...+.+++. .++++|+++++..++..++++|.++||...
T Consensus 130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~rvvil~~~~~~~~~~l~~a~~~~~~~~ 207 (348)
T PF01094_consen 130 DDDYGNSLADSFQDLLRERGGICVAFISVVISS--DSDAEELLKKLKEIKSGARVVILCSSPEDARQFLEAAYELGMTSG 207 (348)
T ss_dssp SSHHHHHHHHHHHHHHHHHTTCEEEEEEEEETT--TSHHHHHHHHHHHHTTTTSEEEEESBHHHHHHHHHHHHHTTTSST
T ss_pred ccccccccchhhhhhhcccccceeccccccccc--ccchhhhhhhhhhccccceeeeeecccccccccccchhhhhcccc
Confidence 99999999999999999965444433 333322 2455555555555 999999999999999999999999999999
Q ss_pred CeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccC-CCCCCCCCCCcchhhhhhHHHH
Q 003093 158 GYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 158 ~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~ 236 (848)
+|+||.++.+...... ..........|++++.+..+..+.+++|.++|++.... +.......+..+++++||||++
T Consensus 208 ~~~~i~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~yDAv~~ 284 (348)
T PF01094_consen 208 DYVWILTDLDNSSFWQ---NNEDFREAFQGVLGFTPPPPSSPEFEDFMKKWKESNNQSSTSGSDQEPSPYAAYAYDAVYL 284 (348)
T ss_dssp TSEEEEETTTTTTHTS---THCHHHCCHTTEEEEEESTTTSHHHHHHHHHHHTTTHTTTTTTTTSSGCHHHHHHHHHHHH
T ss_pred ceeEEeeccccccccc---ccccccccccceeeeeeecccccchhhhhcccChhhccCcccccccccceeeeeehhhhHH
Confidence 9999999987655321 11466788999999999999999999999999976421 1222345678899999999999
Q ss_pred HHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEecc-CCCCCCCcEEEEEee
Q 003093 237 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNS-HGDLINPAYEIINVI 315 (848)
Q Consensus 237 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~-~g~~~~~~~~I~~~~ 315 (848)
+|+|++++.++++.... ..+.|.+|..|.++|++++|+|++|++.||+ +|++....|+|+|+|
T Consensus 285 ~a~al~~~~~~~~~~~~----------------~~~~~~~g~~l~~~l~~~~f~G~tG~v~f~~~~G~~~~~~~~i~~~~ 348 (348)
T PF01094_consen 285 LAHALNRALQDGGPVTN----------------GRNPWQNGSQLLKYLRNVSFEGLTGRVSFDSNDGDRTNYDYDILNMQ 348 (348)
T ss_dssp HHHHHHHHHHHHSTTTS----------------SSGTSTTHHHHHHHHHTEEEEETTEEEEEETTTSBEESEEEEEEEE-
T ss_pred HHHHHHHHHHhccCCCC----------------CccccccHHHHHHHHhheeeeCCCCCEEEeCCCCCcCCCEEEEEECC
Confidence 99999999876543211 0145667999999999999999999999999 999889999999985
No 35
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=100.00 E-value=1.1e-33 Score=300.81 Aligned_cols=265 Identities=23% Similarity=0.376 Sum_probs=208.3
Q ss_pred CCCeEEEEccCCchh-HHHHHHhhccCCccEEecccCC-CCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVT-SHVVSHVANELQVPLLSFSATD-PTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIY 79 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~-~~ava~i~~~~~vP~Is~~at~-p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~ 79 (848)
+++|+|||||.+|.. +.+++++|++.+||+|+++... |.+...++++ +++.|++..|++|+++++++|+|++|++||
T Consensus 63 ~~gV~AIiGp~ss~~~~~~v~~i~~~~~VP~Is~~~~~~~~~~~~~~~~-i~l~P~~~~~~~Ai~dli~~~~W~~v~~iY 141 (333)
T cd06394 63 PKGVVSVLGPSSSPASSSIVSHICGEKEIPHFKVGPEETPKLQYLRFAS-VNLHPSNEDISVAVAGILNSFNYPTASLIC 141 (333)
T ss_pred hcCeEEEECCCCchHHHHHHHHHhhccCCceEEeccccCcccccccceE-EEecCCHHHHHHHHHHHHHhcCCCEEEEEE
Confidence 579999999999975 6799999999999999986443 4443344444 899999999999999999999999999999
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCC--CChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVE--ATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~--~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
+++++ ...|++.++..++ +...++.. .++.|++.+|++|+.+++|+||++|+++.+..++++|+++||+.+
T Consensus 142 e~d~~----l~~L~~~l~~~~~---~~~~i~~~~~~~~~d~~~~L~~ik~~~~~~iVv~~~~~~a~~il~qa~~lGm~~~ 214 (333)
T cd06394 142 AKAEC----LLRLEELLRQFLI---SKETLSVRMLDDSRDPTPLLKEIRDDKTATIIIDANASMSHTILLKASELGMTSA 214 (333)
T ss_pred eCcHH----HHHHHHHHHhhcc---cCCceeeEEccCcccHHHHHHHHHhcCCCEEEEECChHHHHHHHHHHHHcCCCCC
Confidence 99986 4555566655432 12222221 134789999999999999999999999999999999999999999
Q ss_pred CeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccC-CCCCCCCCCCcchhhhhhHHHH
Q 003093 158 GYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 158 ~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~ 236 (848)
+|+|+.|+......+.. +.......+.+++..+++.+..++|.++|++++.+ +...........++++||||++
T Consensus 215 ~y~~i~T~l~~~~~~L~-----~~~~~~~niTgF~l~d~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~~al~~D~v~~ 289 (333)
T cd06394 215 FYKYILTTMDFPLLRLD-----SIVDDRSNILGFSMFNQSHAFYQEFIRSLNQSWRENCDHSPYTGPALSSALLFDAVYA 289 (333)
T ss_pred ceEEEEecCCcccccHH-----HhhcCCcceEEEEeecCCcHHHHHHHHHHHHhhhhhcccccCCCcccceeeecceEEE
Confidence 99999998776543332 22222455788888999999999999999887631 1111111122356677777653
Q ss_pred HHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeec
Q 003093 237 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIG 316 (848)
Q Consensus 237 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~ 316 (848)
+ |+||+|+||++|+|.+..++|+++..
T Consensus 290 ~-----------------------------------------------------glTg~i~f~~~g~R~~~~l~v~~l~~ 316 (333)
T cd06394 290 V-----------------------------------------------------GLTGRIEFNSKGQRSNYTLKILQKTR 316 (333)
T ss_pred E-----------------------------------------------------eeecceecCCCCcCcccEEEEEEecC
Confidence 3 89999999999999999999999999
Q ss_pred ccEEEEEEeeCCCCCc
Q 003093 317 TGYRRIGYWSNYSGLS 332 (848)
Q Consensus 317 ~~~~~Vg~w~~~~gl~ 332 (848)
+|.++||+|++..||+
T Consensus 317 ~g~~kig~W~~~~gl~ 332 (333)
T cd06394 317 SGFRQIGQWHSNETLS 332 (333)
T ss_pred CcceEEEEEeCCCCcC
Confidence 9999999999998875
No 36
>cd06382 PBP1_iGluR_Kainate N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeri
Probab=100.00 E-value=5.4e-33 Score=301.12 Aligned_cols=262 Identities=22% Similarity=0.317 Sum_probs=219.4
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+++|++||||.+|..+.++++++++++||+|+++++++.++ .++|+||+.|++..++.++++++++++|++|+++|++
T Consensus 61 ~~~V~aiiG~~~S~~~~av~~~~~~~~vP~Is~~~~~~~~~--~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vavl~~~ 138 (327)
T cd06382 61 QQGVAAIFGPSSSEASSIVQSICDAKEIPHIQTRWDPEPKS--NRQFTINLYPSNADLSRAYADIVKSFNWKSFTIIYES 138 (327)
T ss_pred hcCcEEEECCCChhHHHHHHHHHhccCCCceeccCCcCccc--cccceEEeCCCHHHHHHHHHHHHHhcCCcEEEEEecC
Confidence 35899999999999999999999999999999988888776 5689999999999999999999999999999999998
Q ss_pred CCCccchHHHHHHHHhccCc---EEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 82 DDHGRNGIAALGDTLAAKRC---RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~---~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
++++.. +.+.+++.|. .|.. +.++.+ . |++.+|.+|++.++|+|++++...++..+++||+++||..+.
T Consensus 139 ~~~~~~----l~~~~~~~~~~g~~v~~-~~~~~~--~-d~~~~l~~i~~~~~d~vv~~~~~~~~~~~~~qa~~~g~~~~~ 210 (327)
T cd06382 139 AEGLLR----LQELLQAFGISGITITV-RQLDDD--L-DYRPLLKEIKNSGDNRIIIDCSADILIELLKQAQQVGMMSEY 210 (327)
T ss_pred hHHHHH----HHHHHHhhccCCCeEEE-EEccCC--c-cHHHHHHHHHhcCceEEEEECCHHHHHHHHHHHHHhCccccc
Confidence 886543 4555555554 4444 455543 2 999999999999999999999999999999999999999999
Q ss_pred eEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccC-CCCCCCCCCCcchhhhhhHHHHH
Q 003093 159 YVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLL 237 (848)
Q Consensus 159 ~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~ 237 (848)
|+|+.++......+.. .......++.++.++.++++.+++|.++|+++++. .++.....|+.+++.+|||++++
T Consensus 211 ~~~i~~~~~~~~~~l~-----~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~~a~~yDav~~~ 285 (327)
T cd06382 211 YHYIITNLDLHTLDLE-----DYRYSGVNITGFRLVDPDSPEVKEVIRSLELSWDEGCRILPSTGVTTESALMYDAVYLF 285 (327)
T ss_pred eEEEEecCCccccchh-----hhccCceeEEEEEEecCCchhHHHHHHHHHhhcccccccCCCCCcchhhhhhhceEEEe
Confidence 9999987755443331 12223447888888888889999999999999974 22223345788899999997754
Q ss_pred HHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecc
Q 003093 238 ARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGT 317 (848)
Q Consensus 238 a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~ 317 (848)
|+||+++||++|+|.+..++|+|++++
T Consensus 286 -----------------------------------------------------g~tG~v~f~~~g~r~~~~~~~~~~~~~ 312 (327)
T cd06382 286 -----------------------------------------------------GLTGRIEFDSSGQRSNFTLDVIELTES 312 (327)
T ss_pred -----------------------------------------------------ecccceeeCCCCCEeeeEEEEEecccc
Confidence 899999999999999999999999999
Q ss_pred cEEEEEEeeCCCCC
Q 003093 318 GYRRIGYWSNYSGL 331 (848)
Q Consensus 318 ~~~~Vg~w~~~~gl 331 (848)
++++||+|++..||
T Consensus 313 ~~~~vg~w~~~~~~ 326 (327)
T cd06382 313 GLRKVGTWNSSEGL 326 (327)
T ss_pred CceEEEEECCCCCc
Confidence 99999999988775
No 37
>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=99.97 E-value=3.2e-30 Score=279.48 Aligned_cols=277 Identities=16% Similarity=0.207 Sum_probs=208.5
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccC---CCC-----CCC-CCCCceEeccCChHHHHHHHHHHHHHcCc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSAT---DPT-----LSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGW 72 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at---~p~-----ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w 72 (848)
+++|+|||||.+|..+.+++++++..+||+|++.+. +|. +.+ ...+|.|++.|++ .+..++++++++|||
T Consensus 60 ~~gV~AI~G~~~s~~~~av~~i~~~~~IP~Is~~~~~~~~~~~~~~~~~~~~~~~~~f~~rp~~-~~~~ai~~lv~~~~w 138 (363)
T cd06381 60 NQGILALVTSTGCASAIALQSLTDAMHIPHLFIQRGYGGSPRTACGLNPSPRGQQYTLALRPPV-RLNDVMLRLVTEWRW 138 (363)
T ss_pred hcCcEEEEecCChhHHHHHHHHhhCCCCCEEEeecCcCCCcccccccCCCcccceeEEEEeccH-HHHHHHHHHHHhCCC
Confidence 459999999999999999999999999999996532 211 111 1224545555664 688999999999999
Q ss_pred EEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHh-------cCCCeEEEEEccCCcHHHH
Q 003093 73 REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVA-------LTESRIIVVHTHYNRGPVV 145 (848)
Q Consensus 73 ~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~-------~~~~~viv~~~~~~~~~~~ 145 (848)
++|+++|++++ |....+.+.+++++.|+.+... ....+ ....+..+++.++ ..+.++||++|+++.+..+
T Consensus 139 kkvavly~~d~-g~~~l~~~~~~~~~~g~~v~~~-~~~~~-~~~~~~~l~~~~~~~~l~~~~~~~~~vIl~~~~~~~~~~ 215 (363)
T cd06381 139 QKFVYFYDNDY-DIRGLQEFLDQLSRQGIDVLLQ-KVDLN-ISKMATALFTTMRCEELNRYRDTLRRALLLLSPNGAYTF 215 (363)
T ss_pred eEEEEEEECCc-hHHHHHHHHHHHHhcCceEEEE-ecccc-cchhhhhhhhHHHHHHHHhhcccceEEEEEcCcHHHHHH
Confidence 99999998876 5566688888999999876643 23221 1123444444332 3455688999999999999
Q ss_pred HHHHHHcCCCCCCeEEEecCccccc-cCCCCCCCcccccccceeEEEEEecCCchhHH----HHHHHHHhhccCCCCCCC
Q 003093 146 FHVAQYLGMLGTGYVWIATSWLSTA-LDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKR----KFISRWRNLTDAKTPNGY 220 (848)
Q Consensus 146 ~~~a~~~g~~~~~~~wi~~~~~~~~-~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~----~f~~~~~~~~~~~~~~~~ 220 (848)
+++|+++||+..+|+||+++.+... .+. +.......|+++++..++..+..+ .|.+.|++.+...++ ..
T Consensus 216 l~~a~~~gm~~~~~~wi~~~~l~~~~~~l-----~~~~~~~~nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 289 (363)
T cd06381 216 IDASVETNLAIKDSHWFLINEEISDTEID-----ELVRYAHGRMTVIRQTFSKEKTNQRCLRNNHRISSLLCDPKDG-YL 289 (363)
T ss_pred HHHHHHcCCCcCceEEEEeccccccchhh-----HHHhhcCccEEEEEEecCCcCchHHHHHHHHHHHHhhcCCCCC-CC
Confidence 9999999999999999887766542 222 345677899999999988777666 455566543322222 22
Q ss_pred CCCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEecc
Q 003093 221 IGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNS 300 (848)
Q Consensus 221 ~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~ 300 (848)
..+...++++|||||++. ++|++++|+|+||+|+||+
T Consensus 290 ~~~~~~~al~yDaV~~~~-------------------------------------------~~~~~~~~~GLTG~i~F~~ 326 (363)
T cd06381 290 QMLEISNLYIYDSVLLLL-------------------------------------------ETIKKGPITGLTGKLEFNE 326 (363)
T ss_pred CChhHHHHHHHHHHHHHH-------------------------------------------HHHHhcCccCcceeEEeCC
Confidence 356678999999999981 2566678999999999999
Q ss_pred CCCCCCCcEEEEEeeccc-----EEEEEEeeCCCCC
Q 003093 301 HGDLINPAYEIINVIGTG-----YRRIGYWSNYSGL 331 (848)
Q Consensus 301 ~g~~~~~~~~I~~~~~~~-----~~~Vg~w~~~~gl 331 (848)
+|+|.+..++|+++...+ .+.||+|++..||
T Consensus 327 ~g~r~~~~l~i~~~~~~~~~~~~~~~~~~w~~~~~~ 362 (363)
T cd06381 327 GGDNSNVQFEILGTGYSETLGKDGRWLATWNPSKGL 362 (363)
T ss_pred CCCccccEEEEEEeccCCccccceEEeeeccCCCCC
Confidence 999999999999998555 7889999998876
No 38
>cd06368 PBP1_iGluR_non_NMDA_like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-d -aspartate (NMDA) and non-NMDA receptors. NMDA receptors
Probab=99.97 E-value=1.5e-30 Score=281.86 Aligned_cols=263 Identities=23% Similarity=0.368 Sum_probs=216.9
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+++|.+||||.+|..+.++++++++++||+|+++++++.++ ..++|.| .|++..|+.++++++++++|++|++||++
T Consensus 60 ~~~V~aiiG~~~S~~~~av~~i~~~~~ip~is~~~~~~~~~-~~~~~~~--~~~~~~~~~a~~~~~~~~~w~~vaii~~~ 136 (324)
T cd06368 60 SQGVAAIFGPSSSSSANTVQSICDALEIPHITTSWSPNPKP-RQFTINL--YPSMRDLSDALLDLIKYFGWRKFVYIYDS 136 (324)
T ss_pred hcCcEEEECCCCHHHHHHHHHHHhccCCCcEEecCCcCCCC-CcceEEe--cCCHHHHHHHHHHHHHhcCCCEEEEEECC
Confidence 46899999999999999999999999999999999998886 3344444 47777999999999999999999999977
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++++ ...+.+.+.+++.|++|+.....+ . + +|++.+|.+|++.++|+|+++++..++..++++|+++||..++|+|
T Consensus 137 ~~~~-~~l~~~~~~~~~~g~~v~~~~~~~-~-~-~d~~~~l~~i~~~~~d~Vi~~~~~~~~~~i~~qa~~~g~~~~~~~~ 212 (324)
T cd06368 137 DEGL-LRLQELLDALSPKGIQVTVRRLDD-D-T-DMYRPLLKEIKREKERRIILDCSPERLKEFLEQAVEVGMMSEYYHY 212 (324)
T ss_pred cHhH-HHHHHHHHhhccCCceEEEEEecC-C-c-hHHHHHHHHHhhccCceEEEECCHHHHHHHHHHHHHhccccCCcEE
Confidence 6654 455667778888899998765433 2 2 3899999999999999999999999999999999999999899999
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccC-CCCCCCCCCCcchhhhhhHHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLLARA 240 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~a~A 240 (848)
|+++......+. ........++.+.....++++.+++|.++|+++++. ++......|..+++.+||||+++
T Consensus 213 i~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~aa~~yDav~~~--- 284 (324)
T cd06368 213 ILTNLDFHTLDL-----ELFRYGGVNITGFRLVDPDNPEVQKFIQRWERSDHRICPGSGLKPIKTESALTYDAVLLF--- 284 (324)
T ss_pred EEccCCccccch-----hhhhcCCceEEEEEEecCCChHHHHHHHHHHhccccccCCCCCCCcchhhHhhhcEEEEe---
Confidence 998765433221 112233445777777788889999999999999863 22222336788999999998754
Q ss_pred HHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecccEE
Q 003093 241 INSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYR 320 (848)
Q Consensus 241 l~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~ 320 (848)
||+++||++|+|.+..++|+++.+++++
T Consensus 285 ----------------------------------------------------tg~~~f~~~g~~~~~~~~i~~~~~~~~~ 312 (324)
T cd06368 285 ----------------------------------------------------TGRIQFDENGQRSNFTLDILELKEGGLR 312 (324)
T ss_pred ----------------------------------------------------eeeeEeCCCCcCcceEEEEEEEcCCCce
Confidence 6789999999999999999999999999
Q ss_pred EEEEeeCCCCC
Q 003093 321 RIGYWSNYSGL 331 (848)
Q Consensus 321 ~Vg~w~~~~gl 331 (848)
.||+|++..|+
T Consensus 313 ~~g~W~~~~~~ 323 (324)
T cd06368 313 KVGTWNPEDGL 323 (324)
T ss_pred EEEEECCCCCC
Confidence 99999987764
No 39
>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=99.97 E-value=1.7e-29 Score=275.15 Aligned_cols=267 Identities=18% Similarity=0.239 Sum_probs=231.1
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHH-HHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~-~~~~w~~vaii~~d 81 (848)
++|++||||.+|..+.++++++++.+||+|+++++++.+++..||++||+.|++..++.++++++ ++++|++|++++.|
T Consensus 65 ~~v~aiiG~~~s~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~ 144 (334)
T cd06342 65 DGVVGVVGHLNSGVTIPASPIYADAGIVMISPAATNPKLTERGYKNVFRVVARDDQQGPAAAKYAVETLKAKKVAIIDDK 144 (334)
T ss_pred CCceEEECCCccHhHHHhHHHHHhCCCeEEecCCCCchhhcCCCceEEeccCCcHHHHHHHHHHHHHhcCCCEEEEEeCC
Confidence 48999999999999999999999999999999888777776678999999999999999999985 67899999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++||+...+.+.+.+++.|++|+....++.+. .|+...+.++++.++|+|++.+...++..++++++++|+. ..|
T Consensus 145 ~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~--~d~~~~l~~i~~~~~~~vi~~~~~~~~~~~~~~~~~~g~~---~~~ 219 (334)
T cd06342 145 TAYGQGLADEFKKALKAAGGKVVAREGTTDGA--TDFSAILTKIKAANPDAVFFGGYYPEAGPLVRQMRQLGLK---APF 219 (334)
T ss_pred cchhhHHHHHHHHHHHHcCCEEEEEecCCCCC--ccHHHHHHHHHhcCCCEEEEcCcchhHHHHHHHHHHcCCC---CcE
Confidence 99999999999999999999999988888654 8999999999999999999999999999999999999984 357
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
+.++++... ... ....+..+|++...++.+ ..+..++|.++|+++++ ..++.++..+||+++++++
T Consensus 220 ~~~~~~~~~-~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~yda~~~~~~ 287 (334)
T cd06342 220 MGGDGLCDP-EFI----KIAGDAAEGTYATFPGGPLEKMPAGKAFVARYKAKFG-------DPPGAYAPYAYDAANVLAE 287 (334)
T ss_pred EecCccCCH-HHH----HHhhHhhCCcEEEecCCCCCCChHHHHHHHHHHHHhC-------CCCchhHHHHHHHHHHHHH
Confidence 776644321 110 223356789888877665 46889999999999886 3457789999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEe
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV 314 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~ 314 (848)
|++++. .. +++.+.++|++++|+|++|+++|+++|++.+..|.|+||
T Consensus 288 al~~~~---------------------------~~-~~~~v~~~l~~~~~~g~~g~i~f~~~g~~~~~~~~~~~~ 334 (334)
T cd06342 288 AIKKAG---------------------------ST-DPAKVADALRKVDFDGVTGKISFDAKGDLKGAAVTVYQV 334 (334)
T ss_pred HHHHhC---------------------------CC-CHHHHHHHHHhCCCCCcceeeEECCCCCcccCcEEEEeC
Confidence 999841 11 388999999999999999999999999999999999885
No 40
>cd06383 PBP1_iGluR_AMPA_Like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excitatory synaptic current.
Probab=99.97 E-value=2.8e-30 Score=280.48 Aligned_cols=280 Identities=15% Similarity=0.115 Sum_probs=202.2
Q ss_pred CCCe--EEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEE
Q 003093 2 EGQT--VAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIY 79 (848)
Q Consensus 2 ~~~V--~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~ 79 (848)
+++| +|||||.+|..+.+++.+++.++||+|+++.. ..++.++|||+|+.|++..|++|+++++++|+|++|++||
T Consensus 63 ~~gv~~~AIiGp~ss~~a~~V~si~~~~~IP~Is~s~~--~~~~~~~p~~ir~~Ps~~~~~~Ai~dlI~~f~W~~v~iIY 140 (368)
T cd06383 63 DSAIVPHLVLDTTTCGDASEIKSVTGALGIPTFSASYG--QEGDLEQPYLIQLMPPADDIVEAIRDIVSYYNITNAAILY 140 (368)
T ss_pred HccCCcEEEECCCcchhHHHHHHHHhccCCCEEEccCC--CcCcccCceEEEEeCChHHHHHHHHHHHHHCCCcEEEEEE
Confidence 4677 89999999999999999999999999997543 3334589999999999999999999999999999999999
Q ss_pred EcCCCccchHH-HHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEcc-CCcHHHHHHHHHHcCCCCC
Q 003093 80 VDDDHGRNGIA-ALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 80 ~dd~~g~~~~~-~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~-~~~~~~~~~~a~~~g~~~~ 157 (848)
++++++..... .+.+.....+.++. +. ...++..+|++|+..+.+.||+.+. ++.+..++++|.++||++.
T Consensus 141 ddd~gl~~~l~~~l~~~~~~~~~~v~-----~~--~~~~~~~~Lk~lk~~~~~rIIi~~s~~~~~~~il~qA~~lgm~~~ 213 (368)
T cd06383 141 DDDFVMDHKYKSLLQNWPTRHVITII-----NS--IIDEVREQIKRLRNLDIKNIFILGSTEEIIRYVLDQALAEGFMGR 213 (368)
T ss_pred EcCchhhHHHHHHHHhHHhcCCEEEE-----ec--cchhHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHHHHHcCCcCC
Confidence 77664432333 33333344455543 11 2257889999999988855555555 5999999999999999999
Q ss_pred CeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHH
Q 003093 158 GYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLL 237 (848)
Q Consensus 158 ~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~ 237 (848)
+|+||.+++.....+. +.....-.++.++++..+.....+.+.++|.+.. ..+.........++.+||||+++
T Consensus 214 ~y~wilt~ld~~~~dl-----~~~~~~~~Nitgfrl~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~aL~~Dav~~~ 286 (368)
T cd06383 214 KYAWFLGNPDLGIYDD-----LSCQLRNASIFVTRPMMDYQSSVRGALLRTDEPT--LRPVFYFEWAFRLFLAYDAVLAV 286 (368)
T ss_pred ceEEEEcCCCchhhhh-----hhhccccCcEEEeeccccchhhhccceeeccCCc--cCchhHHHHHHHHHHHHHHHHHh
Confidence 9999999987665433 2233344678888886655555577777763321 01111113345689999999999
Q ss_pred HHHHHHHHhcCCCccccCCCcccccc-CccccCcc---ccc-CChHHHHHHHHhccccccccceEeccCCCCC
Q 003093 238 ARAINSFFKQGGNLSFSKDSRLSDIQ-GHLRLDSL---RIF-NGGNLLRDSILQANMTGTAGPARFNSHGDLI 305 (848)
Q Consensus 238 a~Al~~~~~~~~~~~~~~~~~~~~~~-g~~~~~~~---~~~-~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~ 305 (848)
++|++.+........ +.. ....|... -+| ..|..+.++|+.++|+|+||+|+||++|.|.
T Consensus 287 ~~a~~~l~~~~~~~~--------~~~~~~~~~~g~~~~~~w~~~g~~~~~~~k~~~~~gltG~i~f~~~g~R~ 351 (368)
T cd06383 287 GEWPRRMRKKRVEDG--------STGTSVLPGFGISPESPLMTLQSSPFNGSSEIKFEMLAGRVAIDEGSSVS 351 (368)
T ss_pred ccccchhheeeccCC--------CcCccccCCCCCCcccchhhcccccccCccceeEeeecCeEEEecCceee
Confidence 999998632211110 000 01223222 234 5567999999999999999999999999874
No 41
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=99.97 E-value=5.6e-29 Score=272.69 Aligned_cols=274 Identities=12% Similarity=0.161 Sum_probs=233.0
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHH-HHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~-~~~~w~~vaii~~ 80 (848)
+++|.+||||.+|..+.++++++++.+||+|++++++|.+++..+||+||+.+.+..++.++++++ ++++|++|++|++
T Consensus 90 ~~~V~~iiG~~~s~~~~a~~~~~~~~~ip~i~~~s~~~~l~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~k~va~i~~ 169 (369)
T PRK15404 90 NDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATAPELTARGYQLIFRTIGLDSDQGPTAAKYILEKVKPKRIAVLHD 169 (369)
T ss_pred hCCceEEEcCCCchhHHHhHHHHHHCCCeEEecCCCCHHHhcCCCceEEeCCCCcHHHHHHHHHHHHHhcCCCEEEEEeC
Confidence 468999999999999999999999999999999999999988778999999999999999999975 5679999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
|++||+...+.+.+.+++.|++++....++.+. .|+..++.++++.+||+|++.+...+...++++++++|+.. .
T Consensus 170 d~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~g~--~D~~~~v~~l~~~~~d~v~~~~~~~~~~~~~k~~~~~G~~~---~ 244 (369)
T PRK15404 170 KQQYGEGLARSVKDGLKKAGANVVFFEGITAGD--KDFSALIAKLKKENVDFVYYGGYHPEMGQILRQAREAGLKT---Q 244 (369)
T ss_pred CCchhHHHHHHHHHHHHHcCCEEEEEEeeCCCC--CchHHHHHHHHhcCCCEEEECCCchHHHHHHHHHHHCCCCC---e
Confidence 999999999999999999999999888888754 89999999999999999998888888899999999999843 4
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEe-cCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTY-TPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~-~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
|+++++..... .. ....+..+|+++..++ ....|..++|.++|+++++ ..++.++..+||++++++.
T Consensus 245 ~i~~~~~~~~~-~~----~~~~~~~~Gv~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~Y~~~~~l~~ 312 (369)
T PRK15404 245 FMGPEGVGNKS-LS----NIAGPASEGMLVTLPKRYDQDPANKAIVDAFKAKKQ-------DPSGPFVWTTYAAVQSLAA 312 (369)
T ss_pred EEecCcCCCHH-HH----HhhhhhhcCcEEEccCCCccChhHHHHHHHHHHhcC-------CCCccchHHHHHHHHHHHH
Confidence 77665443211 10 1234677898876553 3345788999999998875 3455678899999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeecccE
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGY 319 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~~~ 319 (848)
|++++ +.. +++.|.++|++.+|+|++|+++|+++|++....|.|++|++++.
T Consensus 313 Al~~a---------------------------G~~-~~~~l~~al~~~~~~~~~G~~~~~~~g~~~~~~~~i~~~~~~~~ 364 (369)
T PRK15404 313 GINRA---------------------------GSD-DPAKVAKYLKANTFDTVIGPLSWDEKGDLKGFEFGVFEWHADGT 364 (369)
T ss_pred HHHhh---------------------------CCC-CHHHHHHHHHhCCCCcceEeeEECCCCCcccCCEEEEEEEcCCe
Confidence 99984 222 38899999999999999999999999998788999999987665
Q ss_pred E
Q 003093 320 R 320 (848)
Q Consensus 320 ~ 320 (848)
.
T Consensus 365 ~ 365 (369)
T PRK15404 365 K 365 (369)
T ss_pred E
Confidence 3
No 42
>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=99.97 E-value=7.2e-29 Score=271.27 Aligned_cols=267 Identities=15% Similarity=0.221 Sum_probs=224.1
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcC--cEEEEEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYG--WREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~--w~~vaii~~ 80 (848)
++|.+||||.+|..+.++++++++++||+|+++++++.++...+||+||+.|++..++.++++++++++ |+++++++.
T Consensus 70 ~~v~aviG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~ 149 (345)
T cd06338 70 DKVDFLLGPYSSGLTLAAAPVAEKYGVPMVAGSGASDSIFAQGFKYVFGTLPPASQYAKSLLEMLVALDPRPKKVAILYA 149 (345)
T ss_pred cCccEEecCCcchhHHHHHHHHHHhCCcEEecCCCCchHhhcCCceEEEecCchHHHHHHHHHHHHhcCCCCceEEEEec
Confidence 589999999999999999999999999999999988888766789999999999999999999999888 999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
|++||+...+.+.+.+++.|++|+....++.+. .|++.++++|+..++|+|++.+...+...+++++++.|+..+ ..
T Consensus 150 ~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~--~d~~~~v~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~-~~ 226 (345)
T cd06338 150 DDPFSQDVAEGAREKAEAAGLEVVYDETYPPGT--ADLSPLISKAKAAGPDAVVVAGHFPDAVLLVRQMKELGYNPK-AL 226 (345)
T ss_pred CCcccHHHHHHHHHHHHHcCCEEEEEeccCCCc--cchHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCCC-EE
Confidence 999999999999999999999999888787644 799999999999999999999999999999999999999643 22
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecCC-------chhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPD-------SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDT 233 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~-------~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDA 233 (848)
+. +.+..... .. +..++..+|+++...+.+. .+..++|.++|+++|+ ..|+.++..+||+
T Consensus 227 ~~-~~~~~~~~-~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~p~~~~~~~y~a 293 (345)
T cd06338 227 YM-TVGPAFPA-FV----KALGADAEGVFGPTQWTPALDYKDDLFPSAAEFAAAYKEKYG-------KAPDYHAAGAYAA 293 (345)
T ss_pred EE-ecCCCcHH-HH----HHHhhhhCceeecceeccCcccccccCccHHHHHHHHHHHhC-------CCCCcccHHHHHH
Confidence 22 22221110 00 2234456888887766554 3678999999999997 3467788999999
Q ss_pred HHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEE
Q 003093 234 VWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIIN 313 (848)
Q Consensus 234 v~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~ 313 (848)
++++++|++++. .. +++.+.++|++++|+|++|++.|+++|++.. .+.+++
T Consensus 294 ~~~~~~a~~~ag---------------------------~~-~~~~v~~al~~~~~~~~~G~~~f~~~~~~~~-~~~~~~ 344 (345)
T cd06338 294 GQVLQEAVERAG---------------------------SL-DPAAVRDALASNDFDTFYGPIKFDETGQNNH-PMTVVQ 344 (345)
T ss_pred HHHHHHHHHHhC---------------------------CC-CHHHHHHHHHhCCCcccccCeeECCCCCcCC-Cceeee
Confidence 999999999842 12 3889999999999999999999999999744 555554
Q ss_pred e
Q 003093 314 V 314 (848)
Q Consensus 314 ~ 314 (848)
|
T Consensus 345 ~ 345 (345)
T cd06338 345 W 345 (345)
T ss_pred C
Confidence 3
No 43
>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=99.96 E-value=8e-29 Score=271.33 Aligned_cols=246 Identities=33% Similarity=0.525 Sum_probs=211.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|.+||||.+|..+.++++++++++||+|+++++++.+++ ..|||+||+.|++..++.+++++++++||++|++++.+
T Consensus 90 ~~v~aiiG~~~S~~~~a~~~~~~~~~vp~is~~~~~~~ls~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~~~~v~~l~~~ 169 (348)
T cd06350 90 PKVVAVIGPGSSSVSMAVAELLGLFKIPQISYGATSPLLSDKLQFPSFFRTVPSDTSQALAIVALLKHFGWTWVGLVYSD 169 (348)
T ss_pred CceEEEECCCccHHHHHHHHHHhcCcCceecccCCChhhccccccCCeeEecCCcHHHHHHHHHHHHHCCCeEEEEEEec
Confidence 58999999999999999999999999999999999999976 67899999999999999999999999999999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++||....+.|.+.+++.|++|+..+.++...+..|+..++++|++.++|+|++++...++..++++|+++|+ .+.++|
T Consensus 170 ~~~g~~~~~~~~~~~~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vvv~~~~~~~~~~~~~~a~~~g~-~~~~~i 248 (348)
T cd06350 170 DDYGRSGLSDLEEELEKNGICIAFVEAIPPSSTEEDIKRILKKLKSSTARVIVVFGDEDDALRLFCEAYKLGM-TGKYWI 248 (348)
T ss_pred chhHHHHHHHHHHHHHHCCCcEEEEEEccCCCcHHHHHHHHHHHHhCCCcEEEEEeCcHHHHHHHHHHHHhCC-CCeEEE
Confidence 9999999999999999999999999988875446899999999999999999999999999999999999999 444444
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAI 241 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al 241 (848)
.++.+....... ....++++|+++...+.+.....+.|.+.|++ +++++|||||+
T Consensus 249 -~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~---------------~~~~~YDav~~----- 303 (348)
T cd06350 249 -ISTDWDTSTCLL----LFTLDAFQGVLGFSGHAPRSGEIPGFKDFLRK---------------YAYNVYDAVYA----- 303 (348)
T ss_pred -EEccccCccccc----cCCcceeeeEEEEEEEeecCCcCCChHHHHHH---------------HHHHHHhheeE-----
Confidence 554443321111 33456789999999888766556666666664 67889999986
Q ss_pred HHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEeec----c
Q 003093 242 NSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIG----T 317 (848)
Q Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~----~ 317 (848)
.+.||++|++ ...|.|++++. .
T Consensus 304 -----------------------------------------------------~v~f~~~gd~-~~~~~i~~~~~~~~~~ 329 (348)
T cd06350 304 -----------------------------------------------------EVKFDENGDR-LASYDIINWQIFPGGG 329 (348)
T ss_pred -----------------------------------------------------EEEecCCCCc-ccceeEEEEEEcCCcE
Confidence 3899999996 57799999976 6
Q ss_pred cEEEEEEeeCC
Q 003093 318 GYRRIGYWSNY 328 (848)
Q Consensus 318 ~~~~Vg~w~~~ 328 (848)
+++.||.|++.
T Consensus 330 ~~~~vg~~~~~ 340 (348)
T cd06350 330 GFVKVGFWDPQ 340 (348)
T ss_pred EEEEEEEEcCC
Confidence 79999999863
No 44
>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=99.96 E-value=2.6e-28 Score=266.47 Aligned_cols=259 Identities=17% Similarity=0.207 Sum_probs=217.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC----CCCCceEeccCChHHHHHHHHHHHHH-----cCcE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS----LQFPYFVRTTQSDQYQMAAIAEIVDH-----YGWR 73 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~----~~~p~f~r~~p~d~~q~~ai~~~~~~-----~~w~ 73 (848)
++|.+||||.+|..+.++++++++++||+|+++++++.++. ..+||+||+.|++..++.++++++.+ ++|+
T Consensus 66 ~~v~aiiG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~~t~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (344)
T cd06345 66 DKVDAVVGGYSSEVVLALQDVAAENKVPFIVTGAASPEITTADDYETYKYVFRAGPTNSSYAQSVADALKETLVDKHGFK 145 (344)
T ss_pred CCceEEECCcchHHHHHHHHHHHHcCCcEEeccCCCCcccccccccCCceEEecCCCcHHHHHHHHHHHHHhhcccCCCc
Confidence 48999999999999999999999999999999998888873 46899999999999999999998876 8999
Q ss_pred EEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcC
Q 003093 74 EVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLG 153 (848)
Q Consensus 74 ~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g 153 (848)
+|++++.+++||......+++.+++.|++|+....++.+. .|++.++.+|+..++|+|++.+...++..++++++++|
T Consensus 146 ~va~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g 223 (344)
T cd06345 146 TAAIVAEDAAWGKGIDAGIKALLPEAGLEVVSVERFSPDT--TDFTPILQQIKAADPDVIIAGFSGNVGVLFTQQWAEQK 223 (344)
T ss_pred eEEEEecCchhhhHHHHHHHHHHHHcCCeEEEEEecCCCC--CchHHHHHHHHhcCCCEEEEeecCchHHHHHHHHHHcC
Confidence 9999999999999999999999999999999888887653 78999999999999999999999999999999999999
Q ss_pred CCCCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecC----CchhHHHHHHHHHhhccCCCCCCCCCCCcchhh
Q 003093 154 MLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP----DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFY 229 (848)
Q Consensus 154 ~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~ 229 (848)
+..+ ++..+.+....... ....+..+|++....+.+ .++..++|.++|+++|+ ..|+.+++.
T Consensus 224 ~~~~---~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g-------~~p~~~~~~ 289 (344)
T cd06345 224 VPIP---TIGISVEGNSPAFW----KATNGAGNYVITAESGAPGVEAITDKTVPFTEAYEAKFG-------GPPNYMGAS 289 (344)
T ss_pred CCCc---eEEecCCcCCHHHH----HhhchhcceEEeecccccCccCCCHHHHHHHHHHHHHhC-------CCCcccchH
Confidence 8432 33332221111110 122345677766555443 56788999999999997 457889999
Q ss_pred hhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCC
Q 003093 230 AYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLI 305 (848)
Q Consensus 230 ~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~ 305 (848)
+||+++++++|++++. .. +++.+.++|++++|+|++|+++||++|++.
T Consensus 290 ~yda~~~l~~A~~~ag---------------------------~~-~~~~i~~al~~~~~~g~~G~i~f~~~g~~~ 337 (344)
T cd06345 290 TYDSIYILAEAIERAG---------------------------ST-DGDALVEALEKTDFVGTAGRIQFYGDDSAF 337 (344)
T ss_pred HHHHHHHHHHHHHHhc---------------------------CC-CHHHHHHHHHhCCCcCCceeEEECCCCCcC
Confidence 9999999999999842 11 378999999999999999999999999964
No 45
>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=99.96 E-value=3.9e-28 Score=261.00 Aligned_cols=243 Identities=21% Similarity=0.231 Sum_probs=207.7
Q ss_pred CCCeEEEEccCCchhHHHH-HHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVV-SHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIY 79 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~av-a~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~ 79 (848)
+++|++||||.+|..+.++ ++++++.++|+|+++++++.+++ ..++|+||+.|++..++.++++++++++|+++++||
T Consensus 65 ~~~v~~viG~~~s~~~~a~~~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~~vail~ 144 (312)
T cd06346 65 VDGVPGIVGAACSGVTIAALTSVAVPNGVVMISPSSTSPTLTTLDDNGLFFRTAPSDALQGQALAQLAAERGYKSVATTY 144 (312)
T ss_pred hcCCCEEEccccchhhHhhhhhhhccCCcEEEecCCCCccceecCCCceEEEecCCcHHHHHHHHHHHHHcCCCeEEEEE
Confidence 3589999999999999999 99999999999999999999987 457999999999999999999999999999999999
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
.|++||+...+.+++.+++.|++|+....++.+. .|+.+++++|++.+||+|++.+...++..++++++++|+..
T Consensus 145 ~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~--- 219 (312)
T cd06346 145 INNDYGVGLADAFTKAFEALGGTVTNVVAHEEGK--SSYSSEVAAAAAGGPDALVVIGYPETGSGILRSAYEQGLFD--- 219 (312)
T ss_pred ccCchhhHHHHHHHHHHHHcCCEEEEEEeeCCCC--CCHHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCCCC---
Confidence 9999999999999999999999999988888764 89999999999999999999999999999999999999843
Q ss_pred EEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
.|+.+++........ ....+.++|+++..+..+. +..++|.++|+++|+ ..|+.+++.+||+++++++
T Consensus 220 ~~~~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~-~~~~~f~~~~~~~~g-------~~p~~~~~~~Yd~~~~l~~ 287 (312)
T cd06346 220 KFLLTDGMKSDSFLP----ADGGYILAGSYGTSPGAGG-PGLEAFTSAYKAAYG-------ESPSAFADQSYDAAALLAL 287 (312)
T ss_pred ceEeeccccChHHHH----hhhHHHhCCcEEccCCCCc-hhHHHHHHHHHHHhC-------CCCCccchhhHHHHHHHHH
Confidence 367665533221110 1223567888877665443 888999999999997 3578899999999999876
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEE
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYE 310 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~ 310 (848)
| |.|++|+++||++|++.. .|.
T Consensus 288 A------------------------------------------------~~g~~g~~~f~~~g~~~~-~~~ 309 (312)
T cd06346 288 A------------------------------------------------YQGASGVVDFDENGDVAG-SYD 309 (312)
T ss_pred H------------------------------------------------hCCCccceeeCCCCCccc-cee
Confidence 5 568999999999998643 444
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=99.96 E-value=3.4e-27 Score=257.77 Aligned_cols=273 Identities=18% Similarity=0.296 Sum_probs=219.6
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHH-HHHHHHHHc-CcEEEEEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMA-AIAEIVDHY-GWREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~-ai~~~~~~~-~w~~vaii~~ 80 (848)
++|++||||.+|.++.++.+++++.+||+|+++++++.+.. .+||+||+.+++..+.. .+..+++++ +|+++++||.
T Consensus 66 ~~v~~iiG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~~~~-~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~ 144 (344)
T cd06348 66 DRVLAIIGPTLSQQAFAADPIAERAGVPVVGPSNTAKGIPE-IGPYVFRVSAPEAVVAPAAIAAALKLNPGIKRVAVFYA 144 (344)
T ss_pred cCceEEECCCCcHHHHhhhHHHHhCCCCEEeccCCCCCcCC-CCCeEEEccCcHHHHHHHHHHHHHHHhcCCeEEEEEEe
Confidence 48999999999999999999999999999999888776643 56899999887765544 455567787 9999999997
Q ss_pred cCC-CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 81 DDD-HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 81 dd~-~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
+++ ||+.....+++.+++.|++|+....++.+. .|+..++.+|++.++|+|++.+...++..+++++++.|+..
T Consensus 145 ~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~--~d~~~~v~~i~~~~~d~vi~~~~~~~~~~~~~~~~~~g~~~--- 219 (344)
T cd06348 145 QDDAFSVSETEIFQKALRDQGLNLVTVQTFQTGD--TDFQAQITAVLNSKPDLIVISALAADGGNLVRQLRELGYNG--- 219 (344)
T ss_pred CCchHHHHHHHHHHHHHHHcCCEEEEEEeeCCCC--CCHHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCC---
Confidence 655 999999999999999999999988888654 79999999999999999999999999999999999999954
Q ss_pred EEEecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHH
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLL 237 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~ 237 (848)
.|+.++++.... .. ....+..+|++...++.+ +.+..++|.++|+++++ ..|+.++..+|||++++
T Consensus 220 ~~~~~~~~~~~~-~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g-------~~p~~~~~~~yda~~~~ 287 (344)
T cd06348 220 LIVGGNGFNTPN-VF----PVCQAACDGVLVAQAYSPENDTPVNRDFVEAYKKKYG-------KAPPQFSAQAFDAVQVV 287 (344)
T ss_pred ceeccccccCHH-HH----HhhhHhhcCeEEEeeccCCCCCHHHHHHHHHHHHHHC-------CCccHHHHHHHHHHHHH
Confidence 355554432211 11 234467789888777654 34778999999999987 35677889999999999
Q ss_pred HHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEE
Q 003093 238 ARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEI 311 (848)
Q Consensus 238 a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I 311 (848)
++|++++...+.... |. ..+.++.|.++|++++|+|++|++.||++|++....|.|
T Consensus 288 ~~A~~~a~~~~~~~~---------------~~---~~~~~~~l~~~l~~~~~~g~~G~v~f~~~g~~~~~~~~~ 343 (344)
T cd06348 288 AEALKRLNQKQKLAE---------------LP---LPELRTALNAALLSGQYDTPLGEISFTPDGEVLQKAFYV 343 (344)
T ss_pred HHHHHHhcCCCcccc---------------ch---hhhHHHHHHHHHhccCCccceeeeEECCCCCcccCceec
Confidence 999999754321100 00 001367899999999999999999999999987666654
No 47
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.95 E-value=2.3e-27 Score=258.91 Aligned_cols=262 Identities=16% Similarity=0.216 Sum_probs=219.8
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc------CcEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY------GWREVI 76 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~------~w~~va 76 (848)
++|++||||.+|..+.++++++++.+||+|+++++++.+++..+||+||+.|++..++.++++++.++ +|++++
T Consensus 69 ~~v~aiiG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~fr~~p~~~~~~~~~~~~l~~~~~~~~~~~~~v~ 148 (347)
T cd06340 69 EGVVALVGAYQSAVTLAASQVAERYGVPFVVDGAVSDSITERGFKYTFRITPHDGMFTRDMFDFLKDLNEKTGKPLKTVA 148 (347)
T ss_pred CCceEEecccchHhHHHHHHHHHHhCCCEEeccccchHHhhcCCceEEecCCChHHHHHHHHHHHHHhhHhcCCCCceEE
Confidence 48999999999999999999999999999999999888887778999999999999999999998876 469999
Q ss_pred EEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 77 AIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 77 ii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
+++.|++||....+.+.+.+++.|++|+..+.++.. ..|++.++.+|+..++|+|++.+...++..++++++++|+..
T Consensus 149 ~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~G~~~ 226 (347)
T cd06340 149 LVHEDTEFGTSVAEAIKKFAKERGFEIVEDISYPAN--ARDLTSEVLKLKAANPDAILPASYTNDAILLVRTMKEQRVEP 226 (347)
T ss_pred EEecCchHhHHHHHHHHHHHHHcCCEEEEeeccCCC--CcchHHHHHHHHhcCCCEEEEcccchhHHHHHHHHHHcCCCC
Confidence 999999999999999999999999999998888865 379999999999999999999999999999999999999954
Q ss_pred CCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCC-chhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHH
Q 003093 157 TGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPD-SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVW 235 (848)
Q Consensus 157 ~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~ 235 (848)
+ .++...++..... .. ...+++.+|++...++.++ .+..++|.++|+++|+ ..++.++..+||+++
T Consensus 227 ~-~~~~~~~~~~~~~-~~----~~~g~~~~g~~~~~~~~~~~~~~~~~f~~~y~~~~~-------~~~~~~~~~~Y~a~~ 293 (347)
T cd06340 227 K-AVYSVGGGAEDPS-FV----KALGKDAEGILTRNEWSDPKDPMAKDLNKRFKARFG-------VDLSGNSARAYTAVL 293 (347)
T ss_pred c-EEEecCCCcCcHH-HH----HHhhHhhheEEeccccCCCCChHHHHHHHHHHHHhC-------CCCChHHHHHHHHHH
Confidence 3 3332222222111 11 2334567899988777665 6888999999999997 347889999999999
Q ss_pred HHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHH--HHHHhcccc---ccccceEeccCCCCCCC
Q 003093 236 LLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLR--DSILQANMT---GTAGPARFNSHGDLINP 307 (848)
Q Consensus 236 ~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~--~~l~~~~f~---G~tG~v~Fd~~g~~~~~ 307 (848)
++++|++++. +. +++.+. .+|++..+. ++.|++.||++|+..++
T Consensus 294 ~l~~A~~~ag---------------------------~~-~~~~v~~~~~~~~~~~~~~~~~~g~~~f~~~g~~~~~ 342 (347)
T cd06340 294 VIADALERAG---------------------------SA-DPEKIRDLAALASTSGEDLIMPYGPIKFDAKGQNTNA 342 (347)
T ss_pred HHHHHHHHhc---------------------------CC-CHHHHHHHHHhccCCccccccCCCCeeECCCCCcccc
Confidence 9999999942 22 377888 488877765 56899999999997544
No 48
>cd06344 PBP1_ABC_ligand_binding_like_9 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine/isoleucine/valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.95 E-value=4.5e-27 Score=255.22 Aligned_cols=260 Identities=17% Similarity=0.153 Sum_probs=214.9
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcC-cEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYG-WREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~-w~~vaii~~ 80 (848)
+++|++||||.+|..+.+++++++++++|+|+++++++.++ ..+||+||+.|++..+++++++++++.+ |++|++||.
T Consensus 64 ~~~v~aiiG~~~s~~~~a~~~~~~~~~ip~i~~~a~~~~lt-~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~ 142 (332)
T cd06344 64 DPEILGVVGHYSSDATLAALDIYQKAKLVLISPTSTSVKLS-NPGPYFFRTVPSNAVAARALAKYLKKKNKIKKVAIFYN 142 (332)
T ss_pred ccCceEEEcCCCcHHHHHHHHHHhhcCceEEccCcCchhhc-CCCCcEEEeCCCcHHHHHHHHHHHHhhcCCCeEEEEeC
Confidence 35899999999999999999999999999999988888887 4679999999999999999999998876 999999998
Q ss_pred cCC-CccchHHHHHHHHhc-cCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 81 DDD-HGRNGIAALGDTLAA-KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 81 dd~-~g~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
|++ ||+...+.+.+.+++ .|++++....++. ++.++..++.++++.++|+|++.+.......+++++++.|. .
T Consensus 143 ~~~~~g~~~~~~~~~~~~~~~g~~v~~~~~~~~--~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~~---~ 217 (332)
T cd06344 143 STSPYSQSLKQEFTSALLERGGGIVVTPCDLSS--PDFNANTAVSQAINNGATVLVLFPDTDTLDKALEVAKANKG---R 217 (332)
T ss_pred CCchHhHHHHHHHHHHHHHhcCCeeeeeccCCC--CCCCHHHHHHHHHhcCCCEEEEeCChhHHHHHHHHHHhcCC---C
Confidence 876 999999999999999 5999876554443 34678899999999999999999988888889999998775 3
Q ss_pred eEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 159 YVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 159 ~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
..+++++.+... ... ....+..+|+++..++.++.+..++|.++|+++++ ..|+.+++.+||++++++
T Consensus 218 ~~i~~~~~~~~~-~~~----~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~a~~~Yda~~~l~ 285 (332)
T cd06344 218 LTLLGGDSLYTP-DTL----LDGGKDLEGLVLAVPWHPLASPNSPFAKLAQQLWG-------GDVSWRTATAYDATKALI 285 (332)
T ss_pred ceEEecccccCH-HHH----HhchhhhcCeEEEEecccccccchHHHHHHHHHhc-------CCchHHHHhHHHHHHHHH
Confidence 345555543322 111 12345678999988888877888999999999997 357889999999999999
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHH-HHHHhccccccccceEeccCCCCCCC
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLR-DSILQANMTGTAGPARFNSHGDLINP 307 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~-~~l~~~~f~G~tG~v~Fd~~g~~~~~ 307 (848)
+|++++. +. ++..+. ..+++..|+|+.|+++||++|++..+
T Consensus 286 ~A~~~ag---------------------------~~-~~~~~~~~~~~~~~~~g~~g~i~f~~~g~~~~~ 327 (332)
T cd06344 286 AALSQGP---------------------------TR-EGVQQVELSLRNFSVQGATGKIKFLPSGDRNGQ 327 (332)
T ss_pred HHHHhCC---------------------------Ch-hhhhhhhhhcccccccCCCceeEeCCCCcccCc
Confidence 9999842 11 144454 67778889999999999999997543
No 49
>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=99.95 E-value=1.9e-26 Score=251.39 Aligned_cols=265 Identities=16% Similarity=0.235 Sum_probs=225.8
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|.+||||.+|..+.++++++++.++|+|+++++++.+++ ..+||+||+.+++..++..+++++...+|+++++++.+
T Consensus 64 ~~v~~iig~~~s~~~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~~~~~v~~l~~~ 143 (336)
T cd06360 64 DKVDVVVGPVHSGEALAMVKVLREPGTPLINPNAGADDLTGRLCAPNFFRTSFSNAQWAAPMGKYAADDGYKKVVTVAWD 143 (336)
T ss_pred hCCcEEEccCccHhHHHHHHHHHhcCceEEecCCCCccccccCCCCcEEEEeCchHHHHHHHHHHHHHcCCCeEEEEecc
Confidence 58999999999999999999999999999999988888876 44899999999999999999999998899999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
+.||+...+.+.+.+++.|++++....++... .||+++++++++.+||+|++.....++..+++++++.|+.. ...|
T Consensus 144 ~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~--~d~~~~v~~~~~~~pd~v~~~~~~~~~~~~~~~~~~~g~~~-~~~~ 220 (336)
T cd06360 144 YAFGYEVVEGFKEAFTEAGGKIVKELWVPFGT--SDFASYLAQIPDDVPDAVFVFFAGGDAIKFVKQYDAAGLKA-KIPL 220 (336)
T ss_pred chhhHHHHHHHHHHHHHcCCEEEEEEecCCCC--cchHHHHHHHHhcCCCEEEEecccccHHHHHHHHHHcCCcc-CCeE
Confidence 99999999999999999999999887777643 79999999999999999999999999999999999999853 3456
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
+.+++....... ...+++.+|++...++.+ +.+..++|.++|+++++ ..|+.++..+||+++++++
T Consensus 221 ~~~~~~~~~~~~-----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~~-------~~~~~~~~~~yda~~~~~~ 288 (336)
T cd06360 221 IGSGFLTDGTTL-----GAAGEAAEGVITALHYADTLDNPANQAFVKAYRAAYP-------DTPSVYAVQGYDAGQALIL 288 (336)
T ss_pred EecccccCHHHH-----HhhHhhhcCceeccccCCCCCCHHHHHHHHHHHHHhC-------CCccHHHHHHHHHHHHHHH
Confidence 666554332111 334567889888777654 46889999999999997 3678899999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCc
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPA 308 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~ 308 (848)
|++++... .. +++.+.++|++++|.|+.|+++|+++|++..+.
T Consensus 289 A~~~a~~~-------------------------~~-~~~~v~~al~~~~~~~~~g~~~f~~~~~~~~~~ 331 (336)
T cd06360 289 ALEAVGGD-------------------------LS-DGQALIAAMAAAKIDSPRGPFTLDKAHNPIQDN 331 (336)
T ss_pred HHHHhCCC-------------------------CC-CHHHHHHHHhcCCccCCCcceEECCCCCcccce
Confidence 99995211 01 378899999999999999999999999976554
No 50
>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=99.95 E-value=1.3e-26 Score=251.82 Aligned_cols=259 Identities=24% Similarity=0.387 Sum_probs=207.6
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|.|||||.+|..+.+++++++.++||+|+++++++.+++ ..+||+||+.|++..+++++++++++++|++|++||+
T Consensus 61 ~~~v~ai~G~~~s~~~~~v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~iiy~ 140 (328)
T cd06351 61 SQGVAAIFGPTSSESASAVQSICDALEIPHISISGGSEGLSDKEESSTTLQLYPSLEDLADALLDLLEYYNWTKFAIIYD 140 (328)
T ss_pred ccCcEEEECCCCHHHHHHHHHHhccCCCCeEEeecCcccccccccccceEEecCCHHHHHHHHHHHHHHcCCcEEEEEEe
Confidence 578999999999999999999999999999999998888876 6789999999999999999999999999999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCC-eEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTES-RIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~-~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
+++++... +.+.+.....+..+... .+.... .+++.++++++..++ ++|+.++..+.+..++++|+++||++++|
T Consensus 141 ~~~~~~~l-~~~~~~~~~~~~~v~~~-~~~~~~--~~~~~~l~~l~~~~~~~vil~~~~~~~~~~~l~~a~~~gm~~~~~ 216 (328)
T cd06351 141 SDEGLSRL-QELLDESGIKGIQVTVR-RLDLDD--DNYRQLLKELKRSESRRIILDCSSEEEAKEILEQAVELGMMGYGY 216 (328)
T ss_pred CchHHHHH-HHHHHhhcccCceEEEE-EecCCc--hhHHHHHHHHhhcccceEEEECCcHHHHHHHHHHHHHhccccCCc
Confidence 88854433 33333444444455443 444433 389999999999998 55555555489999999999999999999
Q ss_pred EEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
+||.++......+. ........|++++....+..+....|..+|.... +......+...++.+||+++++
T Consensus 217 ~~i~~~~~~~~~d~-----~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~d~~~~~-- 286 (328)
T cd06351 217 HWILTNLDLSDIDL-----EPFQYGPANITGFRLVDPDSPDVSQFLQRWLEES---PGVNLRAPIYDAALLYDAVLLL-- 286 (328)
T ss_pred EEEEecCCccccch-----hhhccCCcceEEEEEeCCCchHHHHHHHhhhhcc---CCCCcCccchhhHhhhcEEEEE--
Confidence 99999976654432 3445678999999999999999999999994333 2223334444556666654321
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEee-ccc
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI-GTG 318 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~-~~~ 318 (848)
||++.||++|+|.+..++|++++ +.+
T Consensus 287 -----------------------------------------------------tg~i~f~~~g~r~~~~l~i~~l~~~~~ 313 (328)
T cd06351 287 -----------------------------------------------------TGTVSFDEDGVRSNFTLDIIELNRSRG 313 (328)
T ss_pred -----------------------------------------------------EeeEEECCCCcccceEEEEEEecCCCC
Confidence 88999999999999999999999 899
Q ss_pred EEEEEEeeC
Q 003093 319 YRRIGYWSN 327 (848)
Q Consensus 319 ~~~Vg~w~~ 327 (848)
+++||.|++
T Consensus 314 ~~~vg~W~~ 322 (328)
T cd06351 314 WRKVGTWNG 322 (328)
T ss_pred ceEEEEecC
Confidence 999999984
No 51
>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=99.95 E-value=4e-26 Score=248.94 Aligned_cols=277 Identities=13% Similarity=0.123 Sum_probs=221.1
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHH-HcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVD-HYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~-~~~w~~vaii~~ 80 (848)
+++|++||||.+|..+.++.+++++.++|+|++.++.. ...+||+||+.+++..++..+++++. ..++++|++++.
T Consensus 65 ~~~V~~iiG~~~S~~~~a~~~~~~~~~~~~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~k~vaii~~ 141 (348)
T cd06355 65 QDKVAAVFGCWTSASRKAVLPVFERHNGLLFYPVQYEG---LEQSPNVFYTGAAPNQQIIPAVDWLMSNKGGKRFYLVGS 141 (348)
T ss_pred hCCCcEEEeccchhhHHHHHHHHhccCCceecCCCccC---CCCCCCEEEeCCChHHhHHHHHHHHHhccCCCeEEEECC
Confidence 46899999999999999999999999999998654321 23569999999999999999999875 457999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
|++||....+.+++.+++.|++|+....++.+. .|+++++.+|++.+||+|++...+.++..++++++++|+..+...
T Consensus 142 d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~D~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~~~ 219 (348)
T cd06355 142 DYVYPRTANKILKAQLESLGGEVVGEEYLPLGH--TDFQSIINKIKAAKPDVVVSTVNGDSNVAFFKQLKAAGITASKVP 219 (348)
T ss_pred cchHHHHHHHHHHHHHHHcCCeEEeeEEecCCh--hhHHHHHHHHHHhCCCEEEEeccCCchHHHHHHHHHcCCCccCCe
Confidence 999999999999999999999999988888654 899999999999999999999999999999999999999654455
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEec--CCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYT--PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~--~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
++........+. ....+.++|+++...+. .+.+..++|.++|+++|+. ...++.+++.+||++++++
T Consensus 220 ~~~~~~~~~~~~------~~g~~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~g~-----~~~~~~~a~~~Y~a~~~~~ 288 (348)
T cd06355 220 VLSFSVAEEELR------GIGPENLAGHYAAWNYFQSVDTPENKKFVAAFKARYGQ-----DRVTNDPMEAAYIGVYLWK 288 (348)
T ss_pred eEEccccHHHHh------hcChHhhcCCEEeccchhhcCCHHHHHHHHHHHHHcCC-----CCCCCcHHHHHHHHHHHHH
Confidence 565432221111 11224567877655443 3568889999999999962 1234567888999999999
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEee-cc
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI-GT 317 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~-~~ 317 (848)
+|++++ ++. ++++|.++|++++|+++.|.++|+++++.....+.|.+++ ++
T Consensus 289 ~Al~~a---------------------------g~~-~~~~i~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~i~~~~~~g 340 (348)
T cd06355 289 QAVEKA---------------------------GSF-DVDKVRAALPGQSFDAPEGPVTVDPANHHLWKPVRIGRIQADG 340 (348)
T ss_pred HHHHHh---------------------------CCC-CHHHHHHHhccCcccCCCcceEeecCCCeeeeeeEEEEEcCCC
Confidence 999994 222 3899999999999999999999998443344566777875 45
Q ss_pred cEEEE
Q 003093 318 GYRRI 322 (848)
Q Consensus 318 ~~~~V 322 (848)
.++.|
T Consensus 341 ~~~~v 345 (348)
T cd06355 341 QFEIV 345 (348)
T ss_pred cEEEE
Confidence 55443
No 52
>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=99.95 E-value=2.2e-26 Score=250.20 Aligned_cols=261 Identities=13% Similarity=0.100 Sum_probs=218.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCC-CCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSL-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~-~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|.+||||.+|..+.++++++++.+||+|+++++++.++.. .+||+||+.+++..++.++++++...++++|++++.|
T Consensus 65 ~~V~aviG~~~s~~~~a~~~~~~~~~vp~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~ 144 (334)
T cd06327 65 DGVDMIVGGPNSAVALAVQEVAREKKKIYIVTGAGSDDLTGKDCSPYTFHWAYDTYMLANGTAPALVKAGGKKWFFLTAD 144 (334)
T ss_pred cCceEEECCccHHHHHHHHHHHHHhCceEEecCCCccccccCCCCCceEEccCChHHHHHHHHHHHHHhcCCeEEEEecc
Confidence 589999999999999999999999999999999998888874 4799999999999999999999877789999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++||+.....+++.+++.|++|+....++.+. .|+..++.++++.++|+|++.+...++..++++++++|+.. +..+
T Consensus 145 ~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~-~~~~ 221 (334)
T cd06327 145 YAFGHSLERDARKVVKANGGKVVGSVRHPLGT--SDFSSYLLQAQASGADVLVLANAGADTVNAIKQAAEFGLTK-GQKL 221 (334)
T ss_pred hHHhHHHHHHHHHHHHhcCCEEcCcccCCCCC--ccHHHHHHHHHhCCCCEEEEeccchhHHHHHHHHHHhCCcc-CCcE
Confidence 99999999999999999999999888888654 79999999999999999999999999999999999999862 3333
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
+.......... ....+..+|++...++.+ +.+..++|.++|+++++ ..|+.+++.+||+++++++
T Consensus 222 ~~~~~~~~~~~------~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g-------~~p~~~~~~~Y~~~~~~~~ 288 (334)
T cd06327 222 AGLLLFLTDVH------SLGLDAAQGLYLTTAWYWDLPNDETRAFVKRFQAKYG-------KMPSMVQAGAYSAVLHYLK 288 (334)
T ss_pred EEecccHHHHH------hhchhhhcCeEEeeeccccCCCHHHHHHHHHHHHHHC-------cCCCcHHHHHHHHHHHHHH
Confidence 33322221110 122356789888877643 36789999999999997 3477889999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhcc-ccccccceEecc-CCCCCCC
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQAN-MTGTAGPARFNS-HGDLINP 307 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~-f~G~tG~v~Fd~-~g~~~~~ 307 (848)
|++++. +. +++++.++|++++ ++++.|+++|+. +|+...+
T Consensus 289 A~~~ag---------------------------~~-~~~~v~~al~~~~~~~~~~g~~~~~~~~~~~~~~ 330 (334)
T cd06327 289 AVEAAG---------------------------TD-DADKVVAKMKETPIYDLFAGNGYIRACDHQMVHD 330 (334)
T ss_pred HHHHHC---------------------------CC-ChHHHHHhccccceeccCCCCceeeccccchhcc
Confidence 999952 22 3777999999986 688999999987 7775433
No 53
>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=99.95 E-value=1.5e-25 Score=238.11 Aligned_cols=275 Identities=15% Similarity=0.169 Sum_probs=194.7
Q ss_pred CCCeEEEEcc-CCchhHHHHHHhhccCCccEEecccCCCCC-CCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEE
Q 003093 2 EGQTVAIIGP-QDAVTSHVVSHVANELQVPLLSFSATDPTL-SSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIY 79 (848)
Q Consensus 2 ~~~V~aiIGp-~~S~~~~ava~i~~~~~vP~Is~~at~p~l-s~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~ 79 (848)
.+||.||+|| .++..+..+..+|+.++||+|+++..++.. +...+.+..++.|+...++.|+++++++|+|++|++||
T Consensus 79 ~~GV~AIfg~p~s~~~~~~v~sic~~l~IP~I~~~~~~~~~~~~~~~~l~L~l~P~~~~l~~a~~~ll~~~~W~~f~~iy 158 (382)
T cd06377 79 VQGVSALLAFPQTRPELVQLDFVSAALEIPVVSIVRREFPRGSQNPFHLQMSWASPLSTLLDVLLSVLQRNGWEDVSLVL 158 (382)
T ss_pred hCCeEEEEecCCCHHHHHHHHHHhcCCCCCEEEecCCcccccCCCceeEEEEecCCHHHHHHHHHHHHHHCCCcEEEEEE
Confidence 6899999994 888888999999999999999986654333 22333334467999999999999999999999999999
Q ss_pred EcCCCccchHHHHHHHHhccCc----EEEEeeecCCC-CChHHH-HHHHHHHhcCC-CeEEEEEccCCcHHHHHHHHHHc
Q 003093 80 VDDDHGRNGIAALGDTLAAKRC----RISFKAPLSVE-ATEDEI-TDLLVKVALTE-SRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~----~v~~~~~~~~~-~~~~d~-~~~l~~i~~~~-~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
+.+..... |++.++..+. .+......+.. ++..++ +..|++|++.+ +++|+++|+.+.+..+++++.+
T Consensus 159 ~~~~gl~~----lq~l~~~~~~~~~~~~i~v~~~~~~~~d~~~~~~~~L~~i~~~~~~~~ill~cs~e~~~~il~~~~~- 233 (382)
T cd06377 159 CRERDPTG----LLLLWTNHARFHLGSVLNLSRNDPSTADLLDFLRAQLELLKDPPGPAVVLFGCDVARARRVLELTPP- 233 (382)
T ss_pred ecCcCHHH----HHHHHHHhcccccCceEEEEeccCccCChhHHHHHHHHHhhcccCceEEEEECCHHHHHHHHHhhcc-
Confidence 88774332 4444444332 12222223211 133555 99999999999 9999999999999999987744
Q ss_pred CCCCCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhh
Q 003093 153 GMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYD 232 (848)
Q Consensus 153 g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YD 232 (848)
+|+||+++.. +... -.....--|+++ |.+.. .....++.||
T Consensus 234 -----~y~wIv~~~~----~le~---~~~~g~nigLl~-----------------~~~~~----------~~~l~ali~D 274 (382)
T cd06377 234 -----GPHWILGDPL----PPEA---LRTEGLPPGLLA-----------------HGETT----------QPPLEAYVQD 274 (382)
T ss_pred -----ceEEEEcCCc----Chhh---ccCCCCCceEEE-----------------Eeecc----------cccHHHHHHH
Confidence 4999998721 1110 001122233331 21110 1123789999
Q ss_pred HHHHHHHHHHHHHh--cCCCccccCCCccccccCccccCcc--c-ccCChHHHHHHHHhccccccccceEeccCCCC--C
Q 003093 233 TVWLLARAINSFFK--QGGNLSFSKDSRLSDIQGHLRLDSL--R-IFNGGNLLRDSILQANMTGTAGPARFNSHGDL--I 305 (848)
Q Consensus 233 Av~~~a~Al~~~~~--~~~~~~~~~~~~~~~~~g~~~~~~~--~-~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~--~ 305 (848)
||+++|+|++.+.. ....+..+ ..+|... . +|+.|..|.++|++++|+|.||+|.|+ .|.| .
T Consensus 275 AV~lvA~a~~~l~~~~~~~~l~~~----------~~~C~~~~~~~~W~~G~~l~~~Lknv~~eGlTG~I~F~-~g~R~~~ 343 (382)
T cd06377 275 ALELVARAVGSATLVQPELALIPA----------TVNCMDLPTKGNESSGQYLARFLANTSFDGRTGPVWVT-GSSQVHS 343 (382)
T ss_pred HHHHHHHHHHHhhhcccccccCCC----------CCCcccCCCCCCCCchHHHHHHHHhCcccccceeEEEc-cCeeecc
Confidence 99999999998631 11111111 3467544 5 899999999999999999999999994 5777 7
Q ss_pred CCcEEEEEee--ccc---EEEEEEeeCCCCC
Q 003093 306 NPAYEIINVI--GTG---YRRIGYWSNYSGL 331 (848)
Q Consensus 306 ~~~~~I~~~~--~~~---~~~Vg~w~~~~gl 331 (848)
+..++|++++ ..| |++||+|++...+
T Consensus 344 ~~~l~I~~L~~~~~G~~~W~kVG~W~~~~~~ 374 (382)
T cd06377 344 SRHFKVWSLRRDPVGQPTWTTVGSWQGGRKI 374 (382)
T ss_pred cceEEEEEeccccCCCccceEEEEecCCCce
Confidence 8899999998 444 5999999986433
No 54
>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=99.95 E-value=5.8e-26 Score=246.66 Aligned_cols=265 Identities=17% Similarity=0.197 Sum_probs=216.5
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|.+||||.+|..+.++++++++.+||+|+++++.+.+.+ ..+||+||+.+++..++.+++++++..||++|++++.|
T Consensus 64 ~~v~~viG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~g~~~vail~~~ 143 (333)
T cd06359 64 DKVDFVTGVVFSNVLLAVVPPVLESGTFYISTNAGPSQLAGKQCSPYFFSTSWQNDQVHEAMGKYAQDKGYKRVFLIAPN 143 (333)
T ss_pred cCCcEEEccCCcHHHHHHHHHHHHcCCeEEecCCCccccccccCCCcEEEeeCChHhhHHHHHHHHHHhCCCeEEEEecC
Confidence 58999999999999999999999999999998777666665 35899999999999999999999988999999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++||+...+.+.+.++ .+++....++.+ ..|+..++.++++.+||+|++......+..++++++++|+.. ...+
T Consensus 144 ~~~g~~~~~~~~~~~~---~~v~~~~~~~~~--~~d~~~~i~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~-~~~~ 217 (333)
T cd06359 144 YQAGKDALAGFKRTFK---GEVVGEVYTKLG--QLDFSAELAQIRAAKPDAVFVFLPGGMGVNFVKQYRQAGLKK-DIPL 217 (333)
T ss_pred chhhHHHHHHHHHHhC---ceeeeeecCCCC--CcchHHHHHHHHhCCCCEEEEEccCccHHHHHHHHHHcCccc-CCee
Confidence 9999999998988774 356655555543 379999999999999999999888888999999999999853 3445
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
+.+...... ... +..+++.+|++...++.+ +++..++|.++|+++++ ..|+.++..+||+++++++
T Consensus 218 ~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~yda~~~~~~ 285 (333)
T cd06359 218 YSPGFSDEE-DTL----PAVGDAALGLYNTAQWAPDLDNPANKKFVADFEKKYG-------RLPTLYAAQAYDAAQLLDS 285 (333)
T ss_pred eccCcccCH-HHH----HhcchhhcCeeeccccCCCCCCHHHHHHHHHHHHHhC-------CCCcHHHHHHHHHHHHHHH
Confidence 655443321 111 233467789888877766 46889999999999986 3578899999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEE
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEII 312 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~ 312 (848)
|++++... .. +++.+.++|++++|+|++|+++|+++|+.. ..+.|+
T Consensus 286 A~~~ag~~-------------------------~~-~~~~v~~al~~~~~~~~~G~~~~~~~~~~~-~~~~~~ 331 (333)
T cd06359 286 AVRKVGGN-------------------------LS-DKDALRAALRAADFKSVRGAFRFGTNHFPI-QDFYLR 331 (333)
T ss_pred HHHHhcCC-------------------------CC-CHHHHHHHHhcCccccCccceEECCCCCcc-eeEEEE
Confidence 99985211 01 378999999999999999999999998853 344444
No 55
>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=99.94 E-value=4.9e-26 Score=248.05 Aligned_cols=259 Identities=14% Similarity=0.160 Sum_probs=217.1
Q ss_pred CCCeEEEEccCCchhHHHH-------HHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcC-c
Q 003093 2 EGQTVAIIGPQDAVTSHVV-------SHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYG-W 72 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~av-------a~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~-w 72 (848)
+++|++||||.+|..+.++ +++++++++|+|+++++++.++. ..+||+||+.|++..++.++++++...+ |
T Consensus 64 ~~~v~aiiG~~~s~~~~~~~~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~ 143 (342)
T cd06329 64 DDGVRLVVQGNSSSVALALTEAVRKHNQRNPGKEVLYLNYASVAPALTGEKCSFWHFRTDANTDMKMEALASYIKKQPDG 143 (342)
T ss_pred HhCCeEEEcccchHHHHHhhhhhhhhhhhhccCCeEEEecCCCCchhhhccCcceEEEecCChHHHHHHHHHHHHhcccC
Confidence 3589999999999999999 88899999999999888888886 5679999999999999999999998776 9
Q ss_pred EEEEEEEEcCCCccchHHHHHHHHhc--cCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHH
Q 003093 73 REVIAIYVDDDHGRNGIAALGDTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQ 150 (848)
Q Consensus 73 ~~vaii~~dd~~g~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~ 150 (848)
++|++++.|+.||+...+.+.+.+++ .|++|+....++.+. ..|+..++.++++.++|+|++.....++..++++++
T Consensus 144 k~v~i~~~~~~~g~~~~~~~~~~~~~~~~G~~vv~~~~~~~~~-~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~ 222 (342)
T cd06329 144 KKVYLINQDYSWGQDVAAAFKAMLAAKRPDIQIVGEDLHPLGK-VKDFSPYVAKIKASGADTVITGNWGNDLLLLVKQAA 222 (342)
T ss_pred ceEEEEeCChHHHHHHHHHHHHHHHhhcCCcEEeceeccCCCC-CCchHHHHHHHHHcCCCEEEEcccCchHHHHHHHHH
Confidence 99999999999999999999999999 999999887776532 278999999999999999999998889999999999
Q ss_pred HcCCCCCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchh
Q 003093 151 YLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGF 228 (848)
Q Consensus 151 ~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~ 228 (848)
++|+..+ ++...+.... .. ....+..+|++....+.+ +.+..++|.++|+++++ ..|+.++.
T Consensus 223 ~~g~~~~---~~~~~~~~~~--~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~ 286 (342)
T cd06329 223 DAGLKLP---FYTPYLDQPG--NP----AALGEAGLGLVVAVAYWHPNDTPANRAFVEAFKAKYG-------RVPDYYEG 286 (342)
T ss_pred HcCCCce---EEeccccchh--HH----HhhcccccceEEeeeccCCCCCHHHHHHHHHHHHHhC-------CCCCchHH
Confidence 9998532 4544433222 11 234456788887766544 35788999999999986 35677899
Q ss_pred hhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEecc-CCCCC
Q 003093 229 YAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNS-HGDLI 305 (848)
Q Consensus 229 ~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~-~g~~~ 305 (848)
.+||+++++++|++++. .. +++.+.++|++++|+|+.|+++|++ +++..
T Consensus 287 ~~y~~~~~~~~a~~~ag---------------------------~~-~~~~v~~al~~~~~~~~~g~~~~~~~~~~~~ 336 (342)
T cd06329 287 QAYNGIQMLADAIEKAG---------------------------ST-DPEAVAKALEGMEVDTPVGPVTMRASDHQAQ 336 (342)
T ss_pred HHHHHHHHHHHHHHHhC---------------------------CC-CHHHHHHHHhCCccccCCCCeEEcccCcchh
Confidence 99999999999999831 11 3889999999999999999999985 44433
No 56
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=99.94 E-value=1.5e-25 Score=245.01 Aligned_cols=275 Identities=23% Similarity=0.234 Sum_probs=222.3
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCC-CceEeccCChHHHHHHHHHHHH-HcCcEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQF-PYFVRTTQSDQYQMAAIAEIVD-HYGWREVIAIY 79 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~-p~f~r~~p~d~~q~~ai~~~~~-~~~w~~vaii~ 79 (848)
+++|.+||||.+|..+.++++++++.++|+|++++++|.++...+ +++||++|++..|+.++++++. ..+.++|++|+
T Consensus 76 ~~~V~~vvG~~~S~~~~a~~~v~~~~~i~~i~p~st~~~~~~~~~~~~vfr~~~~~~~q~~~~~~~l~~~~~~k~v~ii~ 155 (366)
T COG0683 76 QDGVDAVVGPTTSGVALAASPVAEEAGVPLISPSATAPQLTGRGLKPNVFRTGPTDNQQAAAAADYLVKKGGKKRVAIIG 155 (366)
T ss_pred hcCceEEEEeccCcccccchhhHhhcCceEEeecCCCCcccccccccceEEecCChHHHHHHHHHHHHHhcCCcEEEEEe
Confidence 478999999999999999999999999999999999999877544 5599999999999999999974 56667999999
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
.|+.||++..+.+++.+++.|++++..+.+.+.. .+|..++.++++.++|+|++.+..+++..++++++++|+... .
T Consensus 156 ~~~~yg~~~~~~~~~~l~~~G~~~~~~~~~~~~~--~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~~~~~G~~~~-~ 232 (366)
T COG0683 156 DDYAYGEGLADAFKAALKALGGEVVVEEVYAPGD--TDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQAREQGLKAK-L 232 (366)
T ss_pred CCCCcchhHHHHHHHHHHhCCCeEEEEEeeCCCC--CChHHHHHHHHhcCCCEEEECCCCccchHHHHHHHHcCCCCc-c
Confidence 9999999999999999999999866656676654 459999999999999999999999999999999999999643 2
Q ss_pred EEEecCccccccCCCCCCCcccccccce-eEEEEE-ecC-CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHH
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQG-VLTLRT-YTP-DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G-~~~~~~-~~~-~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~ 236 (848)
.++.......... .......+ .+.... ..+ ..|..+.|+++|+++++ .+..++.++..+|||+++
T Consensus 233 ~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~~g-----~~~~~~~~~~~~y~a~~~ 300 (366)
T COG0683 233 IGGDGAGTAEFEE-------IAGAGGAGAGLLATAYSTPDDSPANKKFVEAYKAKYG-----DPAAPSYFAAAAYDAVKL 300 (366)
T ss_pred ccccccCchhhhh-------hcccCccccEEEEecccccccCcchHHHHHHHHHHhC-----CCCCcccchHHHHHHHHH
Confidence 3333222211111 11222233 333322 222 35678889999999997 335667799999999999
Q ss_pred HHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhcc-ccccccceEeccCCCCCCCcEEEEEee
Q 003093 237 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQAN-MTGTAGPARFNSHGDLINPAYEIINVI 315 (848)
Q Consensus 237 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~-f~G~tG~v~Fd~~g~~~~~~~~I~~~~ 315 (848)
+++|++++.+ .. +++++.++|+... +++.+|.+.||++|++....+.|.+++
T Consensus 301 ~~~ai~~a~~--------------------------~~-d~~~v~~al~~~~~~~~~~G~v~~~~~~~~~~~~~~i~~~~ 353 (366)
T COG0683 301 LAKAIEKAGK--------------------------SS-DREAVAEALKGGKFFDTAGGPVTFDEKGDRGSKPVYVGQVQ 353 (366)
T ss_pred HHHHHHHHhc--------------------------CC-CHHHHHHHHhhCCCCccCCcceeECCCCCcCCCceEEEEEE
Confidence 9999999642 11 2788999999887 789999999999999988999999988
Q ss_pred ccc
Q 003093 316 GTG 318 (848)
Q Consensus 316 ~~~ 318 (848)
..+
T Consensus 354 ~~~ 356 (366)
T COG0683 354 KGG 356 (366)
T ss_pred ecC
Confidence 543
No 57
>cd06347 PBP1_ABC_ligand_binding_like_12 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.94 E-value=1.5e-25 Score=244.14 Aligned_cols=260 Identities=18% Similarity=0.298 Sum_probs=217.3
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHH-HHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~-~~~~w~~vaii~~d 81 (848)
++|++||||.+|..+.++++++++.+||+|+++++.+.+++. .+|+||+.|++..++.++++++ ++++|++|++||.+
T Consensus 66 ~~v~aiiG~~~s~~~~~v~~~~~~~~ip~i~~~~~~~~~~~~-~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~ 144 (334)
T cd06347 66 DKVVAIIGPVTSGATLAAGPIAEDAKVPMITPSATNPKVTQG-KDYVFRVCFIDPFQGTVMAKFATENLKAKKAAVLYDN 144 (334)
T ss_pred cCeEEEEcCCccHhHHHhHHHHHHCCCeEEcCCCCCCCcccC-CCeEEEeeCCcHHHHHHHHHHHHHhcCCcEEEEEEeC
Confidence 489999999999999999999999999999999888777653 3589999999999999999986 67899999999988
Q ss_pred C-CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 82 D-DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 82 d-~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
+ +|+....+.+.+.+++.|++++....++.+. .|+..+++++++.++|+|++.+.......+++++++.|+. ..
T Consensus 145 ~~~~~~~~~~~~~~~~~~~g~~v~~~~~~~~~~--~d~~~~~~~~~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~---~~ 219 (334)
T cd06347 145 SSDYSKGLAKAFKEAFKKLGGEIVAEETFNAGD--TDFSAQLTKIKAKNPDVIFLPGYYTEVGLIAKQARELGIK---VP 219 (334)
T ss_pred CCchhHHHHHHHHHHHHHcCCEEEEEEEecCCC--CcHHHHHHHHHhcCCCEEEEcCchhhHHHHHHHHHHcCCC---Cc
Confidence 6 8999999999999999999999888877653 6899999999999999999999999999999999999983 35
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecCC--chhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPD--SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
|+.++.+...... ....+..+|++...++.+. .+..++|.++|+++++ ..|+.++..+|||+++++
T Consensus 220 i~~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~yda~~~~~ 287 (334)
T cd06347 220 ILGGDGWDSPKLE-----EAGGAAAEGVYFTTHFSADDPTPKAKKFVKAYKAKYG-------KEPDAFAALGYDAYYLLA 287 (334)
T ss_pred EEecccccCHHHH-----HHHHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHC-------CCcchhHHHHHHHHHHHH
Confidence 7776655432111 2234568888877776553 5788999999998886 357788999999999999
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhc-cccccccceEeccCCCCCCCc
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQA-NMTGTAGPARFNSHGDLINPA 308 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~-~f~G~tG~v~Fd~~g~~~~~~ 308 (848)
+|++++. .. +++.+.++|.+. +|+|++|+++|+.+|+.....
T Consensus 288 ~Al~~ag---------------------------~~-~~~~v~~~l~~~~~~~g~~G~v~f~~~g~~~~~~ 330 (334)
T cd06347 288 DAIERAG---------------------------ST-DPEAIRDALAKTKDFDGVTGKITIDENGNPVKSA 330 (334)
T ss_pred HHHHHhC---------------------------CC-CHHHHHHHHHhCCCcccceeeeEECCCCCcCCCc
Confidence 9999831 11 378899998865 699999999999999865443
No 58
>cd06336 PBP1_ABC_ligand_binding_like_3 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.94 E-value=7.8e-26 Score=246.87 Aligned_cols=262 Identities=15% Similarity=0.175 Sum_probs=215.5
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
++|++||||.+|.++.+ ++++++.++|+|+++++++.++...+||+||+.|++..++.++++++.+.+|++|++|+.|+
T Consensus 70 ~~v~~iiG~~~s~~~~~-~~~~~~~~ip~i~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~ 148 (347)
T cd06336 70 DGVKFILGPIGGGITAA-QQITERNKVLLLTAYSSDLSIDTAGNPLTFRVPPIYNVYGVPFLAYAKKPGGKKVALLGPND 148 (347)
T ss_pred cCceEEEeCCCCchhhh-hhhhhhcCceEEeccCCcccccccCCceEEEecCCchhHHHHHHHHHhhcCCceEEEEccCC
Confidence 48999999999999998 99999999999999999998876667999999999999999999998889999999999999
Q ss_pred CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCC-cHHHHHHHHHHcCCCCCCeEE
Q 003093 83 DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~-~~~~~~~~a~~~g~~~~~~~w 161 (848)
+||+...+.+.+.+++.|++|+....++.+. .||+.++.+|++.++|+|++.+... ++..++++++++|+..+ ..+
T Consensus 149 ~~g~~~~~~~~~~l~~~G~~vv~~~~~~~~~--~D~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~g~~~~-~~~ 225 (347)
T cd06336 149 AYGQPWVAAYKAAWEAAGGKVVSEEPYDPGT--TDFSPIVTKLLAEKPDVIFLGGPSPAPAALVIKQARELGFKGG-FLS 225 (347)
T ss_pred chhHHHHHHHHHHHHHcCCEEeeecccCCCC--cchHHHHHHHHhcCCCEEEEcCCCchHHHHHHHHHHHcCCCcc-EEe
Confidence 9999999999999999999999888888654 8999999999999999999999998 99999999999998643 222
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecC----CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP----DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLL 237 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~ 237 (848)
+.......... ....+.++|++...++.+ ..|..++|.++|+++++ ..|+.++..+||+++++
T Consensus 226 ~~~~~~~~~~~------~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~p~~~~~~~y~~~~~~ 292 (347)
T cd06336 226 CTGDKYDELLV------ATGADFMEGVYFQFPDVDDPALAFPRAKAFVEEYKKRYG-------EPPNSEAAVSYDAVYIL 292 (347)
T ss_pred ccCCCchHHHH------HhcHHhhCceEEEeecccccccCCHHHHHHHHHHHHHHC-------CCCcHHHHHHHHHHHHH
Confidence 22211111010 122356789888877655 47888999999999997 34778899999999999
Q ss_pred HHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHh--------ccccccccceEeccCCCCCCCcE
Q 003093 238 ARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQ--------ANMTGTAGPARFNSHGDLINPAY 309 (848)
Q Consensus 238 a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~--------~~f~G~tG~v~Fd~~g~~~~~~~ 309 (848)
++|++++. ..+ +..+.+++.. ..|.++.|.+.||++|++..|.+
T Consensus 293 ~~Al~~ag---------------------------~~~-~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 344 (347)
T cd06336 293 KAAMEAAG---------------------------SVD-DTAAVAALAAMLGVGKPAFGYARWWGKELFGVNGALVGPWP 344 (347)
T ss_pred HHHHHhcC---------------------------CCC-cHHHHHHHhhccCCCcCccccccccccccccCCCccccCcc
Confidence 99999842 122 3344444432 56888999999999999876544
No 59
>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=99.94 E-value=2.3e-25 Score=242.94 Aligned_cols=270 Identities=16% Similarity=0.211 Sum_probs=219.3
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHH-HHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~-~~~~w~~vaii~~ 80 (848)
+++|.+|+||.+|..+.++++++++.+||+|+++++.+.+++ ..+|+||+.|++..++.++++++ ++++|++|++++.
T Consensus 65 ~~~V~~i~G~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~~~~-~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~ 143 (340)
T cd06349 65 DPRIVAVLGDFSSGVSMAASPIYQRAGLVQLSPTNSHPDFTK-GGDFIFRNSTSQAIEAPLLADYAVKDLGFKKVAILSV 143 (340)
T ss_pred cCCeEEEECCCccHhHHHhHHHHHhCCCeEEecCCCCCcccc-CCCeEEEccCCcHHHHHHHHHHHHHHcCCcEEEEEec
Confidence 458999999999999999999999999999999888887765 46899999999999999999985 7789999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
|++||....+.+.+.+++.|++|+....++.+. .|++.++.++++.++|+|++.+...+...+++++++.|+..+
T Consensus 144 ~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~--~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~--- 218 (340)
T cd06349 144 NTDWGRTSADIFVKAAEKLGGQVVAHEEYVPGE--KDFRPTITRLRDANPDAIILISYYNDGAPIARQARAVGLDIP--- 218 (340)
T ss_pred CChHhHHHHHHHHHHHHHcCCEEEEEEEeCCCC--CcHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCCCCc---
Confidence 999999999999999999999999888777653 799999999999999999999999999999999999998543
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecCC--chhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPD--SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
++.+...... ... ....+..+|++...++.++ .+..++|.++|+++|+ ..|+.++..+||++++++
T Consensus 219 ~~~~~~~~~~-~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~p~~~~~~~y~~~~~~~ 286 (340)
T cd06349 219 VVASSSVYSP-KFI----ELGGDAVEGVYTPTAFFPGDPRPEVQSFVSAYEAKYG-------AQPDAFAAQAYDAVGILA 286 (340)
T ss_pred EEccCCcCCH-HHH----HHhHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHC-------CCcchhhhhHHHHHHHHH
Confidence 4444332211 111 2233567898887776654 5788999999999886 346788999999999999
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHH-HHhccccccccceEeccC-CCCCCCcEEEEEeec
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDS-ILQANMTGTAGPARFNSH-GDLINPAYEIINVIG 316 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~-l~~~~f~G~tG~v~Fd~~-g~~~~~~~~I~~~~~ 316 (848)
+|++++. +.+ ...+... +.+..+.|++|+++|+++ |+. ...|.++.+++
T Consensus 287 ~a~~~ag---------------------------~~~-~~~~~~~~~~~~~~~~~~g~i~~~~~~~~~-~~~~~~~~~~~ 337 (340)
T cd06349 287 AAVRRAG---------------------------TDR-RAARDGFAKAEDVYSGVTGSTKFDPNTRRV-IKRFVPLVVRN 337 (340)
T ss_pred HHHHHhC---------------------------CCC-HHHHHHHHHhccCcccceEeEEECCCCCCc-cCceEEEEEeC
Confidence 9999842 111 2333333 245568899999999987 654 45888888877
Q ss_pred cc
Q 003093 317 TG 318 (848)
Q Consensus 317 ~~ 318 (848)
++
T Consensus 338 g~ 339 (340)
T cd06349 338 GK 339 (340)
T ss_pred Cc
Confidence 65
No 60
>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=99.94 E-value=3e-25 Score=242.49 Aligned_cols=278 Identities=8% Similarity=0.096 Sum_probs=217.7
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHH-cCcEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDH-YGWREVIAIY 79 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~-~~w~~vaii~ 79 (848)
+++|.+||||.+|.++.++++++++.++|+|.... ++. ...||+||+.|++..++.++++++.. .+ +++++|+
T Consensus 66 ~d~v~~viG~~~S~~~~A~~~~~~~~~~~~i~~~~----~~~~~~~~~~Fr~~~~~~~~~~~~~~~~~~~~g-~~va~l~ 140 (374)
T TIGR03669 66 RDKVDALWAGYSSATREAIRPIIDRNEQLYFYTNQ----YEGGVCDEYTFAVGATARQQLGTVVPYMVEEYG-KKIYTIA 140 (374)
T ss_pred hCCCCEEEcCCchHHHHHHHHHHHhcCceEEcCcc----cccccCCCCEEEcCCChHHHHHHHHHHHHHcCC-CeEEEEc
Confidence 46899999999999999999999999999996422 222 34689999999999999999999754 56 6899999
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
.|++||+...+.+.+.+++.|++|+....++.+. .||..++.+|++.+||+|++.....+...+++|++++|+..+
T Consensus 141 ~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~g~--~Df~~~l~~i~~~~pD~V~~~~~g~~~~~~~kq~~~~G~~~~-- 216 (374)
T TIGR03669 141 ADYNFGQLSADWVRVIAKENGAEVVGEEFIPLSV--SQFSSTIQNIQKADPDFVMSMLVGANHASFYEQAASANLNLP-- 216 (374)
T ss_pred CCcHHHHHHHHHHHHHHHHcCCeEEeEEecCCCc--chHHHHHHHHHHcCCCEEEEcCcCCcHHHHHHHHHHcCCCCc--
Confidence 9999999999999999999999999988888754 899999999999999999999999999999999999999643
Q ss_pred EEEecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHH
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLL 237 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~ 237 (848)
++............ ....+..+|+++...+.+ +.+..++|.++|+++|+.. ..++.+++.+|||++++
T Consensus 217 -~~~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~F~~~y~~~~g~~-----p~~~~~a~~~Yda~~~l 286 (374)
T TIGR03669 217 -MGTSTAMAQGYEHK----RFEPPALKDVYAGVNYMEEIDTPENEAFVERFYAKFPDA-----PYINQEAENNYFSVYMY 286 (374)
T ss_pred -ccchhhhhhhhhhh----hcCchhhCCcEEeeeccccCCCHHHHHHHHHHHHHcCCC-----CCCChHHHHHHHHHHHH
Confidence 22222111111110 112245677776666554 4688899999999999621 12466788999999999
Q ss_pred HHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHh-ccccccccceEeccCCCCCCCcEEEEEeec
Q 003093 238 ARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQ-ANMTGTAGPARFNSHGDLINPAYEIINVIG 316 (848)
Q Consensus 238 a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~-~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~~ 316 (848)
++|++++ ++. +++++.++|++ .+|+|+.|+++||++++.....+.|.+++.
T Consensus 287 ~~Ai~~A---------------------------Gs~-d~~av~~aL~~~~~~~~~~G~i~fd~~~~~~~~~~~v~~~~~ 338 (374)
T TIGR03669 287 KQAVEEA---------------------------GTT-DQDAVRDVLESGVEMDAPEGKVCIDGATHHMSHTMRLARADA 338 (374)
T ss_pred HHHHHHh---------------------------CCC-CHHHHHHHHHcCCeEECCCccEEEcCCCCeeeeeeEEEEEcC
Confidence 9999994 233 38999999997 579999999999977654555666777764
Q ss_pred -ccEEEEEEee
Q 003093 317 -TGYRRIGYWS 326 (848)
Q Consensus 317 -~~~~~Vg~w~ 326 (848)
++...+..|.
T Consensus 339 ~~~~~~~~~~~ 349 (374)
T TIGR03669 339 DHNITFVKEQE 349 (374)
T ss_pred CCCEEEEEecC
Confidence 3345555554
No 61
>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=99.94 E-value=2.7e-25 Score=244.65 Aligned_cols=277 Identities=16% Similarity=0.171 Sum_probs=226.3
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHH-HHHcCcEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEI-VDHYGWREVIAIY 79 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~-~~~~~w~~vaii~ 79 (848)
+++|.+||||.+|..+.++++++++.+||+|+++++++.+++ ..+||+||+.|++..++.+++++ +++++|++|++|+
T Consensus 72 ~~~v~avvG~~~s~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~ii~ 151 (362)
T cd06343 72 SDEVFAMVGGLGTPTNLAVQKYLNEKKVPQLFPASGASKWNDPKPFPWTFGWQPSYQDEARIYAKYLVEEKPNAKIAVLY 151 (362)
T ss_pred hcCeEEEEecCCcHHHHHhHHHHHhcCCceEecccccHhhhCCCCCCceEecCCChHHHHHHHHHHHHHhCCCceEEEEE
Confidence 368999999999999999999999999999998888888877 47999999999999999999997 5678999999999
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
.|++||+...+.+.+.+++.|++++....++.+. .|++.++.++++.++|+|++.+...++..++++++++|+...
T Consensus 152 ~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~-- 227 (362)
T cd06343 152 QNDDFGKDYLKGLKDGLGDAGLEIVAETSYEVTE--PDFDSQVAKLKAAGADVVVLATTPKFAAQAIRKAAELGWKPT-- 227 (362)
T ss_pred eccHHHHHHHHHHHHHHHHcCCeEEEEeeecCCC--ccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHHcCCCce--
Confidence 9999999999999999999999999988888754 799999999999999999999999999999999999998632
Q ss_pred EEEecCccccccC-CCCCCCcccccccceeEEEEEec-------CCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhh
Q 003093 160 VWIATSWLSTALD-TNSPFPSDVMDDIQGVLTLRTYT-------PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAY 231 (848)
Q Consensus 160 ~wi~~~~~~~~~~-~~~~~~~~~~~~~~G~~~~~~~~-------~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~Y 231 (848)
++.+++...... .. ....+..+|++....+. ...+..++|.++|+++++. ...++.++..+|
T Consensus 228 -~~~~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~p~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~~~y 297 (362)
T cd06343 228 -FLLSSVSASVASVLK----PAGLEAAEGVIAAAYLKDPTDPAWADDPGVKEFIAFYKKYFPE-----GDPPDTYAVYGY 297 (362)
T ss_pred -EEEEecccccHHHHH----HhhhHhhCceEEEEEecCCCccccccCHHHHHHHHHHHHhcCC-----CCCCchhhhHHH
Confidence 555554432211 11 12235678887766542 2457889999999999862 124788899999
Q ss_pred hHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccc---cc-cccceEeccCCCCCCC
Q 003093 232 DTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANM---TG-TAGPARFNSHGDLINP 307 (848)
Q Consensus 232 DAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f---~G-~tG~v~Fd~~g~~~~~ 307 (848)
|++.++++|++++. ...+++.+.++|+++++ .+ ..|++.|++++++...
T Consensus 298 ~a~~~~~~a~~~ag---------------------------~~~~~~~v~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~~ 350 (362)
T cd06343 298 AAAETLVKVLKQAG---------------------------DDLTRENIMKQAESLKDVLPDLLPGIRINTSPDDHLPIE 350 (362)
T ss_pred HHHHHHHHHHHHhC---------------------------CCCCHHHHHHHHHhCCCCCccccCccceecCccccccce
Confidence 99999999999841 11138899999999987 33 3458999876555566
Q ss_pred cEEEEEeecccE
Q 003093 308 AYEIINVIGTGY 319 (848)
Q Consensus 308 ~~~I~~~~~~~~ 319 (848)
.+.|.++++++|
T Consensus 351 ~~~i~~~~~g~~ 362 (362)
T cd06343 351 QMQLMRFEGGRW 362 (362)
T ss_pred eEEEEEEecCcC
Confidence 788888877754
No 62
>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=99.94 E-value=2.6e-25 Score=241.65 Aligned_cols=259 Identities=13% Similarity=0.108 Sum_probs=213.0
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
++|++|+||.+|.++.++++++++.+||+|++++.... ...||+||+.|++..++.++++++...+|++|++|+.|+
T Consensus 66 ~~V~aiiG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~ 142 (333)
T cd06331 66 DKVDAVFGCYTSASRKAVLPVVERGRGLLFYPTQYEGG---ECSPNVFYTGATPNQQLLPLIPYLMEKYGKRFYLIGSDY 142 (333)
T ss_pred cCCcEEEecccHHHHHHHHHHHHhcCceEEeCCCCCCC---cCCCCeEEccCChHHhHHHHHHHHHHhcCCeEEEECCCc
Confidence 48999999999999999999999999999987543321 245899999999999999999987665699999999999
Q ss_pred CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003093 83 DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 162 (848)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi 162 (848)
.||......+.+.+++.|.+|+....++.+. .|++.++.+++..++|+|++++...++..+++++++.|+......++
T Consensus 143 ~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 220 (333)
T cd06331 143 VWPRESNRIARALLEELGGEVVGEEYLPLGT--SDFGSVIEKIKAAGPDVVLSTLVGDSNVAFYRQFAAAGLDADRIPIL 220 (333)
T ss_pred hhHHHHHHHHHHHHHHcCCEEEEEEEecCCc--ccHHHHHHHHHHcCCCEEEEecCCCChHHHHHHHHHcCCCcCCCeeE
Confidence 9999999999999999999999888888654 89999999999999999999999999999999999999964333333
Q ss_pred ecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHHH
Q 003093 163 ATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARA 240 (848)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~A 240 (848)
+...... ... .......+|++...++.+ +.+..++|.++|+++++. ...++.+++.+|||++++++|
T Consensus 221 -~~~~~~~-~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~~~yda~~~~~~A 289 (333)
T cd06331 221 -SLTLDEN-ELA----AIGAEAAEGHYSAASYFQSLDTPENKAFVARYRARYGD-----DAVINSPAEAAYEAVYLWAAA 289 (333)
T ss_pred -Ecccchh-hhh----ccChhhhCCcEeechhhhhcCChhHHHHHHHHHHHcCC-----CcCCCchhHHHHHHHHHHHHH
Confidence 3322221 111 122345789888776644 467889999999998862 114678899999999999999
Q ss_pred HHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCC
Q 003093 241 INSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLI 305 (848)
Q Consensus 241 l~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~ 305 (848)
++++. .. +++.|.++|++++|+|++|.+.|++++++.
T Consensus 290 ~~~ag---------------------------~~-~~~~l~~al~~~~~~~~~G~i~f~~~~~~~ 326 (333)
T cd06331 290 VEKAG---------------------------ST-DPEAVRAALEGVSFDAPQGPVRIDPDNHHT 326 (333)
T ss_pred HHHcC---------------------------CC-CHHHHHHHhhcCcccCCCCceEecCCCCcc
Confidence 99831 11 389999999999999999999999877654
No 63
>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=99.94 E-value=2.5e-25 Score=241.32 Aligned_cols=261 Identities=13% Similarity=0.102 Sum_probs=211.3
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCC-CCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSL-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~-~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|++||||.+|.++.++++++++.++|+|+++++++.++.. .++|+||+.+++..++..+++++... +++|++||.|
T Consensus 67 ~~V~avvG~~~S~~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~-~~~v~~i~~~ 145 (333)
T cd06328 67 DGVDILVGSTSSGVALAVLPVAEENKKILIVEPAAADSITGKNWNRYTFRTGRNSSQDAIAAAAALGKP-GKKIATLAQD 145 (333)
T ss_pred cCCeEEEccCCcHHHHHHHHHHHHhCCcEEecCCCCchhhccCCCCcEEEecCChHHHHHHHHHHHHhc-CCeEEEEecC
Confidence 589999999999999999999999999999998999998864 46999999998888899888887665 8999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCC-cHHHHHHHHHHcCCCCCCeE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~-~~~~~~~~a~~~g~~~~~~~ 160 (848)
++||+...+.+.+.+++.|++|+....++.+. .||..++.+|++.+||+|++...+. ....+++++++.|+..+
T Consensus 146 ~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~~g~~~~--- 220 (333)
T cd06328 146 YAFGRDGVAAFKAALEKLGAAIVTEEYAPTDT--TDFTPYAQRLLDALKKVLFVIWAGAGGPWPKLQQMGVLGYGIE--- 220 (333)
T ss_pred ccccHHHHHHHHHHHHhCCCEEeeeeeCCCCC--cchHHHHHHHHhcCCCEEEEEecCchhHHHHHHHhhhhcCCCe---
Confidence 99999999999999999999999988888754 8999999999999999998876555 56778888887776432
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEec-CCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYT-PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~-~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
............. .......+|++....+. +.+|..+.|.++|+++|+ ..|+.+++.+||++.++++
T Consensus 221 ~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g-------~~p~~~~~~~y~a~~~l~~ 288 (333)
T cd06328 221 ITLAGDILANLTM-----YKAGPGMSGASYYYHYFLPKNPVNDWLVEEHKARFG-------SPPDLFTAGGMSAAIAVVE 288 (333)
T ss_pred EEecccccCcccc-----ccccccccceeeeecCCCCCCHHHHHHHHHHHHHhC-------CCcchhhHHHHHHHHHHHH
Confidence 2222222111110 12334567776655554 677888999999999986 4578899999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEecc-CCCCCCCcE
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNS-HGDLINPAY 309 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~-~g~~~~~~~ 309 (848)
|++++. +. +++.+.++|++.+|+++.|+++|+. +|+...+.|
T Consensus 289 Ai~~ag---------------------------~~-~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~ 331 (333)
T cd06328 289 ALEETG---------------------------DT-DTEALIAAMEGMSFETPKGTMTFRKEDHQALQPMY 331 (333)
T ss_pred HHHHhC---------------------------CC-CHHHHHHHHhCCeeecCCCceEECcccchhhhccc
Confidence 999842 12 4889999999999999999999985 555444433
No 64
>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=99.93 E-value=5.7e-25 Score=240.52 Aligned_cols=259 Identities=16% Similarity=0.118 Sum_probs=212.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
++|++||||.+|..+.++++++++.+||+|++.++++.+++ ..+||+||+.|++..+..+++++++++ +|++|++++
T Consensus 66 ~~v~aiig~~~s~~~~~~~~~~~~~~ip~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~ 145 (346)
T cd06330 66 EGVDMLIGLISSGVALAVAPVAEELKVFFIATDPGTPRLTEEPDNPYVFRTRNSTIMDAVAGALYAAKLDKKAKTWATIN 145 (346)
T ss_pred cCCcEEEcccchHHHHHHHHHHHHcCCeEEEcCCCCcccccCCCCCceEEecCChHHHHHHHHHHHHHhCcCccEEEEEC
Confidence 48999999999999999999999999999999888888876 578999999999999999999998877 499999999
Q ss_pred EcCCCccchHHHHHHHHhccC--cEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 80 VDDDHGRNGIAALGDTLAAKR--CRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g--~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
.|++||....+.+++.+++.| ++++....++. ...|+..++.+|+..++|+|++.+...+...++++++++|+..
T Consensus 146 ~~~~~g~~~~~~~~~~~~~~g~~~~~v~~~~~~~--~~~d~~~~v~~i~~~~~d~ii~~~~~~~~~~~~~~~~~~g~~~- 222 (346)
T cd06330 146 PDYAYGQDAWADFKAALKRLRPDVEVVSEQWPKL--GAPDYGSEITALLAAKPDAIFSSLWGGDLVTFVRQANARGLFD- 222 (346)
T ss_pred CchHHHHHHHHHHHHHHHHhCCCCeecccccCCC--CCcccHHHHHHHHhcCCCEEEEecccccHHHHHHHHHhcCccc-
Confidence 999999999999999999984 55665544443 3479999999999999999999999999999999999999854
Q ss_pred CeEEEecCccccccCCCCCCCcccccccceeEEEEEe--cC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhH
Q 003093 158 GYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTY--TP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDT 233 (848)
Q Consensus 158 ~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~--~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDA 233 (848)
+..|+.+.+....+. ....+..+|++....+ .. +.+..++|.++|+++++ ..|+.++..+||+
T Consensus 223 ~~~~~~~~~~~~~~~------~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~g-------~~p~~~~~~~y~a 289 (346)
T cd06330 223 GTTVVLTLTGAPELA------PLGDEMPEGVIIGGRGPYFIPPDTPENKAFVDAYQEKYG-------DYPTYGAYGAYQA 289 (346)
T ss_pred CceEEeeccchhhhh------hhhcccCCceEEeccccCCCCCCChHHHHHHHHHHHHHC-------CCCChHHHHHHHH
Confidence 567887765433211 2233557787655432 21 46889999999999986 4567788999999
Q ss_pred HHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccC
Q 003093 234 VWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSH 301 (848)
Q Consensus 234 v~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~ 301 (848)
++++++|++++...... .+ .+.+.++|++++|.|+.|++.|+++
T Consensus 290 ~~~l~~a~~~a~~~~~~-----------------------~~-~~~v~~al~~~~~~~~~G~~~f~~~ 333 (346)
T cd06330 290 VMALAAAVEKAGATDGG-----------------------AP-PEQIAAALEGLSFETPGGPITMRAA 333 (346)
T ss_pred HHHHHHHHHHhcCCCCC-----------------------Cc-HHHHHHHHcCCCccCCCCceeeecC
Confidence 99999999986432110 01 2579999999999999999999874
No 65
>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=99.93 E-value=1.7e-24 Score=236.98 Aligned_cols=269 Identities=13% Similarity=0.119 Sum_probs=211.9
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHH-cCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~-~~w~~vaii~~ 80 (848)
+++|.+||||.+|.++.++.+++++.++|+|++.... .....||+||+.+++..++.++++++.. .|.++|++++.
T Consensus 66 ~~~V~~iiG~~~S~~~~a~~~~~~~~~~~~i~~~~~~---~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~g~k~v~~l~~ 142 (359)
T TIGR03407 66 QDKVAAVFGCWTSASRKAVLPVFEENNGLLFYPVQYE---GEECSPNIFYTGAAPNQQIIPAVDYLLSKKGAKRFFLLGS 142 (359)
T ss_pred hCCCcEEEcCCcHHHHHHHHHHHhccCCceEeCCccc---CcccCCCEEEcCCChHHHHHHHHHHHHhccCCceEEEecC
Confidence 4689999999999999999999999999999754321 1245789999999999999999998765 59999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
|++||+...+.+.+.+++.|++|+....++.+. .|++.++++|++.+||+|++......+..++++++++|+..+...
T Consensus 143 d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~D~s~~v~~l~~~~pDav~~~~~~~~~~~~~~~~~~~G~~~~~~~ 220 (359)
T TIGR03407 143 DYVFPRTANKIIKAYLKSLGGTVVGEDYTPLGH--TDFQTIINKIKAFKPDVVFNTLNGDSNVAFFKQLKNAGITAKDVP 220 (359)
T ss_pred ccHHHHHHHHHHHHHHHHcCCEEEeeEEecCCh--HhHHHHHHHHHHhCCCEEEEeccCCCHHHHHHHHHHcCCCccCCc
Confidence 999999999999999999999999988887644 899999999999999999988888888899999999999644333
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEe--cCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTY--TPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~--~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
++.+......+. ....+.++|+++...+ ..+.+..++|.++|+++++. ...+..+++.+|||+++++
T Consensus 221 ~~~~~~~~~~~~------~~g~~~~~G~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~~~y~a~~~~~ 289 (359)
T TIGR03407 221 VVSFSVAEEEIR------GIGPENLVGHLAAWNYFQSVDTPANKKFVKAFKAKYGD-----DRVTNDPMEAAYLGVYLWK 289 (359)
T ss_pred EEEeecCHHHHh------hcChHhhCCeEEeccchhcCCCHHHHHHHHHHHHHcCC-----CCCCCcHHHHHHHHHHHHH
Confidence 444432211111 1122457887755333 34568889999999999862 1123445678999999999
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEecc-CCCCCCCcEEEEEee
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNS-HGDLINPAYEIINVI 315 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~-~g~~~~~~~~I~~~~ 315 (848)
+|++++ ++. +++.+.++|++++|+++.|+++|++ +++ ....+.+.+++
T Consensus 290 ~A~~~a---------------------------g~~-~~~~i~~al~~~~~~~~~G~i~f~~~~~~-~~~~~~~~~~~ 338 (359)
T TIGR03407 290 AAVEKA---------------------------GSF-DVDAVRDAAIGIEFDAPEGKVKVDGKNHH-LTKTVRIGEIR 338 (359)
T ss_pred HHHHHh---------------------------CCC-CHHHHHHHhcCCcccCCCccEEEeCCCCe-eeeeeEEEEEc
Confidence 999994 222 3899999999999999999999997 444 33445555654
No 66
>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=99.93 E-value=3.1e-24 Score=235.10 Aligned_cols=280 Identities=15% Similarity=0.121 Sum_probs=219.7
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+++|++||||.+|..+.++++++++.++|++++++... . ...|++|++.+++..++.++++++...+-+++++|+.|
T Consensus 65 ~~~V~aiiG~~~s~~~~a~~~~~~~~~~~~~~~~~~~~-~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~d 141 (360)
T cd06357 65 EDGVRVIFGCYTSSSRKAVLPVVERHDALLWYPTLYEG-F--EYSPNVIYTGAAPNQNSVPLADYLLRHYGKRVFLVGSN 141 (360)
T ss_pred hCCCcEEEeCccHHHHHHHHHHHHhcCceEEeCCCccC-C--cccCCEEEeCCCcHHHHHHHHHHHHhcCCcEEEEECCC
Confidence 46899999999999999999999999999998654321 1 22367888888887788889998765555899999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++||++....+.+.+++.|++++....++.+.+..||.+++.++++.+||+|++.....++..++++++++|+.... ..
T Consensus 142 ~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~~~d~s~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~~~-~~ 220 (360)
T cd06357 142 YIYPYESNRIMRDLLEQRGGEVLGERYLPLGASDEDFARIVEEIREAQPDFIFSTLVGQSSYAFYRAYAAAGFDPAR-MP 220 (360)
T ss_pred CcchHHHHHHHHHHHHHcCCEEEEEEEecCCCchhhHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHHHHcCCCccC-ce
Confidence 99999999999999999999998866666654468999999999999999999999999999999999999996443 23
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
+.+...... ... ....++.+|+++..++.+ +.|..++|.++|+++|+. ...++.+++.+||+++++++
T Consensus 221 ~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~g~-----~~~~~~~~~~~yda~~~l~~ 290 (360)
T cd06357 221 IASLTTSEA-EVA----AMGAEAAAGHITAAPYFSSIDTPANRAFVARYRARFGE-----DAPVSACAEAAYFQVHLFAR 290 (360)
T ss_pred eEEeeccHH-HHh----hcchHhhCCcEEecccccccCChhHHHHHHHHHHHcCC-----CCCCCcHHHHHHHHHHHHHH
Confidence 333222111 111 223467889888766533 568899999999999972 12357789999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEe-eccc
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV-IGTG 318 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~-~~~~ 318 (848)
|++++ +.. +++.+.++|++++|+|+.|.+.||..++.......+.++ ++|+
T Consensus 291 Al~~a---------------------------g~~-~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~~~~~~~~G~ 342 (360)
T cd06357 291 ALQRA---------------------------GSD-DPEDVLAALLGFSFDAPQGPVRIDPDNNHTYLWPRIARVNADGQ 342 (360)
T ss_pred HHHHc---------------------------CCC-CHHHHHHHhccCcccCCCcceEEeCCCCeeeeeeEEEEEcCCCC
Confidence 99984 122 388999999999999999999998765433445566677 5666
Q ss_pred EEEEE
Q 003093 319 YRRIG 323 (848)
Q Consensus 319 ~~~Vg 323 (848)
+..|.
T Consensus 343 ~~~~~ 347 (360)
T cd06357 343 FDIVR 347 (360)
T ss_pred EEEEE
Confidence 66654
No 67
>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=99.93 E-value=1.4e-24 Score=236.31 Aligned_cols=261 Identities=18% Similarity=0.240 Sum_probs=216.2
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCC-CCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSL-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~-~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|++||||.+|..+.++.+.+++.++|+|+++++.+.+++. .+|++||+.|++..++..+++++...||+++++++.+
T Consensus 64 ~~v~~iig~~~s~~~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~g~~~v~il~~~ 143 (333)
T cd06332 64 DKVDVVVGPVFSNVALAVVPSLTESGTFLISPNAGPSDLAGKLCSPNFFRTSWQNDQVHEAMGKYAADKGYKKVVIIAPD 143 (333)
T ss_pred cCCcEEEcCCccHHHHHHHHHHhhcCCeEEecCCCCccccccCCCCcEEEeeCChHHhHHHHHHHHHHhCCceEEEEecC
Confidence 489999999999999999999999999999998888777764 4799999999999999999999999999999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
+.||+...+.+.+.++ ..++....++.+. .|+..+++++++.++|+|++......+..++++++++|+.. ...+
T Consensus 144 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~--~d~~~~i~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~-~~~~ 217 (333)
T cd06332 144 YAAGKDAVAGFKRTFK---GEVVEEVYTPLGQ--LDFSAELAQIRAAKPDAVFVFLPGGMAVNFVKQYDQAGLKK-KIPL 217 (333)
T ss_pred cchhHHHHHHHHHhhc---EEEeeEEecCCCC--cchHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCccc-CCce
Confidence 9999999999999988 4566555666543 68999999999999999999988889999999999999843 4456
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecCC--chhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPD--SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
+.++.+...... ....++++|++...++.++ .+..++|.++|+++++ ..|+.++..+||+++++++
T Consensus 218 ~~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~yda~~~~~~ 285 (333)
T cd06332 218 YGPGFLTDQDTL-----PAQGDAAVGVLTALHWAPDLDNPANKRFVAAYKAAYG-------RVPSVYAAQGYDAAQLLDA 285 (333)
T ss_pred eccCCCCCHHHH-----HhhchhhcCeeeeeccCCCCCCHHHHHHHHHHHHHhC-------CCCcHHHHHHHHHHHHHHH
Confidence 666554332111 2344678898888777653 5788999999999997 3467889999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCC
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINP 307 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~ 307 (848)
|++++... ..+++.+.++|++++|+|++|+++||++|+...+
T Consensus 286 a~~~ag~~--------------------------~~~~~~v~~al~~~~~~~~~g~i~f~~~~~~~~~ 327 (333)
T cd06332 286 ALRAVGGD--------------------------LSDKDALRAALRAADFDSPRGPFKFNPNHNPIQD 327 (333)
T ss_pred HHHHhcCC--------------------------CCCHHHHHHHHhcCceecCccceeECCCCCcccc
Confidence 99995211 0136789999999999999999999999986443
No 68
>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=99.93 E-value=1.4e-24 Score=237.70 Aligned_cols=271 Identities=13% Similarity=0.082 Sum_probs=209.9
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCC-------CCCCCCceEeccCChHHHHHHHHHHHHHcC-cE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTL-------SSLQFPYFVRTTQSDQYQMAAIAEIVDHYG-WR 73 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~l-------s~~~~p~f~r~~p~d~~q~~ai~~~~~~~~-w~ 73 (848)
+++|.+|||+.+|.++.++++++++.+||+|+.++..+.+ ....+||+||..+++..++.+++++++..+ ++
T Consensus 67 ~d~v~~iiG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~k 146 (357)
T cd06337 67 TDKVDLLLAGGTPDTTNPVSDQCEANGVPCISTMAPWQAWFFGRGGNPATGFKWTYHFFWGAEDVVATYVGMWKQLETNK 146 (357)
T ss_pred ccCccEEEecCCcchhhHHHHHHHHhCCCeEEeccchhhhhccCCCCcccCCceeEEecCCHHHHHHHHHHHHHhCCCCc
Confidence 3589999999999999999999999999999865432211 123478999999999888999998888877 99
Q ss_pred EEEEEEEcCCCccchHHHHH---HHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHH
Q 003093 74 EVIAIYVDDDHGRNGIAALG---DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQ 150 (848)
Q Consensus 74 ~vaii~~dd~~g~~~~~~l~---~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~ 150 (848)
+|++++.|++||....+.+. +.+++.|++|+..+.++.+. .||+.++++|++++||+|++.+.+.++..++++++
T Consensus 147 ~v~ii~~~~~~g~~~~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~D~~~~v~~ik~a~pD~v~~~~~~~~~~~~~~~~~ 224 (357)
T cd06337 147 KVGILYPNDPDGNAFADPVIGLPAALADAGYKLVDPGRFEPGT--DDFSSQINAFKREGVDIVTGFAIPPDFATFWRQAA 224 (357)
T ss_pred eEEEEeecCchhHHHHHhhhcccHHHHhCCcEEecccccCCCC--CcHHHHHHHHHhcCCCEEEeCCCccHHHHHHHHHH
Confidence 99999999999998776654 67778999999988888764 79999999999999999999999999999999999
Q ss_pred HcCCCCCCeEEEec-CccccccCCCCCCCcccccccceeEEEEEecCCc--------hhHHHHHHHHHhhccCCCCCCCC
Q 003093 151 YLGMLGTGYVWIAT-SWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDS--------VLKRKFISRWRNLTDAKTPNGYI 221 (848)
Q Consensus 151 ~~g~~~~~~~wi~~-~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~--------~~~~~f~~~~~~~~~~~~~~~~~ 221 (848)
++|+..+ ++.. .+... .... ....+..+|++....+.+.. +..++|.++|+++++ .
T Consensus 225 ~~G~~~~---~~~~~~~~~~-~~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~g-------~ 289 (357)
T cd06337 225 QAGFKPK---IVTIAKALLF-PEDV----EALGDRGDGMSTEVWWSPSHPFRSSLTGQSAAELADAYEAATG-------R 289 (357)
T ss_pred HCCCCCC---eEEEeccccC-HHHH----HHhhhhhcCccccceeccCCCcccccCCccHHHHHHHHHHHhC-------C
Confidence 9998543 2322 22111 1111 12234457777655444432 357899999999997 2
Q ss_pred CCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccC
Q 003093 222 GLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSH 301 (848)
Q Consensus 222 ~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~ 301 (848)
.+.....++||+++++++|++++ ++..+++.|.++|++++++++.|++.||++
T Consensus 290 ~~~~~~~~~~~~~~~l~~Ai~~A---------------------------gs~~d~~~v~~aL~~~~~~~~~G~~~f~~~ 342 (357)
T cd06337 290 QWTQPLGYAHALFEVGVKALVRA---------------------------DDPDDPAAVADAIATLKLDTVVGPVDFGNS 342 (357)
T ss_pred CccCcchHHHHHHHHHHHHHHHc---------------------------CCCCCHHHHHHHHHcCCcccceeeeecCCC
Confidence 34556778999999999999984 222247899999999999999999999865
Q ss_pred CCCCCCcEEEEEeecccE
Q 003093 302 GDLINPAYEIINVIGTGY 319 (848)
Q Consensus 302 g~~~~~~~~I~~~~~~~~ 319 (848)
.+ .+..|+.+++++|
T Consensus 343 --~~-~~~~~~~~~~~~~ 357 (357)
T cd06337 343 --PI-KNVAKTPLVGGQW 357 (357)
T ss_pred --CC-ccccccccccCCC
Confidence 22 3566777776654
No 69
>cd06358 PBP1_NHase Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified int
Probab=99.92 E-value=7.1e-24 Score=230.28 Aligned_cols=258 Identities=16% Similarity=0.156 Sum_probs=208.5
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHH-HHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~-~~~~w~~vaii~~d 81 (848)
++|.+||||.+|.++.++.++++ .+||+|++++.+.. ...||+||+.+++..++.++++++ +..+|++|++++.|
T Consensus 66 ~~v~aviG~~~s~~a~a~~~~~~-~~vp~i~~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~i~~~~ 141 (333)
T cd06358 66 GGVDAIIGWHTSAVRNAVAPVVA-GRVPYVYTSLYEGG---ECNPGVFLTGETPEQQLAPAIPWLAEEKGARRWYLIGND 141 (333)
T ss_pred CCCcEEEecCcHHHHHHHHHHHh-cCceEEeCCCcCCC---CCCCCEEEcCCCcHHHHHHHHHHHHHhcCCCeEEEEecc
Confidence 58999999999999999999999 99999997544322 346999999999999988777775 66799999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++||+...+.+.+.+++.|++|+....++.+ ..||++++.++++.+||+|++.+...+...++++++++|+..+ +
T Consensus 142 ~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~---~ 216 (333)
T cd06358 142 YVWPRGSLAAAKRYIAELGGEVVGEEYVPLG--TTDFTSVLERIAASGADAVLSTLVGQDAVAFNRQFAAAGLRDR---I 216 (333)
T ss_pred chhhHHHHHHHHHHHHHcCCEEeeeeeecCC--hHHHHHHHHHHHHcCCCEEEEeCCCCchHHHHHHHHHcCCCcc---C
Confidence 9999999999999999999999998888865 4899999999999999999999999899999999999999653 2
Q ss_pred Eec-CccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 162 IAT-SWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 162 i~~-~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
+.. ..+...... ......++|++....+.+ ..+..++|.++|+++|+. ....++.++..+||++++++
T Consensus 217 ~~~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~----~~~~~~~~~~~~yda~~~~~ 287 (333)
T cd06358 217 LRLSPLMDENMLL-----ASGAEAAEGLYSSSGYFASLQTPANAAFLARYRARFGD----DAPPLNSLSESCYEAVHALA 287 (333)
T ss_pred ceeecccCHHHHH-----hcChHhhCCcEEeccchhhcCCHHHHHHHHHHHHHcCC----CCCCCChHHHHHHHHHHHHH
Confidence 222 222111100 112245788877665543 568899999999999962 11246778899999999999
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCC
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINP 307 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~ 307 (848)
+|++++ +.. +++.|.++|++++|+|++|+++|++++. +.+
T Consensus 288 ~A~~~a---------------------------g~~-~~~~v~~al~~~~~~~~~G~~~~~~~~~-~~~ 327 (333)
T cd06358 288 AAAERA---------------------------GSL-DPEALIAALEDVSYDGPRGTVTMRGRHA-RQP 327 (333)
T ss_pred HHHHHh---------------------------CCC-CHHHHHHHhccCeeeCCCcceEEccccc-ccc
Confidence 999973 122 3889999999999999999999998864 444
No 70
>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=99.92 E-value=1.2e-23 Score=229.80 Aligned_cols=260 Identities=18% Similarity=0.212 Sum_probs=206.6
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEeccCChHHHHHHHHHHH-HHcCcEEEEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS--LQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~--~~~p~f~r~~p~d~~q~~ai~~~~-~~~~w~~vaii~ 79 (848)
++|++||||.+|..+.++++++++.+||+|++.++.+.++. ..++|+||+.+++..++.++++++ ++.+|++|+++|
T Consensus 66 ~~V~aiiG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~~Fr~~~~~~~~~~~~a~~~~~~~~~~~v~ii~ 145 (347)
T cd06335 66 EKVVAVLGGLHTPVALANLEFIQQNKIPLIGPWAAGTPITRNGAPPNYIFRVSADDSIQAPFLVDEAVKRGGFKKVALLL 145 (347)
T ss_pred CCeEEEEcCCCCHHHHhhhHHHHhcCCcEEecCCCCcccccCCCCCCCEEEeccChHHHHHHHHHHHHHhcCCCeEEEEe
Confidence 48999999999999999999999999999998888777764 456899999999999999999986 566799999999
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
.|++||+...+.+.+.+++.|++++....++... .|++.++.+|++.++|+|++.+...+...+++++++.|+..+
T Consensus 146 ~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~--~d~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~-- 221 (347)
T cd06335 146 DNTGWGRSNRKDLTAALAARGLKPVAVEWFNWGD--KDMTAQLLRAKAAGADAIIIVGNGPEGAQIANGMAKLGWKVP-- 221 (347)
T ss_pred ccCchhhhHHHHHHHHHHHcCCeeEEEeeecCCC--ccHHHHHHHHHhCCCCEEEEEecChHHHHHHHHHHHcCCCCc--
Confidence 9999999999999999999999999888888654 799999999999999999999999999999999999998532
Q ss_pred EEEecCccccccCCCCCCCcccccccceeEEEEEec---CCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHH
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYT---PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~---~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~ 236 (848)
++...... ..... ....+..+|++....+. ++.+..++|.++|+++++..+.. ...++.+++.+||++++
T Consensus 222 -~~~~~~~~-~~~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~-~~~~~~~~~~aYd~~~~ 294 (347)
T cd06335 222 -IISHWGLS-GGNFI----EGAGPAANDALMIQTFIFEPPSNPKAKAFLAAYHKKYPEKKPA-DIPAPVGAAHAYDAVHL 294 (347)
T ss_pred -EecccCCc-Cchhh----hccchhhcCcEEEEeeccccCCCHHHHHHHHHHHHHhCCCccc-ccCcchhHHHHHHHHHH
Confidence 23222211 11111 22345578877765533 25688999999999999731111 11356677899999999
Q ss_pred HHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhc--cccccccc--eEeccC
Q 003093 237 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQA--NMTGTAGP--ARFNSH 301 (848)
Q Consensus 237 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~--~f~G~tG~--v~Fd~~ 301 (848)
+++|++++. .. .++.+.++|+++ .+.|+.|. +.|++.
T Consensus 295 l~~A~~~ag---------------------------~~-~~~~v~~al~~~~~~~~G~~~~~~~~~~~~ 335 (347)
T cd06335 295 LAAAIKQAG---------------------------ST-DGRAIKRALENLKKPVEGLVKTYDKPFSKE 335 (347)
T ss_pred HHHHHHHhc---------------------------CC-CHHHHHHHHHhccCCceeeecccCCCCChh
Confidence 999999842 11 257899999876 46788774 457543
No 71
>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=99.92 E-value=5.2e-24 Score=232.92 Aligned_cols=270 Identities=23% Similarity=0.320 Sum_probs=222.1
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHH-HHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~-~~~~w~~vaii~~ 80 (848)
+++|.+||||.+|..+.++++++++.++|+|++++.++ ...+||+||+.|++..++.++++++ ++++.+++++|+.
T Consensus 67 ~~~v~~vvg~~~s~~~~~~~~~~~~~~ip~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~iv~~ 143 (343)
T PF13458_consen 67 DDGVDAVVGPLSSAQAEAVAPIAEEAGIPYISPSASSP---SPDSPNVFRLSPSDSQQAAALAEYLAKKLGAKKVAIVYP 143 (343)
T ss_dssp TSTESEEEESSSHHHHHHHHHHHHHHT-EEEESSGGGG---TTTHTTEEESS--HHHHHHHHHHHHHHTTTTSEEEEEEE
T ss_pred hcCcEEEEecCCcHHHHHHHHHHHhcCcEEEEeeccCC---CCCCCcEEEEeccccHHHHHHHHHHHHHcCCcEEEEEec
Confidence 37899999999999999999999999999999654442 3567999999999999999999985 5689999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
+++||+...+.+.+.+++.|++++....++.+. .|+..++.++++.++|+|++.+...+...++++++++|+..+.+.
T Consensus 144 ~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~~~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (343)
T PF13458_consen 144 DDPYGRSLAEAFRKALEAAGGKVVGEIRYPPGD--TDFSALVQQLKSAGPDVVVLAGDPADAAAFLRQLRQLGLKPPRIP 221 (343)
T ss_dssp SSHHHHHHHHHHHHHHHHTTCEEEEEEEE-TTS--SHHHHHHHHHHHTTTSEEEEESTHHHHHHHHHHHHHTTGCSCTEE
T ss_pred CchhhhHHHHHHHHHHhhcCceeccceeccccc--ccchHHHHHHhhcCCCEEEEeccchhHHHHHHHHHhhccccccce
Confidence 999999999999999999999998888888655 899999999999999999999999999999999999998643344
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
...+......+. ....+.++|++...++.+ +.+..++|.++|+++++. ...++.++..+||++.+++
T Consensus 222 ~~~~~~~~~~l~------~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~~~yda~~~~~ 290 (343)
T PF13458_consen 222 LFGTSLDDASLQ------QLGGDALEGVYIVSPWFPDPDSPAVKQFQERYRAAYGE-----EPPPSLYAAQGYDAARLLA 290 (343)
T ss_dssp EEEGGGSSHHHH------HHHGGGGTTEEEEESGGGTGGSHHHHHHHHHHHHHHSS-----TGGTCHHHHHHHHHHHHHH
T ss_pred eeccccCcHHHH------HhhhhhccCceeecccCCCCCCHHHHHHHHHHHHHcCC-----CCCCchhHHHHHHHHHHHH
Confidence 443332222211 122346889998888766 458899999999999972 1147889999999999999
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEee
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI 315 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~~ 315 (848)
+|++++. +. +++.+.++|+++.|+|+.|++.|++.++.....+.|++++
T Consensus 291 ~al~~~g---------------------------~~-~~~~v~~al~~~~~~g~~g~~~~~~~~~~~~~~~~i~~v~ 339 (343)
T PF13458_consen 291 QALERAG---------------------------SL-DREAVREALESLKYDGLFGPISFDPPDHQANKPVYIVQVK 339 (343)
T ss_dssp HHHHHHT---------------------------SH-HHHHHHHHHHTSEEEETTEEEEEETTTSBEEEEEEEEEEE
T ss_pred HHHHHhC---------------------------CC-CHHHHHHHHHhCCCcccccceEEeCCCCccccCeEEEEEe
Confidence 9999951 11 4899999999999999999999976555567888999988
No 72
>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=99.92 E-value=2.3e-23 Score=226.09 Aligned_cols=258 Identities=8% Similarity=0.096 Sum_probs=204.5
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+++|++|||+.+|.++.++.+++++.++|+|+.+.... ....||+||+.+++..++.++++++...+-+++++|+.|
T Consensus 65 ~~~V~aiiG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~---~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~vail~~d 141 (334)
T cd06356 65 QDKVDVVWGGISSASREAIRPIMDRTKQLYFYTTQYEG---GVCDRNTFCTGATPAQQFSTLVPYMMEKYGKKVYTIAAD 141 (334)
T ss_pred hCCCCEEEeCcchHHHHHHHHHHHhcCceEEeCCCccC---CcccCCEEEeCCCcHHHHHHHHHHHHHccCCeEEEECCC
Confidence 46899999999999999999999999999997543322 123589999999999999999999766544889999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
++||......+.+.+++.|++++....++.+. .||+.++++|++.+||+|++.....+...+++++++.|+ . ....
T Consensus 142 ~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~-~-~~~~ 217 (334)
T cd06356 142 YNFGQISAEWVRKIVEENGGEVVGEEFIPLDV--SDFGSTIQKIQAAKPDFVMSILVGANHLSFYRQWAAAGL-G-NIPM 217 (334)
T ss_pred chhhHHHHHHHHHHHHHcCCEEEeeeecCCCc--hhHHHHHHHHHhcCCCEEEEeccCCcHHHHHHHHHHcCC-c-cCce
Confidence 99999999999999999999999988888754 899999999999999999999988899999999999998 2 1122
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecCC--chhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPD--SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 239 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 239 (848)
+............ ......++|++....+.++ .+..++|.++|+++++. ...++.+++.+||+++++++
T Consensus 218 ~~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~p~~~~~~~~~y~a~~~~~~ 288 (334)
T cd06356 218 ASSTLGAQGYEHK----RLKPPALKDMYATANYIEELDTPANKAFVERFRAKFPD-----APYINEEAENNYEAIYLYKE 288 (334)
T ss_pred eeeecccchhHHh----ccCchhcCCeEEecchhhhcCCHHHHHHHHHHHHHcCC-----CCCCCchhHHHHHHHHHHHH
Confidence 2221111111010 1123557888777665443 57889999999999962 11235788999999999999
Q ss_pred HHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHh-ccccccccceEeccCCC
Q 003093 240 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQ-ANMTGTAGPARFNSHGD 303 (848)
Q Consensus 240 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~-~~f~G~tG~v~Fd~~g~ 303 (848)
|++++. .. +++.|.++|++ ..|+|+.|+++|+++++
T Consensus 289 A~~~ag---------------------------~~-~~~~v~~aL~~~~~~~~~~g~~~~~~~~h 325 (334)
T cd06356 289 AVEKAG---------------------------TT-DRDAVIEALESGLVCDGPEGKVCIDGKTH 325 (334)
T ss_pred HHHHHC---------------------------CC-CHHHHHHHHHhCCceeCCCceEEEecCCC
Confidence 999842 22 38899999997 56899999999997443
No 73
>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=99.91 E-value=5.1e-23 Score=223.99 Aligned_cols=272 Identities=13% Similarity=0.150 Sum_probs=211.7
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcC-----cEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYG-----WREVI 76 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~-----w~~va 76 (848)
++|++|+ +.+|..+.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.++++++...+ .++|+
T Consensus 66 ~~V~~i~-~~~S~~~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~~Fr~~~~~~~~~~~l~~~~~~~~~~~~~~~kva 144 (351)
T cd06334 66 DGAVAFQ-GWSTGITEALIPKIAADKIPLMSGSYGATLADDGAVFPYNFPVGPTYSDQARALVQYIAEQEGGKLKGKKIA 144 (351)
T ss_pred CCcEEEe-cCcHHHHHHhhHHHhhcCCcEEecccchhhccCCCCCCeeeeCCCCHHHHHHHHHHHHHHhcccCCCCCeEE
Confidence 4788765 588999999999999999999998877777764 6689999999999999999999986654 79999
Q ss_pred EEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 77 AIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 77 ii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
+|+.|++||+...+.+.+.+++.|++|+....++.+. .|++.++.+|++.+||+|++.+...++..++++++++|+..
T Consensus 145 iv~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~D~~~~v~~i~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~ 222 (351)
T cd06334 145 LVYHDSPFGKEPIEALKALAEKLGFEVVLEPVPPPGP--NDQKAQWLQIRRSGPDYVILWGWGVMNPVAIKEAKRVGLDD 222 (351)
T ss_pred EEeCCCccchhhHHHHHHHHHHcCCeeeeeccCCCCc--ccHHHHHHHHHHcCCCEEEEecccchHHHHHHHHHHcCCCc
Confidence 9999999999999999999999999999988888654 89999999999999999999999999999999999999842
Q ss_pred CCeEEEecCccccccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHH
Q 003093 157 TGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTV 234 (848)
Q Consensus 157 ~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv 234 (848)
.|+.+.+.... ... ...++..+|+++..++.+ ++|..++|.++|+++++..+. ....++.++..+|||+
T Consensus 223 ---~~~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~~~~~~-~~~~~~~~~~~gy~a~ 293 (351)
T cd06334 223 ---KFIGNWWSGDE-EDV----KPAGDAAKGYKGVTPFAGGADDPVGKEIVKEVYDKGKGSGN-DKEIGSVYYNRGVVNA 293 (351)
T ss_pred ---eEEEeeccCcH-HHH----HHhhhhhcCcEEeecccCCCCchHHHHHHHHHHHccCCCCC-cccccccHHHHHHHHH
Confidence 25554432221 111 234466789888776654 568899999999999863111 0124567899999999
Q ss_pred HHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccC
Q 003093 235 WLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSH 301 (848)
Q Consensus 235 ~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~ 301 (848)
+++++|++++.+........ .......-+..++.+.+....|+.|+++|...
T Consensus 294 ~~l~~Al~~ag~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 345 (351)
T cd06334 294 MIMVEAIRRAQEKGGETTIA---------------GEEQLENLKLDAARLEELGAEGLGPPVSVSCD 345 (351)
T ss_pred HHHHHHHHHHHHhcCCCCCc---------------HHHHHHhhhhhhhhhhhcCcccccCCceeccc
Confidence 99999999987654321100 00000002234556667778899999999753
No 74
>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=99.91 E-value=2.6e-23 Score=225.33 Aligned_cols=249 Identities=15% Similarity=0.119 Sum_probs=197.1
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+++|.+||||.+|..+.++++++.+.+||+|+++++.+ +.. .|++||+.+++..++.++++++...|+++|++++.+
T Consensus 57 ~~~V~~iiG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~-~~~--~~~~f~~~~~~~~~~~~~~~~~~~~g~k~vaii~~~ 133 (336)
T cd06339 57 AEGADIIVGPLLKENVAALAAAAAELGVPVLALNNDES-VAA--GPNLFYFGLSPEDEARRAAEYARSQGKRRPLVLAPD 133 (336)
T ss_pred HcCCCEEEccCCHHHHHHHHhhhccCCCCEEEccCCcc-ccC--CCCEEEecCChHHHHHHHHHHHHhcCccceEEEecC
Confidence 35899999999999999999999999999999765543 322 589999999999999999999888899999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC---------------------CCeEEEEEccCC
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT---------------------ESRIIVVHTHYN 140 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~---------------------~~~viv~~~~~~ 140 (848)
++||+...+.|.+.+++.|++|+..+.++.+ ..||+.++++|++. ++|+|++.+.+.
T Consensus 134 ~~~g~~~~~~f~~~~~~~G~~vv~~~~~~~~--~~d~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~~~~~~~ 211 (336)
T cd06339 134 GAYGQRVADAFRQAWQQLGGTVVAIESYDPS--PTDLSDAIRRLLGVDDSEQRIAQLKSLESEPRRRQDIDAIDAVALPD 211 (336)
T ss_pred ChHHHHHHHHHHHHHHHcCCceeeeEecCCC--HHHHHHHHHHHhccccchhhhhhhhhcccCccccCCCCcEEEEecCh
Confidence 9999999999999999999999998888864 48999999999998 999999988886
Q ss_pred -cHHHHHHHHHHcCCCCCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCC
Q 003093 141 -RGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNG 219 (848)
Q Consensus 141 -~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 219 (848)
.+..+.++++..+.......+++++++...... ....+..+|++...+.. ....+|.++|+++|+
T Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-----~~~g~~~~g~~~~~~~~---~~~~~f~~~y~~~~~------ 277 (336)
T cd06339 212 GEARLIKPQLLFYYGVPGDVPLYGTSRWYSGTPA-----PLRDPDLNGAWFADPPW---LLDANFELRYRAAYG------ 277 (336)
T ss_pred hhhhhhcchhhhhccCcCCCCEEEeccccCCCCC-----cccCcccCCcEEeCCCc---ccCcchhhhHHHHhc------
Confidence 777777777766531123356777766543211 23346678887655421 123389999999997
Q ss_pred CCCC-CcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHh-ccccccccceE
Q 003093 220 YIGL-NAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQ-ANMTGTAGPAR 297 (848)
Q Consensus 220 ~~~~-~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~-~~f~G~tG~v~ 297 (848)
..| +.+++.+|||+.+++.++++.. .. . ++.+ ..|+|++|+++
T Consensus 278 -~~p~~~~~a~~YDa~~l~~~~~~~~~---------------------------~~--~-----al~~~~~~~g~~G~~~ 322 (336)
T cd06339 278 -WPPLSRLAALGYDAYALAAALAQLGQ---------------------------GD--A-----ALTPGAGFSGVTGVLR 322 (336)
T ss_pred -CCCCchHHHHHHhHHHHHHHHHHccc---------------------------cc--c-----ccCCCCccccCcceEE
Confidence 356 8899999999999988777621 10 1 3333 35999999999
Q ss_pred eccCCCC
Q 003093 298 FNSHGDL 304 (848)
Q Consensus 298 Fd~~g~~ 304 (848)
||++|+.
T Consensus 323 f~~~g~~ 329 (336)
T cd06339 323 LDPDGVI 329 (336)
T ss_pred ECCCCeE
Confidence 9999974
No 75
>KOG1055 consensus GABA-B ion channel receptor subunit GABABR1 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=99.90 E-value=3.5e-24 Score=232.86 Aligned_cols=304 Identities=19% Similarity=0.336 Sum_probs=238.6
Q ss_pred eEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcCC
Q 003093 5 TVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD 83 (848)
Q Consensus 5 V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~ 83 (848)
-++++|+ ||+++..++.-+..++.-++||++++|.|++ ..||+|||+.|++..+...+..++++|+|++|++++++.+
T Consensus 114 k~mll~G-Cs~v~~~iaea~~~w~l~~lsy~~ssp~ls~r~rfp~~frt~PS~~~~np~rl~l~~~~~w~rvgt~~q~e~ 192 (865)
T KOG1055|consen 114 KLMLLGG-CSSVTTLIAEAAKMWNLIVLSYGASSPALSNRKRFPTFFRTHPSANAHNPTRIKLLKKFGWKRVATLQQTEE 192 (865)
T ss_pred hheeccC-CCCcchHHHhhccccceeeecccCCCccccchhhcchhhhcCCccccCCcceeeechhcCcceeeeeeeehh
Confidence 4567888 9999999999999999999999999999998 7899999999999999999999999999999999999988
Q ss_pred CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003093 84 HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 163 (848)
Q Consensus 84 ~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 163 (848)
-.....+.+...+.+.|++++..+.+. .|....+.+++...+|+|+-.-+...|+.+++++++.+|.+..|+|+.
T Consensus 193 ~f~~~~~dl~~~~~~~~ieiv~~qsf~-----~dp~~~vk~l~~~D~RiI~g~f~~~~Arkv~C~~Y~~~myg~ky~w~~ 267 (865)
T KOG1055|consen 193 VFSSTLNDLEARLKEAGIEIVFRQSFS-----SDPADSVKNLKRQDARIIVGLFYETEARKVFCEAYKERLYGRKYVWFL 267 (865)
T ss_pred hhcchHHHHHHhhhccccEEEEeeccc-----cCHHHHHhhccccchhheeccchHhhhhHHHHhhchhhcccceeEEEE
Confidence 888899999999999999999887765 355667899999999999999999999999999999999999999999
Q ss_pred cCccccccCCC-----CCCCcccccccceeEEEEEe--cCCc------hhHHHHHHHHHhhccCCCCCCCCCCCcchhhh
Q 003093 164 TSWLSTALDTN-----SPFPSDVMDDIQGVLTLRTY--TPDS------VLKRKFISRWRNLTDAKTPNGYIGLNAYGFYA 230 (848)
Q Consensus 164 ~~~~~~~~~~~-----~~~~~~~~~~~~G~~~~~~~--~~~~------~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (848)
..|....+... .+.-+++.++++|.+++... ++.. -..++|...+.+..+..+ ........+.++
T Consensus 268 ~g~y~d~w~ev~~~~~~ctveem~~A~eg~~s~e~~pl~~~~~~tisg~T~~~~l~~~~~~r~~~~--~~~~~~~~~~~a 345 (865)
T KOG1055|consen 268 IGWYADNWWEITHPSENCTVEEMTEAAEGHITTEFVMLSPANITTISGMTAQEFLEELTKYRKRHP--EETGGFQEAPLA 345 (865)
T ss_pred EEeeccchhhccCchhhhhHHHHHHHHhhheeeeeeccccccceeeccchhHHHHHHHHhhhcccc--ccccCcccCchH
Confidence 88766544311 22234566788998877543 2221 123445554443332111 113456678899
Q ss_pred hhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEE
Q 003093 231 YDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYE 310 (848)
Q Consensus 231 YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~ 310 (848)
|||+|++|+|+++++...+....+ + .+.+..... -.++|.++|.+++|.|++|.+.|.. |+|. ..-.
T Consensus 346 yd~Iwa~ala~n~t~e~l~~~~~~----l------~~f~y~~k~-i~d~i~eamn~tsF~GvsG~V~F~~-geR~-a~t~ 412 (865)
T KOG1055|consen 346 YDAIWALALALNKTMEGLGRSHVR----L------EDFNYNNKT-IADQIYEAMNSTSFEGVSGHVVFSN-GERM-ALTL 412 (865)
T ss_pred HHHHHHHHHHHHHHHhcCCcccee----c------cccchhhhH-HHHHHHHHhhcccccccccceEecc-hhhH-HHHH
Confidence 999999999999987654321100 0 011111111 2678999999999999999999976 9974 7778
Q ss_pred EEEeecccEEEEEEeeCCC
Q 003093 311 IINVIGTGYRRIGYWSNYS 329 (848)
Q Consensus 311 I~~~~~~~~~~Vg~w~~~~ 329 (848)
|-|+++|+++.+|+|+...
T Consensus 413 ieQ~qdg~y~k~g~Yds~~ 431 (865)
T KOG1055|consen 413 IEQFQDGKYKKIGYYDSTK 431 (865)
T ss_pred HHHHhCCceEeeccccccc
Confidence 8899999999999998654
No 76
>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=99.89 E-value=2.7e-22 Score=214.51 Aligned_cols=165 Identities=35% Similarity=0.580 Sum_probs=155.0
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|.|||||.+|..+.+++++++.++||+|+++++++.+++ ..+|+++|+.|++..++.++++++++++|++|+++|++
T Consensus 70 ~~v~aiiG~~~s~~~~~v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~~v~~~ 149 (298)
T cd06269 70 RGVVAVIGPSSSSSAEAVASLLGALHIPQISYSATSPLLSDKEQFPSFLRTVPSDSSQAQAIVDLLKHFGWTWVGLVYSD 149 (298)
T ss_pred CceEEEECCCCchHHHHHHHHhccCCCcEEecccCchhhcChhhCCCeEecCCCcHHHHHHHHHHHHHCCCeEEEEEEec
Confidence 68999999999999999999999999999999999998887 67999999999999999999999999999999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
+++|....+.+.+.+++.|+++.....++... .++..++++++..++++|++++..+++..++++|+++||+ .+++|
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~--~~~~~~l~~l~~~~~~viv~~~~~~~~~~~l~~a~~~g~~-~~~~~ 226 (298)
T cd06269 150 DDYGRRLLELLEEELEKNGICVAFVESIPDGS--EDIRRLLKELKSSTARVIVVFSSEEDALRLLEEAVELGMM-TGYHW 226 (298)
T ss_pred chhhHHHHHHHHHHHHHCCeeEEEEEEcCCCH--HHHHHHHHHHHhcCCcEEEEEechHHHHHHHHHHHHcCCC-CCeEE
Confidence 99999999999999999999999988887643 7899999999999999999999999999999999999998 89999
Q ss_pred EecCccccc
Q 003093 162 IATSWLSTA 170 (848)
Q Consensus 162 i~~~~~~~~ 170 (848)
|.++.+...
T Consensus 227 i~~~~~~~~ 235 (298)
T cd06269 227 IITDLWLTS 235 (298)
T ss_pred EEEChhhcc
Confidence 999876543
No 77
>TIGR03863 PQQ_ABC_bind ABC transporter, substrate binding protein, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are putative substrate-binding proteins of an ABC transporter family that associates, in gene neighborhood and phylogenomic profile, with pyrroloquinoline-quinone (PQQ)-dependent degradation of certain alcohols, such as 2-phenylethanol in Pseudomonas putida U.
Probab=99.89 E-value=2.3e-22 Score=216.45 Aligned_cols=251 Identities=15% Similarity=0.149 Sum_probs=188.9
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
+++|++|||+.+|+++.++++++++.++|+|+++++++.++. ..+||+||+.|++..++.++++++...+.++|++|+.
T Consensus 57 ~~~V~~vvG~~~S~~~~Av~~~a~~~~vp~i~~~a~~~~lt~~~c~~~~Fr~~~~~~~~~~ala~~~~~~g~kkvaii~~ 136 (347)
T TIGR03863 57 AQGVRFFVLDLPAAALLALADAAKAKGALLFNAGAPDDALRGADCRANLLHTLPSRAMLADALAQYLAAKRWRRILLIQG 136 (347)
T ss_pred HCCCCEEEecCChHHHHHHHHHHHhCCcEEEeCCCCChHHhCCCCCCCEEEecCChHhHHHHHHHHHHHcCCCEEEEEeC
Confidence 467999999999999999999999999999999999999987 5689999999999999999999987779999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCC--hHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEAT--EDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~--~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
|++||....+.+.+.+++.|++|+..+.++...+ ..|+......++.++||+|++.....+....+... .+. .
T Consensus 137 ~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~~~~~d~s~~~~~~~~s~pDvv~~~~~~~~~~~~~~~~--~~~---~ 211 (347)
T TIGR03863 137 PLPADALYADAFRRSAKRFGAKIVAERPFTFSGDPRRTDQSEVPLFTQGADYDVVVVADEAGEFARYLPYA--TWL---P 211 (347)
T ss_pred CCcccHHHHHHHHHHHHHCCCEEEEeEEeccCCchhhhhcccCceeecCCCCCEEEEecchhhHhhhcccc--ccc---c
Confidence 9999999999999999999999999988876431 23555322333348999999875543321111100 000 0
Q ss_pred eEEEecCccccccCCCCCCCcccccccceeEEEEE-ecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHH
Q 003093 159 YVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRT-YTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLL 237 (848)
Q Consensus 159 ~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~-~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~ 237 (848)
... ....|+..... +..+.+..++|.++|+++|+ ..|+.+++.+||+++++
T Consensus 212 ~~~---------------------~g~~G~~~~~~~~~~~~~~~~~f~~~f~~~~g-------~~p~~~~a~aY~av~~~ 263 (347)
T TIGR03863 212 RPV---------------------AGSAGLVPTAWHRAWERWGATQLQSRFEKLAG-------RPMTELDYAAWLAVRAV 263 (347)
T ss_pred ccc---------------------ccccCccccccCCcccchhHHHHHHHHHHHhC-------CCCChHHHHHHHHHHHH
Confidence 000 11122221111 12234677899999999997 45677889999999999
Q ss_pred HHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccc--ccccc-ceEecc-CCCCCCCcEEEEE
Q 003093 238 ARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANM--TGTAG-PARFNS-HGDLINPAYEIIN 313 (848)
Q Consensus 238 a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f--~G~tG-~v~Fd~-~g~~~~~~~~I~~ 313 (848)
+.|++++ ++.+ ++++.++|+++++ +++.| +++|.+ ||+...+ ..+.+
T Consensus 264 a~Ai~~A---------------------------Gs~d-~~aV~~aL~~~~~~~~~~~g~~~~~R~~Dhq~~~~-~~~~~ 314 (347)
T TIGR03863 264 GEAVTRT---------------------------RSAD-PATLRDYLLSDEFELAGFKGRPLSFRPWDGQLRQP-VLLVH 314 (347)
T ss_pred HHHHHHh---------------------------cCCC-HHHHHHHHcCCCceecccCCCcceeeCCCcccccc-eEecc
Confidence 9999994 3343 9999999999887 57887 699985 7775533 34444
Q ss_pred e
Q 003093 314 V 314 (848)
Q Consensus 314 ~ 314 (848)
.
T Consensus 315 ~ 315 (347)
T TIGR03863 315 P 315 (347)
T ss_pred c
Confidence 3
No 78
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.88 E-value=2e-21 Score=201.27 Aligned_cols=218 Identities=25% Similarity=0.393 Sum_probs=188.9
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
..+|+||+.. +|+||.+. +++.+.|+++||++++++++|.+++++.. +|.+++.++.+|++|++++++
T Consensus 24 ~~~l~v~~~~--~~~P~~~~-~~g~~~G~~vdl~~~ia~~lg~~~~~~~~---------~~~~~~~~l~~G~vDi~~~~~ 91 (247)
T PRK09495 24 DKKLVVATDT--AFVPFEFK-QGDKYVGFDIDLWAAIAKELKLDYTLKPM---------DFSGIIPALQTKNVDLALAGI 91 (247)
T ss_pred CCeEEEEeCC--CCCCeeec-CCCceEEEeHHHHHHHHHHhCCceEEEeC---------CHHHHHHHHhCCCcCEEEecC
Confidence 4689999764 68899873 46789999999999999999998666543 499999999999999998779
Q ss_pred eeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcc
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVV 534 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 534 (848)
+.+++|.+.++||.||+..++.+++++..
T Consensus 92 ~~t~~R~~~~~fs~p~~~~~~~~~~~~~~--------------------------------------------------- 120 (247)
T PRK09495 92 TITDERKKAIDFSDGYYKSGLLVMVKANN--------------------------------------------------- 120 (247)
T ss_pred ccCHHHHhhccccchheecceEEEEECCC---------------------------------------------------
Confidence 99999999999999999999999998665
Q ss_pred hhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHH
Q 003093 535 TIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFAR 614 (848)
Q Consensus 535 ~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~ 614 (848)
.++++++||. +++||+..|+...
T Consensus 121 -------------------------------------------------------~~~~~~~dL~--g~~I~v~~g~~~~ 143 (247)
T PRK09495 121 -------------------------------------------------------NDIKSVKDLD--GKVVAVKSGTGSV 143 (247)
T ss_pred -------------------------------------------------------CCCCChHHhC--CCEEEEecCchHH
Confidence 4688999997 8899999998888
Q ss_pred HHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCC--cEEEeCCccccCCceeeecCCCCc
Q 003093 615 NYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC--EFSIVGQVFTKNGWGFAFPRDSPL 692 (848)
Q Consensus 615 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~~~~~~k~spl 692 (848)
.++.. ..+..+++.+++.++.+++|.+ |++|+++.+...+.+++++.. ++..++.......++++++|++.+
T Consensus 144 ~~l~~--~~~~~~i~~~~~~~~~~~~L~~----grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l 217 (247)
T PRK09495 144 DYAKA--NIKTKDLRQFPNIDNAYLELGT----GRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSEL 217 (247)
T ss_pred HHHHh--cCCCCceEEcCCHHHHHHHHHc----CceeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcHHH
Confidence 88854 3344567788899999999999 999999999988888887643 577777666677899999999999
Q ss_pred hHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 693 AVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 693 ~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
.+.+|++|.++.++|.++++.+||+.
T Consensus 218 ~~~~n~al~~~~~~g~~~~i~~k~~~ 243 (247)
T PRK09495 218 REKVNGALKTLKENGTYAEIYKKWFG 243 (247)
T ss_pred HHHHHHHHHHHHHCCcHHHHHHHHcC
Confidence 99999999999999999999999987
No 79
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.87 E-value=4.1e-21 Score=203.53 Aligned_cols=223 Identities=18% Similarity=0.284 Sum_probs=186.3
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHH----hCCC-CcceEEeeCCCCCCCCChhHHHHHHhcCeeeE
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAIN----LLPY-AVPYKLIPFGDGHNNPSCTELVRLITAGVYDA 449 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~----~l~~-~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~ 449 (848)
.+.|+||+.. +|+||.+.++++++.||++|++++|++ ++|. .++++++++ +|..++..|..|++||
T Consensus 39 ~g~L~Vg~~~--~~pP~~f~~~~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~-------~~~~~i~~L~~G~~Di 109 (302)
T PRK10797 39 NGVIVVGHRE--SSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPI-------TSQNRIPLLQNGTFDF 109 (302)
T ss_pred CCeEEEEEcC--CCCCcceECCCCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEEc-------ChHhHHHHHHCCCccE
Confidence 3569999885 788998866678899999997777655 6664 355777763 4888999999999999
Q ss_pred EeeceeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCC
Q 003093 450 AVGDIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPP 529 (848)
Q Consensus 450 ~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~ 529 (848)
+++++++|++|.+.++||.||+..+..+++++..
T Consensus 110 ~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~---------------------------------------------- 143 (302)
T PRK10797 110 ECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG---------------------------------------------- 143 (302)
T ss_pred EecCCccCcchhhcceecccEeeccEEEEEECCC----------------------------------------------
Confidence 9988999999999999999999999999998654
Q ss_pred CCCcchhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEe
Q 003093 530 KRQVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQV 609 (848)
Q Consensus 530 ~~~~~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~ 609 (848)
.+++++||. |++||+..
T Consensus 144 -------------------------------------------------------------~i~sl~dL~--Gk~V~v~~ 160 (302)
T PRK10797 144 -------------------------------------------------------------DIKDFADLK--GKAVVVTS 160 (302)
T ss_pred -------------------------------------------------------------CCCChHHcC--CCEEEEeC
Confidence 478899997 89999999
Q ss_pred CchHHHHHHhhhC--CCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhc--CC-cEEEeCCccccCCcee
Q 003093 610 NSFARNYLVDELN--IDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLST--RC-EFSIVGQVFTKNGWGF 684 (848)
Q Consensus 610 ~s~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~--~~-~l~~~~~~~~~~~~~~ 684 (848)
|+....++..... .+..+++.+.+.++.+++|.. |++|+++.+...+.+.+.+ .. .++++++.+...++++
T Consensus 161 gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~----GrvDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~~ 236 (302)
T PRK10797 161 GTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLES----GRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGC 236 (302)
T ss_pred CCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHc----CCceEEEccHHHHHHHHHcCCCCcceEECCccCCcCceeE
Confidence 9988887743211 223567888999999999999 9999999998877654433 22 4888888777788999
Q ss_pred eecCCCC-chHHHHHHHHhhhccCchHHHHHhhccc
Q 003093 685 AFPRDSP-LAVDISTAILKLSENGDLQRIHDKWLLR 719 (848)
Q Consensus 685 ~~~k~sp-l~~~in~~i~~l~e~G~~~~~~~kw~~~ 719 (848)
+++|+++ ++..+|.+|.++.++|.+++|.+||+..
T Consensus 237 a~~k~~~~L~~~in~~L~~l~~~G~l~~i~~kw~~~ 272 (302)
T PRK10797 237 MLRKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFKN 272 (302)
T ss_pred EEeCCCHHHHHHHHHHHHHHHhCchHHHHHHHHcCC
Confidence 9999988 9999999999999999999999999983
No 80
>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=99.86 E-value=1.4e-20 Score=194.29 Aligned_cols=275 Identities=16% Similarity=0.200 Sum_probs=209.8
Q ss_pred CeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHH------HHcCcEEEEE
Q 003093 4 QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV------DHYGWREVIA 77 (848)
Q Consensus 4 ~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~------~~~~w~~vai 77 (848)
.-.+++||.|..++.+|+.+...+++|+||-++-. ++=...+.+-|+.|+....+..+.++. ++++|+++.
T Consensus 81 ~gcv~lGP~CtYat~~~~~~~~~~~~P~ISaGsfg--lscd~k~~LTR~~pparK~~~~~~~f~~~~~~~~~~~W~~ay- 157 (380)
T cd06369 81 LGCVLLGPSCTYATFQMVDDEFNLSLPIISAGSFG--LSCDYKENLTRLLPPARKISDFFVDFWKEKNFPKKPKWETAY- 157 (380)
T ss_pred cCcEEEcCccceehhhhhhhhhcCCCceEeccccc--cCCCchhhhhhcCchHHHHHHHHHHHHhcccccCCCCCceeE-
Confidence 35789999999999999999999999999866643 332344689999999999999999998 589998665
Q ss_pred EEEcCCC---ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 78 IYVDDDH---GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 78 i~~dd~~---g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
||.+++- +--.+.++....+..+..+...+... +.+++..+|+.++ .+.||||+++++++.+.++.+ |+
T Consensus 158 vyk~~~~~edCf~~i~al~a~~~~f~~~~~~~~~l~---~~~~~~~il~~~~-~~sRIiImCG~p~~ir~lm~~----~~ 229 (380)
T cd06369 158 VYKKQENTEDCFWYINALEAGVAYFSSALKFKELLR---TEEELQKLLTDKN-RKSNVIIMCGTPEDIVNLKGD----RA 229 (380)
T ss_pred EEcCCCCccceeeEhHhhhhhhhhhhhcccceeeec---CchhHHHHHHHhc-cCccEEEEeCCHHHHHHHHhc----Cc
Confidence 9966642 22345566655555555544433332 3378898888877 678999999999999999886 45
Q ss_pred CCCCeEEEecCccccccCCCCCCCcccccccceeEEEEEecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHH
Q 003093 155 LGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTV 234 (848)
Q Consensus 155 ~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv 234 (848)
...+|++|..|........ +..+.++++.++.+++..|..+.+++ .. +.+...+ ..+++..||||
T Consensus 230 ~~gDYVf~~IDlF~~sy~~----d~~a~~amqsVLvIT~~~p~~~~~~~-------~~---~fn~~l~-~~~aa~fyDaV 294 (380)
T cd06369 230 VAEDIVIILIDLFNDVYYE----NTTSPPYMRNVLVLTLPPRNSTNNSS-------FT---TDNSLLK-DDYVAAYHDGV 294 (380)
T ss_pred cCCCEEEEEEecccchhcc----CcchHHHHhceEEEecCCCCCccccc-------CC---CCCcchH-HHHHHHHHHHH
Confidence 5579999999876544321 13556789999999888876655443 11 1111111 28999999999
Q ss_pred HHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEe
Q 003093 235 WLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV 314 (848)
Q Consensus 235 ~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~ 314 (848)
.++|+||++.++.+++. .+.++.+.|+|.+|.|++|.+++|++||| ..+|.++-+
T Consensus 295 LLYa~AL~EtL~~G~~~------------------------~~~~I~~~m~NrTF~GitG~V~IDeNGDR-d~dfsLl~m 349 (380)
T cd06369 295 LLFGHVLKKFLESQEGV------------------------QTFSFINEFRNISFEGAGGPYTLDEYGDR-DVNFTLLYT 349 (380)
T ss_pred HHHHHHHHHHHHhCCCC------------------------CcHHHHHHHhCcceecCCCceEeCCCCCc-cCceEEEEe
Confidence 99999999999876642 14789999999999999999999999997 689999887
Q ss_pred e--cccEEEEEEeeCCC
Q 003093 315 I--GTGYRRIGYWSNYS 329 (848)
Q Consensus 315 ~--~~~~~~Vg~w~~~~ 329 (848)
. .++++.||.|+-..
T Consensus 350 s~~tg~y~vV~~y~t~~ 366 (380)
T cd06369 350 STDTSKYKVLFEFDTST 366 (380)
T ss_pred eCCCCCeEEEEEEECCC
Confidence 5 47899999998644
No 81
>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=99.86 E-value=3e-20 Score=202.44 Aligned_cols=255 Identities=14% Similarity=0.156 Sum_probs=202.5
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
++|++|||+.+|..+.++.+++.+.++|+|+++++++.++....|++||+.+++..++..+++++.+.||++|++++.++
T Consensus 67 ~~v~avig~~~s~~~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~v~~l~~~~ 146 (336)
T cd06326 67 DKVFALFGYVGTPTTAAALPLLEEAGVPLVGPFTGASSLRDPPDRNVFNVRASYADEIAAIVRHLVTLGLKRIAVFYQDD 146 (336)
T ss_pred cCcEEEEeCCCchhHHHHHHHHHHcCCeEEEecCCcHHhcCCCCCceEEeCCChHHHHHHHHHHHHHhCCceEEEEEecC
Confidence 48999999999988888899999999999998777666654456899999999999999999999999999999999999
Q ss_pred CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003093 83 DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 162 (848)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi 162 (848)
.+|....+.+.+.+++.|++++....++.+ ..|+..++.++++.++|+|++......+..++++++++|+..+ ..+
T Consensus 147 ~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~--~~d~~~~~~~l~~~~~dav~~~~~~~~a~~~i~~~~~~G~~~~-~~~- 222 (336)
T cd06326 147 AFGKDGLAGVEKALAARGLKPVATASYERN--TADVAAAVAQLAAARPQAVIMVGAYKAAAAFIRALRKAGGGAQ-FYN- 222 (336)
T ss_pred cchHHHHHHHHHHHHHcCCCeEEEEeecCC--cccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHhcCCCCc-EEE-
Confidence 999999999999999999998877677754 3689999999999999999999988889999999999998532 222
Q ss_pred ecCccccccCCCCCCCcccccccceeEEEEE----ecCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 163 ATSWLSTALDTNSPFPSDVMDDIQGVLTLRT----YTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~----~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
........ .. ...+...+|++.... .....|..++|.++|+++++. .+++.++..+||++++++
T Consensus 223 -~~~~~~~~-~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~------~~~~~~~~~~y~~~~~~~ 290 (336)
T cd06326 223 -LSFVGADA-LA----RLLGEYARGVIVTQVVPNPWSRTLPIVREYQAAMKAYGPG------APPSYVSLEGYIAAKVLV 290 (336)
T ss_pred -EeccCHHH-HH----HHhhhhhcceEEEEEecCccccCCHHHHHHHHHHHhhCCC------CCCCeeeehhHHHHHHHH
Confidence 22221110 10 223456778765432 123457889999999988752 356778899999999999
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccc-cccccceEecc
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANM-TGTAGPARFNS 300 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f-~G~tG~v~Fd~ 300 (848)
+|++++. ...+++.+.++|++++. ++..|.++|++
T Consensus 291 ~a~~~~g---------------------------~~~~~~~v~~al~~~~~~~~~g~~~~~~~ 326 (336)
T cd06326 291 EALRRAG---------------------------PDPTRESLLAALEAMGKFDLGGFRLDFSP 326 (336)
T ss_pred HHHHHcC---------------------------CCCCHHHHHHHHHhcCCCCCCCeEEecCc
Confidence 9999841 11148899999999885 45445899965
No 82
>PRK11260 cystine transporter subunit; Provisional
Probab=99.86 E-value=1.7e-20 Score=196.47 Aligned_cols=221 Identities=19% Similarity=0.351 Sum_probs=190.9
Q ss_pred CCceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeec
Q 003093 374 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 453 (848)
Q Consensus 374 ~g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~ 453 (848)
..++|+||+.. +++||.+.+.++++.|+.+|+++.+++++|.++++... .|.+++.+|.+|++|+++++
T Consensus 39 ~~~~l~v~~~~--~~~P~~~~~~~g~~~G~~~dl~~~i~~~lg~~~e~~~~---------~~~~~~~~l~~G~~D~~~~~ 107 (266)
T PRK11260 39 ERGTLLVGLEG--TYPPFSFQGEDGKLTGFEVEFAEALAKHLGVKASLKPT---------KWDGMLASLDSKRIDVVINQ 107 (266)
T ss_pred cCCeEEEEeCC--CcCCceEECCCCCEEEehHHHHHHHHHHHCCeEEEEeC---------CHHHHHHHHhcCCCCEEEec
Confidence 45789999864 68898876677899999999999999999998666553 39999999999999999988
Q ss_pred eeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCc
Q 003093 454 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 533 (848)
Q Consensus 454 ~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 533 (848)
++.+++|.+.+.||.||+..+..+++++.+
T Consensus 108 ~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~-------------------------------------------------- 137 (266)
T PRK11260 108 VTISDERKKKYDFSTPYTVSGIQALVKKGN-------------------------------------------------- 137 (266)
T ss_pred cccCHHHHhccccCCceeecceEEEEEcCC--------------------------------------------------
Confidence 999999999999999999999999988654
Q ss_pred chhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchH
Q 003093 534 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFA 613 (848)
Q Consensus 534 ~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~ 613 (848)
...+++++||. +++||+..|+..
T Consensus 138 -------------------------------------------------------~~~~~~~~dL~--g~~Igv~~G~~~ 160 (266)
T PRK11260 138 -------------------------------------------------------EGTIKTAADLK--GKKVGVGLGTNY 160 (266)
T ss_pred -------------------------------------------------------cCCCCCHHHcC--CCEEEEecCCcH
Confidence 13678899996 889999999988
Q ss_pred HHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCc-EEEeCCccccCCceeeecCCCC-
Q 003093 614 RNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCE-FSIVGQVFTKNGWGFAFPRDSP- 691 (848)
Q Consensus 614 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~~~~~~k~sp- 691 (848)
..++.+ +.+..++..+++..+.+++|.+ |++|+++.+.....+++++... +.+....+...++++++++++|
T Consensus 161 ~~~l~~--~~~~~~i~~~~~~~~~l~~L~~----GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~ 234 (266)
T PRK11260 161 EQWLRQ--NVQGVDVRTYDDDPTKYQDLRV----GRIDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNPD 234 (266)
T ss_pred HHHHHH--hCCCCceEecCCHHHHHHHHHc----CCCCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCHH
Confidence 888854 4455677888999999999999 9999999999888888877554 5555666777889999999988
Q ss_pred chHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 692 LAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 692 l~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
++..||++|.++.++|.++++.+||+.
T Consensus 235 l~~~ln~~l~~~~~~g~~~~i~~k~~~ 261 (266)
T PRK11260 235 LLKAVNQAIAEMQKDGTLKALSEKWFG 261 (266)
T ss_pred HHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 999999999999999999999999987
No 83
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=99.85 E-value=3.7e-20 Score=192.18 Aligned_cols=253 Identities=16% Similarity=0.147 Sum_probs=184.0
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEeccCChHHHHHHHHHH-HHHcCcEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS--LQFPYFVRTTQSDQYQMAAIAEI-VDHYGWREVIAI 78 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~--~~~p~f~r~~p~d~~q~~ai~~~-~~~~~w~~vaii 78 (848)
+++|.+|+|.++|..-++|.++.++++-++..+ ...+ +..|++|-+.....+|...++++ ++++|-+++.+|
T Consensus 66 ~d~V~~ifGc~TSasRKaVlPvvE~~~~LL~Yp-----~~YEG~E~S~nviYtGa~PNQ~~~pl~~~~~~~~G~~r~~lv 140 (363)
T PF13433_consen 66 EDGVRAIFGCYTSASRKAVLPVVERHNALLFYP-----TQYEGFECSPNVIYTGAAPNQQLLPLIDYLLENFGAKRFYLV 140 (363)
T ss_dssp HS---EEEE--SHHHHHHHHHHHHHCT-EEEE------S--------TTEEE-S--GGGTHHHHHHHHHHHS--SEEEEE
T ss_pred hCCccEEEecchhhhHHHHHHHHHhcCceEEec-----cccccccCCCceEEcCCCchhhHHHHHHHHHhccCCceEEEe
Confidence 579999999999999999999999999999963 3333 45689999999999999999998 588899999999
Q ss_pred EEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 79 YVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 79 ~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
.+|+.|++.....+++.+++.|++|+.+..+|.+. +|+..++.+|++.+||+|+-...++....|+++++++|+....
T Consensus 141 GSdYv~pre~Nri~r~~l~~~GgevvgE~Y~plg~--td~~~ii~~I~~~~Pd~V~stlvG~s~~aF~r~~~~aG~~~~~ 218 (363)
T PF13433_consen 141 GSDYVYPRESNRIIRDLLEARGGEVVGERYLPLGA--TDFDPIIAEIKAAKPDFVFSTLVGDSNVAFYRAYAAAGLDPER 218 (363)
T ss_dssp EESSHHHHHHHHHHHHHHHHTT-EEEEEEEE-S-H--HHHHHHHHHHHHHT-SEEEEE--TTCHHHHHHHHHHHH-SSS-
T ss_pred cCCccchHHHHHHHHHHHHHcCCEEEEEEEecCCc--hhHHHHHHHHHhhCCCEEEEeCcCCcHHHHHHHHHHcCCCccc
Confidence 99999999999999999999999999999999755 9999999999999999999999999999999999999997543
Q ss_pred eEEEecCccc-cccCCCCCCCcccccccceeEEEEEecC--CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHH
Q 003093 159 YVWIATSWLS-TALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVW 235 (848)
Q Consensus 159 ~~wi~~~~~~-~~~~~~~~~~~~~~~~~~G~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~ 235 (848)
.. |.+.... .... ....+...|.++..+|.. ++|.+++|+++|+++|++ +..++.....+|.+|+
T Consensus 219 ~P-i~S~~~~E~E~~------~~g~~~~~Gh~~~~~YFqsidtp~N~~Fv~~~~~~~g~-----~~v~s~~~eaaY~~v~ 286 (363)
T PF13433_consen 219 IP-IASLSTSEAELA------AMGAEAAAGHYTSAPYFQSIDTPENQAFVARFRARYGD-----DRVTSDPMEAAYFQVH 286 (363)
T ss_dssp ---EEESS--HHHHT------TS-HHHHTT-EEEES--TT-SSHHHHHHHHHHHTTS-T-----T----HHHHHHHHHHH
T ss_pred Ce-EEEEecCHHHHh------hcChhhcCCcEEeehhhhhCCcHHHHHHHHHHHHHhCC-----CCCCCcHHHHHHHHHH
Confidence 33 3333222 2221 122357899999988755 579999999999999973 2345667778999999
Q ss_pred HHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccC
Q 003093 236 LLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSH 301 (848)
Q Consensus 236 ~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~ 301 (848)
++|+|++++ ++. +.++++++|.+.+|+++.|.+++|+.
T Consensus 287 l~a~Av~~a---------------------------gs~-d~~~vr~al~g~~~~aP~G~v~id~~ 324 (363)
T PF13433_consen 287 LWAQAVEKA---------------------------GSD-DPEAVREALAGQSFDAPQGRVRIDPD 324 (363)
T ss_dssp HHHHHHHHH---------------------------TS---HHHHHHHHTT--EEETTEEEEE-TT
T ss_pred HHHHHHHHh---------------------------CCC-CHHHHHHHhcCCeecCCCcceEEcCC
Confidence 999999995 333 38999999999999999999999983
No 84
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=99.85 E-value=5.2e-21 Score=195.44 Aligned_cols=221 Identities=27% Similarity=0.416 Sum_probs=185.0
Q ss_pred EEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeee
Q 003093 378 LRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAII 457 (848)
Q Consensus 378 lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t 457 (848)
||||+.. +++||.+.+.++...|+++||++++++++|++++++..+ |.+++.+|.+|++|+++++++.+
T Consensus 1 l~V~~~~--~~~P~~~~~~~~~~~G~~~dl~~~i~~~~g~~~~~~~~~---------~~~~~~~l~~g~~D~~~~~~~~~ 69 (225)
T PF00497_consen 1 LRVGVDE--DYPPFSYIDEDGEPSGIDVDLLRAIAKRLGIKIEFVPMP---------WSRLLEMLENGKADIIIGGLSIT 69 (225)
T ss_dssp EEEEEES--EBTTTBEEETTSEEESHHHHHHHHHHHHHTCEEEEEEEE---------GGGHHHHHHTTSSSEEESSEB-B
T ss_pred CEEEEcC--CCCCeEEECCCCCEEEEhHHHHHHHHhhcccccceeecc---------ccccccccccccccccccccccc
Confidence 6899854 788998867789999999999999999999997777654 99999999999999999889999
Q ss_pred cCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcchhh
Q 003093 458 TNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIF 537 (848)
Q Consensus 458 ~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~ 537 (848)
++|.+.++||.||+....++++++.+..
T Consensus 70 ~~r~~~~~~s~p~~~~~~~~~~~~~~~~---------------------------------------------------- 97 (225)
T PF00497_consen 70 PERAKKFDFSDPYYSSPYVLVVRKGDAP---------------------------------------------------- 97 (225)
T ss_dssp HHHHTTEEEESESEEEEEEEEEETTSTC----------------------------------------------------
T ss_pred ccccccccccccccchhheeeecccccc----------------------------------------------------
Confidence 9999999999999999999999975310
Q ss_pred hhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHHHHH
Q 003093 538 WFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNYL 617 (848)
Q Consensus 538 ~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~~~l 617 (848)
....+++++||. +++||+..|+...+++
T Consensus 98 --------------------------------------------------~~~~~~~~~dl~--~~~i~~~~g~~~~~~l 125 (225)
T PF00497_consen 98 --------------------------------------------------PIKTIKSLDDLK--GKRIGVVRGSSYADYL 125 (225)
T ss_dssp --------------------------------------------------STSSHSSGGGGT--TSEEEEETTSHHHHHH
T ss_pred --------------------------------------------------ccccccchhhhc--CcccccccchhHHHHh
Confidence 014667788996 7889999999888888
Q ss_pred HhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCc--EEEeCCccccCCceeeecCCCC-chH
Q 003093 618 VDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCE--FSIVGQVFTKNGWGFAFPRDSP-LAV 694 (848)
Q Consensus 618 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~--l~~~~~~~~~~~~~~~~~k~sp-l~~ 694 (848)
.+.... ..+++.+.+.++++++|.+ |++++++.+...+.+++++... ...........++++++.++.+ +.+
T Consensus 126 ~~~~~~-~~~~~~~~~~~~~~~~l~~----g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 200 (225)
T PF00497_consen 126 KQQYPS-NINIVEVDSPEEALEALLS----GRIDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKNPELLE 200 (225)
T ss_dssp HHHTHH-TSEEEEESSHHHHHHHHHT----TSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTTHHHHH
T ss_pred hhhccc-hhhhcccccHHHHHHHHhc----CCeeeeeccchhhhhhhhhcccccccccccccccceeEEeecccccHHHH
Confidence 553211 4567788999999999999 9999999999999999988652 3332455566677777877655 999
Q ss_pred HHHHHHHhhhccCchHHHHHhhcc
Q 003093 695 DISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 695 ~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
.||++|.+|.++|.+++|.+||+.
T Consensus 201 ~~n~~i~~l~~~G~~~~i~~ky~g 224 (225)
T PF00497_consen 201 IFNKAIRELKQSGEIQKILKKYLG 224 (225)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHS
T ss_pred HHHHHHHHHHhCcHHHHHHHHHcC
Confidence 999999999999999999999986
No 85
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.85 E-value=4.2e-20 Score=192.89 Aligned_cols=222 Identities=18% Similarity=0.278 Sum_probs=180.2
Q ss_pred CCceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeec
Q 003093 374 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 453 (848)
Q Consensus 374 ~g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~ 453 (848)
..++|+|++.. +|+||.+.+++|++.|+++||++++++++|.+++++.. +|..++.++..|++|++++.
T Consensus 24 ~~~~l~v~~~~--~~pPf~~~~~~g~~~G~~vdl~~~ia~~lg~~~~~~~~---------~~~~~~~~l~~g~~Di~~~~ 92 (260)
T PRK15010 24 LPETVRIGTDT--TYAPFSSKDAKGDFVGFDIDLGNEMCKRMQVKCTWVAS---------DFDALIPSLKAKKIDAIISS 92 (260)
T ss_pred cCCeEEEEecC--CcCCceeECCCCCEEeeeHHHHHHHHHHhCCceEEEeC---------CHHHHHHHHHCCCCCEEEec
Confidence 45789999863 68999886567899999999999999999999766654 49999999999999999988
Q ss_pred eeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCc
Q 003093 454 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 533 (848)
Q Consensus 454 ~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 533 (848)
+..+++|.+.++||.||+..+.++++++..
T Consensus 93 ~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~-------------------------------------------------- 122 (260)
T PRK15010 93 LSITDKRQQEIAFSDKLYAADSRLIAAKGS-------------------------------------------------- 122 (260)
T ss_pred CcCCHHHHhhcccccceEeccEEEEEECCC--------------------------------------------------
Confidence 999999999999999999999999998765
Q ss_pred chhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchH
Q 003093 534 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFA 613 (848)
Q Consensus 534 ~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~ 613 (848)
+...+++||. |++||+..|+..
T Consensus 123 --------------------------------------------------------~~~~~~~dl~--g~~Igv~~gs~~ 144 (260)
T PRK15010 123 --------------------------------------------------------PIQPTLDSLK--GKHVGVLQGSTQ 144 (260)
T ss_pred --------------------------------------------------------CCCCChhHcC--CCEEEEecCchH
Confidence 2223688996 889999999987
Q ss_pred HHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHH-HHhcC--CcEEEeCCcc-----ccCCceee
Q 003093 614 RNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAEL-FLSTR--CEFSIVGQVF-----TKNGWGFA 685 (848)
Q Consensus 614 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~-~~~~~--~~l~~~~~~~-----~~~~~~~~ 685 (848)
..++.........+++.+.+.++++++|.+ |++|+++.+.....+ +.++. .++...+..+ ...+++++
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~----griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a 220 (260)
T PRK15010 145 EAYANETWRSKGVDVVAYANQDLVYSDLAA----GRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVG 220 (260)
T ss_pred HHHHHHhcccCCceEEecCCHHHHHHHHHc----CCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEE
Confidence 777754332223456678888999999999 999999999877654 34432 2455554322 22346789
Q ss_pred ecCCCC-chHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 686 FPRDSP-LAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 686 ~~k~sp-l~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
++++.+ ++..+|++|.++.++|.+++|.+||+.
T Consensus 221 ~~~~~~~L~~~ln~~l~~l~~~G~~~~i~~ky~~ 254 (260)
T PRK15010 221 LRKDDAELTAAFNKALGELRQDGTYDKMAKKYFD 254 (260)
T ss_pred EeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 999877 999999999999999999999999987
No 86
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.85 E-value=4.7e-20 Score=190.82 Aligned_cols=217 Identities=22% Similarity=0.380 Sum_probs=182.1
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
..+||||+.. +++||.+.+.++++.|+++|+++++++++|.+++|+.. +|.+++..+..|++|++++++
T Consensus 20 ~~~l~v~~~~--~~~P~~~~~~~g~~~G~~~dl~~~i~~~lg~~~~~~~~---------~~~~~~~~l~~g~~D~~~~~~ 88 (243)
T PRK15007 20 AETIRFATEA--SYPPFESIDANNQIVGFDVDLAQALCKEIDATCTFSNQ---------AFDSLIPSLKFRRVEAVMAGM 88 (243)
T ss_pred CCcEEEEeCC--CCCCceeeCCCCCEEeeeHHHHHHHHHHhCCcEEEEeC---------CHHHHhHHHhCCCcCEEEEcC
Confidence 4689999863 78899876667899999999999999999999776543 499999999999999998878
Q ss_pred eeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcc
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVV 534 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 534 (848)
+.+++|.+.++||.||+..+.+++.+..
T Consensus 89 ~~~~~r~~~~~fs~p~~~~~~~~v~~~~---------------------------------------------------- 116 (243)
T PRK15007 89 DITPEREKQVLFTTPYYDNSALFVGQQG---------------------------------------------------- 116 (243)
T ss_pred ccCHHHhcccceecCccccceEEEEeCC----------------------------------------------------
Confidence 9999999999999999998877776532
Q ss_pred hhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHH
Q 003093 535 TIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFAR 614 (848)
Q Consensus 535 ~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~ 614 (848)
.+++++||. +++||+..|+...
T Consensus 117 --------------------------------------------------------~~~~~~dL~--g~~Igv~~g~~~~ 138 (243)
T PRK15007 117 --------------------------------------------------------KYTSVDQLK--GKKVGVQNGTTHQ 138 (243)
T ss_pred --------------------------------------------------------CCCCHHHhC--CCeEEEecCcHHH
Confidence 357789997 8899999999888
Q ss_pred HHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEEEeCCc-----cccCCceeeecCC
Q 003093 615 NYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQV-----FTKNGWGFAFPRD 689 (848)
Q Consensus 615 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~~~~~~k~ 689 (848)
+++.+ ..+..+++.+++.++.+++|.+ |++|+++.+...+.+++++...+..++.. ....+++++++++
T Consensus 139 ~~l~~--~~~~~~~~~~~~~~~~~~~L~~----grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 (243)
T PRK15007 139 KFIMD--KHPEITTVPYDSYQNAKLDLQN----GRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQG 212 (243)
T ss_pred HHHHH--hCCCCeEEEcCCHHHHHHHHHc----CCCCEEEeCHHHHHHHHhcCCCceeecCcccccccCCcceEEEEeCC
Confidence 88854 2444567778899999999999 99999999999888888776666555432 2233578999987
Q ss_pred CC-chHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 690 SP-LAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 690 sp-l~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
.+ ++..||++|.++.++|.++++.+||+.
T Consensus 213 ~~~l~~~ln~~l~~l~~~g~~~~i~~~w~~ 242 (243)
T PRK15007 213 NTELQQKLNTALEKVKKDGTYETIYNKWFQ 242 (243)
T ss_pred CHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 76 999999999999999999999999985
No 87
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.84 E-value=6.3e-20 Score=190.81 Aligned_cols=218 Identities=23% Similarity=0.370 Sum_probs=184.8
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
.+|+|++.. +|+||.+.+.++++.|+++|+++.+++.+|.+++++.. +|.+++.++.+|++|+++++++
T Consensus 24 ~~l~v~~~~--~~~P~~~~~~~g~~~G~~~dl~~~i~~~lg~~~~~~~~---------~~~~~~~~l~~G~~D~~~~~~~ 92 (250)
T TIGR01096 24 GSVRIGTET--GYPPFESKDANGKLVGFDVDLAKALCKRMKAKCKFVEQ---------NFDGLIPSLKAKKVDAIMATMS 92 (250)
T ss_pred CeEEEEECC--CCCCceEECCCCCEEeehHHHHHHHHHHhCCeEEEEeC---------CHHHHHHHHhCCCcCEEEecCc
Confidence 689999853 78899886667899999999999999999988666543 4999999999999999988888
Q ss_pred eecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcch
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVT 535 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 535 (848)
.+++|.+.+.||.|++..+..++++...
T Consensus 93 ~~~~r~~~~~~s~p~~~~~~~~~~~~~~---------------------------------------------------- 120 (250)
T TIGR01096 93 ITPKRQKQIDFSDPYYATGQGFVVKKGS---------------------------------------------------- 120 (250)
T ss_pred cCHHHhhccccccchhcCCeEEEEECCC----------------------------------------------------
Confidence 9999999999999999999999998765
Q ss_pred hhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHHH
Q 003093 536 IFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARN 615 (848)
Q Consensus 536 ~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~~ 615 (848)
+.+.+++||. ++++|+..|+....
T Consensus 121 ------------------------------------------------------~~~~~~~dl~--g~~i~~~~g~~~~~ 144 (250)
T TIGR01096 121 ------------------------------------------------------DLAKTLEDLD--GKTVGVQSGTTHEQ 144 (250)
T ss_pred ------------------------------------------------------CcCCChHHcC--CCEEEEecCchHHH
Confidence 3356788997 88999999998888
Q ss_pred HHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCC---cEEEeCCcccc-----CCceeeec
Q 003093 616 YLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC---EFSIVGQVFTK-----NGWGFAFP 687 (848)
Q Consensus 616 ~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~---~l~~~~~~~~~-----~~~~~~~~ 687 (848)
++.+.... ..+++.+.+.++++++|.+ |++|+++.+...+.+++++.. ++.+++..+.. ..++++++
T Consensus 145 ~l~~~~~~-~~~~~~~~s~~~~~~~L~~----g~vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 219 (250)
T TIGR01096 145 YLKDYFKP-GVDIVEYDSYDNANMDLKA----GRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLR 219 (250)
T ss_pred HHHHhccC-CcEEEEcCCHHHHHHHHHc----CCCCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEEe
Confidence 88553321 3567778999999999999 999999999999998887644 37777654332 24789999
Q ss_pred CCCC-chHHHHHHHHhhhccCchHHHHHhhc
Q 003093 688 RDSP-LAVDISTAILKLSENGDLQRIHDKWL 717 (848)
Q Consensus 688 k~sp-l~~~in~~i~~l~e~G~~~~~~~kw~ 717 (848)
++++ ++..||++|.+|.++|.+++|.+||+
T Consensus 220 ~~~~~l~~~ln~~l~~l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 220 KGDTELKAAFNKALAAIRADGTYQKISKKWF 250 (250)
T ss_pred CCCHHHHHHHHHHHHHHHHCCcHHHHHHhhC
Confidence 9887 99999999999999999999999995
No 88
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.84 E-value=1.5e-19 Score=187.70 Aligned_cols=217 Identities=17% Similarity=0.301 Sum_probs=179.7
Q ss_pred CCceEEEEecCCCCccceEEe-CCCcceeeeeHHHHHHHHHhC-CCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEe
Q 003093 374 NGRHLRIGVPNRVSFREFVSV-KGSEMTSGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAV 451 (848)
Q Consensus 374 ~g~~lrv~v~~~~~~~p~~~~-~~~~~~~G~~~dll~~i~~~l-~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~ 451 (848)
..++|+||+.. +++||.+. +.++++.||++|+++++++++ |..+++++.++ +|...+.+|.+|++|+++
T Consensus 36 ~~g~l~vg~~~--~~pP~~~~~~~~g~~~G~~vdl~~~ia~~llg~~~~~~~~~~-------~~~~~~~~l~~g~~D~~~ 106 (259)
T PRK11917 36 SKGQLIVGVKN--DVPHYALLDQATGEIKGFEIDVAKLLAKSILGDDKKIKLVAV-------NAKTRGPLLDNGSVDAVI 106 (259)
T ss_pred hCCEEEEEECC--CCCCceeeeCCCCceeEeeHHHHHHHHHHhcCCCccEEEEEc-------ChhhHHHHHHCCCccEEE
Confidence 45789999985 78999874 457899999999999999994 86656666552 377778999999999999
Q ss_pred eceeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCC
Q 003093 452 GDIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKR 531 (848)
Q Consensus 452 ~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~ 531 (848)
+++++|++|.+.++||.||+.++.++++++..
T Consensus 107 ~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~------------------------------------------------ 138 (259)
T PRK11917 107 ATFTITPERKRIYNFSEPYYQDAIGLLVLKEK------------------------------------------------ 138 (259)
T ss_pred ecccCChhhhheeeeccCceeeceEEEEECCC------------------------------------------------
Confidence 99999999999999999999999999999764
Q ss_pred CcchhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCc
Q 003093 532 QVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNS 611 (848)
Q Consensus 532 ~~~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s 611 (848)
++++++||. |++||+..|+
T Consensus 139 -----------------------------------------------------------~~~s~~dL~--g~~V~v~~gs 157 (259)
T PRK11917 139 -----------------------------------------------------------NYKSLADMK--GANIGVAQAA 157 (259)
T ss_pred -----------------------------------------------------------CCCCHHHhC--CCeEEEecCC
Confidence 578899998 8999999999
Q ss_pred hHHHHHHhhhC--CCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEEEeCCccccCCceeeecCC
Q 003093 612 FARNYLVDELN--IDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQVFTKNGWGFAFPRD 689 (848)
Q Consensus 612 ~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k~ 689 (848)
.....+.+... ....+++.+++..+.+++|.. |++|+++.+...+.++..+ +..++++.+...+++++++|+
T Consensus 158 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~----GrvDa~~~d~~~~~~~~~~--~~~~~~~~~~~~~~~~a~~k~ 231 (259)
T PRK11917 158 TTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDA----KRVDAFSVDKSILLGYVDD--KSEILPDSFEPQSYGIVTKKD 231 (259)
T ss_pred cHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHc----CCCcEEEecHHHHHHhhhc--CCeecCCcCCCCceEEEEeCC
Confidence 77766543221 122356678899999999999 9999999998877666554 345666777778899999999
Q ss_pred CC-chHHHHHHHHhhhccCchHHHHHhh
Q 003093 690 SP-LAVDISTAILKLSENGDLQRIHDKW 716 (848)
Q Consensus 690 sp-l~~~in~~i~~l~e~G~~~~~~~kw 716 (848)
++ +...+|+.|.++.. .+++|.+||
T Consensus 232 ~~~l~~~ln~~l~~~~~--~~~~i~~kw 257 (259)
T PRK11917 232 DPAFAKYVDDFVKEHKN--EIDALAKKW 257 (259)
T ss_pred CHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 88 99999999999864 799999999
No 89
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.83 E-value=2.9e-19 Score=186.44 Aligned_cols=222 Identities=17% Similarity=0.267 Sum_probs=179.0
Q ss_pred CCceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeec
Q 003093 374 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 453 (848)
Q Consensus 374 ~g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~ 453 (848)
...+|+|++.. .|+||.+.+.++++.|+++||++++++++|.+++++..+ |.+++.++.+|++|+++++
T Consensus 24 ~~~~l~v~~~~--~~~P~~~~~~~g~~~G~~vdi~~~ia~~lg~~i~~~~~p---------w~~~~~~l~~g~~D~~~~~ 92 (259)
T PRK15437 24 IPQNIRIGTDP--TYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENP---------LDALIPSLKAKKIDAIMSS 92 (259)
T ss_pred cCCeEEEEeCC--CCCCcceeCCCCCEEeeeHHHHHHHHHHcCCceEEEeCC---------HHHHHHHHHCCCCCEEEec
Confidence 45789999863 588988766678999999999999999999997776654 9999999999999999998
Q ss_pred eeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCc
Q 003093 454 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 533 (848)
Q Consensus 454 ~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 533 (848)
++.|++|.+.++||.||+..+.++++++..
T Consensus 93 ~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~-------------------------------------------------- 122 (259)
T PRK15437 93 LSITEKRQQEIAFTDKLYAADSRLVVAKNS-------------------------------------------------- 122 (259)
T ss_pred CCCCHHHhhhccccchhhcCceEEEEECCC--------------------------------------------------
Confidence 999999999999999999999999998765
Q ss_pred chhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchH
Q 003093 534 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFA 613 (848)
Q Consensus 534 ~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~ 613 (848)
+...+++||. +++||+..|+..
T Consensus 123 --------------------------------------------------------~~~~~~~dl~--g~~Igv~~g~~~ 144 (259)
T PRK15437 123 --------------------------------------------------------DIQPTVESLK--GKRVGVLQGTTQ 144 (259)
T ss_pred --------------------------------------------------------CCCCChHHhC--CCEEEEecCcHH
Confidence 2234688986 889999999987
Q ss_pred HHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHH-HHhcC--CcEEEeCC-----ccccCCceee
Q 003093 614 RNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAEL-FLSTR--CEFSIVGQ-----VFTKNGWGFA 685 (848)
Q Consensus 614 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~-~~~~~--~~l~~~~~-----~~~~~~~~~~ 685 (848)
..++.........+++.+.+.++.+++|.. |++|+++.+.....+ ++++. .++.+.+. .+...+++++
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~----grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia 220 (259)
T PRK15437 145 ETFGNEHWAPKGIEIVSYQGQDNIYSDLTA----GRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMG 220 (259)
T ss_pred HHHHHhhccccCceEEecCCHHHHHHHHHc----CCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEE
Confidence 777754222223466788899999999999 999999988876653 33332 23444322 2223346788
Q ss_pred ecCCCC-chHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 686 FPRDSP-LAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 686 ~~k~sp-l~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
++++.+ +++.+|.+|.++..+|.+++|.+||+.
T Consensus 221 ~~~~~~~l~~~~n~~l~~~~~~G~~~~i~~k~~~ 254 (259)
T PRK15437 221 LRKEDNELREALNKAFAEMRADGTYEKLAKKYFD 254 (259)
T ss_pred EeCCCHHHHHHHHHHHHHHHHCCcHHHHHHHhcC
Confidence 887766 999999999999999999999999987
No 90
>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=99.82 E-value=2.3e-19 Score=188.74 Aligned_cols=222 Identities=18% Similarity=0.203 Sum_probs=181.4
Q ss_pred CCceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCC-cceEEeeCCCCCCCCChhHHHHHHhcCeeeEEee
Q 003093 374 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYA-VPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVG 452 (848)
Q Consensus 374 ~g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~-~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~ 452 (848)
.-+.|+|++. +++||.+.+.++.+.|+++||++++++++|.. +++... +|++++..+.+|++|++++
T Consensus 31 ~~~~l~v~~~---~~pP~~~~~~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~---------~w~~~~~~l~~G~~Di~~~ 98 (275)
T TIGR02995 31 EQGFARIAIA---NEPPFTYVGADGKVSGAAPDVARAIFKRLGIADVNASIT---------EYGALIPGLQAGRFDAIAA 98 (275)
T ss_pred hCCcEEEEcc---CCCCceeECCCCceecchHHHHHHHHHHhCCCceeeccC---------CHHHHHHHHHCCCcCEEee
Confidence 3467999986 57888875667889999999999999999986 455444 4999999999999999988
Q ss_pred ceeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCC
Q 003093 453 DIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQ 532 (848)
Q Consensus 453 ~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 532 (848)
+++++++|.+.++||.||+..+.++++++...
T Consensus 99 ~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~------------------------------------------------ 130 (275)
T TIGR02995 99 GLFIKPERCKQVAFTQPILCDAEALLVKKGNP------------------------------------------------ 130 (275)
T ss_pred cccCCHHHHhccccccceeecceeEEEECCCC------------------------------------------------
Confidence 89999999999999999999999999987651
Q ss_pred cchhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhc-CCCCeeEEeCc
Q 003093 533 VVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRS-SNYPIGYQVNS 611 (848)
Q Consensus 533 ~~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~-s~~~i~~~~~s 611 (848)
..+++++||.. .+.+||+..|+
T Consensus 131 ---------------------------------------------------------~~i~~~~dl~~~~g~~Igv~~g~ 153 (275)
T TIGR02995 131 ---------------------------------------------------------KGLKSYKDIAKNPDAKIAAPGGG 153 (275)
T ss_pred ---------------------------------------------------------CCCCCHHHhccCCCceEEEeCCc
Confidence 34778888864 26789999999
Q ss_pred hHHHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCC--cEEEeCCcc-c--cCCceeee
Q 003093 612 FARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC--EFSIVGQVF-T--KNGWGFAF 686 (848)
Q Consensus 612 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~--~l~~~~~~~-~--~~~~~~~~ 686 (848)
...+++.+ .+.+..+++.+++.++.+++|.+ |++|+++.+...+.+++++.. ++..+.... . ...+++++
T Consensus 154 ~~~~~l~~-~~~~~~~i~~~~~~~~~i~~L~~----grvDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (275)
T TIGR02995 154 TEEKLARE-AGVKREQIIVVPDGQSGLKMVQD----GRADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAAF 228 (275)
T ss_pred HHHHHHHH-cCCChhhEEEeCCHHHHHHHHHc----CCCCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEEE
Confidence 88888843 34444567788999999999999 999999999999988887532 444443211 1 12337888
Q ss_pred cCCCC-chHHHHHHHHhhhccCchHHHHHhhc
Q 003093 687 PRDSP-LAVDISTAILKLSENGDLQRIHDKWL 717 (848)
Q Consensus 687 ~k~sp-l~~~in~~i~~l~e~G~~~~~~~kw~ 717 (848)
+++.+ +++.||++|.++.++|.+++|.+||-
T Consensus 229 ~~~~~~l~~~~n~~l~~~~~sG~~~~i~~ky~ 260 (275)
T TIGR02995 229 RPEDKELRDAFNVELAKLKESGEFAKIIAPYG 260 (275)
T ss_pred CCCCHHHHHHHHHHHHHHHhChHHHHHHHHhC
Confidence 88776 99999999999999999999999993
No 91
>cd06341 PBP1_ABC_ligand_binding_like_7 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.82 E-value=5.1e-19 Score=193.06 Aligned_cols=248 Identities=11% Similarity=0.078 Sum_probs=194.4
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
++|.+|||+.+|..+.++ +++++.++|+|+.+++++.++. .|++|++.+++..++.++++++...+.+++++++.++
T Consensus 66 ~~V~~iig~~~s~~~~~~-~~~~~~~ip~v~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~i~~~~ 142 (341)
T cd06341 66 DKVVAVVGGSSGAGGSAL-PYLAGAGIPVIGGAGTSAWELT--SPNSFPFSGGTPASLTTWGDFAKDQGGTRAVALVTAL 142 (341)
T ss_pred cCceEEEecccccchhHH-HHHhhcCCceecCCCCCchhhc--CCCeEEecCCCcchhHHHHHHHHHcCCcEEEEEEeCC
Confidence 489999999999888776 8999999999998877766654 5788999999999999999999888899999998776
Q ss_pred C-CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEE
Q 003093 83 D-HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 161 (848)
Q Consensus 83 ~-~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~w 161 (848)
. ||+.....+.+.+++.|++++....++.+ ..|+..++.++++.+||+|++......+..++++++++|+..+..
T Consensus 143 ~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~~~~i~~~~pdaV~~~~~~~~a~~~~~~~~~~G~~~~~~-- 218 (341)
T cd06341 143 SAAVSAAAALLARSLAAAGVSVAGIVVITAT--APDPTPQAQQAAAAGADAIITVLDAAVCASVLKAVRAAGLTPKVV-- 218 (341)
T ss_pred cHHHHHHHHHHHHHHHHcCCccccccccCCC--CCCHHHHHHHHHhcCCCEEEEecChHHHHHHHHHHHHcCCCCCEE--
Confidence 5 99999999999999999999877666654 378999999999999999999988889999999999999965422
Q ss_pred EecCccccccCCCCCCCcccccccceeEEEEEecC---CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHHHH
Q 003093 162 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTP---DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 238 (848)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 238 (848)
+........ .. +...++.+|++....+.| +.|..+.|.+.+++.... ....++.++..+||++++++
T Consensus 219 ~~~~~~~~~--~~----~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~----~~~~~~~~~~~~yda~~~~~ 288 (341)
T cd06341 219 LSGTCYDPA--LL----AAPGPALAGVYIAVFYRPFESGTPAVALYLAAMARYAPQ----LDPPEQGFALIGYIAADLFL 288 (341)
T ss_pred EecCCCCHH--HH----HhcCcccCceEEEeeeccccCCCHHHHHHHHHHHHhCCC----CCCCcchHHHHHHHHHHHHH
Confidence 221121111 11 334567899988877665 457888888766543321 11357889999999999999
Q ss_pred HHHHHHHhcCCCccccCCCccccccCccccCcccccCChHH-HHHHHHhcccccccc
Q 003093 239 RAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNL-LRDSILQANMTGTAG 294 (848)
Q Consensus 239 ~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~-l~~~l~~~~f~G~tG 294 (848)
+|++++. ...+++. +.++|++++.....|
T Consensus 289 ~a~~~ag---------------------------~~~~~~~~v~~al~~~~~~~~~g 318 (341)
T cd06341 289 RGLSGAG---------------------------GCPTRASQFLRALRAVTDYDAGG 318 (341)
T ss_pred HHHHhcC---------------------------CCCChHHHHHHHhhcCCCCCCCC
Confidence 9999942 1113676 999999998544434
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=99.82 E-value=2.5e-19 Score=191.54 Aligned_cols=218 Identities=26% Similarity=0.385 Sum_probs=181.8
Q ss_pred CeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 4 QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 4 ~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
+|++||||.++..+.+++.+++..+||+|++.+..+.+.+ ..+|++||+.|++..++..+++++++++|+++++++.++
T Consensus 67 ~v~~iig~~~~~~~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~v~iv~~~~ 146 (299)
T cd04509 67 GVDALVGPVSSGVALAVAPVAEALKIPLISPGATAPGLTDKKGYPYLFRTGPSDEQQAEALADYIKEYNWKKVAILYDDD 146 (299)
T ss_pred CceEEEcCCCcHHHHHHHHHHhhCCceEEeccCCCcccccccCCCCEEEecCCcHHHHHHHHHHHHHcCCcEEEEEecCc
Confidence 8999999999999999999999999999999888777665 568999999999999999999999999999999999999
Q ss_pred CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003093 83 DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 162 (848)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi 162 (848)
.++....+.+.+.+++.|++++....++.+. .++...++++++.++|+|++++....+..++++++++|+. .++.|+
T Consensus 147 ~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~~--~~~~~~~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~g~~-~~~~~i 223 (299)
T cd04509 147 SYGRGLLEAFKAAFKKKGGTVVGEEYYPLGT--TDFTSLLQKLKAAKPDVIVLCGSGEDAATILKQAAEAGLT-GGYPIL 223 (299)
T ss_pred hHHHHHHHHHHHHHHHcCCEEEEEecCCCCC--ccHHHHHHHHHhcCCCEEEEcccchHHHHHHHHHHHcCCC-CCCcEE
Confidence 9999999999999999999998776666543 6788999999988899999999889999999999999998 789999
Q ss_pred ecCccccccCCCCCCCcccccccceeEEEEEecCCc--hhHHHHH---HHHHhhccCCCCCCCCCCCcchhhhhhHHHH
Q 003093 163 ATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDS--VLKRKFI---SRWRNLTDAKTPNGYIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~--~~~~~f~---~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~ 236 (848)
..+.+...... ....+.++|+++..++.+.. +..+.|. ..+++.++ ..++.+++++|||+++
T Consensus 224 ~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~yda~~~ 290 (299)
T cd04509 224 GITLGLSDVLL-----EAGGEAAEGVLTGTPYFPGDPPPESFFFVRAAAREKKKYE-------DQPDYFAALAYDAVLL 290 (299)
T ss_pred ecccccCHHHH-----HHhHHhhcCcEEeeccCCCCCChHHHHHHhHHHHHHHHhC-------CCCChhhhhhcceeee
Confidence 98876543221 13346788998888765543 3333343 34444443 4678899999999998
No 93
>cd06333 PBP1_ABC-type_HAAT_like Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. This subgroup includes the type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. Members of this subgroup are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=99.81 E-value=1.1e-18 Score=187.84 Aligned_cols=219 Identities=19% Similarity=0.238 Sum_probs=176.8
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
++|++|||+.+|..+.++.+++.+.++|+|+++++++.++ ...+|+||+.+++..++..+++++...||++|++++.++
T Consensus 65 ~~v~~vig~~~s~~~~~~~~~~~~~~vP~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~vail~~~~ 143 (312)
T cd06333 65 DKVDAIIGPSTTPATMAVAPVAEEAKTPMISLAPAAAIVE-PKRKWVFKTPQNDRLMAEAILADMKKRGVKTVAFIGFSD 143 (312)
T ss_pred CCeEEEECCCCCHHHHHHHHHHHhcCCCEEEccCCccccC-CCCCcEEEcCCCcHHHHHHHHHHHHHcCCCEEEEEecCc
Confidence 4899999999998888899999999999999877665443 456899999999999999999999999999999999999
Q ss_pred CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003093 83 DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 162 (848)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi 162 (848)
.+|+...+.+.+.+++.|++++....++.+. .|+...+.+++..++|+|++......+..++++++++|+..+ ++
T Consensus 144 ~~~~~~~~~~~~~~~~~G~~v~~~~~~~~~~--~d~~~~~~~l~~~~pdaIi~~~~~~~~~~~~~~l~~~g~~~p---~~ 218 (312)
T cd06333 144 AYGESGLKELKALAPKYGIEVVADERYGRTD--TSVTAQLLKIRAARPDAVLIWGSGTPAALPAKNLRERGYKGP---IY 218 (312)
T ss_pred HHHHHHHHHHHHHHHHcCCEEEEEEeeCCCC--cCHHHHHHHHHhCCCCEEEEecCCcHHHHHHHHHHHcCCCCC---EE
Confidence 9999999999999999999998777776543 578999999988899999999888888889999999998644 33
Q ss_pred ecCccccccCCCCCCCcccccccceeEEEEEe------cC----CchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhh
Q 003093 163 ATSWLSTALDTNSPFPSDVMDDIQGVLTLRTY------TP----DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYD 232 (848)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~------~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YD 232 (848)
.++..... ... +..++..+|++....+ .| ..+..++|.++|+++|+. ..|..+++.+||
T Consensus 219 ~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~f~~~~~~~~g~------~~~~~~~~~~Yd 287 (312)
T cd06333 219 QTHGVASP-DFL----RLAGKAAEGAILPAGPVLVADQLPDSDPQKKVALDFVKAYEAKYGA------GSVSTFGGHAYD 287 (312)
T ss_pred eecCcCcH-HHH----HHhhHhhcCcEeecccceeeeeCCCCCcchHHHHHHHHHHHHHhCC------CCCCchhHHHHH
Confidence 34333221 111 2344667888765421 22 246789999999999972 137889999999
Q ss_pred HHHHHH
Q 003093 233 TVWLLA 238 (848)
Q Consensus 233 Av~~~a 238 (848)
|+++++
T Consensus 288 a~~~~~ 293 (312)
T cd06333 288 ALLLLA 293 (312)
T ss_pred HHHHHH
Confidence 999999
No 94
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.77 E-value=5.2e-18 Score=191.45 Aligned_cols=221 Identities=17% Similarity=0.219 Sum_probs=178.5
Q ss_pred CCceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeec
Q 003093 374 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 453 (848)
Q Consensus 374 ~g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~ 453 (848)
..++||||+... |+.+...++...||++||++++++++|.+++++.. .+|++++.+|.+|++|+++++
T Consensus 41 ~~g~LrVg~~~~----P~~~~~~~~~~~G~~~DLl~~ia~~LGv~~e~v~~--------~~~~~ll~aL~~G~iDi~~~~ 108 (482)
T PRK10859 41 ERGELRVGTINS----PLTYYIGNDGPTGFEYELAKRFADYLGVKLEIKVR--------DNISQLFDALDKGKADLAAAG 108 (482)
T ss_pred hCCEEEEEEecC----CCeeEecCCCcccHHHHHHHHHHHHhCCcEEEEec--------CCHHHHHHHHhCCCCCEEecc
Confidence 356899999742 33221223335999999999999999999776633 369999999999999999888
Q ss_pred eeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCc
Q 003093 454 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 533 (848)
Q Consensus 454 ~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 533 (848)
+++|++|.+.++||.||+....++++++..
T Consensus 109 lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~-------------------------------------------------- 138 (482)
T PRK10859 109 LTYTPERLKQFRFGPPYYSVSQQLVYRKGQ-------------------------------------------------- 138 (482)
T ss_pred CcCChhhhccCcccCCceeeeEEEEEeCCC--------------------------------------------------
Confidence 999999999999999999999999998765
Q ss_pred chhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchH
Q 003093 534 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFA 613 (848)
Q Consensus 534 ~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~ 613 (848)
..+++++||. |++|++..|+..
T Consensus 139 --------------------------------------------------------~~i~~l~dL~--Gk~I~V~~gS~~ 160 (482)
T PRK10859 139 --------------------------------------------------------PRPRSLGDLK--GGTLTVAAGSSH 160 (482)
T ss_pred --------------------------------------------------------CCCCCHHHhC--CCeEEEECCCcH
Confidence 5688999998 899999999988
Q ss_pred HHHHHhhh-CCCccC--cccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEEEeCCccccCCceeeecC-C
Q 003093 614 RNYLVDEL-NIDESR--LVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQVFTKNGWGFAFPR-D 689 (848)
Q Consensus 614 ~~~l~~~~-~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k-~ 689 (848)
.+.+.+.. ..+..+ ...+.+.++++++|.+ |++|+++.+...+.+......++.+........+++++++| +
T Consensus 161 ~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~----G~iDa~v~d~~~~~~~~~~~p~l~v~~~l~~~~~~~~av~k~~ 236 (482)
T PRK10859 161 VETLQELKKKYPELSWEESDDKDSEELLEQVAE----GKIDYTIADSVEISLNQRYHPELAVAFDLTDEQPVAWALPPSG 236 (482)
T ss_pred HHHHHHHHHhCCCceEEecCCCCHHHHHHHHHC----CCCCEEEECcHHHHHHHHhCCCceeeeecCCCceeEEEEeCCC
Confidence 87774321 123232 3446789999999999 99999999988776655555566665554456678999999 4
Q ss_pred CC-chHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 690 SP-LAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 690 sp-l~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
.+ |...+|++|.++.++|.+++|.+||+.
T Consensus 237 ~~~L~~~ln~~L~~i~~~G~l~~L~~kyfg 266 (482)
T PRK10859 237 DDSLYAALLDFFNQIKEDGTLARLEEKYFG 266 (482)
T ss_pred CHHHHHHHHHHHHHhhcCCHHHHHHHHHhh
Confidence 55 999999999999999999999999998
No 95
>cd06268 PBP1_ABC_transporter_LIVBP_like Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC
Probab=99.77 E-value=1.2e-17 Score=178.34 Aligned_cols=220 Identities=25% Similarity=0.317 Sum_probs=183.1
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcC-cEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYG-WREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~-w~~vaii~~ 80 (848)
+++|++||||.++..+.++++.+.+.+||+|++.++.+.+.+..+|++|++.|++..+++++++++...+ |+++++++.
T Consensus 64 ~~~v~~iig~~~~~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~ 143 (298)
T cd06268 64 DDGVDAVIGPLSSGVALAAAPVAEEAGVPLISPGATSPALTGKGNPYVFRTAPSDAQQAAALADYLAEKGKVKKVAIIYD 143 (298)
T ss_pred hCCceEEEcCCcchhHHhhHHHHHhCCCcEEccCCCCcccccCCCceEEEcccCcHHHHHHHHHHHHHhcCCCEEEEEEc
Confidence 4589999999999988899999999999999998887766544579999999999999999999998887 999999999
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
+++++....+.+.+.+++.|++++....++... .++...+++++..++++|++.+....+..+++++++.|+ +..
T Consensus 144 ~~~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~~--~~~~~~~~~l~~~~~~~vi~~~~~~~~~~~~~~~~~~g~---~~~ 218 (298)
T cd06268 144 DYAYGRGLAAAFREALKKLGGEVVAEETYPPGA--TDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQAREAGL---KVP 218 (298)
T ss_pred CCchhHHHHHHHHHHHHHcCCEEEEEeccCCCC--ccHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCC---CCc
Confidence 999999999999999999999998877666543 678999999999899999999988899999999999998 456
Q ss_pred EEecCccccccCCCCCCCcccccccceeEEEEEecCCc--hhHHHHH-HHHHhhccCCCCCCCCCCCcchhhhhhHHHHH
Q 003093 161 WIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDS--VLKRKFI-SRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLL 237 (848)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~--~~~~~f~-~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~ 237 (848)
|+..+.+...... ....+..+|+++..++.+.. +....|. +.|+++++ ..++.++..+||+++++
T Consensus 219 ~~~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~y~~~~~~ 286 (298)
T cd06268 219 IVGGDGAAAPALL-----ELAGDAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAKYG-------RPPDSYAAAAYDAVRLL 286 (298)
T ss_pred EEecCccCCHHHH-----HhhhHhhCCcEEeccCCCCCCChhhhHHHHHHHHHHhC-------CCcccchHHHHHHHHHH
Confidence 7777765443211 12345678988888765543 4445565 77888776 57888999999999999
Q ss_pred H
Q 003093 238 A 238 (848)
Q Consensus 238 a 238 (848)
+
T Consensus 287 ~ 287 (298)
T cd06268 287 A 287 (298)
T ss_pred c
Confidence 8
No 96
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.76 E-value=8.6e-18 Score=213.59 Aligned_cols=216 Identities=14% Similarity=0.203 Sum_probs=179.1
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
.++|+||+. ++|+||.+.+.+|++.||++|++++|++++|.++++... .+|..+..+|.+|++|++.+ +
T Consensus 301 ~~~l~v~~~--~~~pP~~~~d~~g~~~G~~~Dll~~i~~~~g~~~~~v~~--------~~~~~~~~~l~~g~~D~i~~-~ 369 (1197)
T PRK09959 301 HPDLKVLEN--PYSPPYSMTDENGSVRGVMGDILNIITLQTGLNFSPITV--------SHNIHAGTQLNPGGWDIIPG-A 369 (1197)
T ss_pred CCceEEEcC--CCCCCeeEECCCCcEeeehHHHHHHHHHHHCCeEEEEec--------CCHHHHHHHHHCCCceEeec-c
Confidence 357898876 479999997778999999999999999999988544433 35888899999999999876 6
Q ss_pred eeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcc
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVV 534 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 534 (848)
+.+++|.+.++||.||+..++++++++..
T Consensus 370 ~~t~~r~~~~~fs~py~~~~~~~v~~~~~--------------------------------------------------- 398 (1197)
T PRK09959 370 IYSEDRENNVLFAEAFITTPYVFVMQKAP--------------------------------------------------- 398 (1197)
T ss_pred cCCccccccceeccccccCCEEEEEecCC---------------------------------------------------
Confidence 68999999999999999999999987543
Q ss_pred hhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHH
Q 003093 535 TIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFAR 614 (848)
Q Consensus 535 ~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~ 614 (848)
..+.++ . .|++||+..|+...
T Consensus 399 -------------------------------------------------------~~~~~~---~-~g~~vav~~g~~~~ 419 (1197)
T PRK09959 399 -------------------------------------------------------DSEQTL---K-KGMKVAIPYYYELH 419 (1197)
T ss_pred -------------------------------------------------------CCcccc---c-cCCEEEEeCCcchH
Confidence 112222 2 48889999999888
Q ss_pred HHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCC--c-EEEeCCccccCCceeeecCCCC
Q 003093 615 NYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC--E-FSIVGQVFTKNGWGFAFPRDSP 691 (848)
Q Consensus 615 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~--~-l~~~~~~~~~~~~~~~~~k~sp 691 (848)
+++.+ .++..+++.+++.++++++|.+ |++||++.+...+.|++++.. . +......+....++|+++|+.|
T Consensus 420 ~~~~~--~~p~~~~~~~~~~~~~l~av~~----G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~~ 493 (1197)
T PRK09959 420 SQLKE--MYPEVEWIKVDNASAAFHKVKE----GELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEP 493 (1197)
T ss_pred HHHHH--HCCCcEEEEcCCHHHHHHHHHc----CCCCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCCH
Confidence 88854 4556788999999999999999 999999999999999988742 2 3334444556678999999998
Q ss_pred -chHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 692 -LAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 692 -l~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
|...+|++|..+.++ .++++.+||+.
T Consensus 494 ~L~~~lnk~l~~i~~~-~~~~i~~kW~~ 520 (1197)
T PRK09959 494 ELKDIINKALNAIPPS-EVLRLTEKWIK 520 (1197)
T ss_pred HHHHHHHHHHHhCCHH-HHHHHHhhccc
Confidence 999999999999998 88999999987
No 97
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=99.73 E-value=4.8e-17 Score=167.91 Aligned_cols=208 Identities=17% Similarity=0.206 Sum_probs=157.3
Q ss_pred eEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHH---HHHhcCeeeEEeec
Q 003093 377 HLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELV---RLITAGVYDAAVGD 453 (848)
Q Consensus 377 ~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i---~~l~~g~~D~~~~~ 453 (848)
+||||+.. +|+||.+.++ .||++||+++|++++|++++++.. +|.+++ ..|.+|++|++++
T Consensus 1 ~l~vg~~~--~~pPf~~~~~----~Gfdvdl~~~ia~~lg~~~~~~~~---------~~~~~~~~~~~L~~g~~Dii~~- 64 (246)
T TIGR03870 1 TLRVCAAT--KEAPYSTKDG----SGFENKIAAALAAAMGRKVVFVWL---------AKPAIYLVRDGLDKKLCDVVLG- 64 (246)
T ss_pred CeEEEeCC--CCCCCccCCC----CcchHHHHHHHHHHhCCCeEEEEe---------ccchhhHHHHHHhcCCccEEEe-
Confidence 47889874 8999998432 699999999999999999666644 377766 6999999999985
Q ss_pred eeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCc
Q 003093 454 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 533 (848)
Q Consensus 454 ~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 533 (848)
++++++| +.||.||+.++.++++++.+.
T Consensus 65 ~~~t~~r---~~fS~PY~~~~~~~v~~k~~~------------------------------------------------- 92 (246)
T TIGR03870 65 LDTGDPR---VLTTKPYYRSSYVFLTRKDRN------------------------------------------------- 92 (246)
T ss_pred CCCChHH---HhcccCcEEeeeEEEEeCCCC-------------------------------------------------
Confidence 8888877 679999999999999997750
Q ss_pred chhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHH--hhcCCC-CeeEEeC
Q 003093 534 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDS--LRSSNY-PIGYQVN 610 (848)
Q Consensus 534 ~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~d--L~~s~~-~i~~~~~ 610 (848)
..+++++| |. |+ +||+..|
T Consensus 93 --------------------------------------------------------~~~~~~~d~~L~--g~~~vgv~~g 114 (246)
T TIGR03870 93 --------------------------------------------------------LDIKSWNDPRLK--KVSKIGVIFG 114 (246)
T ss_pred --------------------------------------------------------CCCCCccchhhc--cCceEEEecC
Confidence 24777765 65 87 9999999
Q ss_pred chHHHHHHhhhCCC-----ccCcccCC---------CHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcC-CcEE--Ee
Q 003093 611 SFARNYLVDELNID-----ESRLVPLN---------SPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR-CEFS--IV 673 (848)
Q Consensus 611 s~~~~~l~~~~~~~-----~~~~~~~~---------~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~-~~l~--~~ 673 (848)
+..+.++++..... ...++.+. +..+.+++|.. |++||++.+...+.+++.++ .++. .+
T Consensus 115 s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~----GrvDa~i~~~~~~~~~~~~~~~~~~~~~~ 190 (246)
T TIGR03870 115 SPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVAT----GKADLAVAFAPEVARYVKASPEPLRMTVI 190 (246)
T ss_pred ChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHc----CCCCEEEeeHHhHHHHHHhCCCCceEEec
Confidence 99998885421110 11222221 35788999999 99999999877776776653 2333 33
Q ss_pred CCcc-------c--cCCceeeecCCCC-chHHHHHHHHhhhccCchHHHHHhh
Q 003093 674 GQVF-------T--KNGWGFAFPRDSP-LAVDISTAILKLSENGDLQRIHDKW 716 (848)
Q Consensus 674 ~~~~-------~--~~~~~~~~~k~sp-l~~~in~~i~~l~e~G~~~~~~~kw 716 (848)
++.. . ..+++++++|+.+ |++.||++|.+|. |.+++|..+|
T Consensus 191 ~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l~--~~~~~i~~~y 241 (246)
T TIGR03870 191 PDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKAK--PRIDAILKEE 241 (246)
T ss_pred cccccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHhH--HHHHHHHHHc
Confidence 3221 1 1135899999998 9999999999999 4899999988
No 98
>TIGR02285 conserved hypothetical protein. Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown.
Probab=99.72 E-value=7e-17 Score=169.31 Aligned_cols=228 Identities=13% Similarity=0.167 Sum_probs=166.4
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhC-CCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeec
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 453 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l-~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~ 453 (848)
.++|++++. +|+||.+.++++...|+..++++++++++ ++++++...+ |.+++.++ .|+.|+++.+
T Consensus 17 ~~~l~~~~~---~~pPf~~~~~~~~~~G~~~~i~~~i~~~~~~~~~~~~~~p---------w~r~l~~l-~~~~d~~~~~ 83 (268)
T TIGR02285 17 KEAITWIVN---DFPPFFIFSGPSKGRGVFDVILQEIRRALPQYEHRFVRVS---------FARSLKEL-QGKGGVCTVN 83 (268)
T ss_pred cceeEEEec---ccCCeeEeCCCCCCCChHHHHHHHHHHHcCCCceeEEECC---------HHHHHHHH-hcCCCeEEee
Confidence 468888876 68898886566788999999999999998 8887776654 99999999 7777777767
Q ss_pred eeeecCceeeeeecccccc-cceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCC
Q 003093 454 IAIITNRTKMADFTQPYIE-SGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQ 532 (848)
Q Consensus 454 ~~~t~~R~~~~dfs~p~~~-~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 532 (848)
+++|++|.+.++||.||+. ...++++++..... .
T Consensus 84 ~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~-~-------------------------------------------- 118 (268)
T TIGR02285 84 LLRTPEREKFLIFSDPTLRALPVGLVLRKELTAG-V-------------------------------------------- 118 (268)
T ss_pred ccCCcchhhceeecCCccccCCceEEEccchhhh-c--------------------------------------------
Confidence 9999999999999999975 57888888754100 0
Q ss_pred cchhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccC-CCCChHHhhc-CCCCeeEEeC
Q 003093 533 VVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSS-PIKGIDSLRS-SNYPIGYQVN 610 (848)
Q Consensus 533 ~~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~-~i~sl~dL~~-s~~~i~~~~~ 610 (848)
..+.. ++ ++.+|.+ .++++|+..|
T Consensus 119 -----------------------------------------------------~~~~d~~~-~~~~l~~l~g~~vgv~~g 144 (268)
T TIGR02285 119 -----------------------------------------------------RDEQDGDV-DLKKLLASKKKRLGVIAS 144 (268)
T ss_pred -----------------------------------------------------cccCCCCc-cHHHHhcCCCeEEEEecc
Confidence 00001 11 2333321 2778999987
Q ss_pred chHHHHHHh---hhCC-CccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcC----CcEEEeCCcc--ccC
Q 003093 611 SFARNYLVD---ELNI-DESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR----CEFSIVGQVF--TKN 680 (848)
Q Consensus 611 s~~~~~l~~---~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~----~~l~~~~~~~--~~~ 680 (848)
+.....+.+ .... ...++..+.+.++.+++|.. |++|+++.+...+.+++++. ..+....... ...
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~----GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (268)
T TIGR02285 145 RSYGQQIDDILSDSGYQHNTRIIGNAAMGNLFKMLEK----GRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAHI 220 (268)
T ss_pred eeccHHHHHHHHhCCcccceeeeccchHHHHHHHHHc----CCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccce
Confidence 754333221 1121 11235556778889999999 99999999999999888742 1344443221 223
Q ss_pred CceeeecCCC---CchHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 681 GWGFAFPRDS---PLAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 681 ~~~~~~~k~s---pl~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
.++++++|+. .+++.||++|.+|.++|.+++|.+||+.
T Consensus 221 ~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~i~~k~~~ 261 (268)
T TIGR02285 221 SVWVACPKTEWGRKVIADIDQALSELNVDPKYYKYFDRWLS 261 (268)
T ss_pred EEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhCC
Confidence 5789999974 3999999999999999999999999997
No 99
>PF00060 Lig_chan: Ligand-gated ion channel; InterPro: IPR001320 The ability of synapses to modify their synaptic strength in response to activity is a fundamental property of the nervous system and may be an essential component of learning and memory. There are three classes of ionotropic glutamate receptor, namely NMDA (N-methyl-D-aspartate), AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole-4-propionic acid) and kainate receptors. They are believed to play critical roles in synaptic plasticity. At many synapses in the brain, transient activation of NMDA receptors leads to a persistent modification in the strength of synaptic transmission mediated by AMPA receptors and kainate receptors can act as the induction trigger for long-term changes in synaptic transmission [].; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 3FAT_A 3KFM_A 3KEI_A 3EN3_A 3EPE_B 3FAS_A 2F34_A 3C34_B 3S2V_A 3GBB_B ....
Probab=99.70 E-value=6.1e-19 Score=167.11 Aligned_cols=107 Identities=32% Similarity=0.554 Sum_probs=82.2
Q ss_pred chhhHHHHHHHHHHHHHHhhhhhcccCCCCCC-------CCCCCcchhhhhHHHHhhhcC-ccccccchhHHHHHHHHhh
Q 003093 496 TPMMWGVTAIFFLAVGAVVWILEHRLNDEFRG-------PPKRQVVTIFWFSFSTMFFAH-KEKTVSALGRLVLIIWLFV 567 (848)
Q Consensus 496 ~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~-~~~p~s~~~R~~~~~w~~~ 567 (848)
++++|++++++++++++++|++++..+.+++. +...++.+++|+.+++++.|+ ...|++.++|++.++|+++
T Consensus 1 s~~vW~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~s~s~Ril~~~w~l~ 80 (148)
T PF00060_consen 1 SWSVWLLILLSILLVSLVLWLFERFSPYEWRKNQSSPPRRWRFSLSNSFWYTFGTLLQQGSSIRPRSWSGRILLAFWWLF 80 (148)
T ss_dssp -HHHHHHHHHHHHHHHTTGGGT------------------HHHHHHHHHHHCCCCCHHHHH------HHHHHHHHHHHHH
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccccCcccHHHHHHHHHHhhccccccccccchHHHHHHHHHHHH
Confidence 57899999999999999999999987776665 223458899999999999775 5689999999999999999
Q ss_pred hhhhhccccceeeeeeeeccccCCCCChHHhhcCC
Q 003093 568 VLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSN 602 (848)
Q Consensus 568 ~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~ 602 (848)
++++.++|+|+|+|+||.+++.++|+|++||.+++
T Consensus 81 ~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~ 115 (148)
T PF00060_consen 81 SLILIASYTANLTSFLTVPKYEPPIDSLEDLANSG 115 (148)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHTSS-SSHHHHHTHS
T ss_pred HHHHHHHHHHHHHHHhcccCcCCCCCCHHHHHHCC
Confidence 99999999999999999999999999999999766
No 100
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=99.69 E-value=1.2e-15 Score=154.33 Aligned_cols=214 Identities=27% Similarity=0.466 Sum_probs=178.7
Q ss_pred EEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeee
Q 003093 378 LRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAII 457 (848)
Q Consensus 378 lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t 457 (848)
|+|++.. .++||.+.++++.+.|++.++++.+.+++|.++++... .|.+++.+|.+|++|+++.....+
T Consensus 1 l~i~~~~--~~~p~~~~~~~g~~~G~~~~~~~~~~~~~g~~~~~~~~---------~~~~~~~~l~~g~~D~~~~~~~~~ 69 (218)
T cd00134 1 LTVGTAG--TYPPFSFRDANGELTGFDVDLAKAIAKELGVKVKFVEV---------DWDGLITALKSGKVDLIAAGMTIT 69 (218)
T ss_pred CEEecCC--CCCCeeEECCCCCEEeeeHHHHHHHHHHhCCeEEEEeC---------CHHHHHHHHhcCCcCEEeecCcCC
Confidence 5777775 78899887788999999999999999999977555543 399999999999999999877788
Q ss_pred cCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcchhh
Q 003093 458 TNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIF 537 (848)
Q Consensus 458 ~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~ 537 (848)
.+|.+.+.|+.|+.....++++++..
T Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------------------------------------ 95 (218)
T cd00134 70 PERAKQVDFSDPYYKSGQVILVKKGS------------------------------------------------------ 95 (218)
T ss_pred HHHHhhccCcccceeccEEEEEECCC------------------------------------------------------
Confidence 89999999999999999999999765
Q ss_pred hhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHHHHH
Q 003093 538 WFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNYL 617 (848)
Q Consensus 538 ~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~~~l 617 (848)
++.+++||. |+++++..|+....++
T Consensus 96 -----------------------------------------------------~~~~~~dl~--g~~i~~~~~~~~~~~~ 120 (218)
T cd00134 96 -----------------------------------------------------PIKSVKDLK--GKKVAVQKGSTAEKYL 120 (218)
T ss_pred -----------------------------------------------------CCCChHHhC--CCEEEEEcCchHHHHH
Confidence 455899997 8899999888777777
Q ss_pred HhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcC-CcEEEeCCc--cccCCceeeecCCCC-ch
Q 003093 618 VDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR-CEFSIVGQV--FTKNGWGFAFPRDSP-LA 693 (848)
Q Consensus 618 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~-~~l~~~~~~--~~~~~~~~~~~k~sp-l~ 693 (848)
.+... ..++..+.+.++.++++.+ |++++++.+.....+...+. +++.++... ..+..++++..++++ +.
T Consensus 121 ~~~~~--~~~~~~~~~~~~~~~~l~~----g~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~ 194 (218)
T cd00134 121 KKALP--EAKVVSYDDNAEALAALEN----GRADAVIVDEIALAALLKKHPPELKIVGPSIDLEPLGFGVAVGKDNKELL 194 (218)
T ss_pred HHhCC--cccEEEeCCHHHHHHHHHc----CCccEEEeccHHHHHHHHhcCCCcEEeccccCCCccceEEEEcCCCHHHH
Confidence 54332 3456778899999999999 89999999998888877665 677777653 344456777777774 99
Q ss_pred HHHHHHHHhhhccCchHHHHHhhc
Q 003093 694 VDISTAILKLSENGDLQRIHDKWL 717 (848)
Q Consensus 694 ~~in~~i~~l~e~G~~~~~~~kw~ 717 (848)
..++++|.++.++|.++.+.+||+
T Consensus 195 ~~~~~~l~~~~~~g~~~~i~~~~~ 218 (218)
T cd00134 195 DAVNKALKELRADGELKKISKKWF 218 (218)
T ss_pred HHHHHHHHHHHhCccHHHHHHhhC
Confidence 999999999999999999999996
No 101
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.68 E-value=1e-15 Score=161.60 Aligned_cols=224 Identities=25% Similarity=0.337 Sum_probs=181.3
Q ss_pred CCceEEEEecCCCCccceEEeCCC-cceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEee
Q 003093 374 NGRHLRIGVPNRVSFREFVSVKGS-EMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVG 452 (848)
Q Consensus 374 ~g~~lrv~v~~~~~~~p~~~~~~~-~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~ 452 (848)
....++|++... ..+||.+.+.. +++.||++|+++++++.++.......++ .+|.+++..|..|++|++++
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 456788888753 44588885555 6999999999999999998864233333 35999999999999999999
Q ss_pred ceeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCC
Q 003093 453 DIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQ 532 (848)
Q Consensus 453 ~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 532 (848)
.+++|++|.+.++||.||+..+..++++..+.
T Consensus 104 ~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~------------------------------------------------ 135 (275)
T COG0834 104 GMTITPERKKKVDFSDPYYYSGQVLLVKKDSD------------------------------------------------ 135 (275)
T ss_pred ccccCHHHhccccccccccccCeEEEEECCCC------------------------------------------------
Confidence 99999999999999999999999999998761
Q ss_pred cchhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCch
Q 003093 533 VVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSF 612 (848)
Q Consensus 533 ~~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~ 612 (848)
..+.+++||. ++++|++.|+.
T Consensus 136 ---------------------------------------------------------~~~~~~~DL~--gk~v~v~~gt~ 156 (275)
T COG0834 136 ---------------------------------------------------------IGIKSLEDLK--GKKVGVQLGTT 156 (275)
T ss_pred ---------------------------------------------------------cCcCCHHHhC--CCEEEEEcCcc
Confidence 2378899999 89999999998
Q ss_pred --HHHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHH--HhcCCc-EEEeCCcccc-CCceeee
Q 003093 613 --ARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELF--LSTRCE-FSIVGQVFTK-NGWGFAF 686 (848)
Q Consensus 613 --~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~--~~~~~~-l~~~~~~~~~-~~~~~~~ 686 (848)
....... ......++.+++..+.+.+|.. |++|+++.+...+.++ ..+... .......... .++++++
T Consensus 157 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~al~~----Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (275)
T COG0834 157 DEAEEKAKK--PGPNAKIVAYDSNAEALLALKN----GRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIAL 230 (275)
T ss_pred hhHHHHHhh--ccCCceEEeeCCHHHHHHHHHc----CCccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEe
Confidence 4444322 2334677889999999999999 9999999999998883 434333 2333333333 6899999
Q ss_pred cCC--CCchHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 687 PRD--SPLAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 687 ~k~--spl~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
+|+ ..+++.+|.+|.++.++|.++++.++|+.
T Consensus 231 ~~~~~~~l~~~in~~l~~l~~~G~~~~i~~kw~~ 264 (275)
T COG0834 231 RKGDDPELLEAVNKALKELKADGTLQKISDKWFG 264 (275)
T ss_pred ccCCcHHHHHHHHHHHHHHHhCccHHHHHHHhcC
Confidence 999 46999999999999999999999999998
No 102
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.68 E-value=1.7e-15 Score=153.05 Aligned_cols=215 Identities=27% Similarity=0.460 Sum_probs=181.4
Q ss_pred eEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceee
Q 003093 377 HLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAI 456 (848)
Q Consensus 377 ~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~ 456 (848)
+|+||+. +.++||...+.++.+.|+.+|+++.+.+++|+++++... .|..++.++.+|++|++++....
T Consensus 1 ~l~v~~~--~~~~p~~~~~~~g~~~G~~~~~~~~~~~~~g~~~~~~~~---------~~~~~~~~l~~g~~D~~~~~~~~ 69 (219)
T smart00062 1 TLRVGTN--GDYPPFSFADEDGELTGFDVDLAKAIAKELGLKVEFVEV---------SFDNLLTALKSGKIDVVAAGMTI 69 (219)
T ss_pred CEEEEec--CCCCCcEEECCCCCcccchHHHHHHHHHHhCCeEEEEec---------cHHHHHHHHHCCcccEEeccccC
Confidence 4788886 478898886778889999999999999999987555443 49999999999999999987777
Q ss_pred ecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcchh
Q 003093 457 ITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTI 536 (848)
Q Consensus 457 t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~ 536 (848)
+.+|...+.|+.|+...+.++++++..
T Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------------------------- 96 (219)
T smart00062 70 TPERAKQVDFSDPYYKSGQVILVRKDS----------------------------------------------------- 96 (219)
T ss_pred CHHHHhheeeccceeeceeEEEEecCC-----------------------------------------------------
Confidence 888888899999999999999988654
Q ss_pred hhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHHHH
Q 003093 537 FWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNY 616 (848)
Q Consensus 537 ~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~~~ 616 (848)
++.+++||. |+++++..|+....+
T Consensus 97 ------------------------------------------------------~~~~~~dL~--g~~i~~~~g~~~~~~ 120 (219)
T smart00062 97 ------------------------------------------------------PIKSLEDLK--GKKVAVVAGTTGEEL 120 (219)
T ss_pred ------------------------------------------------------CCCChHHhC--CCEEEEecCccHHHH
Confidence 588999997 889999998877777
Q ss_pred HHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcC--CcEEEeCCcccc-CCceeeecCCCC-c
Q 003093 617 LVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR--CEFSIVGQVFTK-NGWGFAFPRDSP-L 692 (848)
Q Consensus 617 l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~--~~l~~~~~~~~~-~~~~~~~~k~sp-l 692 (848)
+... .+..++..+.+..+.+.+|.. |++++++...+...+...+. .++.++...... ..++++++++++ +
T Consensus 121 ~~~~--~~~~~~~~~~~~~~~~~~l~~----g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (219)
T smart00062 121 LKKL--YPEAKIVSYDSQAEALAALKA----GRADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAVRKGDPEL 194 (219)
T ss_pred HHHh--CCCceEEEcCCHHHHHHHhhc----CcccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEEECCCHHH
Confidence 7442 233566778888999999999 89999999999888877765 567777665544 788999999987 9
Q ss_pred hHHHHHHHHhhhccCchHHHHHhhc
Q 003093 693 AVDISTAILKLSENGDLQRIHDKWL 717 (848)
Q Consensus 693 ~~~in~~i~~l~e~G~~~~~~~kw~ 717 (848)
.+.++++|.++.++|.++++.++|+
T Consensus 195 ~~~~~~~l~~~~~~~~~~~i~~~~~ 219 (219)
T smart00062 195 LDKINKALKELKADGTLKKIYEKWF 219 (219)
T ss_pred HHHHHHHHHHHHhCchHHHHHhccC
Confidence 9999999999999999999999985
No 103
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.66 E-value=7.2e-16 Score=196.08 Aligned_cols=220 Identities=11% Similarity=0.137 Sum_probs=183.5
Q ss_pred CCceEEEEecCCCCccceEE-eCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEee
Q 003093 374 NGRHLRIGVPNRVSFREFVS-VKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVG 452 (848)
Q Consensus 374 ~g~~lrv~v~~~~~~~p~~~-~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~ 452 (848)
+.++|+||+.. +++|+.+ .+.+|++.||.+|+++.|++++|.++++ +++ .+|.+++.+|.+|++|++.+
T Consensus 54 ~~~~l~vgv~~--~~~p~~~~~~~~g~~~G~~~D~l~~ia~~lG~~~e~--v~~------~~~~~~l~~l~~g~iDl~~~ 123 (1197)
T PRK09959 54 SKKNLVIAVHK--SQTATLLHTDSQQRVRGINADYLNLLKRALNIKLTL--REY------ADHQKAMDALEEGEVDIVLS 123 (1197)
T ss_pred hCCeEEEEecC--CCCCCceeecCCCccceecHHHHHHHHHhcCCceEE--EeC------CCHHHHHHHHHcCCCcEecC
Confidence 45689999875 4544433 4578999999999999999999998544 442 37999999999999999999
Q ss_pred ceeeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCC
Q 003093 453 DIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQ 532 (848)
Q Consensus 453 ~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 532 (848)
.++.+++|.+.++||.||+....++++++..
T Consensus 124 ~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~------------------------------------------------- 154 (1197)
T PRK09959 124 HLVASPPLNDDIAATKPLIITFPALVTTLHD------------------------------------------------- 154 (1197)
T ss_pred ccccccccccchhcCCCccCCCceEEEeCCC-------------------------------------------------
Confidence 8999999999999999999999999998754
Q ss_pred cchhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCch
Q 003093 533 VVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSF 612 (848)
Q Consensus 533 ~~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~ 612 (848)
.+++++|+. ++++++..|+.
T Consensus 155 ----------------------------------------------------------~~~~~~~l~--~~~i~~~~g~~ 174 (1197)
T PRK09959 155 ----------------------------------------------------------SMRPLTSSK--PVNIARVANYP 174 (1197)
T ss_pred ----------------------------------------------------------CCCCccccc--CeEEEEeCCCC
Confidence 456677776 78899999998
Q ss_pred HHHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCC--cEEEeCCc-cccCCceeeecCC
Q 003093 613 ARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC--EFSIVGQV-FTKNGWGFAFPRD 689 (848)
Q Consensus 613 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~--~l~~~~~~-~~~~~~~~~~~k~ 689 (848)
..+++++ .++..+++.+++..+++++|.. |++||++++...+.|+++++. ++.+++.. .......++++|+
T Consensus 175 ~~~~~~~--~~p~~~i~~~~s~~~al~av~~----G~~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 248 (1197)
T PRK09959 175 PDEVIHQ--SFPKATIISFTNLYQALASVSA----GQNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKE 248 (1197)
T ss_pred CHHHHHH--hCCCCEEEeCCCHHHHHHHHHc----CCCCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCC
Confidence 8888865 5677889999999999999999 999999999999999998743 45555432 2234466889999
Q ss_pred CC-chHHHHHHHHhhhccCchHHHHHhhccc
Q 003093 690 SP-LAVDISTAILKLSENGDLQRIHDKWLLR 719 (848)
Q Consensus 690 sp-l~~~in~~i~~l~e~G~~~~~~~kw~~~ 719 (848)
.| |...+|++|..+.++|.. +|.+||+..
T Consensus 249 ~~~L~~~lnkal~~i~~~~~~-~i~~kW~~~ 278 (1197)
T PRK09959 249 SVILNEVLNRFVDALTNEVRY-EVSQNWLDT 278 (1197)
T ss_pred cHHHHHHHHHHHHhCCHHHHH-HHHHhccCC
Confidence 98 899999999999999887 999999973
No 104
>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=99.63 E-value=8.9e-15 Score=150.13 Aligned_cols=210 Identities=17% Similarity=0.223 Sum_probs=159.0
Q ss_pred EEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeee
Q 003093 378 LRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAII 457 (848)
Q Consensus 378 lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t 457 (848)
||||+.. .|+||.+. ...||++||++++++++|.+++++..++ .+..++..+.+|++|++++ +
T Consensus 2 l~v~~~~--~~~P~~~~----~~~G~~~el~~~i~~~~g~~i~~~~~~~-------~~~~~~~~l~~g~~Di~~~----~ 64 (232)
T TIGR03871 2 LRVCADP--NNLPFSNE----KGEGFENKIAQLLADDLGLPLEYTWFPQ-------RRGFVRNTLNAGRCDVVIG----V 64 (232)
T ss_pred eEEEeCC--CCCCccCC----CCCchHHHHHHHHHHHcCCceEEEecCc-------chhhHHHHHhcCCccEEEe----c
Confidence 7888764 78888762 2479999999999999999977776552 2444577899999999876 4
Q ss_pred cCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcchhh
Q 003093 458 TNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIF 537 (848)
Q Consensus 458 ~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~ 537 (848)
++|.+.++||.||+..+.+++++....
T Consensus 65 ~~r~~~~~fs~py~~~~~~lv~~~~~~----------------------------------------------------- 91 (232)
T TIGR03871 65 PAGYEMVLTTRPYYRSTYVFVTRKDSL----------------------------------------------------- 91 (232)
T ss_pred cCccccccccCCcEeeeEEEEEeCCCc-----------------------------------------------------
Confidence 778888999999999999999987740
Q ss_pred hhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHHHHH
Q 003093 538 WFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNYL 617 (848)
Q Consensus 538 ~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~~~l 617 (848)
..+++++|+...+++||+..|+...+++
T Consensus 92 ----------------------------------------------------~~~~~~~d~~l~g~~V~v~~g~~~~~~l 119 (232)
T TIGR03871 92 ----------------------------------------------------LDVKSLDDPRLKKLRIGVFAGTPPAHWL 119 (232)
T ss_pred ----------------------------------------------------ccccchhhhhhcCCeEEEEcCChHHHHH
Confidence 3577888832238899999999888888
Q ss_pred HhhhCCCccCcc---------cCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcC-CcEEEeCCcc------ccCC
Q 003093 618 VDELNIDESRLV---------PLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR-CEFSIVGQVF------TKNG 681 (848)
Q Consensus 618 ~~~~~~~~~~~~---------~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~-~~l~~~~~~~------~~~~ 681 (848)
.+. +.. .++. ...+..+.+.+|.. |++|+++.+...+.+++++. ..+.+..... ...+
T Consensus 120 ~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~----G~~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 (232)
T TIGR03871 120 ARH-GLV-ENVVGYSLFGDYRPESPPGRMVEDLAA----GEIDVAIVWGPIAGYFAKQAGPPLVVVPLLPEDGGIPFDYR 193 (232)
T ss_pred Hhc-Ccc-cccccccccccccccCCHHHHHHHHHc----CCcCEEEeccHHHHHHHHhCCCCceeeccccCCCCCCccce
Confidence 542 211 1211 13477899999999 99999999988888877753 2444433211 2335
Q ss_pred ceeeecCCCC-chHHHHHHHHhhhccCchHHHHHhhc
Q 003093 682 WGFAFPRDSP-LAVDISTAILKLSENGDLQRIHDKWL 717 (848)
Q Consensus 682 ~~~~~~k~sp-l~~~in~~i~~l~e~G~~~~~~~kw~ 717 (848)
++++++++.+ ++..||++|.++. |.+++|.+||-
T Consensus 194 ~~~~~~~~~~~l~~~~n~~l~~~~--~~~~~i~~kyg 228 (232)
T TIGR03871 194 IAMGVRKGDKAWKDELNAVLDRRQ--AEIDAILREYG 228 (232)
T ss_pred EEEEEecCCHHHHHHHHHHHHHHH--HHHHHHHHHcC
Confidence 6888998877 9999999999986 47999999994
No 105
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.37 E-value=3.9e-12 Score=118.10 Aligned_cols=123 Identities=33% Similarity=0.525 Sum_probs=106.7
Q ss_pred CCCChHHhhcC-CCCeeEEeCchHHHHHHhhhCCC------c---cCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHH
Q 003093 591 PIKGIDSLRSS-NYPIGYQVNSFARNYLVDELNID------E---SRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYA 660 (848)
Q Consensus 591 ~i~sl~dL~~s-~~~i~~~~~s~~~~~l~~~~~~~------~---~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~ 660 (848)
+|++++||..+ +++||++.|+..+.++++..... . .+++.+++..+++.+|.. |+ +|++.+.+.+
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~----g~-da~v~d~~~~ 75 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRV----SN-YAFLMESTYL 75 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHc----CC-CEEEeehHhH
Confidence 47899999843 26899999999999985432210 0 256678999999999999 89 9999999999
Q ss_pred HHHHhcCCcEEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 661 ELFLSTRCEFSIVGQVFTKNGWGFAFPRDSPLAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 661 ~~~~~~~~~l~~~~~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
.++.++.|++.+++..+...+++++++|+++|++.+|.+|.+|.++|.++++.++|+.
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~~l~~kw~~ 133 (134)
T smart00079 76 DYELSQNCDLMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQKLENKWWK 133 (134)
T ss_pred HHHHhCCCCeEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHHHHHHhhcc
Confidence 9998888999999988888899999999999999999999999999999999999985
No 106
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.25 E-value=5.6e-11 Score=120.15 Aligned_cols=220 Identities=16% Similarity=0.160 Sum_probs=177.5
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
...|||++.++ |..+...++...|++.++.+.+++.||.++++... .+-+.++.+|.+|++|+++.++
T Consensus 22 rGvLrV~tins----p~sy~~~~~~p~G~eYelak~Fa~yLgV~Lki~~~--------~n~dqLf~aL~ng~~DL~Aagl 89 (473)
T COG4623 22 RGVLRVSTINS----PLSYFEDKGGPTGLEYELAKAFADYLGVKLKIIPA--------DNIDQLFDALDNGNADLAAAGL 89 (473)
T ss_pred cCeEEEEeecC----ccceeccCCCccchhHHHHHHHHHHhCCeEEEEec--------CCHHHHHHHHhCCCcceecccc
Confidence 45899999874 33333446667799999999999999988655543 3578999999999999999999
Q ss_pred eeecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcc
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVV 534 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 534 (848)
...++|.+.+.....|+..++.+|.++.+
T Consensus 90 ~~~~~~l~~~~~gP~y~svs~qlVyRkG~--------------------------------------------------- 118 (473)
T COG4623 90 LYNSERLKNFQPGPTYYSVSQQLVYRKGQ--------------------------------------------------- 118 (473)
T ss_pred cCChhHhcccCCCCceecccHHHHhhcCC---------------------------------------------------
Confidence 99999999999999999999999999887
Q ss_pred hhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHH
Q 003093 535 TIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFAR 614 (848)
Q Consensus 535 ~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~ 614 (848)
....++++|. +..+-+..|+...
T Consensus 119 -------------------------------------------------------~Rp~~l~~L~--g~~i~v~~gs~~~ 141 (473)
T COG4623 119 -------------------------------------------------------YRPRSLGQLK--GRQITVAKGSAHV 141 (473)
T ss_pred -------------------------------------------------------CCCCCHHHcc--CceeeccCCcHHH
Confidence 4567799998 7778888898766
Q ss_pred HHHHh--hhCCCccC--cccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEEEeCCccccCCceeeecCCC
Q 003093 615 NYLVD--ELNIDESR--LVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQVFTKNGWGFAFPRDS 690 (848)
Q Consensus 615 ~~l~~--~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k~s 690 (848)
+.++. +..+|... .-.-...++.++.+.. |.++..+.+...+..+.+-++++.+.-+.-...+.++.+|.+.
T Consensus 142 ~~l~~lk~~kyP~l~~k~d~~~~~~dLle~v~~----Gkldytiads~~is~~q~i~P~laVafd~tde~~v~Wy~~~~d 217 (473)
T COG4623 142 EDLKLLKETKYPELIWKVDDKLGVEDLLEMVAE----GKLDYTIADSVEISLFQRVHPELAVAFDLTDEQPVAWYLPRDD 217 (473)
T ss_pred HHHHHHHHhhcchhhhhhcccccHHHHHHHHhc----CCcceeeeccHHHHHHHHhCccceeeeecccccCceeeccCCc
Confidence 55532 22334221 1223467899999999 8999999999988877777787776666556688999999854
Q ss_pred --CchHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 691 --PLAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 691 --pl~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
.|...++..+..+.|.|.++++++||++
T Consensus 218 d~tL~a~ll~F~~~~~e~g~larleeky~g 247 (473)
T COG4623 218 DSTLSAALLDFLNEAKEDGLLARLEEKYLG 247 (473)
T ss_pred hHHHHHHHHHHHHHhhcchHHHHHHHHHhc
Confidence 4999999999999999999999999997
No 107
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=99.23 E-value=2.1e-10 Score=119.85 Aligned_cols=163 Identities=22% Similarity=0.322 Sum_probs=134.0
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
+++++|||+.++.....+...+.+.++|+|++.+..+... .+++++++.+++..++..+++++.+.+|+++++++.+.
T Consensus 57 ~~~d~ii~~~~~~~~~~~~~~~~~~~ip~v~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~i~~~~ 134 (269)
T cd01391 57 QGVDGIIGPPSSSSALAVVELAAAAGIPVVSLDATAPDLT--GYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDD 134 (269)
T ss_pred cCCCEEEecCCCHHHHHHHHHHHHcCCcEEEecCCCCccC--CCceEEEEcCCcHHHHHHHHHHHHHhCCceEEEEecCC
Confidence 4789999999988777688899999999999887765554 57899999999999999999999999999999999777
Q ss_pred -CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC-CCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 83 -DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT-ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 83 -~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~-~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
.++....+.+.+.+++.|.++......+.. .+.++......++.. ++++|++++. ..+..+++++++.|+...++.
T Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~i~~~~~-~~a~~~~~~~~~~g~~~~~~~ 212 (269)
T cd01391 135 GAYGRERLEGFKAALKKAGIEVVAIEYGDLD-TEKGFQALLQLLKAAPKPDAIFACND-EMAAGALKAAREAGLTPGDIS 212 (269)
T ss_pred cchhhHHHHHHHHHHHhcCcEEEeccccCCC-ccccHHHHHHHHhcCCCCCEEEEcCc-hHHHHHHHHHHHcCCCCCCCE
Confidence 677888899999999999877654444432 225677777788776 7899998877 888899999999999755677
Q ss_pred EEecCcccc
Q 003093 161 WIATSWLST 169 (848)
Q Consensus 161 wi~~~~~~~ 169 (848)
|++.+.+..
T Consensus 213 ii~~~~~~~ 221 (269)
T cd01391 213 IIGFDGSPA 221 (269)
T ss_pred EEecccccc
Confidence 777766543
No 108
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=98.91 E-value=1.5e-08 Score=105.44 Aligned_cols=198 Identities=18% Similarity=0.150 Sum_probs=141.1
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
.+|+||+.. .++|+ .+.+...++.+.+.+++|.++++... ++|+.++..+..|++|+++.+..
T Consensus 32 ~~l~vg~~~--~~~~~-------~~~~~~~~l~~~l~~~~g~~v~~~~~--------~~~~~~~~~l~~g~~Di~~~~~~ 94 (254)
T TIGR01098 32 KELNFGILP--GENAS-------NLTRRWEPLADYLEKKLGIKVQLFVA--------TDYSAVIEAMRFGRVDIAWFGPS 94 (254)
T ss_pred CceEEEECC--CCCHH-------HHHHHHHHHHHHHHHHhCCcEEEEeC--------CCHHHHHHHHHcCCccEEEECcH
Confidence 579999873 34443 23455679999999999988665542 46999999999999999986554
Q ss_pred eec---Cceeeeeeccccccc------ceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCC
Q 003093 456 IIT---NRTKMADFTQPYIES------GLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFR 526 (848)
Q Consensus 456 ~t~---~R~~~~dfs~p~~~~------~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~ 526 (848)
... +|....+|+.|+... ...+++++.
T Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d-------------------------------------------- 130 (254)
T TIGR01098 95 SYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKAD-------------------------------------------- 130 (254)
T ss_pred HHHHHHHhcCCceEEeeccccCCCCceEEEEEEECC--------------------------------------------
Confidence 332 566667888876643 245666643
Q ss_pred CCCCCCcchhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCee
Q 003093 527 GPPKRQVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIG 606 (848)
Q Consensus 527 ~~~~~~~~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~ 606 (848)
.+|++++||. |++|+
T Consensus 131 ---------------------------------------------------------------~~i~~~~dL~--gk~I~ 145 (254)
T TIGR01098 131 ---------------------------------------------------------------SPIKSLKDLK--GKTFA 145 (254)
T ss_pred ---------------------------------------------------------------CCCCChHHhc--CCEEE
Confidence 3689999997 88999
Q ss_pred EEe-CchH-----HHHHHhhhCCC----ccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCC----cEEE
Q 003093 607 YQV-NSFA-----RNYLVDELNID----ESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC----EFSI 672 (848)
Q Consensus 607 ~~~-~s~~-----~~~l~~~~~~~----~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~----~l~~ 672 (848)
+.. ++.. ..++.+..+.. ..++....+..+.++++.+ |++|+.+.+.+....+..++. ++.+
T Consensus 146 ~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~----G~~Da~~~~~~~~~~~~~~~~~~~~~~~~ 221 (254)
T TIGR01098 146 FGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVAN----GKVDAATNNSSAIGRLKKRGPSDMKKVRV 221 (254)
T ss_pred eeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHc----CCCCeEEecHHHHHHHHHhCccchhheEE
Confidence 874 3321 23343332221 1344555667889999999 999999999988877766542 5788
Q ss_pred eCCccccCCceeeecCC-CC-chHHHHHHHHhh
Q 003093 673 VGQVFTKNGWGFAFPRD-SP-LAVDISTAILKL 703 (848)
Q Consensus 673 ~~~~~~~~~~~~~~~k~-sp-l~~~in~~i~~l 703 (848)
+.+.....+++++++|+ .+ +++.+|++|..+
T Consensus 222 ~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 222 IWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred EEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 87665556789999999 44 999999999764
No 109
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.81 E-value=1.8e-08 Score=105.77 Aligned_cols=163 Identities=19% Similarity=0.277 Sum_probs=131.5
Q ss_pred ChhHHHHHHhcCeeeEEeeceeeecCceeeeeeccc--ccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHH
Q 003093 434 SCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQP--YIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVG 511 (848)
Q Consensus 434 s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p--~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~ 511 (848)
+|.+++..|..|++|+++++.+++.+|.+.++|+.| |....+++++|...
T Consensus 52 ~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~---------------------------- 103 (287)
T PRK00489 52 RPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDS---------------------------- 103 (287)
T ss_pred CcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCC----------------------------
Confidence 589999999999999999999999999999999998 77778888888654
Q ss_pred HHhhhhhcccCCCCCCCCCCCcchhhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCC
Q 003093 512 AVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSP 591 (848)
Q Consensus 512 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~ 591 (848)
+
T Consensus 104 -------------------------------------------------------------------------------~ 104 (287)
T PRK00489 104 -------------------------------------------------------------------------------D 104 (287)
T ss_pred -------------------------------------------------------------------------------C
Confidence 6
Q ss_pred CCChHHhhcCCCCeeEEeCchHHHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEE
Q 003093 592 IKGIDSLRSSNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFS 671 (848)
Q Consensus 592 i~sl~dL~~s~~~i~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~ 671 (848)
+++++||. |+++++..+.....++.+ .+. ..+++.+.+..+. ++.. |..+++++.......+.++ ++.
T Consensus 105 i~sl~DL~--Gk~ia~~~~~~~~~~l~~-~gi-~~~iv~~~gs~ea--a~~~----G~aDaivd~~~~~~~l~~~--~L~ 172 (287)
T PRK00489 105 WQGVEDLA--GKRIATSYPNLTRRYLAE-KGI-DAEVVELSGAVEV--APRL----GLADAIVDVVSTGTTLRAN--GLK 172 (287)
T ss_pred CCChHHhC--CCEEEEcCcHHHHHHHHH-cCC-ceEEEECCCchhh--hhcC----CcccEEEeeHHHHHHHHHC--CCE
Confidence 88899998 889999888888888854 333 2355556545554 4555 8999999888887776664 577
Q ss_pred EeCCccccCCceeeecC--CCC-chHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 672 IVGQVFTKNGWGFAFPR--DSP-LAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 672 ~~~~~~~~~~~~~~~~k--~sp-l~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
++ +.......+++.+| .+| ....+|..+.+| .|.+..+..||+.
T Consensus 173 ~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g~l~a~~~k~~~ 219 (287)
T PRK00489 173 IV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QGVLRARESKYLM 219 (287)
T ss_pred EE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HHHHHhhceEEEE
Confidence 77 56666778999999 666 888899999999 5999999999997
No 110
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=98.80 E-value=4e-08 Score=111.40 Aligned_cols=253 Identities=14% Similarity=0.171 Sum_probs=136.7
Q ss_pred CCCeEEEEccCCchhHHHHHHhhcc--CCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANE--LQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIY 79 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~--~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~ 79 (848)
.+|++.||||..-+...+++..... -.||++.....+.. .. -+.++...-+....++.+|+.+..-|+++..||+
T Consensus 276 ~~ga~~ViGPL~k~~V~~l~~~~~~~~~~vp~LaLN~~~~~-~~--~~~l~~f~LspEdEA~q~A~~a~~~g~~~alvl~ 352 (536)
T PF04348_consen 276 ADGADFVIGPLLKSNVEALAQLPQLQAQPVPVLALNQPDNS-QA--PPNLYQFGLSPEDEARQAAQKAFQDGYRRALVLA 352 (536)
T ss_dssp HTT--EEE---SHHHHHHHHH-GG-GGTT-EEEES---TT-------TTEEE----HHHHHHHHHHHHHHTT--S-EEEE
T ss_pred HcCCCEEEcCCCHHHHHHHHhcCcccccCCceeeccCCCcc-cC--ccceEEEeCCcHHHHHHHHHHHHhcCCCCEEEEc
Confidence 4689999999998888877766553 58999987666543 11 2344555555667799999999999999999999
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
.++++|....+.|.+..++.|+.++....+.. ..++...++.-.....|.||+.+.+.+++.|--...-. .....
T Consensus 353 p~~~~g~R~~~aF~~~W~~~gg~~~~~~~~~~---~~~~~~~i~~r~r~d~D~ifl~a~~~~ar~ikP~l~~~--~a~~l 427 (536)
T PF04348_consen 353 PQNAWGQRMAEAFNQQWQALGGQVAEVSYYGS---PADLQAAIQPRRRQDIDAIFLVANPEQARLIKPQLDFH--FAGDL 427 (536)
T ss_dssp ESSHHHHHHHHHHHHHHHHHHSS--EEEEESS---TTHHHHHHHHS--TT--EEEE---HHHHHHHHHHHTT---T-TT-
T ss_pred CCChHHHHHHHHHHHHHHHcCCCceeeEecCC---HHHHHHHHhhcCCCCCCEEEEeCCHHHHHHHhhhcccc--cCCCC
Confidence 99999999999999999999998876666652 36888888865567899999999998888776655432 12233
Q ss_pred EEEecCccccccCCCCCCCcccccccceeEEEEEe---cCCchhHHHHHHHHHhhccCCCCCCCCCCCcchhhhhhHHHH
Q 003093 160 VWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTY---TPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWL 236 (848)
Q Consensus 160 ~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~---~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~ 236 (848)
..+.++....... +......++|+..+... .+..+..+.+...|.+.. .......+.+|||..+
T Consensus 428 PvyatS~~~~g~~-----~~~~~~dL~gv~f~d~Pwll~~~~~~~~~~~~~~~~~~--------~~~~RL~AlG~DA~~L 494 (536)
T PF04348_consen 428 PVYATSRSYSGSP-----NPSQDRDLNGVRFSDMPWLLDPNSPLRQQLAALWPNAS--------NSLQRLYALGIDAYRL 494 (536)
T ss_dssp EEEE-GGG--HHT------HHHHHHTTT-EEEE-GGGG---SHHHHHHH-HHTTT---------HHHHHHHHHHHHHHHH
T ss_pred CEEEeccccCCCC-----CcchhhhhcCCEEeccccccCCCchHHHHHHhhccCCc--------cHHHHHHHHHHHHHHH
Confidence 3444443322111 13344678999888753 233344444444443211 1122334566776555
Q ss_pred HHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHHHHHhccccccccceEeccCCCCCCCcEEEEEe
Q 003093 237 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV 314 (848)
Q Consensus 237 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~~~I~~~ 314 (848)
+.+ +.. +..+....+.|+||.+++|++|. +.....-.++
T Consensus 495 ~~~-l~~-------------------------------------l~~~~~~~~~G~TG~L~~~~~g~-i~R~l~wa~f 533 (536)
T PF04348_consen 495 APR-LPQ-------------------------------------LRQFPGYRLDGLTGQLSLDEDGR-IERQLSWAQF 533 (536)
T ss_dssp HHT-HHH-------------------------------------HHHSTT--EEETTEEEEE-TT-B-EEEE-EEEEE
T ss_pred HHH-HHH-------------------------------------HhhCCCCcccCCceeEEECCCCe-EEEeecceee
Confidence 422 111 12223346899999999999986 4444444443
No 111
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=98.78 E-value=1.1e-09 Score=84.09 Aligned_cols=50 Identities=22% Similarity=0.443 Sum_probs=40.6
Q ss_pred CCCcceeeeeHHHHHHHHHhCCCCcceEEeeCC---CCCCCCChhHHHHHHhc
Q 003093 395 KGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFG---DGHNNPSCTELVRLITA 444 (848)
Q Consensus 395 ~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~---~~~~n~s~~~~i~~l~~ 444 (848)
.++.++.|||+||+++|++.|||++++..++.+ ...+||+|+|++++|.+
T Consensus 13 ~g~~~~eGyciDll~~la~~l~F~y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 13 TGNDRYEGYCIDLLEELAEELNFTYEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp BGGGGEESHHHHHHHHHHHHHT-EEEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred CCCccEEEEHHHHHHHHHHHcCCeEEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 467899999999999999999999888777643 33478999999999874
No 112
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=98.12 E-value=4.1e-05 Score=81.19 Aligned_cols=116 Identities=21% Similarity=0.274 Sum_probs=75.3
Q ss_pred CCCCChHHhhcCCCCeeEE-eCchHHH-----HHHhhhCCCcc---CcccCC-CHHHHHHHhhcCCCCCceEEEEccHHH
Q 003093 590 SPIKGIDSLRSSNYPIGYQ-VNSFARN-----YLVDELNIDES---RLVPLN-SPEEYAKALKDGPHKGGVAAVVDDRAY 659 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~-~~s~~~~-----~l~~~~~~~~~---~~~~~~-~~~~~~~~l~~~~~~~~~~a~~~~~~~ 659 (848)
.+|++++||. |+++++. .++.... .+.+..+.... +.+.+. +..+.+.+|.. |++|+.+.+...
T Consensus 125 s~i~sl~DL~--Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~----G~vDa~~~~~~~ 198 (288)
T TIGR03431 125 SPIKSLEDLK--GKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVAN----GTVDAATTNDEN 198 (288)
T ss_pred CCCCcHHHhC--CCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHc----CCCCeEeccHHH
Confidence 4689999996 8889986 3443221 22122222211 123344 67889999999 899999998887
Q ss_pred HHHHHhcC-----CcEEEeCCccccCCceeeecCCC-C-chHHHHHHHHhhhccCchHH
Q 003093 660 AELFLSTR-----CEFSIVGQVFTKNGWGFAFPRDS-P-LAVDISTAILKLSENGDLQR 711 (848)
Q Consensus 660 ~~~~~~~~-----~~l~~~~~~~~~~~~~~~~~k~s-p-l~~~in~~i~~l~e~G~~~~ 711 (848)
+..+..+. .++.++.........+++++++. + +.+.+++++.++.+++..++
T Consensus 199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~~ 257 (288)
T TIGR03431 199 LDRMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDKACF 257 (288)
T ss_pred HHHHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcHHHH
Confidence 77666532 12444432111224578889984 3 99999999999999866554
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=97.95 E-value=7.5e-05 Score=77.71 Aligned_cols=153 Identities=10% Similarity=0.062 Sum_probs=108.8
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.++++||+...+.........+.+.++|+|.+....+. .++++++..++...+..+++++...+-++++++..++
T Consensus 54 ~~~d~ii~~~~~~~~~~~~~~l~~~~ip~v~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~ 128 (264)
T cd01537 54 RGVDGIIIAPSDLTAPTIVKLARKAGIPVVLVDRDIPD-----GDRVPSVGSDNEQAGYLAGEHLAEKGHRRIALLAGPL 128 (264)
T ss_pred cCCCEEEEecCCCcchhHHHHhhhcCCCEEEeccCCCC-----CcccceEecCcHHHHHHHHHHHHHhcCCcEEEEECCC
Confidence 47888887766655554678888899999998766542 2567778888888999999999888899999998654
Q ss_pred C--CccchHHHHHHHHhccC-cEEEEeeecCCCCChHHHHHHHHHHhcCC--CeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 83 D--HGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~i~~~~--~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
. ++....+.|.+.+++.| ..+....... .+..+....+.++.+.+ +++++...+ ..+..++++++++|+..+
T Consensus 129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~~~~-~~a~~~~~~~~~~g~~i~ 205 (264)
T cd01537 129 GSSTARERVAGFKDALKEAGPIEIVLVQEGD--WDAEKGYQAAEELLTAHPDPTAIFAAND-DMALGALRALREAGLRVP 205 (264)
T ss_pred CCCcHHHHHHHHHHHHHHcCCcChhhhccCC--CCHHHHHHHHHHHHhcCCCCCEEEEcCc-HHHHHHHHHHHHhCCCCC
Confidence 4 66677899999999887 4433222222 23466677777777665 566665443 466678999999998644
Q ss_pred CeEEEe
Q 003093 158 GYVWIA 163 (848)
Q Consensus 158 ~~~wi~ 163 (848)
+.+-+.
T Consensus 206 ~~i~i~ 211 (264)
T cd01537 206 DDISVI 211 (264)
T ss_pred CCeEEE
Confidence 434333
No 114
>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=97.87 E-value=0.00042 Score=72.30 Aligned_cols=154 Identities=9% Similarity=0.001 Sum_probs=102.3
Q ss_pred CCeEEEEccCC-chhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAIIGPQD-AVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiIGp~~-S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
.+|++||+... +.......+.+.+.++|+|......+. .+.+..+.+++...+..+++++... |-+++++++
T Consensus 54 ~~vdgvi~~~~~~~~~~~~~~~l~~~~ip~V~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~ 128 (267)
T cd01536 54 QGVDGIIISPVDSAALTPALKKANAAGIPVVTVDSDIDG-----GNRLAYVGTDNYEAGRLAGEYLAKLLGGKGKVAIIE 128 (267)
T ss_pred cCCCEEEEeCCCchhHHHHHHHHHHCCCcEEEecCCCCc-----cceeEEEecCHHHHHHHHHHHHHHHhCCCceEEEEE
Confidence 47888875433 333334556667889999987665432 2345566777787888888887666 889999998
Q ss_pred EcC--CCccchHHHHHHHHhccC-cEEEEeeecCCCCChHHHHHHHHHHhcCCC--eEEEEEccCCcHHHHHHHHHHcCC
Q 003093 80 VDD--DHGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALTES--RIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~dd--~~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~--~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.++ .++....+.|.+.+++.| +++....... .+..+....+.++.+..+ ++|++ ++...+..+++++++.|+
T Consensus 129 ~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~i~~-~~d~~a~~~~~~l~~~g~ 205 (267)
T cd01536 129 GPPGSSNAQERVKGFRDALKEYPDIEIVAVQDGN--WDREKALQAMEDLLQANPDIDAIFA-ANDSMALGAVAALKAAGR 205 (267)
T ss_pred cccccchHHHHHHHHHHHHHhCCCcEEEEEecCC--CcHHHHHHHHHHHHHhCCCccEEEE-ecCCchHHHHHHHHhcCC
Confidence 654 377778899999999984 6654332222 233566677777765544 44443 444677779999999997
Q ss_pred CCCCeEEEecC
Q 003093 155 LGTGYVWIATS 165 (848)
Q Consensus 155 ~~~~~~wi~~~ 165 (848)
. .+...++.+
T Consensus 206 ~-~~i~ivg~d 215 (267)
T cd01536 206 K-GDVKIVGVD 215 (267)
T ss_pred C-CCceEEecC
Confidence 5 444444433
No 115
>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=97.85 E-value=0.00016 Score=75.21 Aligned_cols=154 Identities=10% Similarity=0.030 Sum_probs=104.2
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++++++||....+..+.. ...+...++|+|.+....+. +.+..+..++...+..+++++...|.+++++++.+
T Consensus 53 ~~~~d~iii~~~~~~~~~-~~~~~~~~ipvv~~~~~~~~------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~ 125 (264)
T cd06267 53 SRRVDGIILAPSRLDDEL-LEELAALGIPVVLVDRPLDG------LGVDSVGIDNRAGAYLAVEHLIELGHRRIAFIGGP 125 (264)
T ss_pred HcCcCEEEEecCCcchHH-HHHHHHcCCCEEEecccccC------CCCCEEeeccHHHHHHHHHHHHHCCCceEEEecCC
Confidence 357888887666555555 66788999999998665432 34556677778888888898877799999999855
Q ss_pred CC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCC--CeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 DD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~--~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
.. ++....+.+.+.+++.|..+..........+..+....+.++.... +++|+.. +...+..+++++++.|+..+
T Consensus 126 ~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~al~~~g~~~~ 204 (264)
T cd06267 126 PDLSTARERLEGYREALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIFAA-NDLMAIGALRALRELGLRVP 204 (264)
T ss_pred CccchHHHHHHHHHHHHHHcCCCCCcceEEecccchhhHHHHHHHHHhcCCCCcEEEEc-CcHHHHHHHHHHHHhCCCCC
Confidence 43 6677778899999998854322222222222355666777766555 6666643 44566778899999998544
Q ss_pred CeEEEe
Q 003093 158 GYVWIA 163 (848)
Q Consensus 158 ~~~wi~ 163 (848)
+.+.|.
T Consensus 205 ~~i~i~ 210 (264)
T cd06267 205 EDVSVV 210 (264)
T ss_pred CceEEE
Confidence 444333
No 116
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=97.76 E-value=0.00042 Score=74.54 Aligned_cols=254 Identities=11% Similarity=0.120 Sum_probs=152.0
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
++|+..||||.--....++..-.. ..+|++....++..-...+ -..|-..|. +.++..|+.+-.-|-+...++...
T Consensus 317 q~G~~~VVGPLlK~nVe~L~~~~q-~~i~vLALN~~~n~r~~~~-~cyfaLSPE--DEa~~AA~~l~~qG~R~plvlvPr 392 (604)
T COG3107 317 QDGADFVVGPLLKPNVEALLASNQ-QPIPVLALNQPENSRNPAQ-LCYFALSPE--DEARDAANHLWDQGKRNPLVLVPR 392 (604)
T ss_pred hcCCcEEeccccchhHHHHHhCcC-CCCceeeecCCccccCccc-ceeeecChh--HHHHHHHHHHHHccccCceEEecc
Confidence 478999999999988887655443 7788887554432211111 133445554 458889999988899999999999
Q ss_pred CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHH-----------------------HhcCC-CeEEEEEc
Q 003093 82 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVK-----------------------VALTE-SRIIVVHT 137 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~-----------------------i~~~~-~~viv~~~ 137 (848)
+++|+...++|.++.++.|+..+..+.|... .++...+.. +.+.. .|.|++..
T Consensus 393 ~~lG~Rv~~AF~~~Wq~~gg~~v~~~~fg~~---~~l~~~i~~~a~ir~~~~p~~~~~~~g~~~~p~~~~d~iDaVyivA 469 (604)
T COG3107 393 NDLGDRVANAFNQEWQKLGGGTVLQQKFGST---SELRQGINDGAGIRLTGLPADLTTTNGLQTPPLDDQDTIDAVYIVA 469 (604)
T ss_pred hHHHHHHHHHHHHHHHHhcCCchhHhhcCcH---HHHHhhcccccceeecCCccchhcccCCCCCCcccccccceEEEEe
Confidence 9999999999999999998855544444321 111111111 12223 78899888
Q ss_pred cCCcHHHHHHHHHHcCCCCCCeEEEecCccccccCCCCCCCcccccccceeEEEEE---ecCCchhHHHHHHHHHhhccC
Q 003093 138 HYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRT---YTPDSVLKRKFISRWRNLTDA 214 (848)
Q Consensus 138 ~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~---~~~~~~~~~~f~~~~~~~~~~ 214 (848)
.++++..|--...-.+.... -.-..++.... +..+++....++|+..... ..+..|.+++...+|...
T Consensus 470 tp~el~~IKP~ia~~~~~~~-~p~yaSSr~~~-----gT~~P~~~~~m~GiqysdiP~l~~~~~p~~qq~a~~~p~~--- 540 (604)
T COG3107 470 TPSELALIKPMIAMANGSDS-PPLYASSRSSQ-----GTNGPDFRLEMEGIQYSDIPWLAQPNPPLMQQAAAAWPND--- 540 (604)
T ss_pred cchhHhHHhhHHHhhcCCCC-cceeeeccccc-----cCCCccHHHhccCccccCCchhcCCCchHHHHHHHhcCCc---
Confidence 88887765444432232111 12222322111 1111455567888765433 234557777777666542
Q ss_pred CCCCCCCCCCcchhhhhhHHHHHHHHHHHHHhcCCCccccCCCccccccCccccCcccccCChHHHHH---HHH---hcc
Q 003093 215 KTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRD---SIL---QAN 288 (848)
Q Consensus 215 ~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~l~~---~l~---~~~ 288 (848)
|..+.++|.+++.- .|.. .|+ +-.
T Consensus 541 ----------------~sl~RLyAmGvDAw----------------------------------rLan~f~elrqV~G~~ 570 (604)
T COG3107 541 ----------------YSLARLYAMGVDAW----------------------------------RLANHFSELRQVPGYQ 570 (604)
T ss_pred ----------------hHHHHHHHhcchHH----------------------------------HHHHHhHHhhcCCCcc
Confidence 33555555555441 1111 222 235
Q ss_pred ccccccceEeccCCCCCCCcEEEEEeecccEEEE
Q 003093 289 MTGTAGPARFNSHGDLINPAYEIINVIGTGYRRI 322 (848)
Q Consensus 289 f~G~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~V 322 (848)
++|+||.++.|+++. +.....-.+++.|+.+.|
T Consensus 571 i~G~TG~Lsad~~c~-I~R~l~Waqy~~G~vvP~ 603 (604)
T COG3107 571 IDGLTGTLSADPDCV-IERKLSWAQYQQGQVVPV 603 (604)
T ss_pred cccccceeecCCCce-EeecchHHHhcCCCeeeC
Confidence 789999999999886 445545555555555543
No 117
>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=97.58 E-value=0.0016 Score=68.28 Aligned_cols=145 Identities=14% Similarity=0.013 Sum_probs=97.7
Q ss_pred CCeEEEEccCCc-hhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAIIGPQDA-VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiIGp~~S-~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
++|++||....+ .....+...+.+.++|+|......+ . +.+.++.+++...+..+++++... |-++++++.
T Consensus 59 ~~vdgiIi~~~~~~~~~~~l~~~~~~~iPvv~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~ 132 (272)
T cd06300 59 QGVDAIIINPASPTALNPVIEEACEAGIPVVSFDGTVT---T---PCAYNVNEDQAEFGKQGAEWLVKELGGKGNVLVVR 132 (272)
T ss_pred cCCCEEEEeCCChhhhHHHHHHHHHCCCeEEEEecCCC---C---CceeEecCCHHHHHHHHHHHHHHHcCCCceEEEEE
Confidence 478888875443 3233345567778999998754321 1 456678888888899999987665 888999997
Q ss_pred Ec--CCCccchHHHHHHHHhccC-cEEEEeeecCCCCChHHHHHHHHHHhcCCC--eEEEEEccCCcHHHHHHHHHHcCC
Q 003093 80 VD--DDHGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALTES--RIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~d--d~~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~--~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.+ ...+....+.+.+.+++.| +.+.... ....+..+....+.++.+.++ ++|+...+. +..+++++++.|+
T Consensus 133 ~~~~~~~~~~R~~g~~~a~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~d~--A~g~~~al~~~g~ 208 (272)
T cd06300 133 GLAGHPVDEDRYAGAKEVLKEYPGIKIVGEV--YGDWDQAVAQKAVADFLASNPDVDGIWTQGGD--AVGAVQAFEQAGR 208 (272)
T ss_pred CCCCCcchHHHHHHHHHHHHHCCCcEEEeec--CCCCCHHHHHHHHHHHHHhCCCcCEEEecCCC--cHHHHHHHHHcCC
Confidence 43 3345566788999999987 7765322 222233556667777765554 544444333 8889999999998
Q ss_pred CCC
Q 003093 155 LGT 157 (848)
Q Consensus 155 ~~~ 157 (848)
..+
T Consensus 209 ~~p 211 (272)
T cd06300 209 DIP 211 (272)
T ss_pred CCc
Confidence 433
No 118
>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=97.42 E-value=0.0017 Score=67.66 Aligned_cols=148 Identities=11% Similarity=0.099 Sum_probs=94.5
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc-
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD- 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d- 81 (848)
.+|++||....+.........+.+.++|+|......+ ...+++ ..++...+..+++++...|.++++++..+
T Consensus 54 ~~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~~~~~----~~~~~v---~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~ 126 (266)
T cd06282 54 QRVDGLILTVADAATSPALDLLDAERVPYVLAYNDPQ----PGRPSV---SVDNRAAARDVAQALAALGHRRIAMLAGRL 126 (266)
T ss_pred cCCCEEEEecCCCCchHHHHHHhhCCCCEEEEeccCC----CCCCEE---eeCcHHHHHHHHHHHHHcCcccEEEecccc
Confidence 4688888533333333455677888999987654321 223433 45677788889999888899999999732
Q ss_pred --CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHH-hcC-CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 --DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKV-ALT-ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 --d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i-~~~-~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
++++....+.|.+.++++|+.+......+. +..+....+.++ ++. .+++|+. ++...+..+++++++.|+..+
T Consensus 127 ~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~~p 203 (266)
T cd06282 127 AASDRARQRYAGYRAAMRAAGLAPLPPVEIPF--NTAALPSALLALLTAHPAPTAIFC-SNDLLALAVIRALRRLGLRVP 203 (266)
T ss_pred ccCchHHHHHHHHHHHHHHcCCCCCccccCCC--cHHHHHHHHHHHhcCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCC
Confidence 345667789999999999876433222221 223333444443 333 4666665 455667789999999998644
Q ss_pred CeE
Q 003093 158 GYV 160 (848)
Q Consensus 158 ~~~ 160 (848)
+-+
T Consensus 204 ~di 206 (266)
T cd06282 204 DDL 206 (266)
T ss_pred Cce
Confidence 333
No 119
>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=97.32 E-value=0.0056 Score=64.29 Aligned_cols=154 Identities=8% Similarity=0.024 Sum_probs=94.8
Q ss_pred CCeEE-EEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVA-IIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~a-iIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
++|++ ||.|..+....+....+.+.++|+|.+....+ ....+ .+..++...+..+++++... |.++++++.
T Consensus 56 ~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~~~---~~~~~---~V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~ 129 (275)
T cd06320 56 KGYKGLLFSPISDVNLVPAVERAKKKGIPVVNVNDKLI---PNATA---FVGTDNKANGVRGAEWIIDKLAEGGKVAIIE 129 (275)
T ss_pred hCCCEEEECCCChHHhHHHHHHHHHCCCeEEEECCCCC---Cccce---EEecCcHHHHHHHHHHHHHHhCCCceEEEEe
Confidence 46777 45766555444455667789999998754321 11112 24566677788888887655 889999997
Q ss_pred EcC--CCccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEc-cCCcHHHHHHHHHHcCCC
Q 003093 80 VDD--DHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT-HYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 80 ~dd--~~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~-~~~~~~~~~~~a~~~g~~ 155 (848)
... .......+.+.+.++++ |+++..... ...+..+....+.++....+++-.+++ +...+..+++++++.|+.
T Consensus 130 ~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~~~~~al~~~g~~ 207 (275)
T cd06320 130 GKAGAFAAEQRTEGFTEAIKKASGIEVVASQP--ADWDREKAYDVATTILQRNPDLKAIYCNNDTMALGVVEAVKNAGKQ 207 (275)
T ss_pred CCCCCccHHHHHHHHHHHHhhCCCcEEEEecC--CCccHHHHHHHHHHHHHhCCCccEEEECCchhHHHHHHHHHhcCCC
Confidence 432 23345568899999999 988754321 122234455566666554444433344 445566788889999974
Q ss_pred CCCeEEEecC
Q 003093 156 GTGYVWIATS 165 (848)
Q Consensus 156 ~~~~~wi~~~ 165 (848)
.+...++.+
T Consensus 208 -~di~vig~d 216 (275)
T cd06320 208 -GKVLVVGTD 216 (275)
T ss_pred -CCeEEEecC
Confidence 343344433
No 120
>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=97.24 E-value=0.0079 Score=62.73 Aligned_cols=153 Identities=10% Similarity=0.069 Sum_probs=92.5
Q ss_pred CCeEE-EEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVA-IIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~a-iIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
.+++| |++|..+.........+...++|+|......+ ..+.+-.+..++...+..+++++... |-+++++++
T Consensus 54 ~~~dgii~~~~~~~~~~~~l~~l~~~~ipvv~~~~~~~-----~~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~l~ 128 (268)
T cd06323 54 RGVDAIIINPTDSDAVVPAVKAANEAGIPVFTIDREAN-----GGEVVSQIASDNVAGGKMAAEYLVKLLGGKGKVVELQ 128 (268)
T ss_pred cCCCEEEEcCCChHHHHHHHHHHHHCCCcEEEEccCCC-----CCceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEe
Confidence 46777 55666555444444556678999998755322 11223335555565678888887666 789999998
Q ss_pred Ec--CCCccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcCC--CeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 80 VD--DDHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~d--d~~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~--~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.+ ..++....+.|.++++++ |+++....... .+..+....+.++.... +++| ++.+...+..+++++++.|.
T Consensus 129 ~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~~l~~~g~ 205 (268)
T cd06323 129 GIPGASAARERGKGFHEVVDKYPGLKVVASQPAD--FDRAKGLNVMENILQAHPDIKGV-FAQNDEMALGAIEALKAAGK 205 (268)
T ss_pred CCCCCccHHHHHHHHHHHHHhCCCcEEEecccCC--CCHHHHHHHHHHHHHHCCCcCEE-EEcCCchHHHHHHHHHHcCC
Confidence 53 335666778999999985 77765322111 12233334455554333 4443 33444555568999999998
Q ss_pred CCCCeEEEecC
Q 003093 155 LGTGYVWIATS 165 (848)
Q Consensus 155 ~~~~~~wi~~~ 165 (848)
++...++.+
T Consensus 206 --~di~iig~d 214 (268)
T cd06323 206 --DDVKVVGFD 214 (268)
T ss_pred --CCcEEEEeC
Confidence 444455443
No 121
>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=97.20 E-value=0.0092 Score=62.64 Aligned_cols=156 Identities=10% Similarity=0.095 Sum_probs=93.4
Q ss_pred CCeEEE-EccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc------CcEEE
Q 003093 3 GQTVAI-IGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY------GWREV 75 (848)
Q Consensus 3 ~~V~ai-IGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~------~w~~v 75 (848)
+++++| ++|..+.....+...+.+.++|+|.+....+ ...++..+.+++..-+..+++++... |-+++
T Consensus 54 ~~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~~~-----~~~~~~~v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i 128 (277)
T cd06319 54 KGVSGIIISPTNSSAAVTLLKLAAQAKIPVVIADIGAE-----GGDYVSYIKSDNYEGAYDLGKFLAAAMKAQGWADGKV 128 (277)
T ss_pred cCCCEEEEcCCchhhhHHHHHHHHHCCCCEEEEecCCC-----CCceEEEEeeccHHHHHHHHHHHHHHHHhhCCCCCcE
Confidence 467766 5776665555666778889999998643211 11233345556555566777765433 66899
Q ss_pred EEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEE-EEEccCCcHHHHHHHHHHc
Q 003093 76 IAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRII-VVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 76 aii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~vi-v~~~~~~~~~~~~~~a~~~ 152 (848)
+++... ...+....+.|.+.+++.|+.+.... ...+.+..+....+.++....++.- +++.+...+..+++++++.
T Consensus 129 ~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~al~~~ 207 (277)
T cd06319 129 GMVAIPQKRKNGQKRTKGFKEAMKEAGCDLAGIR-QQKDFSYQETFDYTNDLLTANPDIRAIWLQGSDRYQGALDAIATA 207 (277)
T ss_pred EEEeccCCCccHHHHHHHHHHHHHhcCCceEeec-cCCCCCHHHHHHHHHHHHHhCCCCCEEEECCCccchHHHHHHHHc
Confidence 999743 34466778899999999998754221 1112222344445555554444432 2334455566799999999
Q ss_pred CCCCCCeEEEecC
Q 003093 153 GMLGTGYVWIATS 165 (848)
Q Consensus 153 g~~~~~~~wi~~~ 165 (848)
|+. .+...++.+
T Consensus 208 g~~-~di~vvg~d 219 (277)
T cd06319 208 GKT-GKVLLICFD 219 (277)
T ss_pred CCC-CCEEEEEcC
Confidence 985 344444434
No 122
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=97.06 E-value=0.0031 Score=64.89 Aligned_cols=121 Identities=21% Similarity=0.274 Sum_probs=74.4
Q ss_pred CCCCChHHhhcCCCCeeEEeCch-----HHHHHH-hhhCCCc---cCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHH
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNSF-----ARNYLV-DELNIDE---SRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYA 660 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s~-----~~~~l~-~~~~~~~---~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~ 660 (848)
++|++++||. |+++++...+. ...... ++.+... .+.+...+.+..+.+|.+ |++|+.+......
T Consensus 95 s~i~~l~dL~--Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~----G~~Da~~~~~~~~ 168 (243)
T PF12974_consen 95 SPITSLADLK--GKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLN----GKADAAAIPSDAF 168 (243)
T ss_dssp SS--SHHHHG--GSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHT----TSSSEEEEEHHHH
T ss_pred CCCCChhhcC--CCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHc----CCccEEEEechhH
Confidence 4799999998 99999875432 222222 2223331 133345688889999999 8999888888777
Q ss_pred HHHHhcC----CcEEEeCCccccCCceeeecCCCC--chHHHHHHHHhhhccCchHHHHHhh
Q 003093 661 ELFLSTR----CEFSIVGQVFTKNGWGFAFPRDSP--LAVDISTAILKLSENGDLQRIHDKW 716 (848)
Q Consensus 661 ~~~~~~~----~~l~~~~~~~~~~~~~~~~~k~sp--l~~~in~~i~~l~e~G~~~~~~~kw 716 (848)
+-+...+ .+++++...-.-....++..++-| .++.|-.+++.+..+-.-.++.+.+
T Consensus 169 ~~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~~~~~l~~~ 230 (243)
T PF12974_consen 169 ERLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPEGKAILDAF 230 (243)
T ss_dssp HHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHHHHHHHHHT
T ss_pred HHHHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChhhHHHHHhc
Confidence 7666543 357777654333345677777766 8999999999999764444444444
No 123
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.03 E-value=0.0033 Score=67.49 Aligned_cols=71 Identities=23% Similarity=0.295 Sum_probs=48.0
Q ss_pred CCCCChHHhhcCCCCeeEEeCchHHHHHHhh---hCCCccCc-ccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHh
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNSFARNYLVDE---LNIDESRL-VPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLS 665 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s~~~~~l~~~---~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~ 665 (848)
++|.+++||. |++|++..|+....++... .+.....+ ..+.+..+...++.. |++|+++...++......
T Consensus 119 s~i~s~~dL~--Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~----G~vDa~~~~ep~~~~~~~ 192 (314)
T PRK11553 119 SPIKTVADLK--GHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQ----GNVDAWAIWDPYYSAALL 192 (314)
T ss_pred CCCCCHHHhC--CCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHc----CCCCEEEEcCcHHHHHHh
Confidence 3688999998 8889998887666554332 22221111 123466677899999 999999887777666555
Q ss_pred c
Q 003093 666 T 666 (848)
Q Consensus 666 ~ 666 (848)
+
T Consensus 193 ~ 193 (314)
T PRK11553 193 Q 193 (314)
T ss_pred c
Confidence 4
No 124
>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=97.02 E-value=0.0069 Score=63.78 Aligned_cols=144 Identities=15% Similarity=0.135 Sum_probs=94.8
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCC----CCCCCceEeccCChHHHHHHHHHHHHHc--CcEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLS----SLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREV 75 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls----~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~v 75 (848)
+++|++||+..++. ...+ ...+.++|+|.++...+... ....+....+..++...+..+++++... |.+++
T Consensus 58 ~~~vd~iI~~~~~~-~~~~--~~~~~~iPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~i 134 (281)
T cd06325 58 ADKPDLIVAIATPA-AQAA--ANATKDIPIVFTAVTDPVGAGLVKSLEKPGGNVTGVSDLVPVETQLELLKKLLPDAKTV 134 (281)
T ss_pred hcCCCEEEEcCcHH-HHHH--HHcCCCCCEEEEecCCccccccccccccCCCceeCeecccchHHHHHHHHHHCCCCcEE
Confidence 35788999865442 2222 25678999998865543211 1111222223445566677888887765 99999
Q ss_pred EEEEEcC-CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 76 IAIYVDD-DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 76 aii~~dd-~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
++++.+. .++....+.+.+.+++.|+++.... . .+..++...++++.+ ++|+|++..+ ..+..+++++++.|+
T Consensus 135 ~~l~~~~~~~~~~r~~g~~~~~~~~g~~~~~~~-~---~~~~~~~~~~~~~~~-~~dai~~~~d-~~a~~~~~~~~~~~~ 208 (281)
T cd06325 135 GVLYNPSEANSVVQVKELKKAAAKLGIEVVEAT-V---SSSNDVQQAAQSLAG-KVDAIYVPTD-NTVASAMEAVVKVAN 208 (281)
T ss_pred EEEeCCCCccHHHHHHHHHHHHHhCCCEEEEEe-c---CCHHHHHHHHHHhcc-cCCEEEEcCc-hhHHhHHHHHHHHHH
Confidence 9998554 3677778999999999999876532 2 133667777777764 4687776544 466678888888875
No 125
>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=96.97 E-value=0.0078 Score=62.83 Aligned_cols=148 Identities=12% Similarity=0.090 Sum_probs=92.8
Q ss_pred CCeEEEE--ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 3 GQTVAII--GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiI--Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
.+|+||| |+..+ ..+...+.+.++|+|......+ ....++ +..++...+..+++.+...|.+++++|..
T Consensus 54 ~~vdgiii~~~~~~---~~~~~~l~~~~iPvv~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~ 124 (268)
T cd06273 54 RGVDGLALIGLDHS---PALLDLLARRGVPYVATWNYSP---DSPYPC---VGFDNREAGRLAARHLIALGHRRIAMIFG 124 (268)
T ss_pred cCCCEEEEeCCCCC---HHHHHHHHhCCCCEEEEcCCCC---CCCCCE---EEeChHHHHHHHHHHHHHCCCCeEEEEec
Confidence 3565544 44333 2334566778999998754322 122343 34667778888899887779999999974
Q ss_pred c---CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 81 D---DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 81 d---d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
. +.++......|.+.++++|+.+.....+....+..+....+.++.+ ..+++|+. ++...+..+++++++.|+.
T Consensus 125 ~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~~~~a~~~~~~l~~~g~~ 203 (268)
T cd06273 125 PTQGNDRARARRAGVRAALAEAGLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVIC-GNDVLALGALYEARRLGLS 203 (268)
T ss_pred cccCCccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCcHHHHHHHHHHHHcCCCCCCEEEE-cChHHHHHHHHHHHHcCCC
Confidence 3 2346677889999999998654322222212222334455556543 34777765 5556677899999999986
Q ss_pred CCCeE
Q 003093 156 GTGYV 160 (848)
Q Consensus 156 ~~~~~ 160 (848)
.++.+
T Consensus 204 ~p~~i 208 (268)
T cd06273 204 VPEDL 208 (268)
T ss_pred CCCce
Confidence 54433
No 126
>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=96.91 E-value=0.026 Score=58.98 Aligned_cols=156 Identities=13% Similarity=0.055 Sum_probs=94.0
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
.+|+++| .|..+.....+...+.+.++|+|......+.. .+.+..+..++...+..+++++... +-++++++.
T Consensus 55 ~~vdgiii~~~~~~~~~~~~~~l~~~~iPvv~~~~~~~~~----~~~~~~V~~d~~~~g~~~~~~l~~~~~~~~~i~~i~ 130 (272)
T cd06301 55 QGVDAIIVVPVDTAATAPIVKAANAAGIPLVYVNRRPENA----PKGVAYVGSDEVVAGRLQAEYVADKLGGKGNVAILM 130 (272)
T ss_pred cCCCEEEEecCchhhhHHHHHHHHHCCCeEEEecCCCCCC----CCeeEEEecChHHHHHHHHHHHHHHhCCCccEEEEE
Confidence 4677775 66655544455566788999999875432211 1234456677777888888887554 557999997
Q ss_pred EcC--CCccchHHHHHHHHhccC-cEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 80 VDD--DHGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~dd--~~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
... .......+.|.+++++.| +.+... .....+.......+.++.+. .+++| ++.+...+..+++.+++.|.
T Consensus 131 ~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~~l~~~g~ 207 (272)
T cd06301 131 GPLGQSAQIDRTKGVEEVLAKYPDIKVVEE--QTANWSRAEAMDLMENWLSSGGKIDAV-VANNDEMALGAIMALKAAGK 207 (272)
T ss_pred CCCCCccHHHHHHHHHHHHHHCCCcEEEec--CCCCccHHHHHHHHHHHHHhCCCCCEE-EECCCchHHHHHHHHHHcCC
Confidence 433 234455688999999888 444321 11122222233444554332 45654 34455566689999999998
Q ss_pred CCCCeEEEecC
Q 003093 155 LGTGYVWIATS 165 (848)
Q Consensus 155 ~~~~~~wi~~~ 165 (848)
...+...++.+
T Consensus 208 ~~~di~ivg~d 218 (272)
T cd06301 208 SDKDVPVAGID 218 (272)
T ss_pred CCCCcEEEeeC
Confidence 63355555544
No 127
>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=96.87 E-value=0.023 Score=59.56 Aligned_cols=158 Identities=13% Similarity=0.094 Sum_probs=90.2
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEec-cCChHHHHHHHHHHHHHc--CcEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRT-TQSDQYQMAAIAEIVDHY--GWREVIAI 78 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~-~p~d~~q~~ai~~~~~~~--~w~~vaii 78 (848)
++|++|| .|..+.........+.+.++|+|......+ ....++.+.. .+++...+..+++.+... |-++++++
T Consensus 55 ~~vdgiii~~~~~~~~~~~l~~~~~~~iPvV~~~~~~~---~~~~~~v~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l 131 (275)
T cd06317 55 QKVDGIILWPTDGQAYIPGLRKAKQAGIPVVITNSNIS---EKGFEFIKSFTGPDDISQGERSAEAMCKALGGKGQIVVI 131 (275)
T ss_pred cCCCEEEEecCCccccHHHHHHHHHCCCcEEEeCCCCC---CCccchhhhhccccHHHHHHHHHHHHHHHcCCCceEEEE
Confidence 4677774 454444444445666789999998754321 2234544333 344455666777776444 77899999
Q ss_pred EEcCCC--ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc---CCCeEEEEEccCCcHHHHHHHHHHcC
Q 003093 79 YVDDDH--GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL---TESRIIVVHTHYNRGPVVFHVAQYLG 153 (848)
Q Consensus 79 ~~dd~~--g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~---~~~~viv~~~~~~~~~~~~~~a~~~g 153 (848)
..+.++ +....+.|.+.++++|..+..........+..+....+.++-+ .++++|++ ++...+..+++++++.|
T Consensus 132 ~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~-~~d~~a~g~~~~l~~~g 210 (275)
T cd06317 132 AGQPGNGTAIERQKGFEDELAEVCPGVEVLDTQPADWDREKAQVAMEALITKFGDDIDGVYA-GDDNMARGALNAAKEAG 210 (275)
T ss_pred ecCCCCchHHHHHHHHHHHHHhhCCCCEEEeccCCCCCHHHHHHHHHHHHHhCCCCccEEEE-CCCcHHHHHHHHHHhcC
Confidence 754443 3444688999999986433222222111121222333444322 24677764 44455778999999999
Q ss_pred CCCCCeEEEecC
Q 003093 154 MLGTGYVWIATS 165 (848)
Q Consensus 154 ~~~~~~~wi~~~ 165 (848)
+. .+...++.+
T Consensus 211 ~~-~dv~v~g~d 221 (275)
T cd06317 211 LA-GGIVIVGAN 221 (275)
T ss_pred Cc-CCcEEEEeC
Confidence 85 344444333
No 128
>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=96.86 E-value=0.013 Score=61.30 Aligned_cols=157 Identities=13% Similarity=0.114 Sum_probs=95.7
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+++|+|||....+.......+.+...++|+|......+. ..+++ +..++...+..+++.+...|.++++++..+
T Consensus 54 ~~~vdgiii~~~~~~~~~~~~~~~~~~ipvv~i~~~~~~---~~~~~---V~~d~~~~g~~a~~~l~~~g~~~i~~i~~~ 127 (270)
T cd01545 54 RSRVDGVILTPPLSDNPELLDLLDEAGVPYVRIAPGTPD---PDSPC---VRIDDRAAAREMTRHLIDLGHRRIAFIAGP 127 (270)
T ss_pred HCCCCEEEEeCCCCCccHHHHHHHhcCCCEEEEecCCCC---CCCCe---EEeccHHHHHHHHHHHHHCCCceEEEEeCC
Confidence 357888887554433344556677899999987654332 22233 334566667888888877899999999855
Q ss_pred CCCc--cchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 DDHG--RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d~~g--~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
..+. ......|.+.+++.|+.+..........+..+-...+.++.+ .++++|+. ++...+..+++++++.|...+
T Consensus 128 ~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~-~~d~~a~~~~~~~~~~g~~~p 206 (270)
T cd01545 128 PDHRASAERLEGYRDALAEAGLPLDPELVAQGDFTFESGLEAAEALLALPDRPTAIFA-SNDDMAAGVLAVAHRRGLRVP 206 (270)
T ss_pred CCchhHHHHHHHHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCC
Confidence 5443 334678999999888765210011111111222234445443 34677664 455677789999999998544
Q ss_pred C-eEEEecC
Q 003093 158 G-YVWIATS 165 (848)
Q Consensus 158 ~-~~wi~~~ 165 (848)
+ ...++.+
T Consensus 207 ~~i~vig~d 215 (270)
T cd01545 207 DDLSVVGFD 215 (270)
T ss_pred CceEEEEEC
Confidence 3 3444444
No 129
>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=96.74 E-value=0.038 Score=57.82 Aligned_cols=155 Identities=13% Similarity=0.106 Sum_probs=95.8
Q ss_pred CCeEEEEccC-CchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHH-cCcEEEEEEEE
Q 003093 3 GQTVAIIGPQ-DAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiIGp~-~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~-~~w~~vaii~~ 80 (848)
.++++||... ...........+.+.++|+|......+... ..+.+..+..++...+..+++++.. .|-++++++..
T Consensus 56 ~~vdgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~~~~~~--~~~~~~~V~~d~~~~g~~~~~~l~~~~g~~~i~~i~g 133 (271)
T cd06312 56 AKPDGIVVTIPDPDALDPAIKRAVAAGIPVISFNAGDPKYK--ELGALAYVGQDEYAAGEAAGERLAELKGGKNVLCVIH 133 (271)
T ss_pred hCCCEEEEeCCChHHhHHHHHHHHHCCCeEEEeCCCCCccc--cccceEEeccChHHHHHHHHHHHHHhcCCCeEEEEec
Confidence 4677777533 322233344556778999998764332211 1244566778888889999999877 89999999974
Q ss_pred c--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 81 D--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 81 d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
+ +..+....+.|.++++++|+.+... ....+..+....++++.+. ++++|+... ...+..+++.+++.|+.
T Consensus 134 ~~~~~~~~~r~~g~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~aI~~~~-d~~a~g~~~al~~~g~~- 208 (271)
T cd06312 134 EPGNVTLEDRCAGFADGLGGAGITEEVI---ETGADPTEVASRIAAYLRANPDVDAVLTLG-APSAAPAAKALKQAGLK- 208 (271)
T ss_pred CCCCccHHHHHHHHHHHHHhcCceeeEe---ecCCCHHHHHHHHHHHHHhCCCccEEEEeC-CccchHHHHHHHhcCCC-
Confidence 3 3345667889999999988754321 1111223344445554333 356555444 45566788899999985
Q ss_pred CCeEEEec
Q 003093 157 TGYVWIAT 164 (848)
Q Consensus 157 ~~~~wi~~ 164 (848)
.....++.
T Consensus 209 ~di~vvg~ 216 (271)
T cd06312 209 GKVKLGGF 216 (271)
T ss_pred CCeEEEEe
Confidence 34333333
No 130
>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=96.66 E-value=0.032 Score=58.33 Aligned_cols=156 Identities=13% Similarity=-0.032 Sum_probs=91.5
Q ss_pred CCeEEEEcc-CCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHH--cCcEEEEEEE
Q 003093 3 GQTVAIIGP-QDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH--YGWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiIGp-~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~--~~w~~vaii~ 79 (848)
.+|++||-. ..+.....+...+.+.++|+|.+....+. +.+..+..++...++.+++++.. .|.++++++.
T Consensus 54 ~~vdgii~~~~~~~~~~~~i~~~~~~~ipvV~~~~~~~~------~~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~ 127 (273)
T cd06305 54 QKVDAIIIQHGRAEVLKPWVKRALDAGIPVVAFDVDSDN------PKVNNTTQDDYSLARLSLDQLVKDLGGKGNVGYVN 127 (273)
T ss_pred cCCCEEEEecCChhhhHHHHHHHHHcCCCEEEecCCCCC------CccceeeechHHHHHHHHHHHHHHhCCCCCEEEEE
Confidence 468888764 33333344445567889999987553221 22334666777788888888755 5889999997
Q ss_pred Ec-CCCccchHHHHHHHHhccC-cEEEEeeecCCCCChHHHHHHHHHHhcCCCeE---EEEEccCCcHHHHHHHHHHcCC
Q 003093 80 VD-DDHGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALTESRI---IVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~d-d~~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~v---iv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.. ..........+.+.+++.+ +.+..........+..+....++++....++. .+++.+...+..++.++++.|.
T Consensus 128 ~~~~~~~~~R~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~~d~~a~g~~~~l~~~g~ 207 (273)
T cd06305 128 VAGFPPLDRRYDVWQAVLKAYPGIKEVAELGDVSNNTAQDAAAQVEAVLKKYPKGGIDAIWAAWDEFAKGAKQALDEAGR 207 (273)
T ss_pred ccCCchHHHHHHHHHHHHHHCCCcEEecccccccccchhHHHHHHHHHHHHCCCcccCeEEEcChhhhHHHHHHHHHcCC
Confidence 43 2223344567888888887 65543221111112234444555554444433 2333345566778899999998
Q ss_pred CCCCeEEEecC
Q 003093 155 LGTGYVWIATS 165 (848)
Q Consensus 155 ~~~~~~wi~~~ 165 (848)
.. +...++.+
T Consensus 208 ~~-di~iig~d 217 (273)
T cd06305 208 TD-EIKIYGVD 217 (273)
T ss_pred CC-CceEEEec
Confidence 53 44444444
No 131
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=96.54 E-value=0.058 Score=56.44 Aligned_cols=158 Identities=8% Similarity=-0.003 Sum_probs=95.0
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
++|++|| .|..+.........+.+.++|+|......+.. ...+++.++.+++...+..+++++... |-++++++.
T Consensus 54 ~~vdgiIi~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~~~--~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~ 131 (273)
T cd06309 54 QGVDVIILAPVVETGWDPVLKEAKAAGIPVILVDRGVDVK--DDSLYVTFIGSDFVEEGRRAADWLAKATGGKGNIVELQ 131 (273)
T ss_pred cCCCEEEEcCCccccchHHHHHHHHCCCCEEEEecCcCCc--cCcceeeEecCChHHHHHHHHHHHHHHcCCCceEEEEe
Confidence 4566664 55544433344456778899999876532211 112467778888888889898987666 889999997
Q ss_pred EcCC--CccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcC---CCeEEEEEccCCcHHHHHHHHHHcC
Q 003093 80 VDDD--HGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVHTHYNRGPVVFHVAQYLG 153 (848)
Q Consensus 80 ~dd~--~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~---~~~viv~~~~~~~~~~~~~~a~~~g 153 (848)
.+.+ ......+.|.++++++ +.++... .....+..+....+.++... .+++|+ +.+...+..+++++++.|
T Consensus 132 ~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~aI~-~~~d~~a~g~~~a~~~~g 208 (273)
T cd06309 132 GTVGSSVAIDRKKGFAEVIKKYPNMKIVAS--QTGDFTRAKGKEVMEALLKAHGDDIDAVY-AHNDEMALGAIQAIKAAG 208 (273)
T ss_pred CCCCCchHHHHHHHHHHHHHHCCCCEEeec--cCCcccHHHHHHHHHHHHHhCCCCccEEE-ECCcHHHHHHHHHHHHcC
Confidence 5432 2234568899999987 4554421 11111223333445554433 355543 334455567899999999
Q ss_pred CCCCCeE-EEecC
Q 003093 154 MLGTGYV-WIATS 165 (848)
Q Consensus 154 ~~~~~~~-wi~~~ 165 (848)
+..++-+ .++.+
T Consensus 209 ~~ip~di~iig~d 221 (273)
T cd06309 209 KKPGKDIKIVSID 221 (273)
T ss_pred CCCCCCeEEEecC
Confidence 8654444 44433
No 132
>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=96.48 E-value=0.029 Score=58.44 Aligned_cols=153 Identities=14% Similarity=0.089 Sum_probs=94.3
Q ss_pred CCeEEEE--ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 3 GQTVAII--GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiI--Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
.+|+||| ++..+ ..+...+...++|+|.+....+ ....++ +.+++...+..+++++...|-++++++..
T Consensus 54 ~~vdgiii~~~~~~---~~~~~~l~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~l~~ 124 (268)
T cd06298 54 KQVDGIIFMGGKIS---EEHREEFKRSPTPVVLAGSVDE---DNELPS---VNIDYKKAAFEATELLIKNGHKKIAFISG 124 (268)
T ss_pred hcCCEEEEeCCCCc---HHHHHHHhcCCCCEEEEccccC---CCCCCE---EEECcHHHHHHHHHHHHHcCCceEEEEeC
Confidence 4677776 43222 2344556677999998765322 122232 45667777788888887789999999974
Q ss_pred cC---CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCC-CeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 81 DD---DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTE-SRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 81 dd---~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~-~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
+. ..+....+.|.+.++++|+.+.....+....+.......+.++.+.. +++|++ ++...+..+++++++.|+..
T Consensus 125 ~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~v 203 (268)
T cd06298 125 PLEDSINGDERLAGYKEALSEANIEFDESLIFEGDYTYESGYELAEELLEDGKPTAAFV-TDDELAIGILNAAQDAGLKV 203 (268)
T ss_pred CcccccchhHHHHHHHHHHHHcCCCCCHHHeEeCCCChhHHHHHHHHHhcCCCCCEEEE-cCcHHHHHHHHHHHHcCCCC
Confidence 33 35677788999999999876422111111111223334555655444 677775 44455778999999999865
Q ss_pred CC-eEEEecC
Q 003093 157 TG-YVWIATS 165 (848)
Q Consensus 157 ~~-~~wi~~~ 165 (848)
++ ..+++.+
T Consensus 204 p~di~vvg~d 213 (268)
T cd06298 204 PEDFEIIGFN 213 (268)
T ss_pred ccceEEEeec
Confidence 43 3444444
No 133
>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=96.34 E-value=0.05 Score=56.65 Aligned_cols=152 Identities=13% Similarity=0.056 Sum_probs=92.0
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
++|++||...+...... ...+.+.++|+|.+....+ ...+++ +.+++...+..+++++...|-++++++....
T Consensus 58 ~~vdgiii~~~~~~~~~-~~~~~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~ 130 (268)
T cd06271 58 GLVDGVIISRTRPDDPR-VALLLERGFPFVTHGRTEL---GDPHPW---VDFDNEAAAYQAVRRLIALGHRRIALLNPPE 130 (268)
T ss_pred CCCCEEEEecCCCCChH-HHHHHhcCCCEEEECCcCC---CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEecCcc
Confidence 46888886433322222 3455678999998754322 123444 3456677778888888778999999997433
Q ss_pred --CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 83 --DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 83 --~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
..+....+.|.+.++++|..+.....+....+.......+.++... .+++|+.. +...+..+++++++.|+..++
T Consensus 131 ~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~vp~ 209 (268)
T cd06271 131 DLTFAQHRRAGYRRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIVCS-SELMALGVLAALAEAGLRPGR 209 (268)
T ss_pred ccchHHHHHHHHHHHHHHhCCCCCCceEEeCCCChHHHHHHHHHHHhCCCCCCEEEEc-CcHHHHHHHHHHHHhCCCCCc
Confidence 2344567889999999887642211122112223333445554332 36666664 445667799999999987654
Q ss_pred eEEE
Q 003093 159 YVWI 162 (848)
Q Consensus 159 ~~wi 162 (848)
-+-+
T Consensus 210 ~i~i 213 (268)
T cd06271 210 DVSV 213 (268)
T ss_pred ceeE
Confidence 4433
No 134
>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=96.33 E-value=0.033 Score=58.01 Aligned_cols=157 Identities=13% Similarity=0.018 Sum_probs=92.0
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+++|+|||...+......+...+...++|+|.+....+. ...+ .+.+++...+..+++++...|-++|+++..+
T Consensus 53 ~~~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~~~~~~---~~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~ 126 (268)
T cd06289 53 EHGVAGIILCPAAGTSPDLLKRLAESGIPVVLVAREVAG---APFD---YVGPDNAAGARLATEHLISLGHRRIAFIGGL 126 (268)
T ss_pred HcCCCEEEEeCCCCccHHHHHHHHhcCCCEEEEeccCCC---CCCC---EEeecchHHHHHHHHHHHHCCCCCEEEecCC
Confidence 356888876544333333455677889999987543221 1222 2445666777888888777788999988743
Q ss_pred C--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 D--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
. .......+.|.+.+++.|..+.....++...+.......+.++... .+++|+. .+...+..+++++++.|+..+
T Consensus 127 ~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~-~~~~~a~~~~~al~~~g~~~p 205 (268)
T cd06289 127 EDSSTRRERLAGYRAALAEAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAIVC-FNDLVAFGAMSGLRRAGLTPG 205 (268)
T ss_pred ccccchHHHHHHHHHHHHHcCCCCCchhEEecCcchhhHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCC
Confidence 2 3445667899999998885422111111111222233444444333 4566553 344456678999999998654
Q ss_pred C-eEEEecC
Q 003093 158 G-YVWIATS 165 (848)
Q Consensus 158 ~-~~wi~~~ 165 (848)
+ ...++.+
T Consensus 206 ~di~iig~d 214 (268)
T cd06289 206 RDIAVVGFD 214 (268)
T ss_pred cceEEEeec
Confidence 3 3344433
No 135
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=96.33 E-value=0.019 Score=61.16 Aligned_cols=70 Identities=17% Similarity=0.190 Sum_probs=47.8
Q ss_pred CCCCChHHhhcCCCCeeEEeCchHHHHHHh---hhCCCcc--CcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHH
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNSFARNYLVD---ELNIDES--RLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFL 664 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s~~~~~l~~---~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~ 664 (848)
..|++++||. |++||+..++....++.. ..+.... +++.+ ...+...++.+ |++||++...++.....
T Consensus 90 s~I~s~~DLk--GK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~----G~vDa~~~~~p~~~~~~ 162 (300)
T TIGR01729 90 SGIEKPEDLK--GKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQR----GDIDAAYVWPPALSELL 162 (300)
T ss_pred CCCCChhHcC--CCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHc----CCcCEEEEecHHHHHHH
Confidence 4799999998 999999877654443322 2233222 23333 46778899999 89999998888776555
Q ss_pred hc
Q 003093 665 ST 666 (848)
Q Consensus 665 ~~ 666 (848)
+.
T Consensus 163 ~~ 164 (300)
T TIGR01729 163 KS 164 (300)
T ss_pred hc
Confidence 44
No 136
>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=96.30 E-value=0.14 Score=53.49 Aligned_cols=155 Identities=10% Similarity=0.026 Sum_probs=92.0
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
++|++|| -|..+........-+.+.+||+|.+....+ ....+.+..+.+++...+..+++++... |.++++++.
T Consensus 54 ~~vdgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~---~~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~ 130 (272)
T cd06313 54 QGWDFIAVDPLGIGTLTEAVQKAIARGIPVIDMGTLIA---PLQINVHSFLAPDNYFMGASVAQALCNAMGGKGKIAMLQ 130 (272)
T ss_pred cCCCEEEEcCCChHHhHHHHHHHHHCCCcEEEeCCCCC---CCCCceEEEECCCcHHHHHHHHHHHHHHcCCCceEEEEE
Confidence 4565544 444444333333445667999998765332 1111233446677787888899987666 889999997
Q ss_pred EcCCC--ccchHHHHHHHHhccC-cEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 80 VDDDH--GRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~dd~~--g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.+... .....+.|.+.+++.+ .++... .....+.......+.++... .+++|+ +.+...+..+++.+++.|+
T Consensus 131 g~~~~~~~~~R~~gf~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~a~g~~~al~~~g~ 207 (272)
T cd06313 131 GALGHTGAQGRAQGFNDVIKKYPDIEVVDE--QPANWDVSKAARIWETWLTKYPQLDGAF-CHNDSMALAAYQIMKAAGR 207 (272)
T ss_pred CCCCCcchhHHHHHHHHHHHhCCCCEEEec--cCCCCCHHHHHHHHHHHHHhCCCCCEEE-ECCCcHHHHHHHHHHHcCC
Confidence 54332 3456788999999876 655431 12122223334455554433 355544 3555667778999999997
Q ss_pred CCCCeEEEecC
Q 003093 155 LGTGYVWIATS 165 (848)
Q Consensus 155 ~~~~~~wi~~~ 165 (848)
.+...++-+
T Consensus 208 --~di~vvgfd 216 (272)
T cd06313 208 --TKIVIGGVD 216 (272)
T ss_pred --CceEEEeec
Confidence 444444443
No 137
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=96.29 E-value=0.12 Score=54.78 Aligned_cols=154 Identities=10% Similarity=0.116 Sum_probs=88.7
Q ss_pred CCeE-EEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHH-cCcE-EEEEEE
Q 003093 3 GQTV-AIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWR-EVIAIY 79 (848)
Q Consensus 3 ~~V~-aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~-~~w~-~vaii~ 79 (848)
++++ .|++|..+.........+.+.++|+|.+....+ ..+.+..+.+++..-+..+++++.. .+.+ +++++.
T Consensus 81 ~~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~~~-----~~~~~~~V~~D~~~~g~~~~~~l~~~~~~~~~i~~~~ 155 (295)
T PRK10653 81 RGTKILLINPTDSDAVGNAVKMANQANIPVITLDRGAT-----KGEVVSHIASDNVAGGKMAGDFIAKKLGEGAKVIQLE 155 (295)
T ss_pred cCCCEEEEcCCChHHHHHHHHHHHHCCCCEEEEccCCC-----CCceeeEEccChHHHHHHHHHHHHHHhCCCceEEEEE
Confidence 3565 455766555544556677788999998754321 1123344555555556888887654 4543 566555
Q ss_pred EcC--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEE-ccCCcHHHHHHHHHHcCCCC
Q 003093 80 VDD--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVH-THYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 80 ~dd--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~-~~~~~~~~~~~~a~~~g~~~ 156 (848)
.+. .......+.|.+++++.|+.+... .....+..+....+.++.+..++.-.+. .+...+..+++++++.|+
T Consensus 156 ~~~~~~~~~~R~~gf~~al~~~g~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~A~g~l~al~~~G~-- 231 (295)
T PRK10653 156 GIAGTSAARERGEGFKQAVAAHKFNVLAS--QPADFDRTKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK-- 231 (295)
T ss_pred ccCCCccHHHHHHHHHHHHhhCCCEEEEe--cCCCCCHHHHHHHHHHHHHhCCCcCEEEECCChhHHHHHHHHHHcCC--
Confidence 322 234466789999999999876432 1112222334445556654444433333 444555568999999997
Q ss_pred CCeEEEecC
Q 003093 157 TGYVWIATS 165 (848)
Q Consensus 157 ~~~~wi~~~ 165 (848)
.+...++.+
T Consensus 232 ~dv~vig~d 240 (295)
T PRK10653 232 SDVMVVGFD 240 (295)
T ss_pred CceEEEEeC
Confidence 344444433
No 138
>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=96.18 E-value=0.2 Score=52.32 Aligned_cols=156 Identities=8% Similarity=-0.032 Sum_probs=89.8
Q ss_pred CCeEEEEccCCc-hhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAIIGPQDA-VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiIGp~~S-~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
.++++||--... .....+...+...++|+|......+ + ..+ +--+..++...+..+++++... |.++++++.
T Consensus 56 ~~vdgvii~~~~~~~~~~~l~~~~~~~ipvV~~~~~~~---~-~~~-~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~ 130 (273)
T cd06310 56 RGPDAILLAPTDAKALVPPLKEAKDAGIPVVLIDSGLN---S-DIA-VSFVATDNVAAGKLAAEALAELLGKKGKVAVIS 130 (273)
T ss_pred hCCCEEEEcCCChhhhHHHHHHHHHCCCCEEEecCCCC---C-Ccc-eEEEeeChHHHHHHHHHHHHHHcCCCceEEEEe
Confidence 467777643222 2223344555678999998753221 1 111 2224455556677888887666 899999997
Q ss_pred EcCCC--ccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEE-EEEccCCcHHHHHHHHHHcCCC
Q 003093 80 VDDDH--GRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRII-VVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 80 ~dd~~--g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~vi-v~~~~~~~~~~~~~~a~~~g~~ 155 (848)
...++ .....+.|.+++++. |+.+... .....+..+-...+.++....+++- +++.+...+..+++.+++.|+.
T Consensus 131 ~~~~~~~~~~r~~gf~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~d~~a~g~~~~l~~~g~~ 208 (273)
T cd06310 131 FVPGSSTTDQREEGFLEGLKEYPGIEIVAT--QYSDSDYAKALDITEDLLTANPDLKGIFGANEGSAVGAARAVRQAGKA 208 (273)
T ss_pred CCCCCccHHHHHHHHHHHHHhCCCcEEEec--ccCCcCHHHHHHHHHHHHHhCCCceEEEecCchhHHHHHHHHHhcCCC
Confidence 44333 334568899999998 8776432 1111122333345555544333333 3344456677799999999985
Q ss_pred CCCeEEEecCc
Q 003093 156 GTGYVWIATSW 166 (848)
Q Consensus 156 ~~~~~wi~~~~ 166 (848)
.+...++.+.
T Consensus 209 -~di~vig~d~ 218 (273)
T cd06310 209 -GKVKVVGFDA 218 (273)
T ss_pred -CCeEEEEeCC
Confidence 4555555443
No 139
>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=96.17 E-value=0.064 Score=57.92 Aligned_cols=146 Identities=10% Similarity=0.052 Sum_probs=90.5
Q ss_pred CCeEEEE--ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 3 GQTVAII--GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiI--Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
.+|++|| |+..+ ..+.....+.++|+|......+ ...++ .+..++..-+..+++++...|.++++++..
T Consensus 114 ~~vdGiIi~~~~~~---~~~~~~l~~~~iPvV~~~~~~~---~~~~~---~V~~D~~~~~~~a~~~L~~~G~~~I~~i~g 184 (329)
T TIGR01481 114 KQVDGIIFMGGTIT---EKLREEFSRSPVPVVLAGTVDK---ENELP---SVNIDYKQATKEAVGELIAKGHKSIAFVGG 184 (329)
T ss_pred CCCCEEEEeCCCCC---hHHHHHHHhcCCCEEEEecCCC---CCCCC---EEEECcHHHHHHHHHHHHHCCCCeEEEEec
Confidence 4566665 43322 2344556677999997654321 12223 245566666777888887789999999963
Q ss_pred cC--C-CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 81 DD--D-HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 81 dd--~-~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
+. . .+..-.+.|.+.++++|+.+..........+..+-...+.++.+.++++|+.. +...+..+++++++.|+..+
T Consensus 185 ~~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~p~ai~~~-~d~~A~g~~~al~~~g~~vP 263 (329)
T TIGR01481 185 PLSDSINGEDRLEGYKEALNKAGIQFGEDLVCEGKYSYDAGYKAFAELKGSLPTAVFVA-SDEMAAGILNAAMDAGIKVP 263 (329)
T ss_pred CcccccchHHHHHHHHHHHHHcCCCCCcceEEecCCChHHHHHHHHHHhCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCC
Confidence 32 2 24667789999999998764321111111122333445566655678876664 44577789999999998655
Q ss_pred C
Q 003093 158 G 158 (848)
Q Consensus 158 ~ 158 (848)
+
T Consensus 264 ~ 264 (329)
T TIGR01481 264 E 264 (329)
T ss_pred C
Confidence 4
No 140
>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=95.79 E-value=0.12 Score=53.70 Aligned_cols=146 Identities=10% Similarity=0.002 Sum_probs=86.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc-
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD- 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d- 81 (848)
.+|+|||......... +.... ..++|+|..+...+ . +.+..+..++...++.+++++...|.++++++..+
T Consensus 54 ~~vdgiii~~~~~~~~-~~~~~-~~~ipvv~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~ 125 (267)
T cd06284 54 KQADGIILLDGSLPPT-ALTAL-AKLPPIVQACEYIP---G---LAVPSVSIDNVAAARLAVDHLISLGHRRIALITGPR 125 (267)
T ss_pred cCCCEEEEecCCCCHH-HHHHH-hcCCCEEEEecccC---C---CCcceEEecccHHHHHHHHHHHHcCCceEEEEcCCc
Confidence 4788877633222222 22223 45999997642211 1 22333566677778888888877899999999753
Q ss_pred -CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 -DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 -d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
+..+....+.|.+.++++|+++..........+..+....+.++... .+++|+.. +...+..+++++++.|...+
T Consensus 126 ~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~~~~a~g~~~al~~~g~~~p 203 (267)
T cd06284 126 DNPLARDRLEGYRQALAEAGLPADEELIQEGDFSLESGYAAARRLLALPDRPTAIFCF-SDEMAIGAISALKELGLRVP 203 (267)
T ss_pred cchhHHHHHHHHHHHHHHcCCCCCcceEEeCCCChHHHHHHHHHHHhCCCCCcEEEEc-CcHHHHHHHHHHHHcCCCCc
Confidence 34566678899999999985432111111111223334445554333 45666654 44556789999999998543
No 141
>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=95.74 E-value=0.13 Score=53.77 Aligned_cols=153 Identities=12% Similarity=0.092 Sum_probs=90.7
Q ss_pred CCeEEEE--ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 3 GQTVAII--GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiI--Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
.++++|| ++... . .....+...++|+|.++...+. .. +..+.+++...+..+++++...|.++++++..
T Consensus 63 ~~~dgiii~~~~~~--~-~~~~~~~~~~ipvV~~~~~~~~---~~---~~~V~~d~~~~g~~~a~~l~~~g~~~i~~i~~ 133 (275)
T cd06295 63 GRADGVILIGQHDQ--D-PLPERLAETGLPFVVWGRPLPG---QP---YCYVGSDNVGGGRLATEHLLARGRRRIAFLGG 133 (275)
T ss_pred CCCCEEEEeCCCCC--h-HHHHHHHhCCCCEEEECCccCC---CC---CCEEEECcHHHHHHHHHHHHHCCCCeEEEEcC
Confidence 4677765 33222 1 2234557789999987653322 22 23355677778888888888889999999975
Q ss_pred cCC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 81 DDD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 81 dd~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
+.. .+....+.|.+.+++.|..+..........+..+....+.++... .+++|+... ...+..+++.+++.|...
T Consensus 134 ~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~-~~~a~g~~~~l~~~g~~i 212 (275)
T cd06295 134 PQDMPEGEERLEGYREALAEAGLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFAAS-DLMALGALRALREAGRRV 212 (275)
T ss_pred CCCcchhHHHHHHHHHHHHHcCCCCChhhEEeccCCHHHHHHHHHHHHhCCCCCCEEEECC-cHHHHHHHHHHHHhCCCC
Confidence 432 344567889999998885432211112111222333445544433 356665553 455667889999999854
Q ss_pred CCeE-EEecC
Q 003093 157 TGYV-WIATS 165 (848)
Q Consensus 157 ~~~~-wi~~~ 165 (848)
++-+ .++.+
T Consensus 213 p~~i~ii~~d 222 (275)
T cd06295 213 PEDVAVVGFD 222 (275)
T ss_pred ccceEEEeeC
Confidence 4433 34433
No 142
>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=95.71 E-value=0.084 Score=54.65 Aligned_cols=149 Identities=11% Similarity=0.076 Sum_probs=94.7
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc-Cc-EEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-GW-REVIAIY 79 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~-~w-~~vaii~ 79 (848)
+++++|| .|..+........-+...+||+|.+... .....+....+.+++...+..+++++... +- .+++++.
T Consensus 54 ~~~d~Iiv~~~~~~~~~~~l~~~~~~gIpvv~~d~~----~~~~~~~~~~v~~d~~~~G~~~a~~l~~~~~~~~~v~~~~ 129 (257)
T PF13407_consen 54 QGVDGIIVSPVDPDSLAPFLEKAKAAGIPVVTVDSD----EAPDSPRAAYVGTDNYEAGKLAAEYLAEKLGAKGKVLILS 129 (257)
T ss_dssp TTESEEEEESSSTTTTHHHHHHHHHTTSEEEEESST----HHTTSTSSEEEEE-HHHHHHHHHHHHHHHHTTTEEEEEEE
T ss_pred hcCCEEEecCCCHHHHHHHHHHHhhcCceEEEEecc----ccccccceeeeeccHHHHHHHHHHHHHHHhccCceEEecc
Confidence 4666665 7777776667777889999999987554 11223455566778888889999987443 32 6888886
Q ss_pred EcCCC--ccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 80 VDDDH--GRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 80 ~dd~~--g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
...++ .....+.+.+.+++. ++++... .+....+..+....+.++...++-..|++++...+..+++++++.|+.+
T Consensus 130 ~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~l~~~~~~~i~~~~~~~~~g~~~al~~~g~~~ 208 (257)
T PF13407_consen 130 GSPGNPNTQERLEGFRDALKEYPGVEIVDE-YEYTDWDPEDARQAIENLLQANPVDAIIACNDGMALGAAQALQQAGRAG 208 (257)
T ss_dssp SSTTSHHHHHHHHHHHHHHHHCTTEEEEEE-EEECTTSHHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHHHHHHTTCTT
T ss_pred CCCCchHHHHHHHHHHHHHhhcceeeeeee-eeccCCCHHHHHHHHHHhhhcCCceEEEeCCChHHHHHHHHHHHcCCcc
Confidence 44433 334678888999884 5666552 2222334455555555555544322234455556666899999999843
No 143
>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=95.69 E-value=0.1 Score=54.37 Aligned_cols=153 Identities=10% Similarity=0.013 Sum_probs=90.7
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+++|||-........ .......++|++......+. ..++ .+.+++...+..+++++...|-++++++..+.
T Consensus 55 ~~~dgiii~~~~~~~~--~~~~~~~~ipvv~~~~~~~~---~~~~---~v~~d~~~~~~~a~~~l~~~g~~~i~~l~~~~ 126 (269)
T cd06288 55 HRVDGIIYATMYHREV--TLPPELLSVPTVLLNCYDAD---GALP---SVVPDEEQGGYDATRHLLAAGHRRIAFINGEP 126 (269)
T ss_pred cCCCEEEEecCCCChh--HHHHHhcCCCEEEEecccCC---CCCC---eEEEccHHHHHHHHHHHHHcCCceEEEEeCCc
Confidence 3567766543322111 22335578999987543221 1223 35567777788888888777999999997443
Q ss_pred C--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 83 D--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
. ......+.|.+.++++|+.+..........+..+....++++.+. ++++|+. .+...+..+++++++.|+..++
T Consensus 127 ~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~vp~ 205 (269)
T cd06288 127 WMLAAKDRLKGYRQALAEAGIPFDPDLVVHGDWSADDGYEAAAALLDLDDRPTAIFC-GNDRMAMGAYQALLERGLRIPQ 205 (269)
T ss_pred cchhHHHHHHHHHHHHHHcCCCCCHHHeEeCCCChHHHHHHHHHHHhCCCCCCEEEE-eCcHHHHHHHHHHHHcCCCCcc
Confidence 2 334567889999999886532111111111223333445555443 4677654 5555677799999999986555
Q ss_pred eEEEec
Q 003093 159 YVWIAT 164 (848)
Q Consensus 159 ~~wi~~ 164 (848)
-+.+++
T Consensus 206 di~v~g 211 (269)
T cd06288 206 DVSVVG 211 (269)
T ss_pred cceEEe
Confidence 444444
No 144
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=95.57 E-value=0.31 Score=51.08 Aligned_cols=110 Identities=20% Similarity=0.237 Sum_probs=74.1
Q ss_pred CCCCChHHhhcCCCCeeEEeCc-----hHH-HHHHhhhCCCc---cCcccCC-CHHHHHHHhhcCCCCCceEEEEccHHH
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNS-----FAR-NYLVDELNIDE---SRLVPLN-SPEEYAKALKDGPHKGGVAAVVDDRAY 659 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s-----~~~-~~l~~~~~~~~---~~~~~~~-~~~~~~~~l~~~~~~~~~~a~~~~~~~ 659 (848)
++|++++||. |+++++..-+ ..- .+|..+.+.+. -.-+.+. .-+..+.+|.+ |.+|+.......
T Consensus 134 s~i~sl~dlk--gk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~a~~aV~n----G~vDva~~~~~~ 207 (299)
T COG3221 134 SPIKSLEDLK--GKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDAAVLAVAN----GQVDVAAVNSSA 207 (299)
T ss_pred CCcchHHHhc--CCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHHHHHHHHc----CCceEEeccHHH
Confidence 7999999999 9999997532 222 22222221221 1112233 47888999999 899988887766
Q ss_pred HHHHHhcC-----CcEEEeCCccccCCceeeecCCCC--chHHHHHHHHhhhc
Q 003093 660 AELFLSTR-----CEFSIVGQVFTKNGWGFAFPRDSP--LAVDISTAILKLSE 705 (848)
Q Consensus 660 ~~~~~~~~-----~~l~~~~~~~~~~~~~~~~~k~sp--l~~~in~~i~~l~e 705 (848)
...+.... .+++++...-.-.+..++++++-| ++++|..+++.+.+
T Consensus 208 ~~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 208 RGLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred HhhhhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 66555442 257777765444556788888877 99999999999986
No 145
>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=95.54 E-value=0.18 Score=52.39 Aligned_cols=150 Identities=11% Similarity=0.063 Sum_probs=88.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+|+|||--..... ......+...++|+|......+ . +....+..++...+..+++++...|-++++++..+.
T Consensus 54 ~~vdgiii~~~~~~-~~~~~~~~~~~ipvv~~~~~~~---~---~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~ 126 (268)
T cd01575 54 RRPAGLILTGLEHT-ERTRQLLRAAGIPVVEIMDLPP---D---PIDMAVGFSHAEAGRAMARHLLARGYRRIGFLGARM 126 (268)
T ss_pred cCCCEEEEeCCCCC-HHHHHHHHhcCCCEEEEecCCC---C---CCCCeEEeCcHHHHHHHHHHHHHCCCCcEEEecCCC
Confidence 46777764222111 2233445677999997643221 1 112234566677788888888888999999998554
Q ss_pred --CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 83 --DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 83 --~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
.......+.|.+.+++.|.............+.......+.++.+. ++++|+. ++...+..+++.+++.|...++
T Consensus 127 ~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~~p~ 205 (268)
T cd01575 127 DDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFC-SNDDLALGALFECQRRGISVPE 205 (268)
T ss_pred CcccHHHHHHHHHHHHHHcCCCCCceeEeccCCCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHhCCCCCc
Confidence 3445556889999999886432211111111223334455555433 4676654 4445566799999999976554
Q ss_pred eE
Q 003093 159 YV 160 (848)
Q Consensus 159 ~~ 160 (848)
.+
T Consensus 206 di 207 (268)
T cd01575 206 DI 207 (268)
T ss_pred ce
Confidence 43
No 146
>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=95.52 E-value=0.41 Score=49.98 Aligned_cols=156 Identities=8% Similarity=-0.005 Sum_probs=88.1
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
++|++|| .|............+.+.+||+|.+....+ ... .....+.+++...+..+++++... |-++++++.
T Consensus 59 ~~vDgiii~~~~~~~~~~~i~~~~~~gIpvV~~d~~~~---~~~-~~~~~V~~d~~~~g~~aa~~l~~~~~g~~~i~~~~ 134 (274)
T cd06311 59 RKIDALVILPFESAPLTQPVAKAKKAGIFVVVVDRGLS---SPG-AQDLYVAGDNYGMGRVAGEYIATKLGGNGNIVVLR 134 (274)
T ss_pred cCCCEEEEeCCCchhhHHHHHHHHHCCCeEEEEcCCCC---CCc-ccceEEcCCcHHHHHHHHHHHHHHhCCCCeEEEEE
Confidence 4566655 444433322333445678999998754321 111 111235666677778888887655 788999997
Q ss_pred EcC-CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 80 VDD-DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 80 ~dd-~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
.+. .......+.|.+.+++.|+++... .....+.......+.++... ++++|+.. +...+..++.++++.|..
T Consensus 135 g~~~~~~~~R~~gf~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~- 210 (274)
T cd06311 135 GIPTPIDNERVDAFDAAIAKYPIKILDR--QYANWNRDDAFSVMQDLLTKFPKIDAVWAH-DDDMAVGVLAAIKQAGRT- 210 (274)
T ss_pred CCCCcchhHHHHHHHHHHhhCCcEEEec--cCCCCcHHHHHHHHHHHHHhCCCcCEEEEC-CCcHHHHHHHHHHHcCCC-
Confidence 433 223345688999999999766532 22222222333444444333 35665443 344567789999999974
Q ss_pred CCeEEEecCc
Q 003093 157 TGYVWIATSW 166 (848)
Q Consensus 157 ~~~~wi~~~~ 166 (848)
.+...++.++
T Consensus 211 ~~~~ivg~d~ 220 (274)
T cd06311 211 DIKFVVGGAG 220 (274)
T ss_pred CCceEEEeCC
Confidence 2333444343
No 147
>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=95.51 E-value=0.39 Score=50.60 Aligned_cols=163 Identities=9% Similarity=0.034 Sum_probs=89.2
Q ss_pred CCeEEEEc-cCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHH----HcCc--EEE
Q 003093 3 GQTVAIIG-PQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVD----HYGW--REV 75 (848)
Q Consensus 3 ~~V~aiIG-p~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~----~~~w--~~v 75 (848)
.+|++||= |..+.....+...+.+.++|+|.+....+.......+.+-.+..++...+..+++++. ..|+ +++
T Consensus 53 ~~~dgiii~~~~~~~~~~~~~~~~~~~iPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~~~~~g~~~~~i 132 (289)
T cd01540 53 QGAKGFVICVPDVKLGPAIVAKAKAYNMKVVAVDDRLVDADGKPMEDVPHVGMSATKIGEQVGEAIADEMKKRGWDPKEV 132 (289)
T ss_pred cCCCEEEEccCchhhhHHHHHHHHhCCCeEEEecCCCcccCCCccccceEecCCHHHHHHHHHHHHHHHHHhhcCCCcce
Confidence 45665552 3333344555566778999999875432211100112223345566666666666543 4577 788
Q ss_pred EEEE-Ec--CCCccchHHHHHHHHhccCcEEEEeeecCCC-CChHHHHHHHHHHhcC--CCeE-EEEEccCCcHHHHHHH
Q 003093 76 IAIY-VD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVE-ATEDEITDLLVKVALT--ESRI-IVVHTHYNRGPVVFHV 148 (848)
Q Consensus 76 aii~-~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~-~~~~d~~~~l~~i~~~--~~~v-iv~~~~~~~~~~~~~~ 148 (848)
+++. .. ........+.+.+.+++.|+........... .+...-...++++... .++. .+++.+...+..++++
T Consensus 133 ~~i~~~~~~~~~~~~R~~G~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~~d~~a~g~~~a 212 (289)
T cd01540 133 GALRITYDELDTAKPRTDGALEALKAPGFPEANIFQAPQKTTDTEGAFDAAASTLTKNPNVKNWIIYGLNDETVLGAVRA 212 (289)
T ss_pred EEEEecCCCCcchhhHHHHHHHHHhcCCCCcceEecccccCcchhhHHHHHHHHHHhCCCcCeeEEEeCCcHHHHHHHHH
Confidence 8875 22 2345667889999999888753211111111 1112222344554433 3453 4555666678889999
Q ss_pred HHHcCCCCCCeEEEecC
Q 003093 149 AQYLGMLGTGYVWIATS 165 (848)
Q Consensus 149 a~~~g~~~~~~~wi~~~ 165 (848)
+++.|....+...++.+
T Consensus 213 l~~~g~~~~di~vig~d 229 (289)
T cd01540 213 TEQSGIAAADVIGVGIN 229 (289)
T ss_pred HHHcCCCCcceEEEecC
Confidence 99999874344444444
No 148
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=95.47 E-value=0.046 Score=58.55 Aligned_cols=68 Identities=18% Similarity=0.164 Sum_probs=49.4
Q ss_pred CCChHHhhcCCCCeeEEeCchHHHHHHhhh---CCC--ccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhc
Q 003093 592 IKGIDSLRSSNYPIGYQVNSFARNYLVDEL---NID--ESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLST 666 (848)
Q Consensus 592 i~sl~dL~~s~~~i~~~~~s~~~~~l~~~~---~~~--~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~ 666 (848)
|+|++||. |++||+..|+....++.+.+ +.. +.+++.. .+.+...++.+ |.+||.+...++......+
T Consensus 98 i~svaDLK--GKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~-~~~d~~aAl~~----G~VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 98 GKSLADLK--GQKVNLVELSVSHYLLARALESVGLSEKDVKVVNT-SDADIVAAFIT----KDVTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred CCCHHHcC--CCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeC-ChHHHHHHHhc----CCCcEEEEcCchHHHHHhC
Confidence 89999999 99999999987665554322 332 2344444 45778899999 9999999888886655544
No 149
>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=95.42 E-value=0.18 Score=52.41 Aligned_cols=141 Identities=13% Similarity=0.080 Sum_probs=85.4
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+|++||--.+.... .+...+.+.++|+|.+....+ . +.+..+.+++...+..+++++...|-++++++..+.
T Consensus 53 ~~vdgiii~~~~~~~-~~~~~~~~~~ipvV~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~ 125 (266)
T cd06278 53 YRVDGVIVTSGTLSS-ELAEECRRNGIPVVLINRYVD---G---PGVDAVCSDNYEAGRLAAELLLAKGCRRIAFIGGPA 125 (266)
T ss_pred cCCCEEEEecCCCCH-HHHHHHhhcCCCEEEECCccC---C---CCCCEEEEChHHHHHHHHHHHHHCCCceEEEEcCCC
Confidence 467777643222222 234556678999998754322 1 123346677888888888988778999999998543
Q ss_pred C--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcC
Q 003093 83 D--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLG 153 (848)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g 153 (848)
. ......+.|.+.+++.|..+... ... ..+..+....+.++.+. .+++|+.. +...+..+++.+++.+
T Consensus 126 ~~~~~~~R~~gf~~~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~~l~~~~ 197 (266)
T cd06278 126 DTSTSRERERGFRDALAAAGVPVVVE-EAG-DYSYEGGYEAARRLLASRPRPDAIFCA-NDLLAIGVMDAARQEG 197 (266)
T ss_pred cccchHHHHHHHHHHHHHcCCChhhh-ccC-CCCHHHHHHHHHHHHhcCCCCCEEEEc-CcHHHHHHHHHHHHhc
Confidence 3 44556788999999988764321 111 11223334445554433 45665554 3445566778887753
No 150
>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=95.41 E-value=0.49 Score=49.65 Aligned_cols=158 Identities=8% Similarity=0.003 Sum_probs=87.7
Q ss_pred CCeEEEEc-cCCchhHHHHHHhhccCCccEEeccc-CCCCCCCCCCCceEeccCChHHHHHHHHHHHHH--cCcEEEEEE
Q 003093 3 GQTVAIIG-PQDAVTSHVVSHVANELQVPLLSFSA-TDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH--YGWREVIAI 78 (848)
Q Consensus 3 ~~V~aiIG-p~~S~~~~ava~i~~~~~vP~Is~~a-t~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~--~~w~~vaii 78 (848)
++|++||= |........+.. +.+.++|.+.... ..|.-.....+..-.+.+++..-+..+++.+.. .|.++++++
T Consensus 59 ~~vDgiIv~~~~~~~~~~~~~-l~~~~~p~V~i~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~L~~~~~g~~~i~~l 137 (280)
T cd06303 59 SKPDYLIFTLDSLRHRKLIER-VLASGKTKIILQNITTPVKAWLKHQPLLYVGFDHAAGARLLADYFIKRYPNHARYAML 137 (280)
T ss_pred cCCCEEEEcCCchhhHHHHHH-HHhCCCCeEEEeCCCCCccccccCCCceEeCCCHHHHHHHHHHHHHHhcCCCcEEEEE
Confidence 46676663 222212233333 3345677665422 222100000122334566777777888888766 799999999
Q ss_pred EEcC-CCccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 79 YVDD-DHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 79 ~~dd-~~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.... .......+.|.++++++ |+.+... +....+..+....+.++.+. ++++|+ +++...+..+++++++.|+
T Consensus 138 ~~~~~~~~~~R~~gf~~al~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~l~al~~~G~ 214 (280)
T cd06303 138 YFSPGYISTARGDTFIDCVHARNNWTLTSE--FYTDATRQKAYQATSDILSNNPDVDFIY-ACSTDIALGASDALKELGR 214 (280)
T ss_pred ECCCCcchhHHHHHHHHHHHhCCCceEEEe--ecCCCCHHHHHHHHHHHHHhCCCCcEEE-ECCcHHHHHHHHHHHHcCC
Confidence 6432 23344568899999998 7664322 22222223334455555433 355544 4555667789999999998
Q ss_pred CCCCeEEEecC
Q 003093 155 LGTGYVWIATS 165 (848)
Q Consensus 155 ~~~~~~wi~~~ 165 (848)
. .+...++-+
T Consensus 215 ~-~dv~vvg~d 224 (280)
T cd06303 215 E-DDILINGWG 224 (280)
T ss_pred C-CCcEEEecC
Confidence 5 444455444
No 151
>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=95.39 E-value=0.5 Score=49.09 Aligned_cols=143 Identities=12% Similarity=0.056 Sum_probs=84.4
Q ss_pred CCeEEEEc-cCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAIIG-PQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiIG-p~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
.++++||- |..+.........+.+.++|+|.+....+ ..+.+..+.+++...+..+++++... |-+++++++
T Consensus 54 ~~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~~~~~-----~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~ 128 (267)
T cd06322 54 KKVDAIVLSPVDSKGIRAAIAKAKKAGIPVITVDIAAE-----GVAVVSHVATDNYAGGVLAGELAAKVLNGKGQVAIID 128 (267)
T ss_pred cCCCEEEEcCCChhhhHHHHHHHHHCCCCEEEEcccCC-----CCceEEEEecChHHHHHHHHHHHHHHhCCCceEEEEe
Confidence 46777664 44433223333456678999998753211 11223345566666777788887654 778999997
Q ss_pred EcCC-CccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 80 VDDD-HGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~dd~-~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
..+. ......+.|.+++++. |+++... ....+.+.....+.++... ++++|+. .+...+..+++++++.|.
T Consensus 129 ~~~~~~~~~R~~gf~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~al~~~g~ 203 (267)
T cd06322 129 YPTVQSVVDRVRGFKEALADYPNIKIVAV---QPGITRAEALTAAQNILQANPDLDGIFA-FGDDAALGAVSAIKAAGR 203 (267)
T ss_pred cCCCccHHHHHHHHHHHHHhCCCcEEEEe---cCCCChHHHHHHHHHHHHhCCCCCEEEE-cCCcHHHHHHHHHHHCCC
Confidence 4322 2344568899999998 8876422 1111222333344444332 4565444 444566678899999997
No 152
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=95.39 E-value=0.073 Score=55.01 Aligned_cols=74 Identities=23% Similarity=0.190 Sum_probs=49.0
Q ss_pred CCCCChHHhhc-----CCCCeeE-EeCchHHHHHH---hhhCCCc---cCcccCCCHHHHHHHhhcCCCCCceEEEEccH
Q 003093 590 SPIKGIDSLRS-----SNYPIGY-QVNSFARNYLV---DELNIDE---SRLVPLNSPEEYAKALKDGPHKGGVAAVVDDR 657 (848)
Q Consensus 590 ~~i~sl~dL~~-----s~~~i~~-~~~s~~~~~l~---~~~~~~~---~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~ 657 (848)
+.+++++||.+ .|++|++ ..|+.....+. +..+... .+++.++. .+..+++.. |++|+++...
T Consensus 104 ~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~----g~iDa~~~~e 178 (252)
T PF13379_consen 104 SDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRA----GEIDAAVLWE 178 (252)
T ss_dssp STTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHT----TS-SEEEEET
T ss_pred CCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhC----CCcCEEEecC
Confidence 57899999932 2778998 45664433332 3334333 45666665 999999999 9999999999
Q ss_pred HHHHHHHhcCC
Q 003093 658 AYAELFLSTRC 668 (848)
Q Consensus 658 ~~~~~~~~~~~ 668 (848)
++......+..
T Consensus 179 P~~~~~~~~g~ 189 (252)
T PF13379_consen 179 PFASQAEAKGI 189 (252)
T ss_dssp THHHHHHHTTS
T ss_pred CHHHHHHhccC
Confidence 99887776654
No 153
>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=95.31 E-value=0.2 Score=51.83 Aligned_cols=149 Identities=13% Similarity=0.087 Sum_probs=91.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc-
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD- 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d- 81 (848)
.+|+++|...... ...+...+.+.++|+|......+ ..+ .+..++...+..+++++...|-++++++...
T Consensus 54 ~~~dgii~~~~~~-~~~~~~~~~~~~ipvv~~~~~~~-----~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~v~~~~ 124 (259)
T cd01542 54 QKVDGIILLATTI-TDEHREAIKKLNVPVVVVGQDYP-----GIS---SVVYDDYGAGYELGEYLAQQGHKNIAYLGVSE 124 (259)
T ss_pred cCCCEEEEeCCCC-CHHHHHHHhcCCCCEEEEeccCC-----CCC---EEEECcHHHHHHHHHHHHHcCCCcEEEEcCCc
Confidence 5677877543322 23444566677999998754221 122 3556777778889998877888999998632
Q ss_pred C--CCccchHHHHHHHHhccCc-EEEEeeecCCCCChHHHHHHHHHHhcCC-CeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 D--DHGRNGIAALGDTLAAKRC-RISFKAPLSVEATEDEITDLLVKVALTE-SRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d--~~g~~~~~~l~~~l~~~g~-~v~~~~~~~~~~~~~d~~~~l~~i~~~~-~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
+ ..+....+.|.+.+++.|. .+.. +....+.......+.++.+.. +++|+... ...+..+++.+++.|+..+
T Consensus 125 ~~~~~~~~r~~gf~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~~i~~~~-d~~a~g~~~~l~~~g~~vp 200 (259)
T cd01542 125 SDIAVGILRKQGYLDALKEHGICPPNI---VETDFSYESAYEAAQELLEPQPPDAIVCAT-DTIALGAMKYLQELGRRIP 200 (259)
T ss_pred ccchhHHHHHHHHHHHHHHcCCChHHe---eeccCchhhHHHHHHHHhcCCCCCEEEEcC-cHHHHHHHHHHHHcCCCCC
Confidence 2 2334567889999999887 2111 111111123334455554444 67666554 4567789999999998766
Q ss_pred CeEEEec
Q 003093 158 GYVWIAT 164 (848)
Q Consensus 158 ~~~wi~~ 164 (848)
+-+.+.+
T Consensus 201 ~di~v~g 207 (259)
T cd01542 201 EDISVAG 207 (259)
T ss_pred CceEEEe
Confidence 6555554
No 154
>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=95.27 E-value=0.19 Score=52.37 Aligned_cols=154 Identities=11% Similarity=-0.012 Sum_probs=88.5
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+|++||--.+......+...+.+.++|+|......+ ...++ +..++..-+..+++.+...|-++++++....
T Consensus 54 ~~vdgii~~~~~~~~~~~~~~~~~~~ipvV~i~~~~~----~~~~~---V~~d~~~~g~~a~~~l~~~G~~~i~~l~~~~ 126 (269)
T cd06281 54 RRMDGIIIAPGDERDPELVDALASLDLPIVLLDRDMG----GGADA---VLFDHAAGMRQAVEYLISLGHRRIALVGGGS 126 (269)
T ss_pred cCCCEEEEecCCCCcHHHHHHHHhCCCCEEEEecccC----CCCCE---EEECcHHHHHHHHHHHHHCCCcEEEEecCcc
Confidence 4677777422222224445566678999998765432 12232 3445555556677777677999999996432
Q ss_pred --CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 83 --DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 83 --~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
..+....+.|.+.++++|+.+.....+.... ...-...+.++.. ..+++|+. .+...+..+++++++.|+..++
T Consensus 127 ~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~ip~ 204 (269)
T cd06281 127 NTRPGRERLEGYKAAFAAAGLPPDPALVRLSTP-AASGFDATRALLALPDRPTAIIA-GGTQVLVGVLRALREAGLRIPR 204 (269)
T ss_pred ccccHHHHHHHHHHHHHHcCCCCCHHHeecCcH-HHHHHHHHHHHHcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCCc
Confidence 2334556889999999987542111111111 1222334444432 34787763 4555666789999999986544
Q ss_pred e-EEEecC
Q 003093 159 Y-VWIATS 165 (848)
Q Consensus 159 ~-~wi~~~ 165 (848)
- ..++.+
T Consensus 205 dv~iig~d 212 (269)
T cd06281 205 DLSVISIG 212 (269)
T ss_pred ceeEEEec
Confidence 3 344333
No 155
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=95.19 E-value=0.22 Score=54.11 Aligned_cols=154 Identities=6% Similarity=0.038 Sum_probs=87.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhcc-CCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE-
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANE-LQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV- 80 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~-~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~- 80 (848)
.+++|||=-........+ ..+.. .++|+|.+....+ +..++.+ +.+++...+..+++.+...|-+++++|..
T Consensus 114 ~~vdgiii~~~~~~~~~~-~~l~~~~~iPvV~~d~~~~---~~~~~~~--v~~d~~~~g~~a~~~L~~~G~~~i~~i~~~ 187 (341)
T PRK10703 114 KRVDGLLVMCSEYPEPLL-AMLEEYRHIPMVVMDWGEA---KADFTDA--IIDNAFEGGYLAGRYLIERGHRDIGVIPGP 187 (341)
T ss_pred cCCCEEEEecCCCCHHHH-HHHHhcCCCCEEEEecccC---CcCCCCe--EEECcHHHHHHHHHHHHHCCCCcEEEEeCC
Confidence 456766521111112223 33444 7999998754322 1121222 34444556778888877779999999963
Q ss_pred -cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 81 -DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 81 -dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
++..+....+.|.+.++++|+.+.............+....+.++... .+++|+. ++...+..+++++++.|...+
T Consensus 188 ~~~~~~~~R~~Gf~~~l~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~nd~~a~g~~~al~~~g~~ip 266 (341)
T PRK10703 188 LERNTGAGRLAGFMKAMEEANIKVPEEWIVQGDFEPESGYEAMQQILSQKHRPTAVFC-GGDIMAMGAICAADEMGLRVP 266 (341)
T ss_pred ccccchHHHHHHHHHHHHHcCCCCChHHeEeCCCCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCC
Confidence 233445567899999999998654221111111223344455555433 4676664 455566789999999998655
Q ss_pred CeEEEe
Q 003093 158 GYVWIA 163 (848)
Q Consensus 158 ~~~wi~ 163 (848)
+-+.|+
T Consensus 267 ~dv~vv 272 (341)
T PRK10703 267 QDISVI 272 (341)
T ss_pred CceEEE
Confidence 544443
No 156
>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=95.18 E-value=0.32 Score=50.48 Aligned_cols=152 Identities=13% Similarity=0.071 Sum_probs=88.9
Q ss_pred CCeEEEEc-cCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIG-PQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIG-p~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|++||= |... ....+ ..+...++|+|.+....+ ....+ .+..++...+..+++.+...|-++++++...
T Consensus 54 ~~~dgiii~~~~~-~~~~l-~~~~~~~ipvV~~~~~~~---~~~~~---~v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~ 125 (267)
T cd06283 54 YQVDGLIVNPTGN-NKELY-QRLAKNGKPVVLVDRKIP---ELGVD---TVTLDNYEAAKEAVDHLIEKGYERILFVTEP 125 (267)
T ss_pred cCcCEEEEeCCCC-ChHHH-HHHhcCCCCEEEEcCCCC---CCCCC---EEEeccHHHHHHHHHHHHHcCCCcEEEEecC
Confidence 45666652 2222 22233 445678999998765322 11222 3445666778888888888899999999744
Q ss_pred CC--C-ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 82 DD--H-GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 82 d~--~-g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
.. . .......+.+.+++.|.............+..+....+.++.+. .+++|+.. +...+..+++.+++.|+..
T Consensus 126 ~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~v 204 (267)
T cd06283 126 LDEISPRMERYEGFKEALAEHGIGVNEELIEIDDEDADELDERLRQLLNKPKKKTAIFAA-NGLILLEVLKALKELGIRI 204 (267)
T ss_pred ccccccHHHHHHHHHHHHHHcCCCCCcceeEecccchHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCC
Confidence 32 1 23556889999998875322111111111224445566666544 35665554 4455667899999999865
Q ss_pred CCeEEEe
Q 003093 157 TGYVWIA 163 (848)
Q Consensus 157 ~~~~wi~ 163 (848)
++-+-|.
T Consensus 205 p~di~v~ 211 (267)
T cd06283 205 PEDVGLI 211 (267)
T ss_pred ccceEEE
Confidence 5444333
No 157
>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=95.16 E-value=0.31 Score=50.57 Aligned_cols=153 Identities=14% Similarity=0.089 Sum_probs=88.5
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|+||| -|..... ..+. .+...++|+|.+....+ ....++ +..++..-+..+++.+...|-++++++..+
T Consensus 54 ~~vdgiii~~~~~~~-~~~~-~~~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~ 125 (264)
T cd06274 54 RQVDALIVAGSLPPD-DPYY-LCQKAGLPVVALDRPGD---PSRFPS---VVSDNRDGAAELTRELLAAPPEEVLFLGGL 125 (264)
T ss_pred cCCCEEEEcCCCCch-HHHH-HHHhcCCCEEEecCccC---CCCCCE---EEEccHHHHHHHHHHHHHCCCCcEEEEeCC
Confidence 4566665 3332222 2233 35668899998754422 122333 344555556778888777899999999744
Q ss_pred CC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC---CCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 82 DD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 82 d~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~---~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
.. ......+.|.+.++++|+.+..........+...-...+.++... .+++|+.. +...+..+++++++.|+..
T Consensus 126 ~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~~-~d~~A~g~~~al~~~g~~i 204 (264)
T cd06274 126 PELSPSRERLAGFRQALADAGLPVQPDWIYAEGYSPESGYQLMAELLARLGRLPRALFTT-SYTLLEGVLRFLRERPGLA 204 (264)
T ss_pred CcccchHHHHHHHHHHHHHcCCCCCcceeecCCCChHHHHHHHHHHHccCCCCCcEEEEc-ChHHHHHHHHHHHHcCCCC
Confidence 32 344567899999999886432111111111222333444554332 36766644 4556778999999999865
Q ss_pred CCeEEEec
Q 003093 157 TGYVWIAT 164 (848)
Q Consensus 157 ~~~~wi~~ 164 (848)
++-+-|++
T Consensus 205 p~dv~v~g 212 (264)
T cd06274 205 PSDLRIAT 212 (264)
T ss_pred CcceEEEE
Confidence 55444443
No 158
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=95.13 E-value=0.3 Score=53.07 Aligned_cols=147 Identities=8% Similarity=0.012 Sum_probs=87.5
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.++++|| -|.. .........+.+.++|+|...... ....+++ +..++...+..+++++...|.++++++..+
T Consensus 119 ~~vdgiIi~~~~-~~~~~~~~~l~~~~iPvV~~~~~~---~~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~ 191 (342)
T PRK10014 119 QGVDGVVIAGAA-GSSDDLREMAEEKGIPVVFASRAS---YLDDVDT---VRPDNMQAAQLLTEHLIRNGHQRIAWLGGQ 191 (342)
T ss_pred CCCCEEEEeCCC-CCcHHHHHHHhhcCCCEEEEecCC---CCCCCCE---EEeCCHHHHHHHHHHHHHCCCCEEEEEcCC
Confidence 4566666 2222 222344556677899999864321 1122232 456667778888888888899999999643
Q ss_pred CC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 DD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
.. ....-.+.|.+++++.|+.+.....+....+.......+.++.+. .+++|+ +.+...+..+++.+.+.|+..+
T Consensus 192 ~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~~~~l~~~g~~vp 270 (342)
T PRK10014 192 SSSLTRAERVGGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVV-CYNETIAMGAWFGLLRAGRQSG 270 (342)
T ss_pred cccccHHHHHHHHHHHHHHcCCCCCcceEecCCCChHHHHHHHHHHHcCCCCCCEEE-ECCcHHHHHHHHHHHHcCCCCC
Confidence 32 223456789999999987643211111111222333444554433 456655 4555667778999999998654
No 159
>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=95.13 E-value=0.3 Score=50.69 Aligned_cols=153 Identities=10% Similarity=0.042 Sum_probs=87.0
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+|++||=-........ ..-+.+.++|+|......+ ...++++ ..++...+..+++++...|-++++++....
T Consensus 54 ~~vdgiIi~~~~~~~~~-~~~l~~~~ipvV~~~~~~~---~~~~~~v---~~d~~~~~~~~~~~l~~~g~~~I~~i~~~~ 126 (265)
T cd06299 54 QRVDGIIVVPHEQSAEQ-LEDLLKRGIPVVFVDREIT---GSPIPFV---TSDPQPGMTEAVSLLVALGHKKIGYISGPQ 126 (265)
T ss_pred cCCCEEEEcCCCCChHH-HHHHHhCCCCEEEEecccC---CCCCCEE---EECcHHHHHHHHHHHHHcCCCcEEEEeCCC
Confidence 46776663222222333 3455667999998765422 2233443 234444455666777777999999996433
Q ss_pred --CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 83 --DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 83 --~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
.........|.+.++++|+.+.............+....+.++.+.++++|+. ++...+..+++++++.|+..++-+
T Consensus 127 ~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~av~~-~~d~~a~gv~~al~~~g~~vp~dv 205 (265)
T cd06299 127 DTSTGRERLEAFRQACASLGLEVNEDLVVLGGYSQESGYAGATKLLDQGATAIIA-GDSMMTIGAIRAIHDAGLVIGEDI 205 (265)
T ss_pred CcccHHHHHHHHHHHHHHCCCCCChHhEEecCcchHHHHHHHHHHHcCCCCEEEE-cCcHHHHHHHHHHHHhCCCCCcce
Confidence 23345567899999998854321111111111123334455554445776555 445567789999999998655434
Q ss_pred EEe
Q 003093 161 WIA 163 (848)
Q Consensus 161 wi~ 163 (848)
.|.
T Consensus 206 ~v~ 208 (265)
T cd06299 206 SLI 208 (265)
T ss_pred eEE
Confidence 343
No 160
>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=95.12 E-value=0.46 Score=50.64 Aligned_cols=158 Identities=15% Similarity=0.087 Sum_probs=91.5
Q ss_pred CeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCC-----C--CCC-CceEeccCChHHHHHHHHHHHHHcCcEE
Q 003093 4 QTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLS-----S--LQF-PYFVRTTQSDQYQMAAIAEIVDHYGWRE 74 (848)
Q Consensus 4 ~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls-----~--~~~-p~f~r~~p~d~~q~~ai~~~~~~~~w~~ 74 (848)
+|++|| .|... ....+...+.+.++|+|.+....+... . ..+ +++-.+.+++...++.+++.+...|-++
T Consensus 58 ~vdgiIi~~~~~-~~~~~~~~~~~~giPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~g~~~ 136 (305)
T cd06324 58 KPDALIFTNEKS-VAPELLRLAEGAGVKLFLVNSGLTEAQARELGPPREKFPDWLGQLLPNDEEAGYLMAEALISQARSV 136 (305)
T ss_pred CCCEEEEcCCcc-chHHHHHHHHhCCCeEEEEecCCCcchhhcccccccccCceeeeeccCcHHHHHHHHHHHHHHhhcc
Confidence 677755 33332 233334556778999998865432211 0 111 2345566777888888889887666663
Q ss_pred --------EEEEEEcC--CCccchHHHHHHHHhccC-cEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCc
Q 003093 75 --------VIAIYVDD--DHGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNR 141 (848)
Q Consensus 75 --------vaii~~dd--~~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~ 141 (848)
++++..+. .......+.|++.++++| ..+.. .+....+..+-...+.++.+. ++++|+ +.+...
T Consensus 137 ~~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~g~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~ 213 (305)
T cd06324 137 QAPGGRIDLLAISGDPTTPAAILREAGLRRALAEHPDVRLRQ--VVYAGWSEDEAYEQAENLLKRYPDVRLIW-AANDQM 213 (305)
T ss_pred cCCCCceeEEEEeCCCCChHHHHHHHHHHHHHHHCCCceEee--eecCCCCHHHHHHHHHHHHHHCCCccEEE-ECCchH
Confidence 66665322 233455778999999987 43322 222222223334455555433 466655 345566
Q ss_pred HHHHHHHHHHcCCCCCC-eEEEecC
Q 003093 142 GPVVFHVAQYLGMLGTG-YVWIATS 165 (848)
Q Consensus 142 ~~~~~~~a~~~g~~~~~-~~wi~~~ 165 (848)
+..+++++++.|+..++ ...++-+
T Consensus 214 A~g~~~al~~~g~~vp~di~vig~D 238 (305)
T cd06324 214 AFGALRAAKEAGRKPGRDVLFGGVN 238 (305)
T ss_pred HHHHHHHHHHcCCCcCCCEEEEecC
Confidence 77899999999986543 4444434
No 161
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=95.11 E-value=0.94 Score=43.38 Aligned_cols=70 Identities=21% Similarity=0.310 Sum_probs=45.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..++++.+.++.+ .+++.... ....+++..|.+|++|++++..... ...++ ..+.....+++++++
T Consensus 13 ~~l~~~i~~~~~~~p-~i~i~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~~~~~ 80 (197)
T cd05466 13 YLLPPLLAAFRQRYP-GVELSLVE-------GGSSELLEALLEGELDLAIVALPVD---DPGLE-SEPLFEEPLVLVVPP 80 (197)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEE-------CChHHHHHHHHcCCceEEEEcCCCC---CCcce-EeeeeccceEEEecC
Confidence 345667777777654 24455543 3466899999999999999754432 22233 446667788888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (197)
T cd05466 81 DH 82 (197)
T ss_pred CC
Confidence 65
No 162
>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=94.96 E-value=0.88 Score=48.43 Aligned_cols=162 Identities=8% Similarity=0.030 Sum_probs=85.8
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcE------
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWR------ 73 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~------ 73 (848)
.+|++|| .|..+.....+...+...++|+|.+....+...-...+-+..+.+++...+..+++++... +-+
T Consensus 56 ~~vdgiii~~~~~~~~~~~~~~~~~~giPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~a~~l~~~~~~~~~~~~~~ 135 (303)
T cd01539 56 KGVDLLAVNLVDPTAAQTVINKAKQKNIPVIFFNREPEEEDIKSYDKAYYVGTDAEQSGILQGKLIADYWNANKDALDKN 135 (303)
T ss_pred cCCCEEEEecCchhhHHHHHHHHHHCCCCEEEeCCCCcccccccccccceeeecHHHHHHHHHHHHHHHhhccccccccC
Confidence 4566544 5555443344445567789999987653221111111223445666666677777776443 221
Q ss_pred ---E--EEEEEEcCC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC---CCeEEEEEccCCcHH
Q 003093 74 ---E--VIAIYVDDD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVHTHYNRGP 143 (848)
Q Consensus 74 ---~--vaii~~dd~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~---~~~viv~~~~~~~~~ 143 (848)
+ ++++..+.. ......+.|.+.++++|..+..........+.......+.++... ++++|+. .+...+.
T Consensus 136 ~~g~~~i~~~~g~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~~ai~~-~~d~~a~ 214 (303)
T cd01539 136 GDGIIQYVMLKGEPGHPDAIARTKYSIETLNDAGIKTEELASDTANWDRAQAKDKMDALLLKYGDKIEAVIA-NNDAMAL 214 (303)
T ss_pred CCCceEEEEEEcCCCCchhhhhhhhHHHHHHhcCCCeEEEEeecCCCCHHHHHHHHHHHHHhcCCCccEEEE-CCchHHH
Confidence 2 344443322 223446788999999887653222222222222333344554332 2565444 4445556
Q ss_pred HHHHHHHHcCCCCC----CeEEEecC
Q 003093 144 VVFHVAQYLGMLGT----GYVWIATS 165 (848)
Q Consensus 144 ~~~~~a~~~g~~~~----~~~wi~~~ 165 (848)
.+++++++.|...+ +...++.+
T Consensus 215 g~~~al~~~g~~~p~~~~di~iig~d 240 (303)
T cd01539 215 GAIEALQKYGYNKGDKSKNIPVVGVD 240 (303)
T ss_pred HHHHHHHHcCCCcCCCCCceEEEccC
Confidence 78899999998654 44444444
No 163
>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=94.96 E-value=0.33 Score=50.46 Aligned_cols=155 Identities=13% Similarity=0.059 Sum_probs=87.4
Q ss_pred CeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcCC
Q 003093 4 QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD 83 (848)
Q Consensus 4 ~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~ 83 (848)
++++||-...... ......+.+.++|+|.+....+ . .+.+..+..++...++.+++.+...|-++++++..+..
T Consensus 60 ~~dgiii~~~~~~-~~~~~~~~~~~ipvV~~~~~~~---~--~~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~ 133 (270)
T cd06294 60 RVDGFILLYSRED-DPIIDYLKEEKFPFVVIGKPED---D--KENITYVDNDNIQAGYDATEYLIKLGHKKIAFVGGDLD 133 (270)
T ss_pred CcCEEEEecCcCC-cHHHHHHHhcCCCEEEECCCCC---C--CCCCCeEEECcHHHHHHHHHHHHHcCCccEEEecCCcc
Confidence 4666554221111 2333445678999998754321 1 01122244566666778888877779999999974433
Q ss_pred C--ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCC-
Q 003093 84 H--GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG- 158 (848)
Q Consensus 84 ~--g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~- 158 (848)
+ .....+.|.+.+++.|+.+..........+..+....+.++.+. ++++|+. .+...+..+++++++.|+..++
T Consensus 134 ~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~iP~d 212 (270)
T cd06294 134 LEVTQDRLQGYKQALEDHGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIVA-TDDLLALGVLKVLNELGLKVPED 212 (270)
T ss_pred cHHHHHHHHHHHHHHHHcCCCCCcceEEecCCchHHHHHHHHHHHhCCCCCCEEEE-CChHHHHHHHHHHHHcCCCCCcc
Confidence 2 33456889999999885321111111111223334455555433 3666655 3455777899999999986544
Q ss_pred eEEEecC
Q 003093 159 YVWIATS 165 (848)
Q Consensus 159 ~~wi~~~ 165 (848)
..+++.+
T Consensus 213 v~vig~d 219 (270)
T cd06294 213 LSIIGFN 219 (270)
T ss_pred eEEEeeC
Confidence 3344433
No 164
>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=94.91 E-value=0.34 Score=50.43 Aligned_cols=135 Identities=7% Similarity=-0.041 Sum_probs=80.3
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC--CCccchHHHHHHHHhcc
Q 003093 22 HVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLAAK 99 (848)
Q Consensus 22 ~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd--~~g~~~~~~l~~~l~~~ 99 (848)
.+....++|+|......+ ...+++ +..++...+..+++++...|-++++++.... .......+.|.+.+++.
T Consensus 73 ~l~~~~~ipvV~i~~~~~---~~~~~~---V~~d~~~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~ 146 (269)
T cd06275 73 MLERYRHIPMVVMDWGPE---DDFADK---IQDNSEEGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEA 146 (269)
T ss_pred HHHhcCCCCEEEEecccC---CCCCCe---EeeCcHHHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHc
Confidence 344456999998754322 122333 4455666677888888778999999997432 23445568899999998
Q ss_pred CcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003093 100 RCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 163 (848)
Q Consensus 100 g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 163 (848)
|+.+..........+.......++++.+. .+++|+. ++...+..+++.+++.|...++-+-++
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vp~di~vv 211 (269)
T cd06275 147 GLPVNPGWIVEGDFECEGGYEAMQRLLAQPKRPTAVFC-GNDLMAMGALCAAQEAGLRVPQDLSII 211 (269)
T ss_pred CCCCCHHHhccCCCChHHHHHHHHHHHcCCCCCcEEEE-CChHHHHHHHHHHHHcCCCCCcceEEE
Confidence 87653211111111223334455555443 3555444 445566678899999998655444433
No 165
>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=94.90 E-value=0.53 Score=48.97 Aligned_cols=153 Identities=10% Similarity=0.020 Sum_probs=90.3
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.++++||--.+......+..+. ..++|+|......+. ...+ .+.+++...+..+++.+...|-++++++..+.
T Consensus 54 ~~~dgiii~~~~~~~~~~~~~~-~~~~pvV~i~~~~~~---~~~~---~V~~d~~~~~~~~~~~L~~~G~~~i~~i~~~~ 126 (269)
T cd06293 54 NHVDGLIFVTNRPDDGALAKLI-NSYGNIVLVDEDVPG---AKVP---KVFCDNEQGGRLATRHLARAGHRRIAFVGGPD 126 (269)
T ss_pred CCCCEEEEeCCCCCHHHHHHHH-hcCCCEEEECCCCCC---CCCC---EEEECCHHHHHHHHHHHHHCCCceEEEEecCc
Confidence 4677777432221222233333 357999987654321 1122 35577888888999988888999999997443
Q ss_pred C--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 83 D--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
. ......+.|.+++++.|..+..........+..+....+.++.+ ..+++|+.. +...+..+++++++.|...++
T Consensus 127 ~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~vp~ 205 (269)
T cd06293 127 ALISARERYAGYREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPTAIFAA-SDEIAIGLLEVLRERGLSIPG 205 (269)
T ss_pred ccccHHHHHHHHHHHHHHcCCCCChheEEecCCCHHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCcc
Confidence 3 23345688999999988653211111111122233344555433 346765554 555666799999999986555
Q ss_pred eEEEe
Q 003093 159 YVWIA 163 (848)
Q Consensus 159 ~~wi~ 163 (848)
-+-|.
T Consensus 206 di~i~ 210 (269)
T cd06293 206 DMSLV 210 (269)
T ss_pred ceEEE
Confidence 44443
No 166
>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=94.88 E-value=0.34 Score=50.26 Aligned_cols=152 Identities=13% Similarity=0.083 Sum_probs=90.1
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.++++|| .|.... ...+ ..+...++|++.+....+ .+++ +..++..-+..+++++...|-++++++..+
T Consensus 54 ~~~dgiii~~~~~~-~~~~-~~~~~~~iPvv~~~~~~~-----~~~~---V~~d~~~ag~~a~~~L~~~g~~~i~~i~~~ 123 (265)
T cd06285 54 RRVDGLILGDARSD-DHFL-DELTRRGVPFVLVLRHAG-----TSPA---VTGDDVLGGRLATRHLLDLGHRRIAVLAGP 123 (265)
T ss_pred cCCCEEEEecCCCC-hHHH-HHHHHcCCCEEEEccCCC-----CCCE---EEeCcHHHHHHHHHHHHHCCCccEEEEeCC
Confidence 3566555 543322 2333 445668999998764321 2333 345666677788888888899999999744
Q ss_pred C--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 D--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
. ..+....+.|.+.+++.|+.+.....+....+.......+.++... .+++|+. .+...+..+++.+++.|+..+
T Consensus 124 ~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~~p 202 (265)
T cd06285 124 DYASTARDRLAGFRAALAEAGIEVPPERIVYSGFDIEGGEAAAEKLLRSDSPPTAIFA-VNDFAAIGVMGAARDRGLRVP 202 (265)
T ss_pred cccccHHHHHHHHHHHHHHcCCCCChhhEEeCCCCHHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCC
Confidence 3 2345667889999999887643211111111222333455555433 3565444 455566789999999998644
Q ss_pred C-eEEEecC
Q 003093 158 G-YVWIATS 165 (848)
Q Consensus 158 ~-~~wi~~~ 165 (848)
+ ...++-+
T Consensus 203 ~di~iig~d 211 (265)
T cd06285 203 DDVALVGYN 211 (265)
T ss_pred cceEEEeec
Confidence 3 3344433
No 167
>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=94.84 E-value=0.88 Score=47.33 Aligned_cols=155 Identities=10% Similarity=0.094 Sum_probs=90.6
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
.+|++|| .|............+.+.++|+|.+....+ +. .++..+..++...+..+++++... |-++++++.
T Consensus 55 ~~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~~~~~---~~--~~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~ 129 (270)
T cd06308 55 QGVDLLIISPNEAAPLTPVVEEAYRAGIPVILLDRKIL---SD--KYTAYIGADNYEIGRQAGEYIANLLPGKGNILEIW 129 (270)
T ss_pred hCCCEEEEecCchhhchHHHHHHHHCCCCEEEeCCCCC---Cc--cceEEeecCcHHHHHHHHHHHHHHcCCCceEEEEE
Confidence 3555543 343332222333445678999998754221 11 233345667777788888887664 889999997
Q ss_pred EcCCC--ccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 80 VDDDH--GRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~dd~~--g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.+... .....+.+.+.++++ |+++.... ....+..+....+.++.+ .++++|+ +.+...+..+++++++.|+
T Consensus 130 ~~~~~~~~~~R~~g~~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~aI~-~~~d~~a~g~~~al~~~g~ 206 (270)
T cd06308 130 GLEGSSPAIERHDGFKEALSKYPKIKIVAQQ--DGDWLKEKAEEKMEELLQANPDIDLVY-AHNDPMALGAYLAAKRAGR 206 (270)
T ss_pred CCCCCchHHHHHHHHHHHHHHCCCCEEEEec--CCCccHHHHHHHHHHHHHhCCCCcEEE-eCCcHHHHHHHHHHHHcCC
Confidence 44333 234568899999998 88765321 111121222233444432 2466544 4455667789999999998
Q ss_pred CCCCeEEEecCc
Q 003093 155 LGTGYVWIATSW 166 (848)
Q Consensus 155 ~~~~~~wi~~~~ 166 (848)
. .+...++.|.
T Consensus 207 ~-~dv~vvg~d~ 217 (270)
T cd06308 207 E-KEIKFIGIDG 217 (270)
T ss_pred C-CCcEEEEecC
Confidence 6 5555555543
No 168
>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=94.83 E-value=0.44 Score=49.58 Aligned_cols=148 Identities=12% Similarity=0.013 Sum_probs=87.3
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+|++||--.+... ......+...++|+|.+....+ ...+++ +..++...+..+++++...|-++++++..+.
T Consensus 54 ~~vdgii~~~~~~~-~~~~~~~~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~ 126 (268)
T cd06270 54 RRCDALILHSKALS-DDELIELAAQVPPLVLINRHIP---GLADRC---IWLDNEQGGYLATEHLIELGHRKIACITGPL 126 (268)
T ss_pred cCCCEEEEecCCCC-HHHHHHHhhCCCCEEEEeccCC---CCCCCe---EEECcHHHHHHHHHHHHHCCCceEEEEeCCc
Confidence 46666664222111 1213344677999998754332 122232 4567777788888988778999999997443
Q ss_pred C--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 83 D--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
. ......+.|.+.++++|+.+..........+..+....+.++.+. .+++|+.. +...+..+++.+++.|+..++
T Consensus 127 ~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~ip~ 205 (268)
T cd06270 127 TKEDARLRLQGYRDALAEAGIALDESLIIEGDFTEEGGYAAMQELLARGAPFTAVFCA-NDEMAAGAISALREHGISVPQ 205 (268)
T ss_pred ccccHHHHHHHHHHHHHHcCCCCCcceEEECCCCHHHHHHHHHHHHhCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCC
Confidence 2 233456788999999887542111111112223444555555444 35655543 345667799999999986543
No 169
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=94.81 E-value=0.45 Score=51.35 Aligned_cols=147 Identities=10% Similarity=0.059 Sum_probs=97.9
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+.+|++||=-. ............+.++|+|-.....+ +..+ -.+..++..-+..+++++...|-+++++|...
T Consensus 112 ~~~vdGiIi~~-~~~~~~~~~~l~~~~~P~V~i~~~~~---~~~~---~~V~~Dn~~~~~~a~~~L~~~G~~~i~~i~~~ 184 (333)
T COG1609 112 QKRVDGLILLG-ERPNDSLLELLAAAGIPVVVIDRSPP---GLGV---PSVGIDNFAGAYLATEHLIELGHRRIAFIGGP 184 (333)
T ss_pred HcCCCEEEEec-CCCCHHHHHHHHhcCCCEEEEeCCCc---cCCC---CEEEEChHHHHHHHHHHHHHCCCceEEEEeCC
Confidence 34677766322 23334445667777999998765544 2222 33557788888899999999999999999965
Q ss_pred --CCCccchHHHHHHHHhccCcEE--EEeeecCCCCChHHHHHHHHHHhcCC---CeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 82 --DDHGRNGIAALGDTLAAKRCRI--SFKAPLSVEATEDEITDLLVKVALTE---SRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 82 --d~~g~~~~~~l~~~l~~~g~~v--~~~~~~~~~~~~~d~~~~l~~i~~~~---~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
...+..-.+.+.++++++|+.. .....-.. +..+-...+.++.... +++|| +++...|..+++++++.|.
T Consensus 185 ~~~~~~~~R~~Gf~~al~~~~~~~~~~~i~~~~~--~~~~g~~~~~~ll~~~~~~ptAif-~~nD~~Alg~l~~~~~~g~ 261 (333)
T COG1609 185 LDSSASRERLEGYRAALREAGLPINPEWIVEGDF--SEESGYEAAERLLARGEPRPTAIF-CANDLMALGALRALRELGL 261 (333)
T ss_pred CccccHhHHHHHHHHHHHHCCCCCCcceEEecCC--ChHHHHHHHHHHHhcCCCCCcEEE-EcCcHHHHHHHHHHHHcCC
Confidence 4455777899999999999875 22211111 2244444555555432 66655 4556678889999999998
Q ss_pred CCCC
Q 003093 155 LGTG 158 (848)
Q Consensus 155 ~~~~ 158 (848)
..++
T Consensus 262 ~vP~ 265 (333)
T COG1609 262 RVPE 265 (333)
T ss_pred CCCC
Confidence 7665
No 170
>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=94.80 E-value=1.3 Score=46.17 Aligned_cols=154 Identities=10% Similarity=0.005 Sum_probs=85.7
Q ss_pred CeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc-C--cEEEEEEE
Q 003093 4 QTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-G--WREVIAIY 79 (848)
Q Consensus 4 ~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~-~--w~~vaii~ 79 (848)
+|++|| .|............+.+.++|+|.+....+. ... +..+..++...+..+++++... | -++++++.
T Consensus 58 ~vdgiii~~~~~~~~~~~i~~~~~~~ipvV~~~~~~~~--~~~---~~~V~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~ 132 (275)
T cd06307 58 RSDGVALVAPDHPQVRAAVARLAAAGVPVVTLVSDLPG--SPR---AGYVGIDNRAAGRTAAWLIGRFLGRRPGKVAVLA 132 (275)
T ss_pred cCCEEEEeCCCcHHHHHHHHHHHHCCCcEEEEeCCCCC--Cce---eeEEccChHHHHHHHHHHHHHHhCCCCCeEEEEe
Confidence 566554 4444333223335555689999987543211 111 1224455556666667766544 5 36999887
Q ss_pred EcCC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 80 VDDD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 80 ~dd~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
.+.. ......+.|.++++++|..+..........+..+....++++.+ .++++|+...+. +..+++.+++.|+.
T Consensus 133 ~~~~~~~~~~R~~gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~--~~g~~~al~~~g~~ 210 (275)
T cd06307 133 GSHRFRGHEEREMGFRSVLREEFPGLRVLETLEGLDDPARAYEATRKLLARHPDLVGIYNAGGG--NRGVIRALREAGRA 210 (275)
T ss_pred cCCCCcchHHHHHHHHHHHHhhCCCcEEEeeccCCCChHHHHHHHHHHHHhCCCceEEEECCCC--hHHHHHHHHHcCCC
Confidence 5432 23445688999999887554322222222222333445555533 356777766543 36899999999985
Q ss_pred CCCeEEEecC
Q 003093 156 GTGYVWIATS 165 (848)
Q Consensus 156 ~~~~~wi~~~ 165 (848)
.+...++.|
T Consensus 211 -~di~Ivg~d 219 (275)
T cd06307 211 -GKVVFVGHE 219 (275)
T ss_pred -CCcEEEEec
Confidence 344444444
No 171
>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=94.79 E-value=0.37 Score=49.89 Aligned_cols=149 Identities=12% Similarity=0.071 Sum_probs=86.7
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+|++||=..+...... .......++|+|......+ ..+++ +..++...+..+++.+...|-++++++....
T Consensus 50 ~~vdgii~~~~~~~~~~-~~~~~~~~ipvV~~~~~~~----~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~ 121 (261)
T cd06272 50 NRFDGVIIFGESASDVE-YLYKIKLAIPVVSYGVDYD----LKYPI---VNVDNEKAMELAVLYLAEKGHKKIAYIGDLS 121 (261)
T ss_pred cCcCEEEEeCCCCChHH-HHHHHHcCCCEEEEcccCC----CCCCE---EEEChHHHHHHHHHHHHHcCchhEEEeeccc
Confidence 35666652212222222 2445578999998754322 12233 4566777788888888778999999997443
Q ss_pred C--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCC--CeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 83 D--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~--~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
. ........|.+.+++.|+.+..........+.......+.++.+.. +++|+ +++...+..+++.+++.|+..++
T Consensus 122 ~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~vp~ 200 (261)
T cd06272 122 LDRRQRKRFKGFLETCDENGISISDSHIDVDGLSAEGGDNAAKKLLKESDLPTAII-CGSYDIALGVLSALNKQGISIPE 200 (261)
T ss_pred ccccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCCHHHHHHHHHHHHcCCCCCCEEE-ECCcHHHHHHHHHHHHhCCCCCC
Confidence 3 3344567899999998864321111111112233334555554433 56544 45555677899999999986554
Q ss_pred eE
Q 003093 159 YV 160 (848)
Q Consensus 159 ~~ 160 (848)
-+
T Consensus 201 dv 202 (261)
T cd06272 201 DI 202 (261)
T ss_pred ce
Confidence 33
No 172
>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=94.74 E-value=0.51 Score=48.87 Aligned_cols=144 Identities=10% Similarity=0.057 Sum_probs=86.8
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|++|| -+...... .+.. ..+.++|+|.+....+ ...+ .+..++...++.+++++...|-++|+++..+
T Consensus 55 ~~vdgiii~~~~~~~~-~~~~-~~~~~ipvv~~~~~~~----~~~~---~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~ 125 (264)
T cd01574 55 QRVDGVIVNAPLDDAD-AALA-AAPADVPVVFVDGSPS----PRVS---TVSVDQEGGARLATEHLLELGHRTIAHVAGP 125 (264)
T ss_pred cCCCEEEEeCCCCChH-HHHH-HHhcCCCEEEEeccCC----CCCC---EEEeCcHHHHHHHHHHHHHCCCCEEEEEecC
Confidence 4677776 23222222 3333 3568999998765321 1223 3556677778888888888899999999744
Q ss_pred CCC--ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC-CCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 82 DDH--GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT-ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 82 d~~--g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~-~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
... .....+.|.+.+++.|+.+... +....+...-...+.++.+. .+++|+. ++...+..+++++++.|...++
T Consensus 126 ~~~~~~~~r~~gf~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~ai~~-~~d~~a~g~~~~~~~~g~~ip~ 202 (264)
T cd01574 126 EEWLSARARLAGWRAALEAAGIAPPPV--LEGDWSAESGYRAGRELLREGDPTAVFA-ANDQMALGVLRALHELGLRVPD 202 (264)
T ss_pred CccchHHHHHHHHHHHHHHCCCCccee--eecCCCHHHHHHHHHHHHhCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCcc
Confidence 332 2345578999998888765422 21111223333444455433 3666554 4555677899999999975443
No 173
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=94.69 E-value=1.9 Score=41.79 Aligned_cols=72 Identities=22% Similarity=0.253 Sum_probs=46.4
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++...+..+|.+|++|++++..... .....+ -..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~-~~~~l~~~~~~~v~~~ 82 (201)
T cd08418 13 TLMPAVINRFKEQFP-DVQISIYE-------GQLSSLLPELRDGRLDFAIGTLPDE-MYLKEL-ISEPLFESDFVVVARK 82 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CcHHHHHHHHHcCCCcEEEEecCCC-CCCcce-eEEeecCCceEEEeCC
Confidence 455677777877764 34455543 4577899999999999999732211 111223 2456677888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 83 ~~ 84 (201)
T cd08418 83 DH 84 (201)
T ss_pred CC
Confidence 54
No 174
>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=94.69 E-value=1.2 Score=43.35 Aligned_cols=70 Identities=17% Similarity=0.167 Sum_probs=46.5
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++.+.+..+|.+|++|+++...... ...+. +.|.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~v~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~v~~~ 80 (201)
T cd08459 13 YFLPRLLAALREVAP-GVRIETVR-------LPVDELEEALESGEIDLAIGYLPDL---GAGFF-QQRLFRERYVCLVRK 80 (201)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe-------cCccCHHHHhhCCCceEEEEcCCCC---cccce-EEEeecCceEEEEcC
Confidence 345677888887764 23344443 3467889999999999998643221 22233 567888888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (201)
T cd08459 81 DH 82 (201)
T ss_pred CC
Confidence 54
No 175
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=94.67 E-value=0.57 Score=47.49 Aligned_cols=135 Identities=9% Similarity=0.086 Sum_probs=95.2
Q ss_pred HHHHHHhhccCCccEEecccCCCCCCCC--C-CCce--EeccCChHHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHH
Q 003093 17 SHVVSHVANELQVPLLSFSATDPTLSSL--Q-FPYF--VRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAA 91 (848)
Q Consensus 17 ~~ava~i~~~~~vP~Is~~at~p~ls~~--~-~p~f--~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~ 91 (848)
..+++.+....++=.|.|++|+.++-.. + ..-. -+...+-..-+.|+.+-++++|.++++++. +|-....+.
T Consensus 60 ~~aa~~ll~~a~~dvi~~~cTsgs~~~G~~~~~~~i~~~~~g~p~tt~~~A~~~AL~alg~~RIalvT---PY~~~v~~~ 136 (239)
T TIGR02990 60 TEAAALILPDEELDVVAYSCTSASVVIGDDEVTRAINAAKPGTPVVTPSSAAVDGLAALGVRRISLLT---PYTPETSRP 136 (239)
T ss_pred HHHHHHhcCCCCCCEEEEccchhheecCHHHHHHHHHhcCCCCCeeCHHHHHHHHHHHcCCCEEEEEC---CCcHHHHHH
Confidence 3445555566788899999998766310 0 0000 011223334467888889999999999997 588889999
Q ss_pred HHHHHhccCcEEEEeeecCCC-------CChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHH-cCC
Q 003093 92 LGDTLAAKRCRISFKAPLSVE-------ATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQY-LGM 154 (848)
Q Consensus 92 l~~~l~~~g~~v~~~~~~~~~-------~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~-~g~ 154 (848)
+.+.+++.|++|+....+... .+...+...+.++...++|+|++.|-.-....++.++.+ +|.
T Consensus 137 ~~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAifisCTnLrt~~vi~~lE~~lGk 207 (239)
T TIGR02990 137 MAQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADALFLSCTALRAATCAQRIEQAIGK 207 (239)
T ss_pred HHHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEEEEeCCCchhHHHHHHHHHHHCC
Confidence 999999999999877555432 234566666777767899999999988777788888754 554
No 176
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=94.61 E-value=1.5 Score=42.99 Aligned_cols=73 Identities=18% Similarity=0.198 Sum_probs=47.6
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..+++..+.++.+ .+++.... ++...++++|.+|++|+++........-...+. +.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~ 83 (202)
T cd08468 13 AVMPRLMARLEELAP-SVRLNLVH-------AEQKLPLDALLAGEIDFALGYSHDDGAEPRLIE-ERDWWEDTYVVIASR 83 (202)
T ss_pred HHhHHHHHHHHhhCC-CCEEEEEE-------CChHhHHHHHHCCCccEEEecccccccCCCCEE-EEEEecCcEEEEEeC
Confidence 456778888888774 23455543 457899999999999999874322100012233 356777788888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 84 ~h 85 (202)
T cd08468 84 DH 85 (202)
T ss_pred CC
Confidence 65
No 177
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=94.55 E-value=0.13 Score=55.33 Aligned_cols=60 Identities=25% Similarity=0.209 Sum_probs=39.2
Q ss_pred CCCCChHHhhcCCCCeeEEeC-chHH----HHHHhhhCCCccC--cccCCCHHHHHHHhhcCCCCCceEEEEcc
Q 003093 590 SPIKGIDSLRSSNYPIGYQVN-SFAR----NYLVDELNIDESR--LVPLNSPEEYAKALKDGPHKGGVAAVVDD 656 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~-s~~~----~~l~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~a~~~~ 656 (848)
.++++++||. ++++++... +... .++ +..+..... .+.+.+..+...+|.+ |++|+++..
T Consensus 131 ~~i~sl~dL~--gk~v~~~~~~s~~~~~~~~~l-~~~G~~~~~~~~v~~~~~~~~~~al~~----G~vDa~~~~ 197 (320)
T TIGR02122 131 SGIKTVADLK--GKRVAVGAPGSGTELNARAVL-KAAGLTYDDVKKVEYLGYAEAADALKD----GKIDAAFYT 197 (320)
T ss_pred CCCCcHHHcC--CCEEecCCCCcchHHHHHHHH-HHcCCCHHHccchhcCCHHHHHHHHHC----CCccEEEEe
Confidence 4688999998 777777543 3222 223 223332222 3566778899999999 899999877
No 178
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=94.52 E-value=2 Score=41.34 Aligned_cols=70 Identities=19% Similarity=0.158 Sum_probs=45.6
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..+++..+.++.+ .+++.... ++..+++..+.+|++|+++... ......+ -..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~-~~~~l~~~~~~~v~~~ 80 (193)
T cd08442 13 VRLPPLLAAYHARYP-KVDLSLST-------GTTGALIQAVLEGRLDGAFVAG---PVEHPRL-EQEPVFQEELVLVSPK 80 (193)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCccEEEEeC---CCCCCCc-EEEEeecCcEEEEecC
Confidence 455778888887764 22344443 4567899999999999998632 1122222 2456677788888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (193)
T cd08442 81 GH 82 (193)
T ss_pred CC
Confidence 54
No 179
>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=94.51 E-value=0.55 Score=48.93 Aligned_cols=136 Identities=14% Similarity=0.046 Sum_probs=82.1
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC--CCccchHHHHHHHHhcc
Q 003093 22 HVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLAAK 99 (848)
Q Consensus 22 ~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd--~~g~~~~~~l~~~l~~~ 99 (848)
.-+.+.++|+|.+....+. ...+++ +..++...+..+++.+...|-++++++.... .......+.|.+.++++
T Consensus 77 ~~~~~~~ipvV~i~~~~~~--~~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~ 151 (273)
T cd06292 77 ERLAERGLPVVLVNGRAPP--PLKVPH---VSTDDALAMRLAVRHLVALGHRRIGFASGPGRTVPRRRKIAGFRAALEEA 151 (273)
T ss_pred HHHHhCCCCEEEEcCCCCC--CCCCCE---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHc
Confidence 3346789999987654322 012332 5567777788888888778999999986432 23445578899999998
Q ss_pred CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003093 100 RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 163 (848)
Q Consensus 100 g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 163 (848)
|+.......+....+.......+.++...++++|++. +...+..+++.+++.|+..++-+-+.
T Consensus 152 ~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~ai~~~-~d~~a~g~~~~l~~~g~~ip~di~ii 214 (273)
T cd06292 152 GLEPPEALVARGMFSVEGGQAAAVELLGSGPTAIVAA-SDLMALGAIRAARRRGLRVPEDVSVV 214 (273)
T ss_pred CCCCChhheEeCCCCHHHHHHHHHHHhcCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCcceEEE
Confidence 8642111011111111223334445444447876644 45566778999999998655444443
No 180
>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=94.47 E-value=1.1 Score=47.24 Aligned_cols=147 Identities=7% Similarity=0.015 Sum_probs=84.0
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc------CcEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY------GWREV 75 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~------~w~~v 75 (848)
.+|++|| .|..+.........+...++|+|......+. ...++. +..++...+..+++.+... |-+++
T Consensus 54 ~~vdgiii~~~~~~~~~~~l~~l~~~~ipvV~~~~~~~~---~~~~~~--v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i 128 (288)
T cd01538 54 KGVDVLVIAPVDGEALASAVEKAADAGIPVIAYDRLILN---SNVDYY--VSFDNEKVGELQGQALVDGLGAKGKPPGNI 128 (288)
T ss_pred cCCCEEEEecCChhhHHHHHHHHHHCCCCEEEECCCCCC---CCcceE--EEeChHHHHHHHHHHHHHHHhhcCCCCceE
Confidence 4566655 4443333334444566789999987654322 122222 3445555667777776544 88899
Q ss_pred EEEEEcCC--CccchHHHHHHHHhccC----cEEEEeeecCCCCChHHHHHHHHHHhcC---CCeEEEEEccCCcHHHHH
Q 003093 76 IAIYVDDD--HGRNGIAALGDTLAAKR----CRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVHTHYNRGPVVF 146 (848)
Q Consensus 76 aii~~dd~--~g~~~~~~l~~~l~~~g----~~v~~~~~~~~~~~~~d~~~~l~~i~~~---~~~viv~~~~~~~~~~~~ 146 (848)
+++..+.. ......+.|.+.+++.| +.+... ......+...-...+.++.+. .+++|+.. +...+..++
T Consensus 129 ~~l~g~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~I~~~-~d~~a~g~~ 206 (288)
T cd01538 129 ELIAGSPTDNNAKLFFNGAMSVLKPLIDSGKITIVGE-VATPDWDPETAQKRMENALTANYNKVDGVLAA-NDGTAGGAI 206 (288)
T ss_pred EEEECCCCCchHHHHHHHHHHHHHhccccCCeeEEec-cccCCCCHHHHHHHHHHHHHhCCCCccEEEeC-CcHHHHHHH
Confidence 99974433 23345678899999987 554332 112122222233444454333 35555543 345667789
Q ss_pred HHHHHcCCCC
Q 003093 147 HVAQYLGMLG 156 (848)
Q Consensus 147 ~~a~~~g~~~ 156 (848)
.++++.|+..
T Consensus 207 ~al~~~g~~~ 216 (288)
T cd01538 207 AALKAAGLAG 216 (288)
T ss_pred HHHHHcCCCC
Confidence 9999999854
No 181
>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=94.46 E-value=1.5 Score=46.36 Aligned_cols=158 Identities=14% Similarity=0.063 Sum_probs=88.1
Q ss_pred CCeEEE-EccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEE
Q 003093 3 GQTVAI-IGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIY 79 (848)
Q Consensus 3 ~~V~ai-IGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~ 79 (848)
.++++| |.|........+...+.+.++|+|.+....+..... -+++.-+..++..-+..+++++... |-++++++.
T Consensus 55 ~~~dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~~~~~~-~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~ 133 (294)
T cd06316 55 QKPDIIISIPVDPVSTAAAYKKVAEAGIKLVFMDNVPSGLEHG-KDYAGIVTDDNYGNGQIAADALAKALPGKGKVGLIY 133 (294)
T ss_pred hCCCEEEEcCCCchhhhHHHHHHHHcCCcEEEecCCCcccccC-cceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEe
Confidence 355554 445433322333455667899999876543322211 1233345556666678888887665 788999997
Q ss_pred EcCCC--ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 80 VDDDH--GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 80 ~dd~~--g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
.+.+. .....+.|.+.+++++..+......... +.......++++... .+++|+. .+...+..+++.+++.|+
T Consensus 134 ~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~- 210 (294)
T cd06316 134 HGADYFVTNQRDQGFKETIKKNYPDITIVAEKGID-GPSKAEDIANAMLTQNPDLKGIYA-VWDVPAEGVIAALRAAGR- 210 (294)
T ss_pred CCCCcccHHHHHHHHHHHHHHhCCCcEEEeecCCc-chhHHHHHHHHHHHhCCCeeEEEe-CCCchhHHHHHHHHHcCC-
Confidence 54333 3445688888888765332211111111 112223344444333 4555554 445567789999999997
Q ss_pred CCCeEEEecC
Q 003093 156 GTGYVWIATS 165 (848)
Q Consensus 156 ~~~~~wi~~~ 165 (848)
.+...++.+
T Consensus 211 -~di~vvg~d 219 (294)
T cd06316 211 -DDIKVTTVD 219 (294)
T ss_pred -CCceEEEeC
Confidence 344455444
No 182
>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=94.45 E-value=1.1 Score=46.58 Aligned_cols=150 Identities=11% Similarity=-0.018 Sum_probs=88.7
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCc-----EEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGW-----REVI 76 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w-----~~va 76 (848)
.+|++|| -|........+ ..+...++|+|......+ +. .....+..++...+..+++++...+- ++++
T Consensus 56 ~~vdgiI~~~~~~~~~~~~-~~~~~~giPvV~~~~~~~---~~--~~~~~V~~d~~~~g~~~~~~l~~~g~~~~~~~~i~ 129 (268)
T cd06306 56 WGADAILLGAVSPDGLNEI-LQQVAASIPVIALVNDIN---SP--DITAKVGVSWYEMGYQAGEYLAQRHPKGSKPAKVA 129 (268)
T ss_pred cCCCEEEEcCCChhhHHHH-HHHHHCCCCEEEeccCCC---Cc--ceeEEecCChHHHHHHHHHHHHHHhhcCCCCceEE
Confidence 4666665 33332222223 345678999997643211 11 12223556667777888888766665 8999
Q ss_pred EEEEcCC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 77 AIYVDDD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 77 ii~~dd~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
++..... ......+.|.+++++.++++... .....+...-...++++.+ .++++|+. ....+..+++.+++.
T Consensus 130 ~l~g~~~~~~~~~R~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~--~d~~a~~~~~~l~~~ 205 (268)
T cd06306 130 WFPGPKGAGWVKAVEKGFRDALAGSAIEISAI--KYGDTGKEVQRKLVEEALEAHPDIDYIVG--SAVAAEAAVGILRQR 205 (268)
T ss_pred EEeCCCCCchHHHHHHHHHHHHhhcCcEEeee--ccCCccHHHHHHHHHHHHHhCCCcCEEee--cchhhhHHHHHHHhc
Confidence 9974332 34556788999999999887542 1111122333445555443 35677764 366777799999999
Q ss_pred CCCCCCeEEEe
Q 003093 153 GMLGTGYVWIA 163 (848)
Q Consensus 153 g~~~~~~~wi~ 163 (848)
|+ ..+...++
T Consensus 206 g~-p~di~vig 215 (268)
T cd06306 206 GL-TDQIKIVS 215 (268)
T ss_pred CC-CCCeEEEe
Confidence 97 33434443
No 183
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=94.37 E-value=0.93 Score=48.81 Aligned_cols=150 Identities=11% Similarity=0.016 Sum_probs=88.9
Q ss_pred CCeEEEEc-cCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAIIG-PQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIG-p~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|++||= |........+ ....+.++|+|......+ ...+++ +..++...+..+++.+...|-++++++...
T Consensus 116 ~~vdgiIi~~~~~~~~~~~-~~l~~~~iPvV~v~~~~~---~~~~~~---V~~d~~~~~~~a~~~L~~~G~r~I~~i~~~ 188 (328)
T PRK11303 116 RQVDALIVSTSLPPEHPFY-QRLQNDGLPIIALDRALD---REHFTS---VVSDDQDDAEMLAESLLKFPAESILLLGAL 188 (328)
T ss_pred cCCCEEEEcCCCCCChHHH-HHHHhcCCCEEEECCCCC---CCCCCE---EEeCCHHHHHHHHHHHHHCCCCeEEEEeCc
Confidence 46777653 3222222233 334567999998654321 122333 346677777888888877899999999744
Q ss_pred C--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 D--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
. ..+..-.+.|.++++++|+.+.... ....+..+-...+.++.+. .+++|+.. +...+..+++++++.|+..+
T Consensus 189 ~~~~~~~~R~~Gf~~al~~~g~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~A~g~~~al~~~g~~vP 265 (328)
T PRK11303 189 PELSVSFEREQGFRQALKDDPREVHYLY--ANSFEREAGAQLFEKWLETHPMPDALFTT-SYTLLQGVLDVLLERPGELP 265 (328)
T ss_pred cccccHHHHHHHHHHHHHHcCCCceEEE--eCCCChHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCC
Confidence 3 2345567899999999987643221 1111212233345555433 46776654 44556678999999998655
Q ss_pred CeEEE
Q 003093 158 GYVWI 162 (848)
Q Consensus 158 ~~~wi 162 (848)
+-+=|
T Consensus 266 ~disv 270 (328)
T PRK11303 266 SDLAI 270 (328)
T ss_pred CceEE
Confidence 44433
No 184
>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=94.36 E-value=1.4 Score=45.82 Aligned_cols=152 Identities=8% Similarity=-0.034 Sum_probs=88.2
Q ss_pred CeEEE-EccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEEEE
Q 003093 4 QTVAI-IGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYV 80 (848)
Q Consensus 4 ~V~ai-IGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~~ 80 (848)
++++| |.|............+.+.++|+|......+ + . ...+..++...++.+++++... |.++++++..
T Consensus 57 ~~dgiIi~~~~~~~~~~~i~~~~~~~ipvv~~~~~~~---~-~---~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~g 129 (271)
T cd06321 57 KVDLILLNAVDSKGIAPAVKRAQAAGIVVVAVDVAAE---G-A---DATVTTDNVQAGEISCQYLADRLGGKGNVAILNG 129 (271)
T ss_pred CCCEEEEeCCChhHhHHHHHHHHHCCCeEEEecCCCC---C-c---cceeeechHHHHHHHHHHHHHHhCCCceEEEEeC
Confidence 45554 4554333223333445667999999865332 1 1 1235667777788888888776 9999999974
Q ss_pred cC-CCccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 81 DD-DHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 81 dd-~~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
+. .......+.+.+.+++. +++.... ......+...-...+.++.+. .+++|++ .+...+..+++++++.|+
T Consensus 130 ~~~~~~~~R~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~-- 205 (271)
T cd06321 130 PPVSAVLDRVAGCKAALAKYPGIKLLSD-DQNGKGSRDGGLRVMQGLLTRFPKLDGVFA-INDPTAIGADLAAKQAGR-- 205 (271)
T ss_pred CCCchHHHHHHHHHHHHHhCCCcEEEee-ecCCCCChhhHHHHHHHHHHhCCCCCEEEE-CCchhHHHHHHHHHHcCC--
Confidence 43 23345568889999988 6653321 111111112222344444333 4566554 445566779999999997
Q ss_pred CCeEEEecCc
Q 003093 157 TGYVWIATSW 166 (848)
Q Consensus 157 ~~~~wi~~~~ 166 (848)
.+..+++.+.
T Consensus 206 ~di~v~g~d~ 215 (271)
T cd06321 206 NDIKITSVDG 215 (271)
T ss_pred CCcEEEEecC
Confidence 3555555543
No 185
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=94.34 E-value=2.3 Score=41.22 Aligned_cols=70 Identities=23% Similarity=0.314 Sum_probs=46.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++..+++++|.+|++|+++..... ....+. ..+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 80 (198)
T cd08421 13 EFLPEDLASFLAAHP-DVRIDLEE-------RLSADIVRAVAEGRADLGIVAGNV---DAAGLE-TRPYRTDRLVVVVPR 80 (198)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------cCcHHHHHHHhcCCceEEEEecCC---CCCCcE-EEEeecCcEEEEeCC
Confidence 344577888887763 33344443 346789999999999999863222 223333 467778888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (198)
T cd08421 81 DH 82 (198)
T ss_pred CC
Confidence 54
No 186
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=94.34 E-value=1.1 Score=44.05 Aligned_cols=183 Identities=18% Similarity=0.176 Sum_probs=112.2
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+- +++.... ++...++++|.+|++|+++......... +. ..|+....+++++++
T Consensus 19 ~~l~~~l~~~~~~~P~-i~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~---~~-~~~l~~~~~~~~~~~ 86 (209)
T PF03466_consen 19 SLLPPLLAEFRERHPN-IRIEIRE-------GDSDELIEALRSGELDLAITFGPPPPPG---LE-SEPLGEEPLVLVVSP 86 (209)
T ss_dssp HTHHHHHHHHHHHSTT-EEEEEEE-------ESHHHHHHHHHTTSSSEEEESSSSSSTT---EE-EEEEEEEEEEEEEET
T ss_pred HHHHHHHHHHHHHCCC-cEEEEEe-------ccchhhhHHHhcccccEEEEEeeccccc---cc-cccccceeeeeeeec
Confidence 4456778888777752 4455543 4578999999999999998855542222 22 567778899999987
Q ss_pred cCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcchhhhhHHHHhhhcCccccccchhHHHH
Q 003093 482 RKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMFFAHKEKTVSALGRLVL 561 (848)
Q Consensus 482 ~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~s~~~R~~~ 561 (848)
..+...
T Consensus 87 ~~pl~~-------------------------------------------------------------------------- 92 (209)
T PF03466_consen 87 DHPLAQ-------------------------------------------------------------------------- 92 (209)
T ss_dssp TSGGGT--------------------------------------------------------------------------
T ss_pred cccccc--------------------------------------------------------------------------
Confidence 652110
Q ss_pred HHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEe-CchHHHHHHh---hhCCCccCcccCCCHHHH
Q 003093 562 IIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQV-NSFARNYLVD---ELNIDESRLVPLNSPEEY 637 (848)
Q Consensus 562 ~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~-~s~~~~~l~~---~~~~~~~~~~~~~~~~~~ 637 (848)
..++ +++||. +.++.... +......+.+ ..+........+++.+..
T Consensus 93 ---------------------------~~~i-~~~dL~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 142 (209)
T PF03466_consen 93 ---------------------------KKPI-TLEDLA--DYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESI 142 (209)
T ss_dssp ---------------------------TSSS-SGGGGT--TSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHH
T ss_pred ---------------------------cccc-hhhhhh--hccccccccccccccccccccccccccccccccccchhhh
Confidence 0344 789998 66654443 4433443332 223332344567899999
Q ss_pred HHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEEEeCCccccCCceeeecCCCCchHHHHHHHHhhh
Q 003093 638 AKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQVFTKNGWGFAFPRDSPLAVDISTAILKLS 704 (848)
Q Consensus 638 ~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k~spl~~~in~~i~~l~ 704 (848)
...+.. |...+++-+.....+.....-....+.+.-.+..+.++.+++.+....+...+..+.
T Consensus 143 ~~~v~~----g~gi~~~p~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~ 205 (209)
T PF03466_consen 143 LSLVAS----GDGIAILPDSLAQDELESGELVFLPLPDPPLPRPIYLVWRKDRPLSPAIQWFIDLLR 205 (209)
T ss_dssp HHHHHT----TSEBEEEEHHHHHHHHHCTTEEEEEESSSTEEEEEEEEEETTGTTHHHHHHHHHHHH
T ss_pred cccccc----ccceeecCcccccccccCCCEEEEECCCCCCceEEEEEEECCCCCCHHHHHHHHHHH
Confidence 999998 666677665444344322222333444422337788888988876666666555444
No 187
>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=94.31 E-value=0.55 Score=48.83 Aligned_cols=155 Identities=11% Similarity=0.026 Sum_probs=90.6
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+++++|| .|.... . .....+...++|+|.+....+. ...+++ ..+++...+..+++.+...|.++++++..+
T Consensus 54 ~~~dgiii~~~~~~-~-~~~~~~~~~~ipvV~i~~~~~~--~~~~~~---v~~d~~~~~~~a~~~l~~~g~~~i~~i~~~ 126 (270)
T cd06296 54 RRTDGVILVTPELT-S-AQRAALRRTGIPFVVVDPAGDP--DADVPS---VGATNWAGGLAATEHLLELGHRRIGFITGP 126 (270)
T ss_pred cCCCEEEEecCCCC-h-HHHHHHhcCCCCEEEEecccCC--CCCCCE---EEeCcHHHHHHHHHHHHHcCCCcEEEEcCC
Confidence 4677765 333322 2 2345567789999987654211 122333 556677778888888877799999999743
Q ss_pred C--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 D--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
. .......+.|.+.+++.|+.+..........+.+.....+.++... .+++|+. .+...+..+++.+++.|...+
T Consensus 127 ~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~~p 205 (270)
T cd06296 127 PDLLCSRARLDGYRAALAEAGIPVDPALVREGDFSTESGFRAAAELLALPERPTAIFA-GNDLMALGVYEAARERGLRIP 205 (270)
T ss_pred CcchhHHHHHHHHHHHHHHcCCCCChHHheeCCCCHHHHHHHHHHHHhCCCCCcEEEE-cCcHHHHHHHHHHHHhCCCCC
Confidence 2 2344557889999998886543211111111223333444444332 3555554 345566779999999998644
Q ss_pred C-eEEEecC
Q 003093 158 G-YVWIATS 165 (848)
Q Consensus 158 ~-~~wi~~~ 165 (848)
+ ...++.+
T Consensus 206 ~~i~v~~~d 214 (270)
T cd06296 206 EDLSVVGFD 214 (270)
T ss_pred CceEEEEEC
Confidence 3 4444444
No 188
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=94.25 E-value=1.9 Score=45.78 Aligned_cols=83 Identities=13% Similarity=0.185 Sum_probs=54.4
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..++|++.... ..++-..++..+.+..+ .+++.... ++-++++++|.+|++|+++....
T Consensus 91 g~l~i~~~~~~-------------~~~~~~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~ 149 (305)
T PRK11151 91 GPLHIGLIPTV-------------GPYLLPHIIPMLHQTFP-KLEMYLHE-------AQTHQLLAQLDSGKLDCAILALV 149 (305)
T ss_pred ceEEEEecchh-------------HHHHHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEecC
Confidence 47888886311 12445566777776553 24455543 34688999999999999997432
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
...+ .+ .+.|+....+++++++..
T Consensus 150 ~~~~---~l-~~~~l~~~~~~~~~~~~h 173 (305)
T PRK11151 150 KESE---AF-IEVPLFDEPMLLAVYEDH 173 (305)
T ss_pred CCCC---Ce-EEEEeccCcEEEEecCCC
Confidence 2211 22 467888899999988665
No 189
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=94.25 E-value=1.4 Score=47.26 Aligned_cols=150 Identities=13% Similarity=0.102 Sum_probs=92.1
Q ss_pred CCeEE-EEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHH-HHcC-cEEEEEEE
Q 003093 3 GQTVA-IIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYG-WREVIAIY 79 (848)
Q Consensus 3 ~~V~a-iIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~-~~~~-w~~vaii~ 79 (848)
++|++ +|.|.++.....+..-+.+.+||+|.+....+.- .+....+...+...+...++++ +.++ .-+++++.
T Consensus 90 ~~~daIiv~~~d~~~~~~~v~~a~~aGIpVv~~d~~~~~~----~~~~~~vg~dn~~~G~~~a~~l~~~~~~~g~v~~~~ 165 (322)
T COG1879 90 QGVDAIIINPVDPDALTPAVKKAKAAGIPVVTVDSDIPGP----GDRVAYVGSDNYKAGRLAAEYLAKALGGKGKVVVLV 165 (322)
T ss_pred cCCCEEEEcCCChhhhHHHHHHHHHCCCcEEEEecCCCCC----CceeEEEecCcHHHHHHHHHHHHHHhCCCCeEEEEe
Confidence 46655 4589999999999999999999999986654322 1222223335555566666665 3343 23466666
Q ss_pred Ec--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHH-HHHHHHHHcCCCC
Q 003093 80 VD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGP-VVFHVAQYLGMLG 156 (848)
Q Consensus 80 ~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~-~~~~~a~~~g~~~ 156 (848)
.. ........+.+.+.+.+.+..+........+.+...-......+....|++-.+++...... ...+++++.|...
T Consensus 166 g~~~~~~~~~R~~G~~~~l~~~~~~~~v~~~~~~~~~~~~a~~~~~~~L~~~pdi~~i~~~~d~~a~ga~~A~~~~g~~~ 245 (322)
T COG1879 166 GSPGNSSAEERVKGFRDALKEHPPDIEVVDVQTGDWDRDKALEVMEDLLAANPDIDGIYAANDGMALGAIQALKAAGRKG 245 (322)
T ss_pred cCCCCchHHHHHhhHHHHHHhCCCcEEEeeccCCcccHHHHHHHHHHHHHhCCCceEEEECCchhHHHHHHHHHHcCCCC
Confidence 33 33445567899999999885322222233222334445556666667778777666654443 5566777788754
No 190
>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=94.23 E-value=0.9 Score=47.26 Aligned_cols=144 Identities=12% Similarity=-0.024 Sum_probs=79.9
Q ss_pred CCeEEEEccCCchhHHHHHHhhccC-CccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHH-cCcEEEEEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANEL-QVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~-~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~-~~w~~vaii~~ 80 (848)
.+|++||--. +........+..++ ++|++......+.. +.+-++..++..-+..++.++.. .|-++++++..
T Consensus 56 ~~vdgiI~~~-~~~~~~~~~~~~~~~~~PiV~i~~~~~~~-----~~~~~v~~d~~~a~~~a~~ll~~~~G~~~I~~i~~ 129 (265)
T cd06354 56 AGYDLIVGVG-FLLADALKEVAKQYPDQKFAIIDAVVDDP-----PNVASIVFKEEEGSFLAGYLAALMTKTGKVGFIGG 129 (265)
T ss_pred CCCCEEEEcC-cchHHHHHHHHHHCCCCEEEEEecccCCC-----CcEEEEEecchhHHHHHHHHHHhhcCCCeEEEEec
Confidence 4677777522 12233445566665 89999865422110 11222334444444555555654 38899999974
Q ss_pred cCCCcc-chHHHHHHHHhccC---cEEEEeeecCCCCC-hHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcC
Q 003093 81 DDDHGR-NGIAALGDTLAAKR---CRISFKAPLSVEAT-EDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLG 153 (848)
Q Consensus 81 dd~~g~-~~~~~l~~~l~~~g---~~v~~~~~~~~~~~-~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g 153 (848)
+..... ...+.|.+.+++.| ..+..........+ ..+-...+.++.+.++|+|+.. +...+..+++++++.|
T Consensus 130 ~~~~~~~~r~~gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~pdaI~~~-nd~~A~gv~~al~~~g 206 (265)
T cd06354 130 MDIPLIRRFEAGFEAGVKYVNPGVPDIEVLVQYAGSFNDPAKGKEIAQAMYDQGADVIFAA-AGGTGNGVFQAAKEAG 206 (265)
T ss_pred ccChHHHHHHHHHHHHHHHHhccCCCceEEEEEcCcccCHHHHHHHHHHHHHCCCcEEEEC-CCCCchHHHHHHHhcC
Confidence 332122 22368899999888 65332211111111 1233345566555568875544 6667778999999988
No 191
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=94.16 E-value=3.1 Score=39.97 Aligned_cols=70 Identities=17% Similarity=0.231 Sum_probs=46.6
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+ .++++... ++..++.+.+.+|++|+++..... ....+ -+.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~~~~~ 80 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRD-------VSAEQVIEAVRSGEVDFGIGSEPE---ADPDL-EFEPLLRDPFVLVCPK 80 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEe-------CChHHHHHHHHcCCccEEEEeCCC---CCCCe-eEEEeecccEEEEecC
Confidence 455678888887764 33454443 457789999999999999863322 22222 2456777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (197)
T cd08440 81 DH 82 (197)
T ss_pred CC
Confidence 54
No 192
>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=94.13 E-value=2.1 Score=44.53 Aligned_cols=152 Identities=13% Similarity=0.099 Sum_probs=84.0
Q ss_pred CCeEEEE-ccCCchh-HHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEEE
Q 003093 3 GQTVAII-GPQDAVT-SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAI 78 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~-~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii 78 (848)
.+|+++| .|..... ...+..+ .+ ++|+|......+. ...++ -+..++..-+..+++++... +-.+++++
T Consensus 54 ~~vDgiIi~~~~~~~~~~~l~~~-~~-~ipvV~~~~~~~~--~~~~~---~V~~D~~~~g~~a~~~l~~~~~~g~~~~~~ 126 (271)
T cd06314 54 EGVDGIAISPIDPKAVIPALNKA-AA-GIKLITTDSDAPD--SGRYV---YIGTDNYAAGRTAGEIMKKALPGGGKVAIF 126 (271)
T ss_pred cCCCEEEEecCChhHhHHHHHHH-hc-CCCEEEecCCCCc--cceeE---EEccChHHHHHHHHHHHHHHcCCCCEEEEE
Confidence 4666665 4544332 2334444 45 9999987543211 11122 24456666677888877553 23456666
Q ss_pred EEcC--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 79 YVDD--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 79 ~~dd--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.... .......+.|.+++++.|+++.... . ...+..+....+.++.+. .+++|+.. +...+..++..+++.|.
T Consensus 127 ~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~l~~~~~~~~i~~~-~d~~a~~~~~al~~~g~ 203 (271)
T cd06314 127 VGSLGADNAKERIQGIKDAIKDSKIEIVDTR-G-DEEDFAKAKSNAEDALNAHPDLKCMFGL-YAYNGPAIAEAVKAAGK 203 (271)
T ss_pred ecCCCCCCHHHHHHHHHHHHhcCCcEEEEEe-c-CccCHHHHHHHHHHHHHhCCCccEEEec-CCccHHHHHHHHHHcCC
Confidence 5432 2345667889999999998765421 1 111223334455555433 35665543 44555668889999988
Q ss_pred CCCCeEEEecC
Q 003093 155 LGTGYVWIATS 165 (848)
Q Consensus 155 ~~~~~~wi~~~ 165 (848)
. .+...++.+
T Consensus 204 ~-~di~vig~d 213 (271)
T cd06314 204 L-GKVKIVGFD 213 (271)
T ss_pred C-CceEEEEeC
Confidence 5 444444444
No 193
>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=94.01 E-value=0.74 Score=47.72 Aligned_cols=125 Identities=10% Similarity=0.022 Sum_probs=76.3
Q ss_pred CCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc--CCCccchHHHHHHHHhccCcEEE
Q 003093 27 LQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD--DDHGRNGIAALGDTLAAKRCRIS 104 (848)
Q Consensus 27 ~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~ 104 (848)
.++|+|......+ ....++ +..++...+..+++.+...|-++++++..+ +.......+.|.+.+++.|+.+.
T Consensus 76 ~~iPvV~i~~~~~---~~~~~~---V~~d~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~ 149 (265)
T cd06290 76 EEIPVLAVGRRVP---GPGAAS---IAVDNFQGGYLATQHLIDLGHRRIAHITGPRGHIDARDRLAGYRKALEEAGLEVQ 149 (265)
T ss_pred cCCCEEEECCCcC---CCCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEeCccccchhhHHHHHHHHHHHHcCCCCC
Confidence 4899998765422 122233 445667777888888777799999999743 23344567889999988886543
Q ss_pred EeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 105 FKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 105 ~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
....+....+.......+.++.+. .+++|+. ++...+..+++.+++.|+..++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~aii~-~~~~~a~~~~~~l~~~g~~ip~ 204 (265)
T cd06290 150 PDLIVQGDFEEESGLEAVEELLQRGPDFTAIFA-ANDQTAYGARLALYRRGLRVPE 204 (265)
T ss_pred HHHEEecCCCHHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCc
Confidence 111111111112223345555433 3576554 5566677899999999986544
No 194
>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=93.99 E-value=0.78 Score=47.78 Aligned_cols=149 Identities=9% Similarity=-0.043 Sum_probs=86.9
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|+++| -+..+. .......+.++|++...... .+..+++ +..++...+..+++.+...|-++++++...
T Consensus 51 ~~vdgii~~~~~~~---~~~~~~~~~~~pvV~~~~~~---~~~~~~~---v~~D~~~a~~~~~~~l~~~g~~~i~~i~~~ 121 (270)
T cd01544 51 EDVDGIIAIGKFSQ---EQLAKLAKLNPNLVFVDSNP---APDGFDS---VVPDFEQAVEKALDYLLELGHTRIGFIGGE 121 (270)
T ss_pred cCcCEEEEecCCCH---HHHHHHHhhCCCEEEECCCC---CCCCCCE---EEECHHHHHHHHHHHHHHcCCCcEEEECCC
Confidence 3566655 222232 33344566789999875432 2223343 556777778888888888899999999754
Q ss_pred CC-------CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC----CCeEEEEEccCCcHHHHHHHHH
Q 003093 82 DD-------HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT----ESRIIVVHTHYNRGPVVFHVAQ 150 (848)
Q Consensus 82 d~-------~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~----~~~viv~~~~~~~~~~~~~~a~ 150 (848)
.. ........|.+.++++|.. .....+....+..+....++++.+. .+++|+. ++...+..+++.++
T Consensus 122 ~~~~~~~~~~~~~R~~gf~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~-~~d~~a~g~~~~l~ 199 (270)
T cd01544 122 EKTTDGHEYIEDPRETAFREYMKEKGLY-DPELIYIGDFTVESGYQLMKEALKSLGDNLPTAFFI-ASDPMAIGALRALQ 199 (270)
T ss_pred cccccccchhhhHHHHHHHHHHHHcCCC-ChheEeeCCCCHHHHHHHHHHHHhccCCCCCCEEEE-cCcHHHHHHHHHHH
Confidence 32 3445578899999998841 1000111111222223344444322 3565554 55667888999999
Q ss_pred HcCCCCCCeEEE
Q 003093 151 YLGMLGTGYVWI 162 (848)
Q Consensus 151 ~~g~~~~~~~wi 162 (848)
+.|+..++-+-|
T Consensus 200 ~~g~~vp~di~v 211 (270)
T cd01544 200 EAGIKVPEDVSV 211 (270)
T ss_pred HcCCCCCCceEE
Confidence 999865543333
No 195
>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=93.95 E-value=0.8 Score=48.13 Aligned_cols=155 Identities=12% Similarity=0.013 Sum_probs=91.5
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+.++++||--...... .....+...++|+|.+....+ +.+-.+..++...+..+++++...|-++++++..+
T Consensus 54 ~~~~dgiii~~~~~~~-~~~~~~~~~~ipvV~~~~~~~-------~~~~~v~~d~~~~g~~~~~~L~~~g~~~i~~i~~~ 125 (283)
T cd06279 54 SALVDGFIVYGVPRDD-PLVAALLRRGLPVVVVDQPLP-------PGVPSVGIDDRAAAREAARHLLDLGHRRIGILGLR 125 (283)
T ss_pred hcCCCEEEEeCCCCCh-HHHHHHHHcCCCEEEEecCCC-------CCCCEEeeCcHHHHHHHHHHHHHcCCCcEEEecCc
Confidence 3567777753322222 334455778999998754321 11223556777788888898888899999999743
Q ss_pred C-------------------CCccchHHHHHHHHhccCcEEEEeeecC-CCCChHHHHHHHHHHhcC--CCeEEEEEccC
Q 003093 82 D-------------------DHGRNGIAALGDTLAAKRCRISFKAPLS-VEATEDEITDLLVKVALT--ESRIIVVHTHY 139 (848)
Q Consensus 82 d-------------------~~g~~~~~~l~~~l~~~g~~v~~~~~~~-~~~~~~d~~~~l~~i~~~--~~~viv~~~~~ 139 (848)
. .......+.|.+++++.|+.......+. ...+.......+.++... .+++|+ +++.
T Consensus 126 ~~~~~~~~~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d 204 (283)
T cd06279 126 LGRDRNTGRVTDERLASATFSVARERLEGYLEALEEAGIDISDVPIWEIPENDRASGEEAARELLDASPRPTAIL-CMSD 204 (283)
T ss_pred ccccccccccccccccccccccHHHHHHHHHHHHHHcCCCCChheEEecCCCchHHHHHHHHHHHcCCCCCcEEE-ECCc
Confidence 2 2234557889999999885432111111 111223444555565443 355544 4455
Q ss_pred CcHHHHHHHHHHcCCCCCC-eEEEecC
Q 003093 140 NRGPVVFHVAQYLGMLGTG-YVWIATS 165 (848)
Q Consensus 140 ~~~~~~~~~a~~~g~~~~~-~~wi~~~ 165 (848)
..+..+++++++.|+..++ ...++-+
T Consensus 205 ~~a~gv~~al~~~g~~ip~di~vig~d 231 (283)
T cd06279 205 VLALGALQVARELGLRVPEDLSVVGFD 231 (283)
T ss_pred HHHHHHHHHHHHcCCCCCCceEEeeeC
Confidence 5667799999999986443 3344333
No 196
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=93.95 E-value=1.4 Score=47.90 Aligned_cols=142 Identities=11% Similarity=-0.002 Sum_probs=82.9
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc-----CcEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-----GWREVI 76 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~-----~w~~va 76 (848)
.+|+||| .|.......... .+.+.++|+|.+..... .+. ....+..++...+..+++++... |-++++
T Consensus 103 ~~vdgIIl~~~~~~~~~~~l-~~~~~giPvV~~~~~~~--~~~---~~~~V~~D~~~~g~~aa~~L~~~~~~~~g~~~i~ 176 (343)
T PRK10936 103 WGADAILLGAVTPDGLNPDL-ELQAANIPVIALVNGID--SPQ---VTTRVGVSWYQMGYQAGRYLAQWHPKGSKPLNVA 176 (343)
T ss_pred hCCCEEEEeCCChHHhHHHH-HHHHCCCCEEEecCCCC--Ccc---ceEEEecChHHHHHHHHHHHHHHHHhcCCCceEE
Confidence 4566655 554443322222 45678999997633211 111 12335567777778888876544 578999
Q ss_pred EEEEcC--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 77 AIYVDD--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 77 ii~~dd--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
++..+. .......+.|.+.+++.|+++.... .. ..+...-...++++.+ .++++|+ +....+..+++.+++.
T Consensus 177 ~i~g~~~~~~~~~R~~Gf~~~l~~~~i~~~~~~-~~-~~~~~~~~~~~~~~l~~~~~~~ai~--~~d~~A~ga~~al~~~ 252 (343)
T PRK10936 177 LLPGPEGAGGSKAVEQGFRAAIAGSDVRIVDIA-YG-DNDKELQRNLLQELLERHPDIDYIA--GSAVAAEAAIGELRGR 252 (343)
T ss_pred EEECCCCCchHHHHHHHHHHHHhcCCCEEEEee-cC-CCcHHHHHHHHHHHHHhCCCccEEE--eCCHHHHHHHHHHHhc
Confidence 997432 2333456789999999998875421 11 1122223344455433 2467776 3445677788999999
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|+
T Consensus 253 g~ 254 (343)
T PRK10936 253 NL 254 (343)
T ss_pred CC
Confidence 97
No 197
>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=93.95 E-value=2.6 Score=43.99 Aligned_cols=155 Identities=12% Similarity=0.057 Sum_probs=86.9
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHH-cCcE--EEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWR--EVIAI 78 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~-~~w~--~vaii 78 (848)
.++++|| .+..+.........+.+.++|+|.+....+ + ..+.+..+..++...+..+++++-. .|-+ +++++
T Consensus 54 ~~~Dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~---~-~~~~~~~v~~d~~~~g~~~~~~l~~~~g~~~~~i~~i 129 (282)
T cd06318 54 RGVNVLIINPVDPEGLVPAVAAAKAAGVPVVVVDSSIN---L-EAGVVTQVQSSNAKNGNLVGEWVVGELGDKPMKIILL 129 (282)
T ss_pred cCCCEEEEecCCccchHHHHHHHHHCCCCEEEecCCCC---C-CcCeEEEEecCcHHHHHHHHHHHHHHhCCCCceEEEE
Confidence 3555554 444333223333555678999998765321 1 0123344667777788888888744 6755 88888
Q ss_pred EEc--CCCccchHHHHHHHHhccCcE------EEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHH
Q 003093 79 YVD--DDHGRNGIAALGDTLAAKRCR------ISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHV 148 (848)
Q Consensus 79 ~~d--d~~g~~~~~~l~~~l~~~g~~------v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~ 148 (848)
..+ ...+....+.|.+.++++|+. ...........+..+-...+.++... ++++|+. .+...+..++++
T Consensus 130 ~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~a 208 (282)
T cd06318 130 SGDAGNLVGQARRDGFLLGVSEAQLRKYGKTNFTIVAQGYGDWTREGGLKAMEDLLVAHPDINVVYS-ENDDMALGAMRV 208 (282)
T ss_pred ECCCCCchHhHHHHhHHHHHhhCcccccccCCeEEEecCCCCCCHHHHHHHHHHHHHhCCCcCEEEE-CCcchHHHHHHH
Confidence 643 334566778899999998642 11111011111222333444444332 4555554 444566779999
Q ss_pred HHHcCCCCCCeEEEe
Q 003093 149 AQYLGMLGTGYVWIA 163 (848)
Q Consensus 149 a~~~g~~~~~~~wi~ 163 (848)
+++.|+. .+...++
T Consensus 209 l~~~g~~-~dv~vvg 222 (282)
T cd06318 209 LAEAGKT-DDVKVAA 222 (282)
T ss_pred HHHcCCC-CCeEEEe
Confidence 9999984 3433333
No 198
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=93.93 E-value=3.2 Score=40.05 Aligned_cols=70 Identities=17% Similarity=0.179 Sum_probs=45.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++-..++.+|.+|++|+++...... ...+. +.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~~~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~ 80 (201)
T cd08420 13 YLLPRLLARFRKRYP-EVRVSLTI-------GNTEEIAERVLDGEIDLGLVEGPVD---HPDLI-VEPFAEDELVLVVPP 80 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCccEEEecCCCC---CcceE-EEeecCccEEEEecC
Confidence 455677888887764 23344433 3466889999999999998743322 22222 467777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (201)
T cd08420 81 DH 82 (201)
T ss_pred CC
Confidence 54
No 199
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=93.91 E-value=1.5 Score=45.47 Aligned_cols=143 Identities=14% Similarity=0.164 Sum_probs=91.5
Q ss_pred CeEEEEccCCchhHHHHHHhhccCCccEEecccCCCC---CCC-CCCCceEeccCChHHHHHHHHHHHHHc--CcEEEEE
Q 003093 4 QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPT---LSS-LQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIA 77 (848)
Q Consensus 4 ~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~---ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~--~w~~vai 77 (848)
+-+.|++-.+ ..|.++..-.. ++|++-.+.|+|. |.. -.-|----|.-||..-...-.+++++. +.+++++
T Consensus 88 ~~dviv~i~t-p~Aq~~~s~~~--~iPVV~aavtd~v~a~Lv~~~~~pg~NvTGvsD~~~v~q~i~lik~~~Pnak~Igv 164 (322)
T COG2984 88 KPDVIVAIAT-PAAQALVSATK--TIPVVFAAVTDPVGAKLVKSLEQPGGNVTGVSDLLPVAQQIELIKALLPNAKSIGV 164 (322)
T ss_pred CCcEEEecCC-HHHHHHHHhcC--CCCEEEEccCchhhccCCccccCCCCceeecCCcchHHHHHHHHHHhCCCCeeEEE
Confidence 4455555333 33443332222 3999987777663 221 111323335566766566666666654 8999999
Q ss_pred EEEcCC-CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCC---cHHHHHHHHHHcC
Q 003093 78 IYVDDD-HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN---RGPVVFHVAQYLG 153 (848)
Q Consensus 78 i~~dd~-~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~---~~~~~~~~a~~~g 153 (848)
+|.-++ ......+.+++.+++.|++|+.. .++. ..|+...++.+. .++|+|+..++.. ....++..|.+.+
T Consensus 165 ~Y~p~E~ns~~l~eelk~~A~~~Gl~vve~-~v~~---~ndi~~a~~~l~-g~~d~i~~p~dn~i~s~~~~l~~~a~~~k 239 (322)
T COG2984 165 LYNPGEANSVSLVEELKKEARKAGLEVVEA-AVTS---VNDIPRAVQALL-GKVDVIYIPTDNLIVSAIESLLQVANKAK 239 (322)
T ss_pred EeCCCCcccHHHHHHHHHHHHHCCCEEEEE-ecCc---ccccHHHHHHhc-CCCcEEEEecchHHHHHHHHHHHHHHHhC
Confidence 995544 77889999999999999998754 3332 246666666665 7899999988763 3344677777766
Q ss_pred C
Q 003093 154 M 154 (848)
Q Consensus 154 ~ 154 (848)
.
T Consensus 240 i 240 (322)
T COG2984 240 I 240 (322)
T ss_pred C
Confidence 5
No 200
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=93.89 E-value=1 Score=48.49 Aligned_cols=130 Identities=7% Similarity=-0.017 Sum_probs=77.4
Q ss_pred CCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc--CCCccchHHHHHHHHhccCcEEE
Q 003093 27 LQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD--DDHGRNGIAALGDTLAAKRCRIS 104 (848)
Q Consensus 27 ~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~ 104 (848)
.++|++....... ...++ .+..++..-+..+++++...|-+++++|..+ ........+.|.++++++|+.+.
T Consensus 135 ~~iPvV~i~~~~~---~~~~~---~v~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~ 208 (327)
T PRK10423 135 PSVPTVMMDWAPF---DGDSD---LIQDNSLLGGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIP 208 (327)
T ss_pred CCCCEEEECCccC---CCCCC---EEEEChHHHHHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCCC
Confidence 4899998753211 11111 2334444557788888888899999999633 23445567899999999997642
Q ss_pred EeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003093 105 FKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 163 (848)
Q Consensus 105 ~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 163 (848)
....+....+...-...+.++.+. .+++|++ ++...+..+++.+++.|+..|+-+-+.
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~A~g~~~~l~~~g~~vP~dvsvi 268 (327)
T PRK10423 209 DGYEVTGDFEFNGGFDAMQQLLALPLRPQAVFT-GNDAMAVGVYQALYQAGLSVPQDIAVI 268 (327)
T ss_pred cceEEeCCCChHHHHHHHHHHhcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 211111111112223344554433 4666554 455666789999999998765544443
No 201
>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=93.71 E-value=0.73 Score=48.00 Aligned_cols=135 Identities=12% Similarity=0.048 Sum_probs=82.5
Q ss_pred HHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC--C------CccchHH
Q 003093 19 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--D------HGRNGIA 90 (848)
Q Consensus 19 ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd--~------~g~~~~~ 90 (848)
.....+.+.++|+|......+ ..++ +.+++..-+..+++.+... .++++++..+. . .+....+
T Consensus 69 ~~~~~l~~~~iPvv~~~~~~~-----~~~~---v~~d~~~~g~~a~~~L~~~-~~~i~~i~~~~~~~~~~~~~~~~~R~~ 139 (269)
T cd06297 69 RLAERRLPTERPVVLVDAENP-----RFDS---FYLDNRLGGRLAGAYLADF-PGRIGAITVEEEPDRAFRRTVFAERRA 139 (269)
T ss_pred HHHHHHhhcCCCEEEEccCCC-----CCCE---EEECcHHHHHHHHHHHHHh-CCceEEEeCccccccccccccHHHHHH
Confidence 344555678999998755321 2233 3466777777888877666 78999886332 2 3455688
Q ss_pred HHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003093 91 ALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 163 (848)
Q Consensus 91 ~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 163 (848)
.|.+.+++.|+.+.....+....+..+....+.++.+. .+++|+.. +...+..+++.+++.|...++-+-+.
T Consensus 140 gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~vP~di~vv 213 (269)
T cd06297 140 GFQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLAVFAS-ADQQALGALQEAVELGLTVGEDVRVV 213 (269)
T ss_pred HHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHcCCCCCcEEEEc-CcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 99999999987643211111111223344556665433 35665554 44566789999999998655544444
No 202
>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=93.57 E-value=1.7 Score=45.24 Aligned_cols=152 Identities=13% Similarity=0.031 Sum_probs=89.4
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|+++| .+... ....+. -..+.++|+|......+. ...+++ +..++...+..+++.+...|-+++++|...
T Consensus 55 ~~vdgiIi~~~~~-~~~~~~-~l~~~~iPvV~i~~~~~~--~~~~~~---V~~d~~~~~~~a~~~L~~~G~~~I~~i~~~ 127 (269)
T cd06287 55 LDIDGAILVEPMA-DDPQVA-RLRQRGIPVVSIGRPPGD--RTDVPY---VDLQSAATARMLLEHLRAQGARQIALIVGS 127 (269)
T ss_pred cCcCeEEEecCCC-CCHHHH-HHHHcCCCEEEeCCCCCC--CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEEeCC
Confidence 3577655 22221 122233 345679999987543210 122333 345666667888888888899999999633
Q ss_pred C--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 D--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
. .........|.+++++.|+...... .....+..+-...++++.+. ++++|+. .+...+..+++.+++.|+..+
T Consensus 128 ~~~~~~~~R~~gf~~a~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~A~gvl~al~~~gl~vP 205 (269)
T cd06287 128 ARRNSYLEAEAAYRAFAAEHGMPPVVLR-VDEAGGEEAGYAACAQLLAQHPDLDALCV-PVDAFAVGAVRAATELGRAVP 205 (269)
T ss_pred cccccHHHHHHHHHHHHHHcCCCcceeE-ecCCCChHHHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCC
Confidence 2 3344567889999999987543211 11111223333445555433 4676664 456677889999999999766
Q ss_pred CeEEEe
Q 003093 158 GYVWIA 163 (848)
Q Consensus 158 ~~~wi~ 163 (848)
+-+=|+
T Consensus 206 ~dvsvi 211 (269)
T cd06287 206 DQLRVV 211 (269)
T ss_pred CceEEE
Confidence 544443
No 203
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=93.49 E-value=4.8 Score=39.42 Aligned_cols=71 Identities=13% Similarity=0.177 Sum_probs=47.1
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... .++..+++++|.+|++|+++...... ...++ ..|+.+..+++++++
T Consensus 13 ~~~~~~l~~~~~~~P-~~~v~~~~------~~~~~~l~~~L~~g~lDl~i~~~~~~---~~~l~-~~~l~~~~~~lv~~~ 81 (203)
T cd08463 13 LFLPELVARFRREAP-GARLEIHP------LGPDFDYERALASGELDLVIGNWPEP---PEHLH-LSPLFSDEIVCLMRA 81 (203)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEe------CCcchhHHHHHhcCCeeEEEeccccC---CCCcE-EeEeecCceEEEEeC
Confidence 566788888888765 23344443 12457899999999999999732221 12233 357778888888886
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~h 83 (203)
T cd08463 82 DH 83 (203)
T ss_pred CC
Confidence 65
No 204
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=93.48 E-value=4.2 Score=39.14 Aligned_cols=70 Identities=17% Similarity=0.240 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..++++.+.+..+ .+++.... ++..+++..|.+|++|+++...... ...+. ..+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~L~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~ 80 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVE-------YGGKKVEQAVLNGELDVGITVLPVD---EEEFD-SQPLCNEPLVAVLPR 80 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEE-------cCcHHHHHHHHcCCCCEEEEecccc---cCCce-eEEeccccEEEEecC
Confidence 456678888888764 33455543 4567889999999999998643221 12222 456677888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (197)
T cd08438 81 GH 82 (197)
T ss_pred CC
Confidence 54
No 205
>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=93.47 E-value=0.42 Score=50.16 Aligned_cols=154 Identities=10% Similarity=0.001 Sum_probs=96.4
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEE-EEEEEEc
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWRE-VIAIYVD 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~-vaii~~d 81 (848)
.+|+++|=.........+..+.+. ++|+|......... ...|++ ..++..-+..+++.+...|-++ ++++..+
T Consensus 55 ~~vDGiI~~s~~~~~~~l~~~~~~-~iPvV~~~~~~~~~--~~~~~V---~~D~~~a~~~a~~~Li~~Gh~~~I~~i~~~ 128 (279)
T PF00532_consen 55 RRVDGIILASSENDDEELRRLIKS-GIPVVLIDRYIDNP--EGVPSV---YIDNYEAGYEATEYLIKKGHRRPIAFIGGP 128 (279)
T ss_dssp TTSSEEEEESSSCTCHHHHHHHHT-TSEEEEESS-SCTT--CTSCEE---EEEHHHHHHHHHHHHHHTTCCSTEEEEEES
T ss_pred cCCCEEEEecccCChHHHHHHHHc-CCCEEEEEeccCCc--ccCCEE---EEcchHHHHHHHHHHHhcccCCeEEEEecC
Confidence 456665522222223555666666 99999765442110 133433 3446666778888888999999 9999976
Q ss_pred CCC--ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCe--EEEEEccCCcHHHHHHHHHHcC-CCC
Q 003093 82 DDH--GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESR--IIVVHTHYNRGPVVFHVAQYLG-MLG 156 (848)
Q Consensus 82 d~~--g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~--viv~~~~~~~~~~~~~~a~~~g-~~~ 156 (848)
.+. +..-.+.+.++++++|+.+..........+..+-...++++.+.+|+ +|| +++...|..+++++++.| ...
T Consensus 129 ~~~~~~~~R~~Gy~~Al~~~Gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~p~idai~-~~nd~~A~ga~~~l~~~gr~~i 207 (279)
T PF00532_consen 129 EDSSTSRERLQGYRDALKEAGLPIDEEWIFEGDFDYESGYEAARELLESHPDIDAIF-CANDMMAIGAIRALRERGRLKI 207 (279)
T ss_dssp TTTHHHHHHHHHHHHHHHHTTSCEEEEEEEESSSSHHHHHHHHHHHHHTSTT-SEEE-ESSHHHHHHHHHHHHHTT-TCT
T ss_pred cchHHHHHHHHHHHHHHHHcCCCCCcccccccCCCHHHHHHHHHHHHhhCCCCEEEE-EeCHHHHHHHHHHHHHcCCccc
Confidence 554 34556789999999999654443333223334444566677666666 544 445567777899999999 766
Q ss_pred CCeEEEe
Q 003093 157 TGYVWIA 163 (848)
Q Consensus 157 ~~~~wi~ 163 (848)
++-+-+.
T Consensus 208 p~di~~~ 214 (279)
T PF00532_consen 208 PEDIVSG 214 (279)
T ss_dssp TTEEEEC
T ss_pred Chhheee
Confidence 6654333
No 206
>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=93.46 E-value=1.3 Score=45.99 Aligned_cols=153 Identities=15% Similarity=0.100 Sum_probs=90.1
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+|+|||=...+. .........++|+|......+. +.+-.+..++...+..+++.+...|-++++++....
T Consensus 49 ~~vdGiI~~~~~~---~~~~~l~~~~~PvV~~~~~~~~------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~ 119 (265)
T cd01543 49 WQGDGIIARIDDP---EMAEALQKLGIPVVDVSGSREK------PGIPRVTTDNAAIGRMAAEHFLERGFRHFAFYGLPG 119 (265)
T ss_pred cccceEEEECCCH---HHHHHHhhCCCCEEEEeCccCC------CCCCEEeeCHHHHHHHHHHHHHHCCCcEEEEEcCCC
Confidence 4678777432222 2224456679999987553221 223346677777888888888888999999987443
Q ss_pred C-CccchHHHHHHHHhccCcEEEEeee--cCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 83 D-HGRNGIAALGDTLAAKRCRISFKAP--LSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 83 ~-~g~~~~~~l~~~l~~~g~~v~~~~~--~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
. ......+.|.+++++.|..+..... .....+..+-...+.++-+. .+++|+. ++...+..+++.+++.|+..+
T Consensus 120 ~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vp 198 (265)
T cd01543 120 ARWSDEREEAFRQLVAEAGYECSFFYRGLSTDAQSWEEEQEELAQWLQSLPKPVGIFA-CTDARARQLLEACRRAGIAVP 198 (265)
T ss_pred CHHHHHHHHHHHHHHHHcCCccccccCccccccccHHHHHHHHHHHHhcCCCCcEEEe-cChHHHHHHHHHHHHhCCCCC
Confidence 3 1233457899999999987521111 11111112223344444322 4565544 455667779999999998543
Q ss_pred -CeEEEecC
Q 003093 158 -GYVWIATS 165 (848)
Q Consensus 158 -~~~wi~~~ 165 (848)
+...++-|
T Consensus 199 ~di~vigfd 207 (265)
T cd01543 199 EEVAVLGVD 207 (265)
T ss_pred CceEEEeeC
Confidence 44445444
No 207
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=93.41 E-value=4.9 Score=38.81 Aligned_cols=70 Identities=17% Similarity=0.239 Sum_probs=45.6
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+ .+++.... ++-..+...|.+|++|+++.... .....+ -+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~~~~~ 80 (198)
T cd08433 13 VLAVPLLRAVRRRYP-GIRLRIVE-------GLSGHLLEWLLNGRLDLALLYGP---PPIPGL-STEPLLEEDLFLVGPA 80 (198)
T ss_pred hcchHHHHHHHHHCC-CcEEEEEe-------cCcHHHHHHHhCCCCcEEEEeCC---CCCCCe-eEEEeccccEEEEecC
Confidence 455677888888764 33444443 23568899999999999986322 112222 3567778888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (198)
T cd08433 81 DA 82 (198)
T ss_pred CC
Confidence 54
No 208
>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=93.40 E-value=1.1 Score=46.31 Aligned_cols=127 Identities=13% Similarity=0.090 Sum_probs=77.2
Q ss_pred hhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC---CCccchHHHHHHHHhcc
Q 003093 23 VANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD---DHGRNGIAALGDTLAAK 99 (848)
Q Consensus 23 i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd---~~g~~~~~~l~~~l~~~ 99 (848)
-+.+.++|+|......+ ...+| +.+++...+..+++++...|.++++++.... .......+.|.+.++++
T Consensus 70 ~~~~~gipvv~~~~~~~----~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~ 142 (265)
T cd06291 70 EYENIDLPIVSFDRYLS----ENIPI---VSSDNYEGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKEN 142 (265)
T ss_pred HHhcCCCCEEEEeCCCC----CCCCe---EeechHHHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHc
Confidence 33567999998765432 22333 4455666678888888777999999996433 23445568899999998
Q ss_pred CcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 100 RCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 100 g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
|+.+.... .....+..+....+.++.+. .+++|+.. +...+..+++.+++.|...++
T Consensus 143 ~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~~~~~al~~~g~~vp~ 201 (265)
T cd06291 143 GLEVRIIE-IQENFDDAEKKEEIKELLEEYPDIDGIFAS-NDLTAILVLKEAQQRGIRVPE 201 (265)
T ss_pred CCCCChhe-eeccccchHHHHHHHHHHhCCCCCCEEEEC-ChHHHHHHHHHHHHcCCCCCc
Confidence 87642211 11111112223344444333 34555543 344567789999999986444
No 209
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=93.39 E-value=3 Score=44.58 Aligned_cols=116 Identities=13% Similarity=0.114 Sum_probs=64.8
Q ss_pred CChHHhhcCCCC-eeEEeCchHHHHHH---hhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCC
Q 003093 593 KGIDSLRSSNYP-IGYQVNSFARNYLV---DELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC 668 (848)
Q Consensus 593 ~sl~dL~~s~~~-i~~~~~s~~~~~l~---~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~ 668 (848)
-+++||. +.+ +.+..++.....+. +..+.........++.+...+++.. |...+++... ..+... ..
T Consensus 184 i~~~dL~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~----g~Gv~~lp~~-~~~~~~--~~ 254 (313)
T PRK12684 184 LTLEDLA--QYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVEL----GLGVGIVADM-AFDPER--DR 254 (313)
T ss_pred cCHHHHh--cCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHh----CCceEEeehh-hccccc--cC
Confidence 3678887 444 44444443333222 2223333334566888999999998 5555666543 222221 22
Q ss_pred cEEEeC--CccccCCceeeecCCCCchHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 669 EFSIVG--QVFTKNGWGFAFPRDSPLAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 669 ~l~~~~--~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
++..+. .......++++.+++.++...+...+..+.+. +..++.++-+.
T Consensus 255 ~l~~~~i~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~-~~~~~~~~~~~ 305 (313)
T PRK12684 255 NLRAIDAGHLFGSSTTRLGLRRGAYLRGYVYTFIELFAPT-LNRKLVEQALK 305 (313)
T ss_pred CeEEEECCCCCcceeEEEEEECCCcCCHHHHHHHHHHHHH-hCHHHHHHHhc
Confidence 455443 23334567889999988777666666655543 55555554443
No 210
>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=93.36 E-value=0.96 Score=47.13 Aligned_cols=154 Identities=14% Similarity=0.156 Sum_probs=89.3
Q ss_pred CCeEEEE-ccCCchh---HHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEE
Q 003093 3 GQTVAII-GPQDAVT---SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAI 78 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~---~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii 78 (848)
.+|++|| -|..+.. ......-+...++|+|......+. .. +..+..++...+..+++++...|.++++++
T Consensus 54 ~~vdgii~~~~~~~~~~~~~~~~~~~~~~~ipvV~~~~~~~~---~~---~~~V~~D~~~~g~~~~~~l~~~G~~~i~~l 127 (273)
T cd01541 54 QGIDGLIIEPTKSALPNPNIDLYLKLEKLGIPYVFINASYEE---LN---FPSLVLDDEKGGYKATEYLIELGHRKIAGI 127 (273)
T ss_pred cCCCEEEEeccccccccccHHHHHHHHHCCCCEEEEecCCCC---CC---CCEEEECcHHHHHHHHHHHHHcCCcCEEEe
Confidence 4677765 4433211 112223456779999987644221 11 223556677778888898888899999988
Q ss_pred EEcC-CCccchHHHHHHHHhccCcEEEEe--eecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcC
Q 003093 79 YVDD-DHGRNGIAALGDTLAAKRCRISFK--APLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLG 153 (848)
Q Consensus 79 ~~dd-~~g~~~~~~l~~~l~~~g~~v~~~--~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g 153 (848)
...+ ..+....+.|.+.+++.|..+... ..+............+.++.+. .+++|+. .+...+..+++++++.|
T Consensus 128 ~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av~~-~~d~~a~g~~~al~~~g 206 (273)
T cd01541 128 FKADDLQGVKRMKGFIKAYREHGIPFNPSNVITYTTEEKEEKLFEKIKEILKRPERPTAIVC-YNDEIALRVIDLLKELG 206 (273)
T ss_pred cCCCcccHHHHHHHHHHHHHHcCCCCChHHEEeccccchhhHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcC
Confidence 7432 234455678999999888643211 1111111112334445555433 4666544 45556667999999999
Q ss_pred CCCCCeEEEe
Q 003093 154 MLGTGYVWIA 163 (848)
Q Consensus 154 ~~~~~~~wi~ 163 (848)
+..++-+-|.
T Consensus 207 ~~~p~dv~vv 216 (273)
T cd01541 207 LKIPEDISVV 216 (273)
T ss_pred CCCCCcEEEE
Confidence 8655444443
No 211
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=93.34 E-value=0.92 Score=49.25 Aligned_cols=111 Identities=10% Similarity=0.026 Sum_probs=68.5
Q ss_pred ccCChHHHHHHHHHHHHHcCcEEEEEEEEcCC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC-
Q 003093 52 TTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT- 128 (848)
Q Consensus 52 ~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~- 128 (848)
+..++..-+..+++.+...|.+++++|..... ....-.+.|.+++++.|+.+..........+...-...+.++...
T Consensus 156 V~~Dn~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 235 (343)
T PRK10727 156 IALDDRYGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLGRG 235 (343)
T ss_pred EEECcHHHHHHHHHHHHHCCCccEEEEeCCccccchHHHHHHHHHHHHHCCCCCChhhEEeCCCChhHHHHHHHHHHhCC
Confidence 44566666777778887789999999974432 345567899999999997642211111111112222344454433
Q ss_pred -CCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003093 129 -ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 163 (848)
Q Consensus 129 -~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 163 (848)
.+++|+. .+...+..++++++++|+..++-+-|.
T Consensus 236 ~~~~ai~~-~nD~~A~g~~~al~~~G~~vP~disVi 270 (343)
T PRK10727 236 RNFTAVAC-YNDSMAAGAMGVLNDNGIDVPGEISLI 270 (343)
T ss_pred CCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcceeEE
Confidence 3666554 455667789999999998665544333
No 212
>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=93.28 E-value=4.2 Score=43.07 Aligned_cols=154 Identities=10% Similarity=-0.030 Sum_probs=85.3
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc-Cc-EEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-GW-REVIAIY 79 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~-~w-~~vaii~ 79 (848)
.++++|| -+..+.........+...++|+|.+....+. .. .-+.....++...+..+++++... +- ++++++.
T Consensus 55 ~~~DgiIi~~~~~~~~~~~~~~~~~~~iPvV~v~~~~~~---~~-~~~~~v~~D~~~~g~~a~~~l~~~~~~~~~I~~l~ 130 (298)
T cd06302 55 QGVDAIAVVPNDPDALEPVLKKAREAGIKVVTHDSDVQP---DN-RDYDIEQADNKAIGETLMDSLAEQMGGKGEYAIFV 130 (298)
T ss_pred cCCCEEEEecCCHHHHHHHHHHHHHCCCeEEEEcCCCCC---Cc-ceeEEeccCHHHHHHHHHHHHHHHcCCCCEEEEEe
Confidence 3566655 3333332233334456789999987543211 01 112334567777788888887555 43 6899987
Q ss_pred EcCC--CccchHHHHHHHHhccC---cEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHc
Q 003093 80 VDDD--HGRNGIAALGDTLAAKR---CRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 80 ~dd~--~g~~~~~~l~~~l~~~g---~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
.+.. ......+.|.+.++++| .++.. ......+...-...++++... .+++|+. .+...+..++++++++
T Consensus 131 g~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~D~~A~g~~~al~~~ 207 (298)
T cd06302 131 GSLTATNQNAWIDAAKAYQKEKYYPMLELVD--RQYGDDDADKSYQTAQELLKAYPDLKGIIG-PTSVGIPGAARAVEEA 207 (298)
T ss_pred CCCCCcchHHHHHHHHHHHhhcCCCCeEEeC--cccCCCCHHHHHHHHHHHHHhCCCceEEEE-CCCcchhHHHHHHHhc
Confidence 4332 23445688999999987 33211 112112222222344444332 3555444 3456777899999999
Q ss_pred CCCCCCeEEEec
Q 003093 153 GMLGTGYVWIAT 164 (848)
Q Consensus 153 g~~~~~~~wi~~ 164 (848)
|+. .+...++-
T Consensus 208 g~~-~dv~vvG~ 218 (298)
T cd06302 208 GLK-GKVAVTGL 218 (298)
T ss_pred CCC-CCEEEEEe
Confidence 985 34333433
No 213
>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=93.19 E-value=1.1 Score=46.41 Aligned_cols=146 Identities=12% Similarity=0.055 Sum_probs=84.2
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+|++||-..... ..+...+...++|+|......+ ....++ +..++...+..+++++...|.++++++..+.
T Consensus 57 ~~vdgiii~~~~~--~~~~~~l~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~ 128 (268)
T cd06277 57 GKVDGIILLGGIS--TEYIKEIKELGIPFVLVDHYIP---NEKADC---VLTDNYSGAYAATEYLIEKGHRKIGFVGDPL 128 (268)
T ss_pred CCCCEEEEeCCCC--hHHHHHHhhcCCCEEEEccCCC---CCCCCE---EEecchHHHHHHHHHHHHCCCCcEEEECCCC
Confidence 4677777422222 2224556778999998754322 122233 3445555666677777777999999997554
Q ss_pred CC--ccchHHHHHHHHhccCcEEEEeeecCC-CCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 83 DH--GRNGIAALGDTLAAKRCRISFKAPLSV-EATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 83 ~~--g~~~~~~l~~~l~~~g~~v~~~~~~~~-~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
.. .....+.|.+.+++.|+.+.....+.. .....++...+..+. ..+++|+.. +...+..+++++++.|+..++
T Consensus 129 ~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~ai~~~-~d~~a~g~~~a~~~~g~~~p~ 205 (268)
T cd06277 129 YSPSFEERYEGYKKALLDHGIPFNEDYDITEKEEDEEDIGKFIDELK-PLPTAFFCS-NDGVAFLLIKVLKEMGIRVPE 205 (268)
T ss_pred CCcchHHHHHHHHHHHHHcCCCCCcceEEEcchhHHHHHHHHHhcCC-CCCCEEEEC-CcHHHHHHHHHHHHcCCCCCC
Confidence 32 234567899999998876432111111 111233333333322 236765544 445566788888999986443
No 214
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=93.19 E-value=3.4 Score=40.06 Aligned_cols=70 Identities=17% Similarity=0.151 Sum_probs=46.6
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++...+..+|.+|++|+++.... .....+ -+.|+....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~lv~~~ 80 (200)
T cd08466 13 LLLPRLLARLKQLAP-NISLRESP-------SSEEDLFEDLRLQEVDLVIDYVP---FRDPSF-KSELLFEDELVCVARK 80 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec-------CchHhHHHHHHcCCccEEEeccc---CCCCCc-eeeeecccceEEEEeC
Confidence 455677778877764 33454443 45778999999999999986321 112223 2457778889988886
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (200)
T cd08466 81 DH 82 (200)
T ss_pred CC
Confidence 65
No 215
>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=93.15 E-value=1.3 Score=47.70 Aligned_cols=149 Identities=11% Similarity=0.062 Sum_probs=87.3
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|++|| -|........+ ......++|++......+ +..+++ +..++..-+..+++.+...|.++++++...
T Consensus 115 ~~vdgiIi~~~~~~~~~~~-~~l~~~~iPvV~~~~~~~---~~~~~~---V~~dn~~~~~~~~~~L~~~G~~~I~~i~~~ 187 (327)
T TIGR02417 115 RQVDALIVASCMPPEDAYY-QKLQNEGLPVVALDRSLD---DEHFCS---VISDDVDAAAELIERLLSQHADEFWYLGAQ 187 (327)
T ss_pred cCCCEEEEeCCCCCChHHH-HHHHhcCCCEEEEccccC---CCCCCE---EEeCcHHHHHHHHHHHHHCCCCeEEEEeCc
Confidence 4677755 33332122233 334567999998754322 122332 445666667777788877899999999744
Q ss_pred CC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC---CCeEEEEEccCCcHHHHHHHHHHcCCCC
Q 003093 82 DD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVHTHYNRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 82 d~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~---~~~viv~~~~~~~~~~~~~~a~~~g~~~ 156 (848)
.. ....-.+.|.++++++|+.+... +....+..+-...+.++... .+++|+.. +...+..++++++++| ..
T Consensus 188 ~~~~~~~~R~~Gf~~al~~~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~~Ai~~~-~D~~A~g~~~al~~~g-~v 263 (327)
T TIGR02417 188 PELSVSRDRLAGFRQALKQATLEVEWV--YGGNYSRESGYQMFAKLCARLGRLPQALFTT-SYTLLEGVLDYMLERP-LL 263 (327)
T ss_pred ccchhHHHHHHHHHHHHHHcCCChHhE--EeCCCChHHHHHHHHHHHhcCCCCCcEEEEc-CcHHHHHHHHHHHHcC-CC
Confidence 32 34556788999999998753211 11111112233445555432 36776654 4456778999999999 66
Q ss_pred CCeEEE
Q 003093 157 TGYVWI 162 (848)
Q Consensus 157 ~~~~wi 162 (848)
++-+-|
T Consensus 264 P~dvsv 269 (327)
T TIGR02417 264 DSQLHL 269 (327)
T ss_pred CCcceE
Confidence 544333
No 216
>PRK09701 D-allose transporter subunit; Provisional
Probab=93.04 E-value=4.5 Score=43.19 Aligned_cols=158 Identities=14% Similarity=0.027 Sum_probs=89.0
Q ss_pred CCeEEEEc-cCCchh-HHHHHHhhccCCccEEecccCCCC--CCCCCCCceEeccCChHHHHHHHHHHH-HHcCc--EEE
Q 003093 3 GQTVAIIG-PQDAVT-SHVVSHVANELQVPLLSFSATDPT--LSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGW--REV 75 (848)
Q Consensus 3 ~~V~aiIG-p~~S~~-~~ava~i~~~~~vP~Is~~at~p~--ls~~~~p~f~r~~p~d~~q~~ai~~~~-~~~~w--~~v 75 (848)
++|++||= |..+.. ...+ ..+.+.++|++.+....+. +....-+...-+..++...+..+++++ +..|- +++
T Consensus 81 ~~vDgiIi~~~~~~~~~~~l-~~~~~~giPvV~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~aa~~L~~~~g~~~~~i 159 (311)
T PRK09701 81 KNYKGIAFAPLSSVNLVMPV-ARAWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEV 159 (311)
T ss_pred cCCCEEEEeCCChHHHHHHH-HHHHHCCCcEEEeCCCCCcccccccCCceEEEeccchHHHHHHHHHHHHHHhCCCCCEE
Confidence 45666653 333322 2333 3345789999988654321 111111122335677777888888876 44464 789
Q ss_pred EEEEEcC--CCccchHHHHHHHHhccC-cEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHH
Q 003093 76 IAIYVDD--DHGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQ 150 (848)
Q Consensus 76 aii~~dd--~~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~ 150 (848)
+++..+. .......+.|.+.++++| +++.... ....+..+-...+.++.+. ++++|+ +.+...+..++.+++
T Consensus 160 ~~l~g~~~~~~~~~R~~Gf~~al~~~~~~~~~~~~--~~~~~~~~~~~~~~~ll~~~~~~~~I~-~~~d~~A~g~~~al~ 236 (311)
T PRK09701 160 AIIEGKAGNASGEARRNGATEAFKKASQIKLVASQ--PADWDRIKALDVATNVLQRNPNIKAIY-CANDTMAMGVAQAVA 236 (311)
T ss_pred EEEECCCCCccHHHHHHHHHHHHHhCCCcEEEEec--CCCCCHHHHHHHHHHHHHhCCCCCEEE-ECCcchHHHHHHHHH
Confidence 8885433 334556788999999887 7654321 1111222233455555433 456544 555567778999999
Q ss_pred HcCCCCCCeEEEecC
Q 003093 151 YLGMLGTGYVWIATS 165 (848)
Q Consensus 151 ~~g~~~~~~~wi~~~ 165 (848)
+.|.. .+...++.+
T Consensus 237 ~~G~~-~dv~vvg~d 250 (311)
T PRK09701 237 NAGKT-GKVLVVGTD 250 (311)
T ss_pred HcCCC-CCEEEEEeC
Confidence 99984 343344433
No 217
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=93.04 E-value=4.6 Score=42.96 Aligned_cols=86 Identities=19% Similarity=0.217 Sum_probs=53.4
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
.++|||+... . ...+-.+++..+.+..+ .+.+.... +....++..|.+|++|+++..-.
T Consensus 95 g~l~ig~~~~--~-----------~~~~~~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~ 153 (305)
T CHL00180 95 GTLIIGASQT--T-----------GTYLMPRLIGLFRQRYP-QINVQLQV-------HSTRRIAWNVANGQIDIAIVGGE 153 (305)
T ss_pred ceEEEEEcCc--c-----------hHhHHHHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHcCCccEEEEcCc
Confidence 4689988731 1 12345567777777653 23344432 34788999999999999987322
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
...+....+ ...++....+++++++..
T Consensus 154 ~~~~~~~~~-~~~~l~~~~~~~v~~~~~ 180 (305)
T CHL00180 154 VPTELKKIL-EITPYVEDELALIIPKSH 180 (305)
T ss_pred cCcccccce-eEEEeccCcEEEEECCCC
Confidence 221111122 357778888999988765
No 218
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=92.93 E-value=3 Score=45.07 Aligned_cols=147 Identities=10% Similarity=0.019 Sum_probs=77.6
Q ss_pred CCCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHH-c--CcEEEEE
Q 003093 2 EGQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-Y--GWREVIA 77 (848)
Q Consensus 2 ~~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~-~--~w~~vai 77 (848)
+++|++|| -|..+.....+..-+.+.+||+|.+.+..+. +. ..++-...++...+..+++++.+ . +-.++++
T Consensus 78 ~~~vdgIiv~~~d~~al~~~l~~a~~~gIpVV~~d~~~~~--~~--~~~~V~~~~~~~~G~~~~~~l~~~l~~g~gki~i 153 (336)
T PRK15408 78 NQGYNAIIVSAVSPDGLCPALKRAMQRGVKVLTWDSDTKP--EC--RSYYINQGTPEQLGSMLVEMAAKQVGKDKAKVAF 153 (336)
T ss_pred HcCCCEEEEecCCHHHHHHHHHHHHHCCCeEEEeCCCCCC--cc--ceEEEecCCHHHHHHHHHHHHHHhcCCCCCEEEE
Confidence 35666655 4555554455666678889999997654221 11 11211112334566666666543 2 3468888
Q ss_pred EEEcCC--CccchHHHHHHHHhc--cCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcH-HHHHHHHHHc
Q 003093 78 IYVDDD--HGRNGIAALGDTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRG-PVVFHVAQYL 152 (848)
Q Consensus 78 i~~dd~--~g~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~-~~~~~~a~~~ 152 (848)
+..... -.....+.+.+.+++ .+++++... + ...+...-...++++....||+=.+++....+ ...++++++.
T Consensus 154 l~g~~~~~~~~~r~~g~~~~l~~~~p~~~vv~~~-~-~~~d~~~a~~~~~~lL~~~pdi~aI~~~~~~~~~Ga~~Al~~~ 231 (336)
T PRK15408 154 FYSSPTVTDQNQWVKEAKAKIAKEHPGWEIVTTQ-F-GYNDATKSLQTAEGILKAYPDLDAIIAPDANALPAAAQAAENL 231 (336)
T ss_pred EECCCCCccHHHHHHHHHHHHHhhCCCCEEEeec-C-CCCcHHHHHHHHHHHHHHCCCCcEEEECCCccHHHHHHHHHhC
Confidence 864322 122334667777754 356665332 1 12222333335555555555544444434433 3588888888
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 232 g~ 233 (336)
T PRK15408 232 KR 233 (336)
T ss_pred CC
Confidence 86
No 219
>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=92.86 E-value=0.81 Score=48.06 Aligned_cols=71 Identities=15% Similarity=0.251 Sum_probs=47.4
Q ss_pred CCCCChHHhhcCCCCeeEEeCchHHHHHHh---hhCCCccCc-ccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHh
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNSFARNYLVD---ELNIDESRL-VPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLS 665 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s~~~~~l~~---~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~ 665 (848)
++|++++||. |++|++..++.....+.. ..+.+...+ ..+.+..+...++.+ |++++++...++...+..
T Consensus 91 ~~i~s~~dL~--Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~----g~vda~~~~~p~~~~~~~ 164 (288)
T TIGR01728 91 SPIRTVADLK--GKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAA----GQVDAWAIWEPWGSALVE 164 (288)
T ss_pred CCCCCHHHcC--CCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHC----CCCCEEEeccchHhHHhh
Confidence 5789999998 888998877644443322 223332222 122356788899999 899999888877766555
Q ss_pred c
Q 003093 666 T 666 (848)
Q Consensus 666 ~ 666 (848)
+
T Consensus 165 ~ 165 (288)
T TIGR01728 165 E 165 (288)
T ss_pred c
Confidence 4
No 220
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=92.82 E-value=7.7 Score=37.37 Aligned_cols=72 Identities=19% Similarity=0.247 Sum_probs=46.2
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+ .+++.... ++..++++++.+|++|+++.... ...+...+. ..|.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~-~~~l~~~~~~~~~~~ 82 (201)
T cd08435 13 VLLPPAIARLLARHP-RLTVRVVE-------GTSDELLEGLRAGELDLAIGRLA-DDEQPPDLA-SEELADEPLVVVARP 82 (201)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHcCCccEEEEecC-cccCCCCcE-EEEcccCcEEEEEeC
Confidence 344577777777764 33454443 44678899999999999986321 111122232 457778888888886
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 83 ~~ 84 (201)
T cd08435 83 GH 84 (201)
T ss_pred CC
Confidence 55
No 221
>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=92.74 E-value=1.5 Score=45.18 Aligned_cols=145 Identities=10% Similarity=0.005 Sum_probs=84.8
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|++|| -|.... ...+..+.+ .+ |++......+ ...+ .+.+++...+..+++.+...|-++++++..+
T Consensus 54 ~~vdgiii~~~~~~-~~~~~~~~~-~~-pvv~~~~~~~----~~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~ 123 (260)
T cd06286 54 KQVDGLILCSREND-WEVIEPYTK-YG-PIVLCEEYDS----KNIS---SVYIDHYEAFYEALKYLIQKGYRKIAYCIGR 123 (260)
T ss_pred cCCCEEEEeCCCCC-HHHHHHHhc-CC-CEEEEecccC----CCCC---EEEECChHHHHHHHHHHHHCCCceEEEEcCC
Confidence 4566655 333222 233444433 34 8876543211 2223 2556677778888888888899999999744
Q ss_pred C--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCC
Q 003093 82 D--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 157 (848)
Q Consensus 82 d--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~ 157 (848)
. .......+.|.+.+++.|+.+.....+....+..+-...+.++.+. .+++|+ +++...+..+++.++++|+..+
T Consensus 124 ~~~~~~~~R~~Gf~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~ip 202 (260)
T cd06286 124 KKSLNSQSRKKAYKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLLKMKDRPDAIF-TGSDEVAAGIITEAKKQGIRVP 202 (260)
T ss_pred cccchhHHHHHHHHHHHHHcCCCCChHheEeCCCCHHHHHHHHHHHHcCCCCCCEEE-EcchHHHHHHHHHHHHcCCCCC
Confidence 2 3445567899999999986542211111111223333445555433 467654 4555667789999999998644
Q ss_pred C
Q 003093 158 G 158 (848)
Q Consensus 158 ~ 158 (848)
+
T Consensus 203 ~ 203 (260)
T cd06286 203 E 203 (260)
T ss_pred c
Confidence 4
No 222
>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=92.70 E-value=0.33 Score=48.65 Aligned_cols=59 Identities=32% Similarity=0.394 Sum_probs=37.7
Q ss_pred CCCCChHHhhcCCCCeeEEeCchHHHHHH---hhhCCCccCcccCC-CHHHHHHHhhcCCCCCceEEEE
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNSFARNYLV---DELNIDESRLVPLN-SPEEYAKALKDGPHKGGVAAVV 654 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s~~~~~l~---~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~a~~ 654 (848)
+.|++++||. |++||+..++.....+. +..+.....+.... +..+...+|.+ |++||.+
T Consensus 83 s~i~~~~DLk--GK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~----g~vDa~~ 145 (216)
T PF09084_consen 83 SGIKSPADLK--GKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLS----GQVDAAI 145 (216)
T ss_dssp TS-SSGGGGT--TSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHT----TSSSEEE
T ss_pred CCCCCHHHhC--CCEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhc----CCCCEEE
Confidence 4699999998 99999998765444332 23344333333222 35666679999 8999888
No 223
>PRK09526 lacI lac repressor; Reviewed
Probab=92.67 E-value=2.1 Score=46.35 Aligned_cols=147 Identities=11% Similarity=0.064 Sum_probs=86.7
Q ss_pred CCeEEEE--ccCCchhHHHHHHhh-ccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEE
Q 003093 3 GQTVAII--GPQDAVTSHVVSHVA-NELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIY 79 (848)
Q Consensus 3 ~~V~aiI--Gp~~S~~~~ava~i~-~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~ 79 (848)
.+|++|| +|..+... ..+. ...++|++.+... + ....+ .+..++..-+..+++++...|-++++++.
T Consensus 119 ~~vdGiii~~~~~~~~~---~~~~~~~~~iPvV~~d~~-~---~~~~~---~V~~d~~~~~~~a~~~L~~~G~~~I~~l~ 188 (342)
T PRK09526 119 QRVSGVIINVPLEDADA---EKIVADCADVPCLFLDVS-P---QSPVN---SVSFDPEDGTRLGVEHLVELGHQRIALLA 188 (342)
T ss_pred cCCCEEEEecCCCcchH---HHHHhhcCCCCEEEEecc-C---CCCCC---EEEECcHHHHHHHHHHHHHCCCCeEEEEe
Confidence 4677766 45443322 2222 2358999876532 1 11222 34566677778888888888999999997
Q ss_pred EcC--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 80 VDD--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 80 ~dd--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
.+. .....-...|.+++++.|+.+... +....+..+-...+.++... .+++|+. .+...+..+++++++.|+.
T Consensus 189 g~~~~~~~~~R~~Gf~~al~~~gi~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~A~g~~~al~~~g~~ 265 (342)
T PRK09526 189 GPESSVSARLRLAGWLEYLTDYQLQPIAV--REGDWSAMSGYQQTLQMLREGPVPSAILV-ANDQMALGVLRALHESGLR 265 (342)
T ss_pred CCCccccHHHHHHHHHHHHHHcCCCcceE--EeCCCchHHHHHHHHHHhcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCC
Confidence 432 233455688999999999864322 11111112222344444332 4666554 4556677899999999987
Q ss_pred CCCeEEE
Q 003093 156 GTGYVWI 162 (848)
Q Consensus 156 ~~~~~wi 162 (848)
.++-+-|
T Consensus 266 vP~disv 272 (342)
T PRK09526 266 VPGQISV 272 (342)
T ss_pred CCCceEE
Confidence 6554433
No 224
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=92.47 E-value=5.1 Score=42.28 Aligned_cols=83 Identities=16% Similarity=0.166 Sum_probs=55.0
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..++||++.. . ...+..+++..+.++.+ .+.+.... +....++..|.+|++|+++....
T Consensus 91 ~~i~I~~~~~--~-----------~~~~l~~~l~~~~~~~p-~~~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~ 149 (296)
T PRK11242 91 GSLRLAMTPT--F-----------TAYLIGPLIDAFHARYP-GITLTIRE-------MSQERIEALLADDELDVGIAFAP 149 (296)
T ss_pred eEEEEEeccc--h-----------hhhhhHHHHHHHHHHCC-CCEEEEEe-------CCHHHHHHHHHCCCCcEEEEecC
Confidence 4688888631 1 22445677888887754 44455543 44678899999999999986322
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.+...+ .+.++....+++++++..
T Consensus 150 ---~~~~~l-~~~~l~~~~~~~~~~~~~ 173 (296)
T PRK11242 150 ---VHSPEI-EAQPLFTETLALVVGRHH 173 (296)
T ss_pred ---CCCcce-eEEEeeeccEEEEEcCCC
Confidence 222223 357778888998888765
No 225
>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=92.41 E-value=4.4 Score=39.18 Aligned_cols=70 Identities=20% Similarity=0.252 Sum_probs=45.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..+++..+.++.+ .+++.... ++...+...|.+|++|+++.... .....+ -..|.....++++++.
T Consensus 13 ~~~~~~i~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~ 80 (200)
T cd08417 13 LLLPPLLARLRQEAP-GVRLRFVP-------LDRDDLEEALESGEIDLAIGVFP---ELPPGL-RSQPLFEDRFVCVARK 80 (200)
T ss_pred HHHHHHHHHHHhhCC-CeEEEecc-------CCHHHHHHHHHcCCCCEEEeecc---cCCCcc-chhhhhcCceEEEecC
Confidence 445567777777653 22344432 45778999999999999987322 222223 2467788889988886
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (200)
T cd08417 81 DH 82 (200)
T ss_pred CC
Confidence 54
No 226
>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=92.35 E-value=5.3 Score=38.49 Aligned_cols=71 Identities=14% Similarity=0.071 Sum_probs=47.4
Q ss_pred eeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEe
Q 003093 401 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 480 (848)
Q Consensus 401 ~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~ 480 (848)
..+-.+++..+.++.+ .+++.... ++..+++.+|.+|++|+++..... ....+ ...|+....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~~~~ 79 (198)
T cd08412 12 PYYLPGLLRRFREAYP-GVEVRVVE-------GNQEELEEGLRSGELDLALTYDLD---LPEDI-AFEPLARLPPYVWLP 79 (198)
T ss_pred hhhhHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEcCCC---CCccc-ceeeeeccceEEEec
Confidence 3566788888888764 23344443 457788999999999999873221 12223 246777888888887
Q ss_pred ccC
Q 003093 481 VRK 483 (848)
Q Consensus 481 ~~~ 483 (848)
+..
T Consensus 80 ~~~ 82 (198)
T cd08412 80 ADH 82 (198)
T ss_pred CCC
Confidence 654
No 227
>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=92.32 E-value=4.6 Score=39.10 Aligned_cols=70 Identities=14% Similarity=0.182 Sum_probs=44.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++..+++..|.+|++|+++...... ...+ -..+..+..++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~ 81 (200)
T cd08411 14 YLLPRLLPALRQAYP-KLRLYLRE-------DQTERLLEKLRSGELDAALLALPVD---EPGL-EEEPLFDEPFLLAVPK 81 (200)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEe-------CcHHHHHHHHHcCCccEEEEeccCC---CCCc-eEEEeeccceEEEecC
Confidence 355677778877764 23344443 4578899999999999998632211 1222 2446677888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~~ 83 (200)
T cd08411 82 DH 83 (200)
T ss_pred CC
Confidence 54
No 228
>PRK09492 treR trehalose repressor; Provisional
Probab=92.17 E-value=2 Score=45.80 Aligned_cols=137 Identities=15% Similarity=0.040 Sum_probs=82.5
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc-
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD- 81 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d- 81 (848)
.+|++||--..+... .......++|++...... +.+-.+..++...+..+++++...|-++++++...
T Consensus 117 ~~vdgiIi~~~~~~~---~~~l~~~~~pvv~i~~~~--------~~~~~V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~ 185 (315)
T PRK09492 117 RNVDGVILFGFTGIT---EEMLAPWQDKLVLLARDA--------KGFSSVCYDDEGAIKLLMQRLYDQGHRHISYLGVDH 185 (315)
T ss_pred cCCCEEEEeCCCccc---HHHHHhcCCCEEEEeccC--------CCCcEEEECcHHHHHHHHHHHHHcCCCeEEEEcCCc
Confidence 467777753222111 122334567777654211 11223455666677778888878899999999632
Q ss_pred C--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 82 D--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 82 d--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
. ..+..-.+.|.+++++.|+.+... ... .+...-...+.++...++++|+... ...+..+++++++.|+
T Consensus 186 ~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~~-~~~~~~~~~~~~~l~~~~~ai~~~~-D~~A~g~~~al~~~g~ 256 (315)
T PRK09492 186 SDVTTGKRRHQAYLAFCKQHKLTPVAA--LGG-LSMQSGYELVAKVLTPETTALVCAT-DTLALGASKYLQEQGR 256 (315)
T ss_pred ccchhHHHHHHHHHHHHHHcCCCceee--cCC-CCchHHHHHHHHHhhcCCCEEEEcC-cHHHHHHHHHHHHcCC
Confidence 2 234567789999999999875432 111 1112222344455445788876544 5677789999999997
No 229
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=92.09 E-value=5 Score=42.57 Aligned_cols=86 Identities=10% Similarity=0.140 Sum_probs=55.7
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
...|+||++.. . ...+-.+++..+.+..+ .+++.... ++..+++.+|.+|++|+++...
T Consensus 94 ~g~l~I~~~~~--~-----------~~~~l~~~l~~~~~~~p-~i~~~~~~-------~~~~~~~~~l~~g~~Di~i~~~ 152 (302)
T PRK09791 94 AGQINIGMGAS--I-----------ARSLMPAVISRFHQQHP-QVKVRIME-------GQLVSMINELRQGELDFTINTY 152 (302)
T ss_pred ceEEEEEechH--H-----------HHhhhHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHCCCccEEEEec
Confidence 36789988731 1 23455677788777765 33444432 4578999999999999998632
Q ss_pred eeecCceeeeeecccccccceEEEEeccC
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.... ....+. ..|+....+++++++..
T Consensus 153 ~~~~-~~~~~~-~~~l~~~~~~l~~~~~~ 179 (302)
T PRK09791 153 YQGP-YDHEFT-FEKLLEKQFAVFCRPGH 179 (302)
T ss_pred CCcc-ccccee-EEEeccceEEEEEcCCC
Confidence 1111 122243 36888899999988665
No 230
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=92.05 E-value=2.4 Score=45.98 Aligned_cols=111 Identities=6% Similarity=-0.096 Sum_probs=69.0
Q ss_pred ccCChHHHHHHHHHHHHHcCcEEEEEEEEcC--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC-
Q 003093 52 TTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT- 128 (848)
Q Consensus 52 ~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~- 128 (848)
+..++..-+..+++++...|-+++++|.... ..+..-.+.|.++++++|+.+..........+...-...+.++.+.
T Consensus 156 V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 235 (346)
T PRK10401 156 VCLDNVSGARMATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRN 235 (346)
T ss_pred EEECcHHHHHHHHHHHHHCCCCeEEEEeCCCcCcchHHHHHHHHHHHHHcCCCCChhheecCCCChHHHHHHHHHHHcCC
Confidence 3445555667777888888999999997433 3345667899999999997543211111111112222344454432
Q ss_pred -CCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003093 129 -ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 163 (848)
Q Consensus 129 -~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 163 (848)
.+++|+. .+...+..+++++++.|+..|+-+-+.
T Consensus 236 ~~~~ai~~-~nd~~A~g~~~al~~~G~~vP~disvi 270 (346)
T PRK10401 236 LQLTAVFA-YNDNMAAGALTALKDNGIAIPLHLSII 270 (346)
T ss_pred CCCcEEEE-CCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 4676664 456677789999999998765544333
No 231
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=92.01 E-value=5.5 Score=38.16 Aligned_cols=70 Identities=23% Similarity=0.261 Sum_probs=45.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-..++..+.++.+ .+++.... +....++.++.+|++|+++..... ....+. ..++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~ 80 (195)
T cd08434 13 SLVPDLIRAFRKEYP-NVTFELHQ-------GSTDELLDDLKNGELDLALCSPVP---DEPDIE-WIPLFTEELVLVVPK 80 (195)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEec-------CcHHHHHHHHHcCCccEEEEccCC---CCCCee-EEEeecceEEEEecC
Confidence 455667777777763 22344432 346788999999999999863322 222333 356777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (195)
T cd08434 81 DH 82 (195)
T ss_pred CC
Confidence 54
No 232
>PF07885 Ion_trans_2: Ion channel; InterPro: IPR013099 This entry includes the two membrane helix type ion channels found in bacteria []. ; PDB: 1KKD_A 2A0L_A 1ORQ_C 3UKM_C 1LNQ_E 3OUS_A 3LDC_A 3LDD_A 3RBZ_A 3LDE_A ....
Probab=91.99 E-value=0.18 Score=41.38 Aligned_cols=55 Identities=22% Similarity=0.422 Sum_probs=45.6
Q ss_pred CCCCcchhhhhHHHHhhhcC--ccccccchhHHHHHHHHhhhhhhhccccceeeeee
Q 003093 529 PKRQVVTIFWFSFSTMFFAH--KEKTVSALGRLVLIIWLFVVLIINSSYTASLTSIL 583 (848)
Q Consensus 529 ~~~~~~~~~~~~~~~l~~~~--~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~L 583 (848)
...++.+++|+++.++...| .-.|.+..+|++.+.+.++++.+.+...+.+++.+
T Consensus 21 ~~~~~~da~yfs~~t~tTvGyGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l 77 (79)
T PF07885_consen 21 EKWSFIDALYFSFVTITTVGYGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVL 77 (79)
T ss_dssp STTSHHHHHHHHHHHHTT---SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHhcccCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35689999999999999775 45899999999999999999999988888776654
No 233
>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=91.76 E-value=4 Score=42.12 Aligned_cols=144 Identities=11% Similarity=-0.024 Sum_probs=79.8
Q ss_pred CCeEEEEccCCchhHHHHHHhhccC-CccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc-CcEEEEEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANEL-QVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-GWREVIAIYV 80 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~-~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~-~w~~vaii~~ 80 (848)
.+|++||=.... ....+....++. ++|++......+. ....+ .+..++..-++.++.++... |-+++++|..
T Consensus 55 ~~vdgiii~~~~-~~~~~~~~~~~~~~ipvv~~~~~~~~--~~~~~---~v~~d~~~~~~~a~~l~~~~~g~~~I~~i~~ 128 (260)
T cd06304 55 QGYDLIFGVGFG-FMDAVEKVAKEYPDVKFAIIDGVVDA--PPNVA---SYVFREYEGSYLAGVLAALMTKTGKVGFVGG 128 (260)
T ss_pred cCCCEEEECCcc-hhHHHHHHHHHCCCCEEEEecCccCC--CCCee---eeecchHHHHHHHHHHHHHhccCCceEEEec
Confidence 456766532222 224444555544 7898876543211 01112 23334444445555556555 8899999975
Q ss_pred cC-CCccchHHHHHHHHhccCcEEEEeeecCCCC-ChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcC
Q 003093 81 DD-DHGRNGIAALGDTLAAKRCRISFKAPLSVEA-TEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLG 153 (848)
Q Consensus 81 dd-~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~-~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g 153 (848)
+. .......+.|.+.++++|............. +..+-...++++.+..+++| ++.+...+..++.+++++|
T Consensus 129 ~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ai-~~~~d~~A~gv~~al~~~g 202 (260)
T cd06304 129 MPIPEVNRFINGFAAGAKSVNPDITVLVIYTGSFFDPAKGKEAALALIDQGADVI-FAAAGGTGPGVIQAAKEAG 202 (260)
T ss_pred cccHHHHHHHHHHHHHHHHhCCCcEEEEEEecCccCcHHHHHHHHHHHhCCCCEE-EEcCCCCchHHHHHHHHcC
Confidence 32 2233446789999999886433211111111 11233445666655567876 5566677778999999988
No 234
>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=91.72 E-value=8.5 Score=36.90 Aligned_cols=71 Identities=15% Similarity=0.140 Sum_probs=47.9
Q ss_pred eeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEe
Q 003093 401 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 480 (848)
Q Consensus 401 ~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~ 480 (848)
..+..+++..+.+..+ .+++.... +...++..++.+|++|+++...... ...+ .+.|+....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~ 79 (196)
T cd08415 12 LSLLPRAIARFRARHP-DVRISLHT-------LSSSTVVEAVLSGQADLGLASLPLD---HPGL-ESEPLASGRAVCVLP 79 (196)
T ss_pred ccccHHHHHHHHHHCC-CcEEEEEe-------cchHHHHHHHHcCCccEEEEeCCCC---CCcc-eeeeecccceEEEEc
Confidence 3556788888888764 23455443 4577899999999999998632221 1222 366777888888887
Q ss_pred ccC
Q 003093 481 VRK 483 (848)
Q Consensus 481 ~~~ 483 (848)
+..
T Consensus 80 ~~~ 82 (196)
T cd08415 80 PGH 82 (196)
T ss_pred CCC
Confidence 654
No 235
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=91.71 E-value=6 Score=42.11 Aligned_cols=84 Identities=19% Similarity=0.193 Sum_probs=53.5
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..|+||+.. .+ ...+-.+++..+.+..+ .+++.... ++-+.+++.|.+|++|++++.-.
T Consensus 93 g~l~Ig~~~--~~-----------~~~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~ 151 (309)
T PRK12682 93 GTLTIATTH--TQ-----------ARYVLPRVVAAFRKRYP-KVNLSLHQ-------GSPDEIARMVISGEADIGIATES 151 (309)
T ss_pred CeEEEeeCc--hH-----------HHHHHHHHHHHHHHhCC-CeEEEEec-------CCHHHHHHHHHcCCccEEEecCc
Confidence 468988863 11 12455677788877764 22344432 34678999999999999987322
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.. ....++ +.|+....++++++...
T Consensus 152 ~~--~~~~l~-~~~l~~~~~~~~~~~~~ 176 (309)
T PRK12682 152 LA--DDPDLA-TLPCYDWQHAVIVPPDH 176 (309)
T ss_pred cc--CCCcce-EEEeeeeeEEEEecCCC
Confidence 11 112233 45778888888888765
No 236
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=91.52 E-value=2.5 Score=45.55 Aligned_cols=152 Identities=8% Similarity=-0.021 Sum_probs=87.0
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
.+|++||=-..... ......+.+.++|+|....... . .... .+..++..-+..+++++...|-++++++....
T Consensus 118 ~~vdgiI~~~~~~~-~~~~~~l~~~~iPvV~~~~~~~---~-~~~~--~V~~Dn~~~~~~a~~~L~~~Gh~~I~~i~~~~ 190 (331)
T PRK14987 118 WNIDGLILTERTHT-PRTLKMIEVAGIPVVELMDSQS---P-CLDI--AVGFDNFEAARQMTTAIIARGHRHIAYLGARL 190 (331)
T ss_pred cCCCEEEEcCCCCC-HHHHHHHHhCCCCEEEEecCCC---C-CCCc--eEEeCcHHHHHHHHHHHHHCCCceEEEEcCCC
Confidence 46677663111111 2223445678999997532110 1 1112 25566777778888888888999999996332
Q ss_pred -CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCCe
Q 003093 83 -DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 159 (848)
Q Consensus 83 -~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~ 159 (848)
.........|.++++++|+.... ..+....+...-...+.++... .+++||. ++...+..+++++++.|+..|+-
T Consensus 191 ~~~~~~R~~Gf~~al~~~g~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~nD~~A~g~~~al~~~g~~vP~d 268 (331)
T PRK14987 191 DERTIIKQKGYEQAMLDAGLVPYS-VMVEQSSSYSSGIELIRQARREYPQLDGVFC-TNDDLAVGAAFECQRLGLKVPDD 268 (331)
T ss_pred cccHHHHHHHHHHHHHHcCCCccc-eeecCCCChhhHHHHHHHHHhcCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCc
Confidence 22334568899999999863211 1111111112222344554433 4676554 45567778999999999876655
Q ss_pred EEEe
Q 003093 160 VWIA 163 (848)
Q Consensus 160 ~wi~ 163 (848)
+-|.
T Consensus 269 isvi 272 (331)
T PRK14987 269 MAIA 272 (331)
T ss_pred cEEE
Confidence 5444
No 237
>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=91.44 E-value=12 Score=35.96 Aligned_cols=70 Identities=10% Similarity=0.061 Sum_probs=45.4
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++..+++.++.+|++|+++...... ...+. +.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~ 80 (199)
T cd08426 13 ELLPSLIARFRQRYP-GVFFTVDV-------ASTADVLEAVLSGEADIGLAFSPPP---EPGIR-VHSRQPAPIGAVVPP 80 (199)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEe-------CCcHHHHHHHHCCCccEEEecCCCC---CCCeE-EEeeccCcEEEEecC
Confidence 445667777777753 23344433 3467899999999999998632221 12232 467778888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~h 82 (199)
T cd08426 81 GH 82 (199)
T ss_pred CC
Confidence 54
No 238
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=91.30 E-value=8 Score=41.65 Aligned_cols=151 Identities=7% Similarity=-0.010 Sum_probs=78.0
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHc-----------
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY----------- 70 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~----------- 70 (848)
.+|++|| -|..+.........+...++|+|.+....+.-.-...+-...+..++...+..+++++...
T Consensus 80 ~~vdgiIi~~~~~~~~~~~l~~l~~~giPvV~vd~~~~~~~~~~~~~~~~V~~D~~~ag~~a~~~l~~~~~~~~~~~~~~ 159 (330)
T PRK15395 80 KGVKALAINLVDPAAAPTVIEKARGQDVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWKANPAWDLNK 159 (330)
T ss_pred cCCCEEEEeccCHHHHHHHHHHHHHCCCcEEEEcCCccccccccccceeEEccChHHHHHHHHHHHHHHHhhccccccCC
Confidence 4566655 2333332333334566789999998653211000111212234555555566555554321
Q ss_pred -CcEEEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC----CCeEEEEEccCCcHH
Q 003093 71 -GWREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT----ESRIIVVHTHYNRGP 143 (848)
Q Consensus 71 -~w~~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~----~~~viv~~~~~~~~~ 143 (848)
|-.++++|... ..........+.++++++|+.+..........+..+-...+.++.+. .+++|+ +++...+.
T Consensus 160 ~g~~~i~~i~g~~~~~~~~~R~~G~~~al~~~g~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~ai~-~~~d~~A~ 238 (330)
T PRK15395 160 DGKIQYVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVI-ANNDAMAM 238 (330)
T ss_pred CCceEEEEEecCCCCchHHHHHHHHHHHHHhcCCCeeeeecccCCcCHHHHHHHHHHHHhhCcCCCeeEEE-ECCchHHH
Confidence 33344555432 22334457889999999987654321111111212233344554332 345554 44556677
Q ss_pred HHHHHHHHcCC
Q 003093 144 VVFHVAQYLGM 154 (848)
Q Consensus 144 ~~~~~a~~~g~ 154 (848)
.+++++++.|+
T Consensus 239 gvl~al~~~Gl 249 (330)
T PRK15395 239 GAVEALKAHNK 249 (330)
T ss_pred HHHHHHHhcCC
Confidence 89999999997
No 239
>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=91.27 E-value=7.1 Score=37.93 Aligned_cols=68 Identities=19% Similarity=0.305 Sum_probs=43.4
Q ss_pred eeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEecc
Q 003093 403 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 403 ~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
+-..++..+.++.+ .+++.... ++. ++++.|.+|++|+++..-... ...+. ..|.....++++++..
T Consensus 14 ~l~~~i~~~~~~~P-~i~l~i~~-------~~~-~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~ 80 (200)
T cd08462 14 LLPPVIERVAREAP-GVRFELLP-------PDD-QPHELLERGEVDLLIAPERFM---SDGHP-SEPLFEEEFVCVVWAD 80 (200)
T ss_pred HHHHHHHHHHHHCC-CCEEEEec-------CCh-hHHHHHhcCCeeEEEecCCCC---CCCce-eeeeeccceEEEEcCC
Confidence 44566777777664 23344443 334 899999999999998732221 12232 4477778888888766
Q ss_pred C
Q 003093 483 K 483 (848)
Q Consensus 483 ~ 483 (848)
.
T Consensus 81 h 81 (200)
T cd08462 81 N 81 (200)
T ss_pred C
Confidence 5
No 240
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=91.25 E-value=13 Score=35.46 Aligned_cols=70 Identities=19% Similarity=0.201 Sum_probs=45.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..+++..+.++.+ .+++.... +....++.+|.+|++|+++....... ..+ ...+.....++++++.
T Consensus 12 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~~~~~ 79 (197)
T cd08419 12 YFAPRLLGAFCRRHP-GVEVSLRV-------GNREQVLERLADNEDDLAIMGRPPED---LDL-VAEPFLDNPLVVIAPP 79 (197)
T ss_pred hHhhHHHHHHHHHCC-CceEEEEE-------CCHHHHHHHHhcCCccEEEecCCCCC---CCe-EEEEeccCCEEEEecC
Confidence 355677788877753 22344443 34778899999999999986332211 112 3567778888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 80 ~~ 81 (197)
T cd08419 80 DH 81 (197)
T ss_pred CC
Confidence 54
No 241
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=91.23 E-value=13 Score=35.96 Aligned_cols=71 Identities=20% Similarity=0.197 Sum_probs=47.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
++..+++..+.++.+ .+.+.... ++...+++.|.+|++|+++..-.. .....+ .+.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~~~~ 81 (198)
T cd08444 13 YALPWVVQAFKEQFP-NVHLVLHQ-------GSPEEIASMLANGQADIGIATEAL--ENHPEL-VSFPYYDWHHHIIVPV 81 (198)
T ss_pred hhhhHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHCCCccEEEecccc--CCCcCc-EEeeccccceeEEecC
Confidence 566778888888764 23344443 457789999999999999862211 111222 2567777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~h 83 (198)
T cd08444 82 GH 83 (198)
T ss_pred CC
Confidence 65
No 242
>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=91.22 E-value=6.8 Score=41.43 Aligned_cols=86 Identities=15% Similarity=0.220 Sum_probs=54.5
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
...|+||+... . ...+-.+++..+.++.+ .+.+.... ++...++.++.+|++|++++..
T Consensus 92 ~~~l~I~~~~~--~-----------~~~~~~~~l~~~~~~~P-~~~i~~~~-------~~~~~~~~~l~~g~~D~~i~~~ 150 (300)
T TIGR02424 92 GPTVRIGALPT--V-----------AARLMPEVVKRFLARAP-RLRVRIMT-------GPNAYLLDQLRVGALDLVVGRL 150 (300)
T ss_pred CceEEEecccH--H-----------HHhhhHHHHHHHHHhCC-CcEEEEEe-------CchHHHHHHHHCCCCCEEEEec
Confidence 45789988631 1 12345567777777765 34455543 4567899999999999999633
Q ss_pred eeecCceeeeeecccccccceEEEEeccC
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
... .....+ -..|.....+++++++..
T Consensus 151 ~~~-~~~~~~-~~~~l~~~~~~~~~~~~h 177 (300)
T TIGR02424 151 GAP-ETMQGL-SFEHLYNEPVVFVVRAGH 177 (300)
T ss_pred CCc-ccccce-eeeeecCCceEEEEcCCC
Confidence 221 112223 245777888888887654
No 243
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=91.19 E-value=7.8 Score=37.42 Aligned_cols=135 Identities=12% Similarity=0.036 Sum_probs=90.3
Q ss_pred hHHHHHHhhccCCccEEecccCCCCCCC-CCCCce--Ee-----ccCChHHHHHHHHHHHHHcCcEEEEEEEEcCCCccc
Q 003093 16 TSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYF--VR-----TTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRN 87 (848)
Q Consensus 16 ~~~ava~i~~~~~vP~Is~~at~p~ls~-~~~p~f--~r-----~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~ 87 (848)
.+...|......++-+|.|++|+.++.. .+|.-= -| -.| -..-+.|.++-++.++.+++.++. +|-..
T Consensus 55 ~t~~aAl~Lada~vdvI~Y~CtsgS~i~G~~~d~ei~~~ie~~~~v~-vvTts~Avv~aL~al~a~ri~vlT---PY~~e 130 (238)
T COG3473 55 YTERAALELADAGVDVIVYGCTSGSLIGGPGYDKEIAQRIEEAKGVP-VVTTSTAVVEALNALGAQRISVLT---PYIDE 130 (238)
T ss_pred HHHHHHHhcCccccCEEEEeccceeeecCCchhHHHHHHHHhccCCc-eeechHHHHHHHHhhCcceEEEec---cchhh
Confidence 3455667778889999999999988764 333100 00 000 011135667778999999999997 67777
Q ss_pred hHHHHHHHHhccCcEEEEeeecCCCC-------ChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHH-HcCC
Q 003093 88 GIAALGDTLAAKRCRISFKAPLSVEA-------TEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQ-YLGM 154 (848)
Q Consensus 88 ~~~~l~~~l~~~g~~v~~~~~~~~~~-------~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~-~~g~ 154 (848)
..+.-.+.++++|++|+....+.... .....-...+++...++|.||+.|-.-....++.... +.|.
T Consensus 131 vn~~e~ef~~~~Gfeiv~~~~Lgi~dn~eigr~~P~~~y~lAk~~~~~~~DaiFiSCTnlRt~eii~~lE~~~G~ 205 (238)
T COG3473 131 VNQREIEFLEANGFEIVDFKGLGITDNLEIGRQEPWAVYRLAKEVFTPDADAIFISCTNLRTFEIIEKLERDTGV 205 (238)
T ss_pred hhhHHHHHHHhCCeEEEEeeccCCcccchhcccChHHHHHHHHHhcCCCCCeEEEEeeccccHHHHHHHHHHhCC
Confidence 88888999999999998776543321 1233444556667789999999887665666665554 3554
No 244
>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=91.12 E-value=8.1 Score=37.27 Aligned_cols=70 Identities=11% Similarity=0.061 Sum_probs=44.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
++-..++..+.++.+ .+++.... ++...++..|.+|++|+++..... . ...+ -..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~-~~~~l~~~~~~~v~~~ 80 (200)
T cd08464 13 WLAPPLLAALRAEAP-GVRLVFRQ-------VDPFNVGDMLDRGEIDLAIGVFGE--L-PAWL-KREVLYTEGYACLFDP 80 (200)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCcccHHHHHhcCcccEEEecCCC--C-cccc-eeeeecccceEEEEeC
Confidence 455677778877763 23354443 346688999999999999863221 1 1222 2457777888888765
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (200)
T cd08464 81 QQ 82 (200)
T ss_pred CC
Confidence 54
No 245
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=90.93 E-value=12 Score=40.07 Aligned_cols=207 Identities=12% Similarity=0.127 Sum_probs=124.9
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..||||+.. .+ ...+-.++++.+.+..+ .+.+.... ++...++++|.+|++|+++....
T Consensus 93 g~lrIg~~~--~~-----------~~~~l~~~l~~f~~~~P-~i~l~l~~-------~~~~~~~~~L~~g~~Dl~i~~~~ 151 (316)
T PRK12679 93 GVLTIATTH--TQ-----------ARYSLPEVIKAFRELFP-EVRLELIQ-------GTPQEIATLLQNGEADIGIASER 151 (316)
T ss_pred ceEEEEech--Hh-----------hhcchHHHHHHHHHHCC-CeEEEEec-------CCHHHHHHHHHcCCCCEEEeccc
Confidence 578999873 11 23556678888887754 22344432 44678999999999999986322
Q ss_pred eecCceeeeeecccccccceEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcch
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVT 535 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 535 (848)
.. . ...+. +.++....+++++++..+...
T Consensus 152 ~~-~-~~~l~-~~~l~~~~~~~v~~~~hpl~~------------------------------------------------ 180 (316)
T PRK12679 152 LS-N-DPQLV-AFPWFRWHHSLLVPHDHPLTQ------------------------------------------------ 180 (316)
T ss_pred CC-C-CCCce-EEEccCCcEEEEecCCCcccc------------------------------------------------
Confidence 11 1 12233 457788888888876652110
Q ss_pred hhhhHHHHhhhcCccccccchhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCe-eEEeCchH-
Q 003093 536 IFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPI-GYQVNSFA- 613 (848)
Q Consensus 536 ~~~~~~~~l~~~~~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i-~~~~~s~~- 613 (848)
...-+++||. +.++ ....+...
T Consensus 181 ------------------------------------------------------~~~i~~~~L~--~~~~i~~~~~~~~~ 204 (316)
T PRK12679 181 ------------------------------------------------------ITPLTLESIA--KWPLITYRQGITGR 204 (316)
T ss_pred ------------------------------------------------------CCCCCHHHHh--CCCeEEecCCCcHH
Confidence 1223688887 4453 33334322
Q ss_pred ---HHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEEEeC--CccccCCceeeecC
Q 003093 614 ---RNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVG--QVFTKNGWGFAFPR 688 (848)
Q Consensus 614 ---~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~k 688 (848)
..++. ..+.........++.+...+++.. |...+++-... ... . +...+..+. .......+.+++++
T Consensus 205 ~~~~~~~~-~~~~~~~~~~~~~s~~~~~~~v~~----g~Gi~~lp~~~-~~~-~-~~~~L~~~~~~~~~~~~~~~l~~~~ 276 (316)
T PRK12679 205 SRIDDAFA-RKGLLADIVLSAQDSDVIKTYVAL----GLGIGLVAEQS-SGE-Q-EESNLIRLDTRHLFDANTVWLGLKR 276 (316)
T ss_pred HHHHHHHH-HcCCCceEEEEeccHHHHHHHHHc----CCcEEEecccc-ccc-c-cCCcEEEEECcccCCCceEEEEEeC
Confidence 33332 223332334556788888999998 55556665432 232 2 233455443 22334568889999
Q ss_pred CCCchHHHHHHHHhhhccCchHHHHHhhcc
Q 003093 689 DSPLAVDISTAILKLSENGDLQRIHDKWLL 718 (848)
Q Consensus 689 ~spl~~~in~~i~~l~e~G~~~~~~~kw~~ 718 (848)
+.+....+...+..+.+.--.+.++++-+.
T Consensus 277 ~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~ 306 (316)
T PRK12679 277 GQLQRNYVWRFLELCNAGLSVEDIKRQVME 306 (316)
T ss_pred CchhhHHHHHHHHHHhcccCHHHHHHHHhh
Confidence 988888888888777776667777766554
No 246
>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=90.85 E-value=7 Score=41.46 Aligned_cols=146 Identities=7% Similarity=-0.031 Sum_probs=81.9
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcE-EEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWR-EVIAIYV 80 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~-~vaii~~ 80 (848)
.+|++|| -|..+.........+.+.++|+|.+....+ ..+....+..++..-++.+++++...+-+ +++++..
T Consensus 53 ~~vDgIIi~~~~~~~~~~~l~~~~~~~iPvV~~d~~~~-----~~~~~~~V~~d~~~~g~~~~~~L~~~g~~~~i~~i~g 127 (302)
T TIGR02634 53 RGVDVLVIIPQNGQVLSNAVQEAKDEGIKVVAYDRLIN-----DADIDFYLSFDNEKVGEMQARAVLEAAPKGNYFLMGG 127 (302)
T ss_pred cCCCEEEEeCCChhHHHHHHHHHHHCCCeEEEecCcCC-----CCCccEEEecCHHHHHHHHHHHHHhhCCCCCEEEEeC
Confidence 3555544 343333334444556778999998754321 11222345566777788888887666555 7887764
Q ss_pred c--CCCccchHHHHHHHHhcc----CcEEEEeeecCCCCChHHHHHHHHHHhc---CCCeEEEEEccCCcHHHHHHHHHH
Q 003093 81 D--DDHGRNGIAALGDTLAAK----RCRISFKAPLSVEATEDEITDLLVKVAL---TESRIIVVHTHYNRGPVVFHVAQY 151 (848)
Q Consensus 81 d--d~~g~~~~~~l~~~l~~~----g~~v~~~~~~~~~~~~~d~~~~l~~i~~---~~~~viv~~~~~~~~~~~~~~a~~ 151 (848)
+ +.......+.+.+.+++. ++.+... .+.......+....+.++.. ..+++|+.. +...+..+++++++
T Consensus 128 ~~~~~~~~~R~~g~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ll~~~~~~~~aI~~~-~D~~A~g~~~al~~ 205 (302)
T TIGR02634 128 SPTDNNAKLLRGGQMKVLQPAIDSGDIKIVGD-QWVDGWLPENALRIMENALTANDNKVDAVVAS-NDATAGGAIQALTA 205 (302)
T ss_pred CCCCcchHHHHHHHHHHHhhhccCCCeEEecC-cCCCCCCHHHHHHHHHHHHHhCCCCccEEEEC-CCchHHHHHHHHHH
Confidence 3 222334457788888764 3554322 11111122334455555543 246665553 44556679999999
Q ss_pred cCCC
Q 003093 152 LGML 155 (848)
Q Consensus 152 ~g~~ 155 (848)
.|+.
T Consensus 206 ~g~~ 209 (302)
T TIGR02634 206 QGLA 209 (302)
T ss_pred CCCC
Confidence 9974
No 247
>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=90.78 E-value=6 Score=41.75 Aligned_cols=141 Identities=11% Similarity=0.020 Sum_probs=78.9
Q ss_pred CCeEEEE-ccCCchh-HHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHH-cC----cEEE
Q 003093 3 GQTVAII-GPQDAVT-SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YG----WREV 75 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~-~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~-~~----w~~v 75 (848)
.+|+||| .|..... ...+..+ . .++|+|.+..-.+ +. ..+-.+..++..-+..+++++.. .. -+++
T Consensus 56 ~~vDgiIi~~~~~~~~~~~l~~~-~-~~iPvV~~~~~~~---~~--~~~~~V~~D~~~~g~~~~~~L~~~~~~~~g~~~I 128 (295)
T TIGR02955 56 WGADAILLGTVSPEALNHDLAQL-T-KSIPVFALVNQID---SN--QVKGRVGVDWYQMGYQAGEYLAQRHPKGSGPTTL 128 (295)
T ss_pred cCCCEEEEecCChhhhhHHHHHH-h-cCCCEEEEecCCC---cc--ceeEEEeecHHHHHHHHHHHHHHhcccCCCCeeE
Confidence 4677765 4432222 2333333 3 4899987532211 11 12233555666666777777654 21 3469
Q ss_pred EEEEEcC--CCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHH
Q 003093 76 IAIYVDD--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQY 151 (848)
Q Consensus 76 aii~~dd--~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~ 151 (848)
+++.... .......+.|.+.+++.|+++... .....+..+-...++++.+ ..+++| +++...+..+++++++
T Consensus 129 ~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~d~i--~~~d~~a~g~l~al~~ 204 (295)
T TIGR02955 129 AWLPGPKNRGGTKPVTQGFRAALEGSDVEISAI--LWADNDKELQRNLLQDLLKKHPDIDYL--VGSAVAAEAAISELRS 204 (295)
T ss_pred EEEeCCCcCCchhHHHHHHHHHHhcCCcEEEEE--ecCCCcHHHHHHHHHHHHHhCCCcCEE--EeccHHHHHHHHHHHh
Confidence 9997443 334556789999999999877532 2211222333344555443 245754 4455567778999988
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|.
T Consensus 205 ~g~ 207 (295)
T TIGR02955 205 LHM 207 (295)
T ss_pred hCc
Confidence 886
No 248
>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=90.69 E-value=8.3 Score=37.38 Aligned_cols=71 Identities=18% Similarity=0.140 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... +....+.+.|.+|++|+++...... ....+. +.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~~-~~~l~~~~~~~v~~~ 81 (198)
T cd08413 13 YVLPPVIAAFRKRYP-KVKLSLHQ-------GTPSQIAEMVLKGEADIAIATEALD--DHPDLV-TLPCYRWNHCVIVPP 81 (198)
T ss_pred hhccHHHHHHHHhCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEEccCCC--CCCCcE-EEEeeeeeEEEEecC
Confidence 455677888888764 23344443 4577899999999999998632211 112233 467778888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~h 83 (198)
T cd08413 82 GH 83 (198)
T ss_pred CC
Confidence 55
No 249
>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=90.65 E-value=0.65 Score=43.85 Aligned_cols=99 Identities=10% Similarity=0.092 Sum_probs=63.8
Q ss_pred HHHHHHcCcEEEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHH-HHHhcCCCeEEEEEccCC
Q 003093 64 AEIVDHYGWREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLL-VKVALTESRIIVVHTHYN 140 (848)
Q Consensus 64 ~~~~~~~~w~~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l-~~i~~~~~~viv~~~~~~ 140 (848)
++.+...|-+++++|..+ +.+.....+.|.+++++.|+........... ...+..... ..++...+++||+ ++..
T Consensus 1 ~~~L~~~G~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~pdaii~-~~~~ 78 (160)
T PF13377_consen 1 VDYLIERGHRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFEELIFFSDD-DSEDAREAQLLWLRRLRPDAIIC-SNDR 78 (160)
T ss_dssp HHHHHHTT-SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEEGEEEEESS-SHHHHHHHHHHHHHTCSSSEEEE-SSHH
T ss_pred ChHHHHCCCCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCCeeEeecCC-cchhHHHHHHHHHhcCCCcEEEE-cCHH
Confidence 456777899999999933 3344566788999999999986544433332 223333222 2344347787666 6667
Q ss_pred cHHHHHHHHHHcCCCCCCeEEEec
Q 003093 141 RGPVVFHVAQYLGMLGTGYVWIAT 164 (848)
Q Consensus 141 ~~~~~~~~a~~~g~~~~~~~wi~~ 164 (848)
.+..+++.+++.|+..++-+-|++
T Consensus 79 ~a~~~~~~l~~~g~~vP~di~vv~ 102 (160)
T PF13377_consen 79 LALGVLRALRELGIRVPQDISVVS 102 (160)
T ss_dssp HHHHHHHHHHHTTSCTTTTSEEEE
T ss_pred HHHHHHHHHHHcCCcccccccEEE
Confidence 788899999999996554444433
No 250
>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=90.64 E-value=3.4 Score=42.71 Aligned_cols=129 Identities=11% Similarity=0.098 Sum_probs=80.1
Q ss_pred ccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC-CCccchHHHHHHHHhccCcEE
Q 003093 25 NELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD-DHGRNGIAALGDTLAAKRCRI 103 (848)
Q Consensus 25 ~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd-~~g~~~~~~l~~~l~~~g~~v 103 (848)
...++|+|......+ ...++++ ..++..-+..+++.+...|-++++++..+. ........+|.+.++++|+..
T Consensus 74 ~~~~iPvV~~~~~~~---~~~~~~v---~~d~~~~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~~~~~~ 147 (263)
T cd06280 74 LRLSFPVVLIDRAGP---AGRVDAV---VLDNRAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAP 147 (263)
T ss_pred HhcCCCEEEECCCCC---CCCCCEE---EECcHHHHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHHcCCCC
Confidence 466899998765432 2334443 356666778888888888999999987432 233455788999999988764
Q ss_pred EEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003093 104 SFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 163 (848)
Q Consensus 104 ~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 163 (848)
... .... +..+....+.++... .+++|+ +.+...+..+++.+++.|+..++-+.|.
T Consensus 148 ~~~-~~~~--~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~~p~di~ii 205 (263)
T cd06280 148 DAR-FVAP--TAEAAEAALAAWLAAPERPEALV-ASNGLLLLGALRAVRAAGLRIPQDLALA 205 (263)
T ss_pred Chh-hccc--CHHHHHHHHHHHhcCCCCCcEEE-ECCcHHHHHHHHHHHHcCCCCCCcEEEE
Confidence 321 1111 223333344444432 466654 4555667789999999998655444343
No 251
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=90.59 E-value=6.9 Score=42.03 Aligned_cols=85 Identities=19% Similarity=0.107 Sum_probs=53.0
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
...|+||+... + ...+-.+++..+.+..+ .+++.... ++...++.+|.+|++|+++..-
T Consensus 92 ~g~l~Ig~~~~--~-----------~~~~l~~~l~~f~~~~P-~i~i~i~~-------~~~~~~~~~L~~g~iDl~i~~~ 150 (324)
T PRK12681 92 KGSLYIATTHT--Q-----------ARYALPPVIKGFIERYP-RVSLHMHQ-------GSPTQIAEAAAKGNADFAIATE 150 (324)
T ss_pred CCeEEEEechh--H-----------HHHhhHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCCCEEEecC
Confidence 35789998631 1 12345567777777664 34455543 5688999999999999998632
Q ss_pred eeecCceeeeeecccccccceEEEEeccC
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.. .....+. ..|.....+++++++..
T Consensus 151 ~~--~~~~~l~-~~~l~~~~~~~v~~~~h 176 (324)
T PRK12681 151 AL--HLYDDLI-MLPCYHWNRSVVVPPDH 176 (324)
T ss_pred cc--cCCCCeE-EEEeccceeEEEeCCCC
Confidence 11 1122232 35667777788877554
No 252
>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=90.58 E-value=11 Score=36.26 Aligned_cols=70 Identities=16% Similarity=0.115 Sum_probs=45.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++...+..++.+|++|+++..... ....+ -+.+.....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Di~i~~~~~---~~~~~-~~~~l~~~~~~lv~~~ 80 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRD-------LESDNLEAQLERGEVDLALTTPEY---APDGL-RSRPLFEERYVCVTRR 80 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEee-------CCcccHHHHHhcCCCcEEEecCcc---CCccc-eeeeeecCcEEEEEcC
Confidence 455677888887764 22344432 335678999999999999863221 12222 2567778888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (198)
T cd08461 81 GH 82 (198)
T ss_pred CC
Confidence 54
No 253
>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=90.55 E-value=4.4 Score=39.38 Aligned_cols=70 Identities=19% Similarity=0.238 Sum_probs=46.2
Q ss_pred eeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEe
Q 003093 401 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 480 (848)
Q Consensus 401 ~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~ 480 (848)
..+-.+++..+.++.+ .+++.... ++. .++++|.+|++|++++.... ....+. ..|..+..++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~v~l~~-------~~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~ 78 (200)
T cd08460 12 AAFGPALLAAVAAEAP-GVRLRFVP-------ESD-KDVDALREGRIDLEIGVLGP---TGPEIR-VQTLFRDRFVGVVR 78 (200)
T ss_pred HHHHHHHHHHHHHHCC-CCEEEEec-------Cch-hHHHHHHCCCccEEEecCCC---CCcchh-eeeeeccceEEEEe
Confidence 3556677888887764 33455543 335 78899999999999873222 112233 46777888888888
Q ss_pred ccC
Q 003093 481 VRK 483 (848)
Q Consensus 481 ~~~ 483 (848)
...
T Consensus 79 ~~h 81 (200)
T cd08460 79 AGH 81 (200)
T ss_pred CCC
Confidence 665
No 254
>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=90.34 E-value=17 Score=34.68 Aligned_cols=71 Identities=15% Similarity=0.127 Sum_probs=45.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+ .+.+.... ++...+.+++.+|++|+++..... .....+ ...+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~~~~ 81 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQ-------AGSDDLLAAVREGRLDLAFVGLPE--RRPPGL-ASRELAREPLVAVVAP 81 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCHHHHHHHHHcCCccEEEEecCC--CCCCCc-EEEEeecceEEEEecC
Confidence 455677778877764 33454443 346788999999999999864322 122222 2456677788888776
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~~ 83 (194)
T cd08436 82 DH 83 (194)
T ss_pred CC
Confidence 54
No 255
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=90.31 E-value=7.9 Score=37.66 Aligned_cols=70 Identities=13% Similarity=0.146 Sum_probs=45.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
++-.+++..+.++.+ .+++.... ++..+++++|.+|++|+++...... ...+. +.+.....+++++++
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~-------~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~lv~~~ 80 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQ-------ASREAMLAQVADGEIDLALGVFPEL---PEELH-AETLFEERFVCLADR 80 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEec-------CChHhHHHHHHCCCccEEEeccccC---CcCee-EEEeeeccEEEEEeC
Confidence 455677777776654 33454443 4588999999999999998633221 12233 346667788888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~h 82 (200)
T cd08465 81 AT 82 (200)
T ss_pred CC
Confidence 54
No 256
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=90.28 E-value=18 Score=37.93 Aligned_cols=83 Identities=16% Similarity=0.169 Sum_probs=51.8
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..++||+... . ...+-.+++..+.+..+ .+++.... +...+++..+.+|++|+++....
T Consensus 89 g~l~i~~~~~--~-----------~~~~~~~~l~~~~~~~P-~i~i~v~~-------~~~~~~~~~l~~g~~Di~i~~~~ 147 (290)
T PRK10837 89 GALRIYASST--I-----------GNYILPAMIARYRRDYP-QLPLELSV-------GNSQDVINAVLDFRVDIGLIEGP 147 (290)
T ss_pred CeEEEEecch--h-----------HhhhhHHHHHHHHHHCC-CceEEEEE-------CCHHHHHHHHHhCCceEEEecCC
Confidence 4788888731 1 12445677777777763 22344432 34678999999999999986322
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.. ...+ -..|+....+++++++..
T Consensus 148 ~~---~~~~-~~~~l~~~~~~lv~~~~h 171 (290)
T PRK10837 148 CH---SPEL-ISEPWLEDELVVFAAPDS 171 (290)
T ss_pred CC---CCce-eEEEeecceEEEEEcCCC
Confidence 11 1122 235667778888887655
No 257
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=90.26 E-value=11 Score=40.12 Aligned_cols=105 Identities=12% Similarity=0.110 Sum_probs=58.2
Q ss_pred CChHHhhcCCCC-eeEEeCchHHHHHH---hhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCC
Q 003093 593 KGIDSLRSSNYP-IGYQVNSFARNYLV---DELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC 668 (848)
Q Consensus 593 ~sl~dL~~s~~~-i~~~~~s~~~~~l~---~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~ 668 (848)
-+++||. +.+ +....++.....+. ...+.........++.+...+.+.. |...+++-.. ..... ...
T Consensus 184 ~~~~~L~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~----g~Gi~~lp~~-~~~~~--~~~ 254 (309)
T PRK12683 184 LTLEAIA--EYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVEL----GMGVGIVAAM-AYDPQ--RDT 254 (309)
T ss_pred cCHHHHh--cCCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHh----CCCeEEeehh-hcccc--CCC
Confidence 5688887 445 44444443333222 2223332334457788888888888 5555666432 22211 123
Q ss_pred cEEEeC--CccccCCceeeecCCCCchHHHHHHHHhhhcc
Q 003093 669 EFSIVG--QVFTKNGWGFAFPRDSPLAVDISTAILKLSEN 706 (848)
Q Consensus 669 ~l~~~~--~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~ 706 (848)
.+..+. +......++++.+|+.++.......+..+.+.
T Consensus 255 ~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~l~~~ 294 (309)
T PRK12683 255 GLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFAPH 294 (309)
T ss_pred ceEEEeCCCCcccceEEEEEECCCcCCHHHHHHHHHHHhh
Confidence 455443 22334568899999988777666666555544
No 258
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=90.13 E-value=12 Score=36.05 Aligned_cols=72 Identities=8% Similarity=0.036 Sum_probs=47.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .++++... ++...+++.|.+|++|+++.... .......++ ..+..+..++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~l~-~~~l~~~~~~~~~~~ 82 (198)
T cd08437 13 YYFPKLAKDLIKTGL-MIQIDTYE-------GGSAELLEQLLQGDLDIALLGSL-TPLENSALH-SKIIKTQHFMIIVSK 82 (198)
T ss_pred HHhHHHHHHHHHhCC-ceEEEEEE-------cCHHHHHHHHHcCCCCEEEecCC-CCCCcccce-EEEeecceEEEEecC
Confidence 345677788887765 34455543 35788999999999999986321 111222333 457777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 83 ~h 84 (198)
T cd08437 83 DH 84 (198)
T ss_pred CC
Confidence 54
No 259
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=89.79 E-value=5.3 Score=42.41 Aligned_cols=112 Identities=7% Similarity=-0.033 Sum_probs=70.6
Q ss_pred ccCChHHHHHHHHHHHHHcCcEEEEEEEEcCC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC-
Q 003093 52 TTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT- 128 (848)
Q Consensus 52 ~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~- 128 (848)
+..++...+..+++.+...|-+++++|..... ......+.|.+.+++.|+++.....+....+.......+.++...
T Consensus 132 V~~Dn~~~g~~a~~~l~~~G~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 211 (309)
T PRK11041 132 VHIDNLTAAFEAVNYLHELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITVDPQYIARGDFTFEAGAKALKQLLDLP 211 (309)
T ss_pred EEECcHHHHHHHHHHHHHcCCceEEEEeCCccccchHHHHHHHHHHHHHcCCCCCHHHeEeCCCCHHHHHHHHHHHHcCC
Confidence 44566677778888887789999999974433 234557889999999987653211111111223334455665443
Q ss_pred -CCeEEEEEccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003093 129 -ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 164 (848)
Q Consensus 129 -~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 164 (848)
.+++|+. ++...+..+++++++.|+..++-+.|++
T Consensus 212 ~~~~ai~~-~~d~~a~gv~~al~~~g~~ip~di~vvg 247 (309)
T PRK11041 212 QPPTAVFC-HSDVMALGALSQAKRMGLRVPQDLSIIG 247 (309)
T ss_pred CCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 3677775 4555666799999999986544444443
No 260
>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=89.66 E-value=12 Score=39.65 Aligned_cols=145 Identities=6% Similarity=-0.014 Sum_probs=72.9
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChH-HHHHHHHHHH-HHc-CcEEEEEE
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQ-YQMAAIAEIV-DHY-GWREVIAI 78 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~-~q~~ai~~~~-~~~-~w~~vaii 78 (848)
++|++|| -|..+........-+.+.+||+|.+....+. + +....+...|. ..++..++.+ +++ +-++|+++
T Consensus 55 ~~vdgiIi~~~~~~~~~~~l~~~~~~giPvV~~~~~~~~--~---~~~~~v~~~Dn~~~g~~aa~~l~~~l~~~~~I~~i 129 (302)
T TIGR02637 55 QKVDAIAISANDPDALVPALKKAMKRGIKVVTWDSGVAP--E---GRNLFLNQASADLIGRTQVQLAAEQIGNGGEIAIL 129 (302)
T ss_pred cCCCEEEEeCCChHHHHHHHHHHHHCCCEEEEeCCCCCC--C---ceeEEEecCCHHHHHHHHHHHHHHHcCCCcEEEEE
Confidence 4555544 3444333333344466789999987543221 1 12233333333 3344445543 332 22689988
Q ss_pred EEcCCC--ccchHHHHHHHHhccC---cEEEEeeecCCCCChHHHHHHHHHHhcCC--CeEEEEEccCCcHHHHHHHHHH
Q 003093 79 YVDDDH--GRNGIAALGDTLAAKR---CRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQY 151 (848)
Q Consensus 79 ~~dd~~--g~~~~~~l~~~l~~~g---~~v~~~~~~~~~~~~~d~~~~l~~i~~~~--~~viv~~~~~~~~~~~~~~a~~ 151 (848)
..+... .....+.+.+.++++| .+++.. .....+..+-...++++.+.+ +++|+. .....+...++++++
T Consensus 130 ~g~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~~ai~~-~~d~~a~ga~~al~~ 206 (302)
T TIGR02637 130 SAASTATNQNAWIEIMKKELKDPKYPKVKLVAT--VYGDDDAQKSYQEAQGLLKSYPNLKGIIA-PTTVGIKAAAQAVSD 206 (302)
T ss_pred ECCCCCccHHHHHHHHHHHHhhccCCCCEEEee--ecCCchHHHHHHHHHHHHHhCCCccEEEe-CCCchHHHHHHHHHh
Confidence 744322 2234577777777653 344322 111112233334444544333 455554 334566668888888
Q ss_pred cCCC
Q 003093 152 LGML 155 (848)
Q Consensus 152 ~g~~ 155 (848)
.|..
T Consensus 207 ~g~~ 210 (302)
T TIGR02637 207 AKLI 210 (302)
T ss_pred cCCC
Confidence 8874
No 261
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=89.41 E-value=4.9 Score=43.15 Aligned_cols=146 Identities=10% Similarity=-0.009 Sum_probs=83.1
Q ss_pred CeEEEEc-cCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcC
Q 003093 4 QTVAIIG-PQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 82 (848)
Q Consensus 4 ~V~aiIG-p~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd 82 (848)
+|+++|= |..+. .......+.++|++......+ ...+++ +..++..-+..+++++...|.++++++..+.
T Consensus 114 ~vDgiI~~~~~~~---~~~~~l~~~~~pvV~~~~~~~---~~~~~~---V~~D~~~~~~~a~~~l~~~G~~~i~~i~~~~ 184 (327)
T PRK10339 114 NVTGILIVGKPTP---ALRAAASALTDNICFIDFHEP---GSGYDA---VDIDLARISKEIIDFYINQGVNRIGFIGGED 184 (327)
T ss_pred cCCEEEEeCCCCH---HHHHHHHhcCCCEEEEeCCCC---CCCCCE---EEECHHHHHHHHHHHHHHCCCCeEEEeCCcc
Confidence 5666553 22222 233445667899987643221 122332 5556666677888888888999999996433
Q ss_pred C--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 83 D--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
. ....-...|.+.+++.|+. .....+....+..+-...+.++.. ..+++|+. ++...+..++++++++|...++
T Consensus 185 ~~~~~~~R~~gf~~~~~~~g~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~D~~A~g~~~al~~~g~~vP~ 262 (327)
T PRK10339 185 EPGKADIREVAFAEYGRLKQVV-REEDIWRGGFSSSSGYELAKQMLAREDYPKALFV-ASDSIAIGVLRAIHERGLNIPQ 262 (327)
T ss_pred ccchhhHHHHHHHHHHHHcCCC-ChhheeecCcChhHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCC
Confidence 2 3344467788888888761 110111111111222334445443 24666544 4556677899999999986554
Q ss_pred eE
Q 003093 159 YV 160 (848)
Q Consensus 159 ~~ 160 (848)
-+
T Consensus 263 di 264 (327)
T PRK10339 263 DI 264 (327)
T ss_pred ce
Confidence 33
No 262
>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=89.23 E-value=6.3 Score=41.95 Aligned_cols=118 Identities=13% Similarity=0.009 Sum_probs=75.1
Q ss_pred ccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc-C--CCccchHHHHHHHHhccCc
Q 003093 25 NELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD-D--DHGRNGIAALGDTLAAKRC 101 (848)
Q Consensus 25 ~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d-d--~~g~~~~~~l~~~l~~~g~ 101 (848)
...++|++...... ..++ .+.+++..-+..+++++...|-+++++|..+ . ..+..-.++|.+++++.|+
T Consensus 133 ~~~~~p~V~i~~~~-----~~~~---~V~~D~~~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~~R~~gf~~a~~~~gi 204 (311)
T TIGR02405 133 ESWNHKAVVIARDT-----GGFS---SVCYDDYGAIELLMANLYQQGHRHISFLGVDPSDKTTGLMRHNAYLAYCESANL 204 (311)
T ss_pred HhcCCCEEEEecCC-----CCcc---EEEeCcHHHHHHHHHHHHHcCCCcEEEEccCcccchhHHHHHHHHHHHHHHcCC
Confidence 44678888765321 1122 3456677777788888888899999999632 2 2445667899999999998
Q ss_pred EEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 102 RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 102 ~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.... .....+..+....+.++...++++|| +++...+..+++.++++|.
T Consensus 205 ~~~~---~~~~~~~~~~~~~~~~~l~~~~tAi~-~~~D~~A~g~~~~l~~~g~ 253 (311)
T TIGR02405 205 EPIY---QTGQLSHESGYVLTDKVLKPETTALV-CATDTLALGAAKYLQELDR 253 (311)
T ss_pred Ccee---eeCCCCHHHHHHHHHHHHhcCCCEEE-ECCcHHHHHHHHHHHHcCC
Confidence 6321 11111212223344444334677765 5666677889999999996
No 263
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=89.04 E-value=18 Score=34.84 Aligned_cols=69 Identities=13% Similarity=0.123 Sum_probs=44.0
Q ss_pred eeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEecc
Q 003093 403 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 403 ~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
+-..++..+.++.+- +++.... ++...+..+|.+|++|+++..-... ...+. ..+.....++++++..
T Consensus 14 ~~~~~l~~~~~~~P~-i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~~~~ 81 (198)
T cd08441 14 WLMPVLDQFRERWPD-VELDLSS-------GFHFDPLPALLRGELDLVITSDPLP---LPGIA-YEPLFDYEVVLVVAPD 81 (198)
T ss_pred hhHHHHHHHHHhCCC-eEEEEEe-------CCchhHHHHHHcCCceEEEecCCcC---CCCcE-EEEccCCcEEEEEcCC
Confidence 445677888777642 2344433 3467899999999999998632211 12222 4566777888887765
Q ss_pred C
Q 003093 483 K 483 (848)
Q Consensus 483 ~ 483 (848)
.
T Consensus 82 ~ 82 (198)
T cd08441 82 H 82 (198)
T ss_pred C
Confidence 4
No 264
>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=88.97 E-value=22 Score=34.00 Aligned_cols=72 Identities=13% Similarity=0.001 Sum_probs=46.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-..++..+.++.+ .+++.... +...++++.|.+|++|++++...... +...+. ..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~-~~~l~~~~~~~v~~~ 82 (197)
T cd08449 13 GGLGPALRRFKRQYP-NVTVRFHE-------LSPEAQKAALLSKRIDLGFVRFADTL-NDPPLA-SELLWREPMVVALPE 82 (197)
T ss_pred hhHHHHHHHHHHHCC-CeEEEEEE-------CCHHHHHHHHhCCCccEEEecccccC-CCCCce-EEEEEEeeEEEEecC
Confidence 456677888887764 33454443 45788999999999999986332210 112222 356777788888776
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 83 ~~ 84 (197)
T cd08449 83 EH 84 (197)
T ss_pred CC
Confidence 54
No 265
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=88.87 E-value=21 Score=34.54 Aligned_cols=70 Identities=16% Similarity=0.170 Sum_probs=45.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... +....++..|.+|++|+++..... . ...+. ..+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~~-~~~l~~~~~~~v~~~ 80 (200)
T cd08467 13 ALLPRLAPRLRERAP-GLDLRLCP-------IGDDLAERGLEQGTIDLAVGRFAV--P-PDGLV-VRRLYDDGFACLVRH 80 (200)
T ss_pred HHHHHHHHHHHhhCC-CCEEEEec-------CCcccHHHHhhCCCcCEEEecCCC--C-Cccce-eEEeeeccEEEEEcC
Confidence 455677788877764 23455543 346689999999999999863211 1 12233 457778888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~h 82 (200)
T cd08467 81 GH 82 (200)
T ss_pred CC
Confidence 54
No 266
>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=88.87 E-value=21 Score=34.33 Aligned_cols=70 Identities=20% Similarity=0.154 Sum_probs=45.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .++++... ++..++...+.+|++|+++....... ..+ -+.+..+..++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~v~~~ 80 (196)
T cd08458 13 SFMSGVIQTFIADRP-DVSVYLDT-------VPSQTVLELVSLQHYDLGISILAGDY---PGL-TTEPVPSFRAVCLLPP 80 (196)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEec-------cChHHHHHHHHcCCCCEEEEeccCCC---CCc-eEEEeccCceEEEecC
Confidence 345677888887765 33455443 34667899999999999987332211 122 2456777788888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~h 82 (196)
T cd08458 81 GH 82 (196)
T ss_pred CC
Confidence 54
No 267
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=88.78 E-value=2.6 Score=43.55 Aligned_cols=103 Identities=13% Similarity=0.093 Sum_probs=62.6
Q ss_pred CCCCChHHhhcCCCCeeEEeCchHHHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHH-HhcCC
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELF-LSTRC 668 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~-~~~~~ 668 (848)
.+|++++||. |+++.+..++.....++. ++ ...+ ..+..|...+|++ |.+|+.+.....+..+ +.+-.
T Consensus 126 ~~i~s~~Dl~--G~kir~~~~~~~~~~~~~-~G---a~~v-~~~~~e~~~aL~~----G~vDg~~~~~~~~~~~~~~ev~ 194 (257)
T TIGR00787 126 KPITKPEDLK--GLKIRIPNSPMNEAQFKA-LG---ANPE-PMAFSEVYTALQT----GVVDGQENPLSNVYSSKFYEVQ 194 (257)
T ss_pred CccCChHHhC--CCEEecCCCHHHHHHHHH-cC---Cccc-ccCHHHHHHHHHc----CCcccccCCHHHHhhcchhhhc
Confidence 5799999998 999998877766777743 33 2233 5577899999999 8899988765443211 11122
Q ss_pred cEEEeCCccccCCceeeecCCC--CchHHHHHHHHhhh
Q 003093 669 EFSIVGQVFTKNGWGFAFPRDS--PLAVDISTAILKLS 704 (848)
Q Consensus 669 ~l~~~~~~~~~~~~~~~~~k~s--pl~~~in~~i~~l~ 704 (848)
++..... .......+.+.++. .|-+....+|.+..
T Consensus 195 ~y~~~~~-~~~~~~~~~~n~~~~~~L~~e~q~~i~~a~ 231 (257)
T TIGR00787 195 KYLSMTN-HGYLGYLVVVNKAFWKSLPPDLQAVVKEAA 231 (257)
T ss_pred chheecC-CcccceEEEEeHHHHhcCCHHHHHHHHHHH
Confidence 3322222 22344566677653 25555555554443
No 268
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=88.77 E-value=1.2 Score=47.76 Aligned_cols=68 Identities=16% Similarity=0.136 Sum_probs=44.9
Q ss_pred CCCCChHHhhcCCCCeeEEeCchHHHHHH---hhhCCCcc--CcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHH
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNSFARNYLV---DELNIDES--RLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFL 664 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s~~~~~l~---~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~ 664 (848)
++|++++||. |++||+..++.....+. +..+.... +++.. ...+...++.+ |.+||++...++..-..
T Consensus 112 ~~I~s~~DLk--GK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~Al~~----G~VDAa~~~~p~~~~~~ 184 (320)
T PRK11480 112 KTISKPEDLI--GKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNL-QPPAIIAAWQR----GDIDGAYVWAPAVNALE 184 (320)
T ss_pred CCCCChHHcC--CCEEecCCCCchHHHHHHHHHHcCCCHhheEEEEC-CcHHHHHHHHc----CCcCEEEEcchHHHHHH
Confidence 3599999998 99999987664433321 23344332 23333 36778899999 89999887777654333
No 269
>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=88.63 E-value=19 Score=34.45 Aligned_cols=70 Identities=11% Similarity=0.102 Sum_probs=46.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+...++..+.++.+ .+.+.... +...++...|.+|++|+++..... ....+ ...++....+++++++
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~v~~~ 81 (197)
T cd08425 14 YLIGPLIDRFHARYP-GIALSLRE-------MPQERIEAALADDRLDLGIAFAPV---RSPDI-DAQPLFDERLALVVGA 81 (197)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEE-------CcHHHHHHHHHcCCccEEEEecCC---CCCCc-EEEEeccccEEEEecC
Confidence 344677888877764 34455543 346788999999999999863221 22222 2466777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
+.
T Consensus 82 ~~ 83 (197)
T cd08425 82 TH 83 (197)
T ss_pred CC
Confidence 65
No 270
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=88.63 E-value=15 Score=39.28 Aligned_cols=82 Identities=10% Similarity=0.106 Sum_probs=53.9
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
..+++||+... . ...+-..++..+.+..+ .+++... .+++++..|.+|++|+++...
T Consensus 116 ~~~l~Ig~~~~--~-----------~~~~l~~~l~~f~~~~P-~i~i~~~---------~~~~~~~~l~~g~~Dl~i~~~ 172 (317)
T PRK11482 116 QRTITIATTPS--V-----------GALVMPVIYQAIKTHYP-QLLLRNI---------PISDAENQLSQFQTDLIIDTH 172 (317)
T ss_pred CceEEEEecHH--H-----------HHHHHHHHHHHHHHHCC-CCEEEEe---------cchhHHHHHHCCCcCEEEecc
Confidence 35789998731 1 12345667777777765 3444432 356899999999999998743
Q ss_pred eeecCceeeeeecccccccceEEEEeccC
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.. ....+. +.|.....++++++...
T Consensus 173 ~~---~~~~~~-~~~l~~~~~~lv~~~~h 197 (317)
T PRK11482 173 SC---SNRTIQ-HHVLFTDNVVLVCRQGH 197 (317)
T ss_pred CC---CCCceE-EEEEecCcEEEEEeCCC
Confidence 32 223343 46778888998888765
No 271
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=88.60 E-value=14 Score=36.47 Aligned_cols=70 Identities=11% Similarity=0.118 Sum_probs=46.1
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..+++..+.++.+ .+++.... .+...+.+.|.+|++|++++... .....+. ..|.....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~Di~i~~~~---~~~~~l~-~~~l~~~~~~~v~~~ 80 (221)
T cd08469 13 VLLPALVRRLETEAP-GIDLRIRP-------VTRLDLAEQLDLGRIDLVIGIFE---QIPPRFR-RRTLFDEDEVWVMRK 80 (221)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEee-------CChhhHHHHHHCCCccEEEecCC---CCCccce-eeeeeccceEEEEeC
Confidence 345667777777664 23444443 34678999999999999987332 1223333 467778888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (221)
T cd08469 81 DH 82 (221)
T ss_pred CC
Confidence 55
No 272
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=88.45 E-value=26 Score=34.30 Aligned_cols=72 Identities=11% Similarity=0.135 Sum_probs=44.5
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+... .+++.... ++...++..|.+|++|+++........-...+ ...|.....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~-------~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~ 83 (204)
T cd08429 13 SIAYRLLEPAMDLHE-PIRLVCRE-------GKLEQLLADLALHRLDMVLADRPMPSSLDVKG-YSHRLGECGVSFFAAP 83 (204)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEecCCCccccchhe-eeccccccceEEEecC
Confidence 455677777777763 33344443 56889999999999999986332211100111 2457777777777654
Q ss_pred c
Q 003093 482 R 482 (848)
Q Consensus 482 ~ 482 (848)
+
T Consensus 84 ~ 84 (204)
T cd08429 84 P 84 (204)
T ss_pred C
Confidence 3
No 273
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=88.32 E-value=18 Score=34.57 Aligned_cols=72 Identities=22% Similarity=0.263 Sum_probs=46.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+ .+++.... ++.+.+++.+.+|++|+++..-.. ......+ .+.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~-~~~~~~~-~~~~l~~~~~~~v~~~ 82 (195)
T cd08427 13 GLLPRALARLRRRHP-DLEVHIVP-------GLSAELLARVDAGELDAAIVVEPP-FPLPKDL-VWTPLVREPLVLIAPA 82 (195)
T ss_pred HHhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCCCEEEEcCCC-CccccCc-eEEEcccCcEEEEECC
Confidence 455677788877764 23344443 457889999999999999873211 1101222 2456777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 83 ~~ 84 (195)
T cd08427 83 EL 84 (195)
T ss_pred CC
Confidence 54
No 274
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=88.28 E-value=2 Score=47.24 Aligned_cols=87 Identities=6% Similarity=0.009 Sum_probs=65.0
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
..+.+.++.+|.+++.+++...-...+..+.+.+.|++.|+.+.....+.+..+.+++...+..+++.++|+||-.+.+
T Consensus 20 ~~l~~~~~~~g~~~~livt~~~~~~~g~~~~v~~~L~~~~i~~~~f~~v~~np~~~~v~~~~~~~~~~~~D~IiaiGGGS 99 (383)
T PRK09860 20 TDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGS 99 (383)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCCch
Confidence 5567788999999999887543334456788999999999987655556556667889999999999999999977554
Q ss_pred -CcHHHHHH
Q 003093 140 -NRGPVVFH 147 (848)
Q Consensus 140 -~~~~~~~~ 147 (848)
-++.+.+.
T Consensus 100 ~iD~AK~ia 108 (383)
T PRK09860 100 PHDCAKGIA 108 (383)
T ss_pred HHHHHHHHH
Confidence 34444443
No 275
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=88.24 E-value=13 Score=40.07 Aligned_cols=146 Identities=6% Similarity=-0.054 Sum_probs=83.2
Q ss_pred CCeEEEE-ccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 3 GQTVAII-GPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 3 ~~V~aiI-Gp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
.+|++|| -|............+.+.++|+|.+....+ .. +....+.+++...+..+++++...|-++++++...
T Consensus 80 ~~vDGiIi~~~~~~~~~~~l~~~~~~~iPvV~id~~~~---~~--~~~~~V~~D~~~~g~~a~~~L~~~g~~~i~~i~~g 154 (330)
T PRK10355 80 RGVDVLVIIPYNGQVLSNVIKEAKQEGIKVLAYDRMIN---NA--DIDFYISFDNEKVGELQAKALVDKVPQGNYFLMGG 154 (330)
T ss_pred cCCCEEEEeCCChhhHHHHHHHHHHCCCeEEEECCCCC---CC--CccEEEecCHHHHHHHHHHHHHHhcCCCCEEEEeC
Confidence 4566654 443332223334556788999998754321 11 12234677888888999999877777887765432
Q ss_pred C---CCccchHHHHHHHHhcc---C-cEEEEeeecCCCCChHHHHHHHHHHh-c--CCCeEEEEEccCCcHHHHHHHHHH
Q 003093 82 D---DHGRNGIAALGDTLAAK---R-CRISFKAPLSVEATEDEITDLLVKVA-L--TESRIIVVHTHYNRGPVVFHVAQY 151 (848)
Q Consensus 82 d---~~g~~~~~~l~~~l~~~---g-~~v~~~~~~~~~~~~~d~~~~l~~i~-~--~~~~viv~~~~~~~~~~~~~~a~~ 151 (848)
. ..+....+.+.+.++++ | +.+....... ..+..+-...++++. + ..+++|+ +.+...+..+++.+++
T Consensus 155 ~~~~~~~~~R~~gf~~~l~~~~~~~~i~~~~~~~~~-~~~~~~~~~~~~~lL~~~~~~~~aI~-~~nD~~A~g~l~al~~ 232 (330)
T PRK10355 155 SPVDNNAKLFRAGQMKVLKPYIDSGKIKVVGDQWVD-GWLPENALKIMENALTANNNKIDAVV-ASNDATAGGAIQALSA 232 (330)
T ss_pred CCCCccHHHHHHHHHHHHhhhccCCCeEEecccCCC-CCCHHHHHHHHHHHHHhCCCCccEEE-ECCCchHHHHHHHHHH
Confidence 2 23345567888888764 4 4432221111 112223334444443 2 2466544 4555667779999999
Q ss_pred cCCC
Q 003093 152 LGML 155 (848)
Q Consensus 152 ~g~~ 155 (848)
+|+.
T Consensus 233 ~g~~ 236 (330)
T PRK10355 233 QGLS 236 (330)
T ss_pred CCCC
Confidence 9985
No 276
>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=88.20 E-value=7.6 Score=37.27 Aligned_cols=102 Identities=11% Similarity=0.030 Sum_probs=70.4
Q ss_pred HHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhcc--CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEE
Q 003093 57 QYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK--RCRISFKAPLSVEATEDEITDLLVKVALTESRIIV 134 (848)
Q Consensus 57 ~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv 134 (848)
......+.+.+...++ ++.++..+.+ ..+.+...+++. |+.|+....-+ .+..+...+++.|++++||+|+
T Consensus 34 ~dl~~~l~~~~~~~~~-~ifllG~~~~----~~~~~~~~l~~~yP~l~ivg~~~g~--f~~~~~~~i~~~I~~~~pdiv~ 106 (172)
T PF03808_consen 34 SDLFPDLLRRAEQRGK-RIFLLGGSEE----VLEKAAANLRRRYPGLRIVGYHHGY--FDEEEEEAIINRINASGPDIVF 106 (172)
T ss_pred HHHHHHHHHHHHHcCC-eEEEEeCCHH----HHHHHHHHHHHHCCCeEEEEecCCC--CChhhHHHHHHHHHHcCCCEEE
Confidence 3446667777766664 7888876654 455666666665 67776543222 2457788899999999999999
Q ss_pred EEccCCcHHHHHHHHHHcCCCCCCeEEEecCccc
Q 003093 135 VHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLS 168 (848)
Q Consensus 135 ~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 168 (848)
+.+..+....++.+.++.. ... +|+..++..
T Consensus 107 vglG~PkQE~~~~~~~~~l--~~~-v~i~vG~~~ 137 (172)
T PF03808_consen 107 VGLGAPKQERWIARHRQRL--PAG-VIIGVGGAF 137 (172)
T ss_pred EECCCCHHHHHHHHHHHHC--CCC-EEEEECchh
Confidence 9999888888887777643 223 777776543
No 277
>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=88.14 E-value=25 Score=33.56 Aligned_cols=70 Identities=13% Similarity=0.036 Sum_probs=46.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++..++..++.+|++|+++.... .....+ .+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Di~i~~~~---~~~~~~-~~~~l~~~~~~~~~~~ 80 (197)
T cd08448 13 RGLPRILRAFRAEYP-GIEVALHE-------MSSAEQIEALLRGELDLGFVHSR---RLPAGL-SARLLHREPFVCCLPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe-------CCHHHHHHHHHcCCcceEEEeCC---CCCcCc-eEEEEecCcEEEEeeC
Confidence 455678888887764 23355443 45788999999999999986222 222223 2456777888888776
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~h 82 (197)
T cd08448 81 GH 82 (197)
T ss_pred CC
Confidence 54
No 278
>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=87.74 E-value=26 Score=33.39 Aligned_cols=70 Identities=19% Similarity=0.202 Sum_probs=45.4
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..+++..+.+..+ .+.+.... ++...+..+|.+|++|+++...... ...+. ..|.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~ 80 (197)
T cd08414 13 GLLPRLLRRFRARYP-DVELELRE-------MTTAEQLEALRAGRLDVGFVRPPPD---PPGLA-SRPLLREPLVVALPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHcCCccEEEEcCCCC---CCCee-EEEEeeccEEEEecC
Confidence 345667777777764 23344443 4467899999999999998633221 22222 466777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (197)
T cd08414 81 DH 82 (197)
T ss_pred CC
Confidence 54
No 279
>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=87.71 E-value=26 Score=33.85 Aligned_cols=72 Identities=19% Similarity=0.178 Sum_probs=46.8
Q ss_pred eeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEe
Q 003093 401 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 480 (848)
Q Consensus 401 ~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~ 480 (848)
..+-.+++..+.++.+ .+++.... ++...+...+.+|++|+++..-.. .....+. +.++....++++++
T Consensus 12 ~~~l~~~l~~f~~~~P-~~~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~ 80 (198)
T cd08443 12 RYVLPPVIKGFIERYP-RVSLQMHQ-------GSPTQIAEMVSKGLVDFAIATEAL--HDYDDLI-TLPCYHWNRCVVVK 80 (198)
T ss_pred eeECcHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHCCCccEEEEeccc--cccCCce-EeeeeeceEEEEEc
Confidence 3566778888887763 23344432 456789999999999999863211 1112232 46777888888887
Q ss_pred ccC
Q 003093 481 VRK 483 (848)
Q Consensus 481 ~~~ 483 (848)
...
T Consensus 81 ~~h 83 (198)
T cd08443 81 RDH 83 (198)
T ss_pred CCC
Confidence 655
No 280
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=87.30 E-value=20 Score=34.24 Aligned_cols=73 Identities=18% Similarity=0.124 Sum_probs=46.5
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeee--cCceeeeeecccccccceEEEE
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAII--TNRTKMADFTQPYIESGLVVVA 479 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t--~~R~~~~dfs~p~~~~~~~~v~ 479 (848)
.+-.+++..+.+..+ .+++.... ++...+..++.+|++|+++...... ......+ ...+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~ 83 (200)
T cd08423 13 ALLPPALAALRARHP-GLEVRLRE-------AEPPESLDALRAGELDLAVVFDYPVTPPPDDPGL-TRVPLLDDPLDLVL 83 (200)
T ss_pred HhhhHHHHHHHHhCC-CCeEEEEe-------CCHHHHHHHHhcCCccEEEEeccccccCCCCCCc-EEEEeccCcEEEEe
Confidence 345677788887764 33455543 3467889999999999998632110 1122222 35677788888888
Q ss_pred eccC
Q 003093 480 PVRK 483 (848)
Q Consensus 480 ~~~~ 483 (848)
+...
T Consensus 84 ~~~~ 87 (200)
T cd08423 84 PADH 87 (200)
T ss_pred cCCC
Confidence 7654
No 281
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=86.90 E-value=3.6 Score=44.55 Aligned_cols=92 Identities=10% Similarity=-0.010 Sum_probs=73.0
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
.+.+.+.++.+|++++-+|.+..-...+..+.+.+.|++.|+.+.....+.++.+.+.+...+..+++.++|.||-.+.+
T Consensus 17 l~~l~~~~~~~g~~r~liVTd~~~~~~g~~~~v~~~L~~~~i~~~if~~v~p~P~~~~v~~~~~~~~~~~~D~iIalGGG 96 (377)
T COG1454 17 LKELGEEVKRLGAKRALIVTDRGLAKLGLLDKVLDSLDAAGIEYEVFDEVEPEPTIETVEAGAEVAREFGPDTIIALGGG 96 (377)
T ss_pred HHHHHHHHHhcCCCceEEEECCccccchhHHHHHHHHHhcCCeEEEecCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 35666778889999999998777666778999999999999888777777777777888889999999999999987654
Q ss_pred --CcHHHHHHHHHH
Q 003093 140 --NRGPVVFHVAQY 151 (848)
Q Consensus 140 --~~~~~~~~~a~~ 151 (848)
-++...+.....
T Consensus 97 S~~D~AK~i~~~~~ 110 (377)
T COG1454 97 SVIDAAKAIALLAE 110 (377)
T ss_pred cHHHHHHHHHHHhh
Confidence 355555444443
No 282
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=86.55 E-value=11 Score=39.98 Aligned_cols=69 Identities=19% Similarity=0.161 Sum_probs=43.4
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..+++..+.++.+ .+++.... +....+...|.+|++|+++..-... ...+ ...|+.+..++++++.
T Consensus 105 ~~~~~~l~~~~~~~p-~i~l~~~~-------~~~~~~~~~l~~g~~Di~i~~~~~~---~~~~-~~~~l~~~~~~lv~~~ 172 (305)
T PRK11233 105 SLTMPLLQAVRAEFP-GIVLYLHE-------NSGATLNEKLMNGQLDMAVIYEHSP---VAGL-SSQPLLKEDLFLVGTQ 172 (305)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEE-------CCcHHHHHHHHCCCCCEEEEcCCcC---CCCc-EEEEEeeeeEEEEEcC
Confidence 344557788877763 33344433 3467889999999999998632211 1122 3457777888888775
Q ss_pred c
Q 003093 482 R 482 (848)
Q Consensus 482 ~ 482 (848)
+
T Consensus 173 ~ 173 (305)
T PRK11233 173 D 173 (305)
T ss_pred c
Confidence 4
No 283
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=86.41 E-value=19 Score=38.31 Aligned_cols=71 Identities=20% Similarity=0.333 Sum_probs=46.6
Q ss_pred eeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEecc
Q 003093 403 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 403 ~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
+-.+++..+.+... .+++.... ++..+++.+|.+|++|+++....... ....+ -..|+.+..+++++++.
T Consensus 111 ~l~~~l~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~~~l-~~~~l~~~~~~lv~~~~ 180 (312)
T PRK10341 111 FMSDMINKFKEVFP-KAQVSMYE-------AQLSSFLPAIRDGRLDFAIGTLSNEM-KLQDL-HVEPLFESEFVLVASKS 180 (312)
T ss_pred hHHHHHHHHHHhCC-CCEEEEEe-------CCHHHHHHHHHcCCCcEEEecCCccc-ccCCe-eEEEEecccEEEEEcCC
Confidence 44577777777654 34455543 45789999999999999986332111 11222 35677888889988765
Q ss_pred C
Q 003093 483 K 483 (848)
Q Consensus 483 ~ 483 (848)
.
T Consensus 181 ~ 181 (312)
T PRK10341 181 R 181 (312)
T ss_pred C
Confidence 4
No 284
>PRK15454 ethanol dehydrogenase EutG; Provisional
Probab=86.39 E-value=2.7 Score=46.43 Aligned_cols=80 Identities=10% Similarity=0.057 Sum_probs=61.0
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
.+.+.++++.+|.+++.++....-...+..+.+.+.|++.|+.+.....+.++.+.+++...+...++.++|+||-.+.+
T Consensus 37 ~~~l~~~~~~~g~~~~lvv~~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~P~~~~v~~~~~~~r~~~~D~IiavGGG 116 (395)
T PRK15454 37 VSSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLAVKGIAMTLWPCPVGEPCITDVCAAVAQLRESGCDGVIAFGGG 116 (395)
T ss_pred HHHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCcCEEEEeCCh
Confidence 35567788899988887776444344456788999999999987655455555566778889999999999999988765
No 285
>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=86.26 E-value=32 Score=32.93 Aligned_cols=70 Identities=19% Similarity=0.264 Sum_probs=44.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... +.-.++...|.+|++|+++..... ....+. ..++.+..++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~ 80 (196)
T cd08457 13 GFLPRFLAAFLRLRP-NLHLSLMG-------LSSSQVLEAVASGRADLGIADGPL---EERQGF-LIETRSLPAVVAVPM 80 (196)
T ss_pred cccHHHHHHHHHHCC-CeEEEEEe-------cCcHHHHHHHHcCCccEEEeccCC---CCCCcE-EEEeccCCeEEEeeC
Confidence 456678888888775 33444443 234688899999999999863322 122222 356667778877776
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (196)
T cd08457 81 GH 82 (196)
T ss_pred CC
Confidence 54
No 286
>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=86.19 E-value=3.3 Score=46.12 Aligned_cols=80 Identities=15% Similarity=0.094 Sum_probs=62.3
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
.+.+.++++.+|.+++.+++....+.....+.+.+.|++.|+++.....+....+.+.+...+..+++.++|+||-.+.+
T Consensus 11 ~~~l~~~l~~~g~~~vlivt~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (414)
T cd08190 11 TAEVGMDLKNLGARRVCLVTDPNLAQLPPVKVVLDSLEAAGINFEVYDDVRVEPTDESFKDAIAFAKKGQFDAFVAVGGG 90 (414)
T ss_pred HHHHHHHHHHcCCCeEEEEECcchhhcchHHHHHHHHHHcCCcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 35567778899999999998666555556788999999999887655455555566788888889999999999988655
No 287
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=86.18 E-value=21 Score=36.83 Aligned_cols=121 Identities=14% Similarity=0.093 Sum_probs=64.2
Q ss_pred CCCCChHHhhcCCCCeeEEeCchHHHH---HHhhhCCC--------------------ccCcccCCCHHHHHHHhhcCCC
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNSFARNY---LVDELNID--------------------ESRLVPLNSPEEYAKALKDGPH 646 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s~~~~~---l~~~~~~~--------------------~~~~~~~~~~~~~~~~l~~~~~ 646 (848)
.++++++||.+ |.+|++..+...... +.+..+.. ..+++++ ...+...++.+
T Consensus 106 ~~~~sl~dlk~-G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel-~~~~~~~al~~--- 180 (258)
T TIGR00363 106 KKIKNVNELQD-GAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITEL-ETSQLPRALDD--- 180 (258)
T ss_pred cCCCCHHHcCC-CCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEc-CHHHHHHHhhc---
Confidence 68999999953 788999866432222 11332221 1233334 34456678877
Q ss_pred CCceEEEEccHHHHHHHHhcC-CcEEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccCchHHHHHhh
Q 003093 647 KGGVAAVVDDRAYAELFLSTR-CEFSIVGQVFTKNGWGFAFPRDSPLAVDISTAILKLSENGDLQRIHDKW 716 (848)
Q Consensus 647 ~~~~~a~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~G~~~~~~~kw 716 (848)
|.+|+.+...+++.-..... .+-......-.++--.++++.+.-=.+.+...+..+.....-+.|.++|
T Consensus 181 -g~vDaa~v~~~~~~~agl~~~~~~i~~e~~~~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 250 (258)
T TIGR00363 181 -PKVDLAVINTTYAGQVGLNPQDDGVFVEDKDSPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQKHF 250 (258)
T ss_pred -ccccEEEEChHHHHHcCCCcCcCceeecCCCCCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 88999888877654331111 1111222111122235566655334555666666666554444454543
No 288
>KOG3857 consensus Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=86.09 E-value=4.9 Score=41.73 Aligned_cols=96 Identities=9% Similarity=0.000 Sum_probs=76.6
Q ss_pred CCCceEeccCChHHHHHHHH----HHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHH
Q 003093 45 QFPYFVRTTQSDQYQMAAIA----EIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITD 120 (848)
Q Consensus 45 ~~p~f~r~~p~d~~q~~ai~----~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~ 120 (848)
.-+|-|-+.|+....+++.. .-++..|.|++.++.+.+.--....+..++.|+++|+++.....+.+..+...+..
T Consensus 39 ~~~~af~m~~s~~rfG~gv~~Evg~dikn~gaKk~llvTDkni~~~~~~~~a~~~L~~~~I~~~vyD~v~~ePtv~s~~~ 118 (465)
T KOG3857|consen 39 MMSVAFFMIPSTSRFGKGVLAEVGDDIKNLGAKKTLLVTDKNIAKLGLVKVAQDSLEENGINVEVYDKVQPEPTVGSVTA 118 (465)
T ss_pred cceeeEEeccchhhhcchhHHHHHHHHHhcCccceEEeeCCChhhcccHHHHHHHHHHcCCceEEecCccCCCchhhHHH
Confidence 34677777787777665433 33789999999999877776677788999999999999987777777677788999
Q ss_pred HHHHHhcCCCeEEEEEccCC
Q 003093 121 LLVKVALTESRIIVVHTHYN 140 (848)
Q Consensus 121 ~l~~i~~~~~~viv~~~~~~ 140 (848)
.|.-+|..+.|.+|..+.+.
T Consensus 119 alefak~~~fDs~vaiGGGS 138 (465)
T KOG3857|consen 119 ALEFAKKKNFDSFVAIGGGS 138 (465)
T ss_pred HHHHHHhcccceEEEEcCcc
Confidence 99999999999999876653
No 289
>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=85.94 E-value=30 Score=33.04 Aligned_cols=70 Identities=13% Similarity=0.074 Sum_probs=45.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..+++..+.+..+ .+++.... +....+++++.+|++|+++...... ...+ -+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 80 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHT-------RDSPTVEQWLSAQQCDLGLVSTLHE---PPGI-ERERLLRIDGVCVLPP 80 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEecCCC---CCCe-eEEEeeccCeEEEecC
Confidence 455678888888774 33455543 4467889999999999998632211 1222 2456677788888776
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (196)
T cd08456 81 GH 82 (196)
T ss_pred CC
Confidence 54
No 290
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=85.76 E-value=28 Score=37.40 Aligned_cols=84 Identities=15% Similarity=0.088 Sum_probs=55.0
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
+.||||+... . ...+-.++++.+.++.+ .+.+.... +...+++++|.+|++|+++....
T Consensus 93 g~lrIg~~~~--~-----------~~~~l~~~l~~f~~~~P-~v~i~l~~-------~~~~~~~~~l~~g~~Dl~i~~~~ 151 (327)
T PRK12680 93 GQLTLTTTHT--Q-----------ARFVLPPAVAQIKQAYP-QVSVHLQQ-------AAESAALDLLGQGDADIAIVSTA 151 (327)
T ss_pred eEEEEEecch--h-----------HHHhhHHHHHHHHHHCC-CcEEEEEe-------CChHHHHHHHHCCCCcEEEEecC
Confidence 5789998741 1 12455678888888776 23344443 45789999999999999986321
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.. ...... ..|+....++++++...
T Consensus 152 ~~--~~~~~~-~~~l~~~~~~l~~~~~h 176 (327)
T PRK12680 152 GG--EPSAGI-AVPLYRWRRLVVVPRGH 176 (327)
T ss_pred CC--CCCcce-EEEeeccceEEEEeCCC
Confidence 11 111222 46788888888888665
No 291
>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=85.46 E-value=3.8 Score=45.00 Aligned_cols=88 Identities=7% Similarity=-0.050 Sum_probs=64.9
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
..+.++++.+|.+++.+++....+-....+.+.+.|++.|+++.....+....+.+++...+...+..++|+||-.+.+
T Consensus 13 ~~l~~~l~~~g~~~~liv~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS 92 (370)
T cd08192 13 KELPAECAELGIKRPLIVTDPGLAALGLVARVLALLEDAGLAAALFDEVPPNPTEAAVEAGLAAYRAGGCDGVIAFGGGS 92 (370)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 4567778889999998887555444446788999999999887655455555666788899999999999999977554
Q ss_pred -CcHHHHHHH
Q 003093 140 -NRGPVVFHV 148 (848)
Q Consensus 140 -~~~~~~~~~ 148 (848)
-++.+++..
T Consensus 93 viD~aK~ia~ 102 (370)
T cd08192 93 ALDLAKAVAL 102 (370)
T ss_pred HHHHHHHHHH
Confidence 455544443
No 292
>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=85.17 E-value=36 Score=32.86 Aligned_cols=70 Identities=13% Similarity=0.058 Sum_probs=45.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.. .+++.... ++...++++|.+|++|+++.... . ....++ +.+..+..++++++.
T Consensus 14 ~~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~l~~~l~~g~~D~~~~~~~--~-~~~~~~-~~~l~~~~~~lv~~~ 81 (198)
T cd08486 14 RSLPLLLRAFLTSTP-TATVSLTH-------MTKDEQVEGLLAGTIHVGFSRFF--P-RHPGIE-IVNIAQEDLYLAVHR 81 (198)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEE-------CCHHHHHHHHHcCCceEEEecCC--C-CCCceE-EEEEeeccEEEEecC
Confidence 445677777777763 33344443 46889999999999999986321 1 122232 456667788888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~h 83 (198)
T cd08486 82 SQ 83 (198)
T ss_pred CC
Confidence 54
No 293
>PRK10624 L-1,2-propanediol oxidoreductase; Provisional
Probab=84.61 E-value=4 Score=44.97 Aligned_cols=80 Identities=10% Similarity=0.094 Sum_probs=60.5
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
...+.+.++.+|.+++.+++...-+-.+..+.+.+.|++.|+++.....+....+.+++...+..+++.++|+||-.+.+
T Consensus 18 l~~l~~~~~~~g~~~~lvvtd~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 97 (382)
T PRK10624 18 IGALTDEVKRRGFKKALIVTDKTLVKCGVVAKVTDVLDAAGLAYEIYDGVKPNPTIEVVKEGVEVFKASGADYLIAIGGG 97 (382)
T ss_pred HHHHHHHHHhcCCCEEEEEeCcchhhCcchHHHHHHHHHCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCh
Confidence 35577788889999998887554444447788999999999887654445555556788888889999999999977554
No 294
>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=84.24 E-value=12 Score=37.36 Aligned_cols=70 Identities=7% Similarity=-0.071 Sum_probs=38.7
Q ss_pred ccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEEEeCCc-cccCCceeeecCCCCchHHHHHHHHhh
Q 003093 629 VPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQV-FTKNGWGFAFPRDSPLAVDISTAILKL 703 (848)
Q Consensus 629 ~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~k~spl~~~in~~i~~l 703 (848)
....+..+..+.+.+ |++++.+......... ........+++. .....+++++.|+++-.+.-.+.|..|
T Consensus 133 ~~~~~~~~~~~~~~~----Ge~~~~~~~~~~~~~~-~~~~~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl 203 (216)
T TIGR01256 133 VYGEDVRQALQFVET----GNAPAGIVALSDVIPS-KKVGSVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYL 203 (216)
T ss_pred eecCcHHHHHHHHHc----CCCCEEeeehhhhccc-CCccEEEEeCccccCCccccEEEEECCCChHHHHHHHHHH
Confidence 334466778888888 8888776644322111 122333344443 233456889989887544444444333
No 295
>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=84.22 E-value=4.9 Score=44.14 Aligned_cols=87 Identities=7% Similarity=0.001 Sum_probs=64.7
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
+.+.++++.++.+++.+++....+-....+.+.+.|++.|+++.....+....+.+++...+..++..++|+||..+.+
T Consensus 12 ~~l~~~l~~~~~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IiaiGGGs 91 (370)
T cd08551 12 EKLGEEIKNLGGRKALIVTDPGLVKTGVLDKVIDSLKEAGIEVVIFDGVEPNPTLSNVDAAVAAYREEGCDGVIAVGGGS 91 (370)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 5667778888999999988655444467788999999999887654455555566889999999998999999977654
Q ss_pred -CcHHHHHH
Q 003093 140 -NRGPVVFH 147 (848)
Q Consensus 140 -~~~~~~~~ 147 (848)
-+..+++.
T Consensus 92 ~~D~AK~va 100 (370)
T cd08551 92 VLDTAKAIA 100 (370)
T ss_pred HHHHHHHHH
Confidence 34444443
No 296
>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=84.14 E-value=4.7 Score=44.26 Aligned_cols=89 Identities=8% Similarity=0.022 Sum_probs=65.2
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
.+.+.+.++.+|-+++.+++....+..+..+.+.+.|++.|+.+.....+....+.+++...+..+++.++|+||..+.+
T Consensus 14 l~~l~~~l~~~g~~~~lvvt~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 93 (374)
T cd08189 14 LAQLPAAISQLGVKKVLIVTDKGLVKLGLLDKVLEALEGAGIEYAVYDGVPPDPTIENVEAGLALYRENGCDAILAVGGG 93 (374)
T ss_pred HHHHHHHHHhcCCCeEEEEeCcchhhcccHHHHHHHHHhcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 34567778888888998887554443446788999999999887655556555666888899999999999999977554
Q ss_pred --CcHHHHHHH
Q 003093 140 --NRGPVVFHV 148 (848)
Q Consensus 140 --~~~~~~~~~ 148 (848)
-++.+++..
T Consensus 94 S~~D~aK~ia~ 104 (374)
T cd08189 94 SVIDCAKAIAA 104 (374)
T ss_pred cHHHHHHHHHH
Confidence 345544433
No 297
>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=84.02 E-value=40 Score=32.13 Aligned_cols=71 Identities=20% Similarity=0.147 Sum_probs=46.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .++++... ++...++.++.+|++|+++...... ....+. ..++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~l~-~~~l~~~~~~~~~~~ 81 (199)
T cd08430 13 SFLPPILERFRAQHP-QVEIKLHT-------GDPADAIDKVLNGEADIAIAARPDK--LPARLA-FLPLATSPLVFIAPN 81 (199)
T ss_pred eeccHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHCCCCCEEEEecCCC--CCcccE-EEeeccceEEEEEeC
Confidence 556778888888874 23354443 4578899999999999998632211 112232 456677778888776
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~~ 83 (199)
T cd08430 82 IA 83 (199)
T ss_pred Cc
Confidence 54
No 298
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=84.02 E-value=2.2 Score=44.94 Aligned_cols=215 Identities=13% Similarity=0.094 Sum_probs=114.4
Q ss_pred eeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEe
Q 003093 401 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 480 (848)
Q Consensus 401 ~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~ 480 (848)
.++ ..+.+.+.++.|-++.++..+.|. -+.-.++++.|..|.+||+.........+..
T Consensus 13 ~~~-~~fa~~v~e~t~G~v~i~v~~~g~---lg~~~e~~~~v~~G~vdm~~~~~~~~~~~~p------------------ 70 (286)
T PF03480_consen 13 QAV-EKFAEEVEERTGGRVKIEVFPAGQ---LGKEAEVLEAVQDGAVDMAVVSPSYLAGFVP------------------ 70 (286)
T ss_dssp HHH-HHHHHHHHHHTTTSEEEEEEETTS---SSSHHHHHHHHHTTSSSEEEEEGGGGTTTSG------------------
T ss_pred HHH-HHHHHHHHHHcCCeEEEEEecCcc---cCCHHHHHHHHhCCCccEEeecchhhhhhch------------------
Confidence 344 677889999999998888877332 2457799999999999999874433333221
Q ss_pred ccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcchhhhhHHHHhhhcCccccccchhHHH
Q 003093 481 VRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMFFAHKEKTVSALGRLV 560 (848)
Q Consensus 481 ~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~s~~~R~~ 560 (848)
.+..+..||-..----+-. +.-+. ..+.+
T Consensus 71 ------~~~~~~lP~~~~~~~~~~~--~~~~~-------------------------------------------~~~~l 99 (286)
T PF03480_consen 71 ------EFGVFDLPFLFRDYEELDR--VMDSG-------------------------------------------YGPEL 99 (286)
T ss_dssp ------GGGGGGSTTTSSSHHHHHH--HHHSH-------------------------------------------HHHHH
T ss_pred ------hheeeeCCCCCCCHHHHHH--HHhCc-------------------------------------------HHHHH
Confidence 1222222321110000000 00000 00000
Q ss_pred HHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCchHHHHHHhhhCCCccCcccCCCHHHHHHH
Q 003093 561 LIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKA 640 (848)
Q Consensus 561 ~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 640 (848)
.--.---.+.+...|......+.+ ...+|++++||. |+++.+..+.....++ +.++.. .+.. ...|...+
T Consensus 100 ~~~~~~~g~~~L~~~~~g~~~~~~---~~~pi~s~~Dlk--G~kiR~~~~~~~~~~~-~~lGa~---pv~i-p~~evy~a 169 (286)
T PF03480_consen 100 REELEEKGIKLLGWFPGGPRQFFS---TKKPIRSPEDLK--GLKIRVPGSPVMSDFF-EALGAS---PVPI-PWSEVYQA 169 (286)
T ss_dssp HHHHHHTTEEEEEEEEEEEEEEEE---SSS--SSGGGGT--TEEEEETSSHHHHHHH-HHCTSE---EEE--TGGGHHHH
T ss_pred HHHHHhhceEEEEEecCCceEEEe---cccCCccHhhHh--hCeEEecCCHHHHHHH-HHcCCe---eecC-cHHHHHHH
Confidence 000011122233334444444444 236899999998 8888887566566666 344422 2223 55688999
Q ss_pred hhcCCCCCceEEEEccHHHHHHH-HhcCCcEEEeCCccccCCceeeecCCCC--chHHHHHHHHhh
Q 003093 641 LKDGPHKGGVAAVVDDRAYAELF-LSTRCEFSIVGQVFTKNGWGFAFPRDSP--LAVDISTAILKL 703 (848)
Q Consensus 641 l~~~~~~~~~~a~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~k~sp--l~~~in~~i~~l 703 (848)
|++ |.+|+........... +.+-+++..... ....++.+++.++.- |-+....+|.+.
T Consensus 170 Lq~----G~vDg~~~~~~~~~~~~~~ev~~y~~~~~-~~~~~~~~~~n~~~w~~L~~e~q~~l~~~ 230 (286)
T PF03480_consen 170 LQQ----GVVDGAENSASSIYSLGLYEVAKYFTDTN-HGWSPYAVIMNKDWWDSLPDEDQEALDDA 230 (286)
T ss_dssp HHT----TSSSEEEEEHHHHHHTTGGGTSSEEEEEE-EEEEEEEEEEEHHHHHHS-HHHHHHHHHH
T ss_pred Hhc----CCcCeEecCHHHHHhcChhhhCCeeEeec-ccCcceEEEEcHHHHhcCCHHHHHHHHHH
Confidence 999 8999998877655221 122355554443 444566777776532 444444444333
No 299
>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=83.98 E-value=4.5 Score=44.51 Aligned_cols=87 Identities=10% Similarity=0.051 Sum_probs=64.3
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
..+.++++.++.+++.+++...-...+..+.+.+.|++.|+++.....+....+.+++...+..+++.++|+||-.+.+
T Consensus 15 ~~l~~~l~~~~~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGs 94 (376)
T cd08193 15 ARLGELLAALGAKRVLVVTDPGILKAGLIDPLLASLEAAGIEVTVFDDVEADPPEAVVEAAVEAARAAGADGVIGFGGGS 94 (376)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 4566778888999998887554334456788999999999887655555555667888999999999999999988655
Q ss_pred -CcHHHHHH
Q 003093 140 -NRGPVVFH 147 (848)
Q Consensus 140 -~~~~~~~~ 147 (848)
-++.+++.
T Consensus 95 ~iD~aK~ia 103 (376)
T cd08193 95 SMDVAKLVA 103 (376)
T ss_pred HHHHHHHHH
Confidence 34444443
No 300
>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=83.75 E-value=3.2 Score=42.71 Aligned_cols=78 Identities=10% Similarity=0.086 Sum_probs=59.9
Q ss_pred EEEEE--EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEc-cCCcHHHHHHHHHH
Q 003093 75 VIAIY--VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT-HYNRGPVVFHVAQY 151 (848)
Q Consensus 75 vaii~--~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~-~~~~~~~~~~~a~~ 151 (848)
|+++. .++.|.......+.+++++.|.++... .+...+.......++++.+.++|.|++.. .+.....+++++++
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 45555 445688888999999999999998765 33333456667778888888999998874 45667789999999
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|+
T Consensus 79 ~gI 81 (257)
T PF13407_consen 79 AGI 81 (257)
T ss_dssp TTS
T ss_pred cCc
Confidence 987
No 301
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=83.32 E-value=17 Score=38.65 Aligned_cols=84 Identities=8% Similarity=0.123 Sum_probs=54.2
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
+..++||+... ...++-.+++..+.+..+ .+.+.... ++...++.+|.+|++|+++...
T Consensus 111 ~~~i~i~~~~~-------------~~~~~l~~~l~~f~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Di~i~~~ 169 (314)
T PRK09508 111 ERVFNLCICSP-------------LDIRLTSQIYNRIEQIAP-NIHVVFKS-------SLNQNIEHQLRYQETEFVISYE 169 (314)
T ss_pred ccEEEEEechh-------------HHHHHHHHHHHHHHHhCC-CcEEEEEe-------CcchhHHHHHhcCCccEEEecC
Confidence 45788887521 012466788888888764 22344443 4467889999999999999743
Q ss_pred eeecCceeeeeecccccccceEEEEeccC
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.. ....+. ..++....++++++...
T Consensus 170 ~~---~~~~l~-~~~l~~~~~~lv~~~~h 194 (314)
T PRK09508 170 EF---DRPEFT-SVPLFKDELVLVASKNH 194 (314)
T ss_pred CC---Cccccc-eeeeecCceEEEEcCCC
Confidence 22 122233 34677788888887665
No 302
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=83.27 E-value=33 Score=36.25 Aligned_cols=85 Identities=13% Similarity=0.036 Sum_probs=51.5
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..++||+... . ...+..+++..+.++.. .+.+.... ++..+++.+|.+|++|++++...
T Consensus 92 g~l~Ig~~~~--~-----------~~~~l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~ 150 (300)
T PRK11074 92 GQLSIAVDNI--V-----------RPDRTRQLIVDFYRHFD-DVELIIRQ-------EVFNGVWDALADGRVDIAIGATR 150 (300)
T ss_pred ceEEEEEcCc--c-----------chhHHHHHHHHHHHhCC-CceEEEEe-------hhhhHHHHHHHCCCCCEEEecCc
Confidence 5789998631 1 12344567777776665 23344433 44678999999999999997322
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.. .....+ -..+.....+++++++..
T Consensus 151 ~~-~~~~~l-~~~~l~~~~~~~v~~~~h 176 (300)
T PRK11074 151 AI-PVGGRF-AFRDMGMLSWACVVSSDH 176 (300)
T ss_pred cC-Cccccc-ceeecccceEEEEEcCCC
Confidence 11 111112 245667777888887655
No 303
>cd08194 Fe-ADH6 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions.
Probab=83.11 E-value=5.4 Score=43.81 Aligned_cols=79 Identities=9% Similarity=0.053 Sum_probs=61.4
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
..+.++++.++.+++.+|+....+..+..+.+.+.|++.|+++.....+....+..++...+..++..++|+||-.+.+
T Consensus 12 ~~l~~~~~~~~~~r~livt~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (375)
T cd08194 12 DETGAVLADLGGKRPLIVTDKVMVKLGLVDKLTDSLKKEGIESAIFDDVVSEPTDESVEEGVKLAKEGGCDVIIALGGG 90 (375)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhcchHHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4556677777889999998555554446788999999999987655556666667888999999999999999987654
No 304
>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=82.40 E-value=49 Score=31.89 Aligned_cols=70 Identities=20% Similarity=0.261 Sum_probs=46.1
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
++..+++..+.++.+ .+++.... ++..+++.++.+|++|++++..... ...+. ..|.....+++++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~ 81 (203)
T cd08445 14 GLLPELIRRFRQAAP-DVEIELIE-------MTTVQQIEALKEGRIDVGFGRLRIE---DPAIR-RIVLREEPLVVALPA 81 (203)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHcCCCcEEEecCCCC---CCCce-eEEEEeccEEEEeeC
Confidence 566777888877764 23344443 3477899999999999998632211 12232 456777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~h 83 (203)
T cd08445 82 GH 83 (203)
T ss_pred CC
Confidence 54
No 305
>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=81.99 E-value=25 Score=34.45 Aligned_cols=102 Identities=20% Similarity=0.202 Sum_probs=62.1
Q ss_pred CCCCChHHhhcCCCCe-eEEeCchHHHHHHhhh---CCCccCcc----cCCCHHHHHHHhhcCCCCCceEEEEccHHHHH
Q 003093 590 SPIKGIDSLRSSNYPI-GYQVNSFARNYLVDEL---NIDESRLV----PLNSPEEYAKALKDGPHKGGVAAVVDDRAYAE 661 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i-~~~~~s~~~~~l~~~~---~~~~~~~~----~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~ 661 (848)
..|.+++||.+.+.++ .=+.||-...+|...+ +.....+. ...+..+...++.. |..|+-+......+
T Consensus 81 ~~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~----G~AD~G~g~~~~A~ 156 (193)
T PF12727_consen 81 KGITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVAS----GKADAGIGIRAAAE 156 (193)
T ss_pred ccCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHc----CCCCEEeehHHHHH
Confidence 4799999998666653 3346777777665433 22322233 34677788888988 88888887655543
Q ss_pred HHHhcCCcEEEeCCccccCCceeeecCCCCchHHHHHHHH
Q 003093 662 LFLSTRCEFSIVGQVFTKNGWGFAFPRDSPLAVDISTAIL 701 (848)
Q Consensus 662 ~~~~~~~~l~~~~~~~~~~~~~~~~~k~spl~~~in~~i~ 701 (848)
-+ ..-++.-+ ....|-+++++..-..+.+.+.|.
T Consensus 157 ~~--~gL~Fvpl----~~E~~dlv~~~~~~~~~~vq~ll~ 190 (193)
T PF12727_consen 157 EF--YGLDFVPL----AEERYDLVIRREDLEDPAVQALLD 190 (193)
T ss_pred hh--cCCCcEEc----cccceEEEEEhhHcCCHHHHHHHH
Confidence 11 11133333 335677888887655555555543
No 306
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=81.92 E-value=53 Score=34.85 Aligned_cols=70 Identities=7% Similarity=0.075 Sum_probs=45.0
Q ss_pred eHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEeccC
Q 003093 404 CIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 404 ~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
-.+++..+.++.+- +++.... ++-.++.+.|.+|++|++++ +.........+. ..+.....++++++...
T Consensus 108 l~~~l~~~~~~~P~-i~l~l~~-------~~~~~~~~~l~~g~~D~~i~-~~~~~~~~~~l~-~~~l~~~~~~~v~~~~h 177 (308)
T PRK10094 108 VAQLLAWLNERYPF-TQFHISR-------QIYMGVWDSLLYEGFSLAIG-VTGTEALANTFS-LDPLGSVQWRFVMAADH 177 (308)
T ss_pred HHHHHHHHHHhCCC-cEEEEEe-------ehhhhHHHHHhCCCccEEEe-cccCccccCCee-EEEecceeEEEEECCCC
Confidence 45778888877754 3454443 34678899999999999987 221111122232 45777788888887654
No 307
>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=81.84 E-value=6 Score=43.55 Aligned_cols=80 Identities=9% Similarity=0.055 Sum_probs=60.1
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
...+.+.++.+|.+++.+++.....-.+..+.+.+.|++.|+++.....+....+.+++...+..+++.++|+||..+.+
T Consensus 17 l~~l~~~l~~~g~~r~lvvt~~~~~~~g~~~~v~~~L~~~~i~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiaiGGG 96 (379)
T TIGR02638 17 IEDIVDEVKRRGFKKALVVTDKDLIKFGVADKVTDLLDEAGIAYELFDEVKPNPTITVVKAGVAAFKASGADYLIAIGGG 96 (379)
T ss_pred HHHHHHHHHhcCCCEEEEEcCcchhhccchHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCh
Confidence 34566778889999998888544333346788999999999887655445555566788888889999999999977654
No 308
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=81.70 E-value=21 Score=37.06 Aligned_cols=120 Identities=14% Similarity=0.136 Sum_probs=59.9
Q ss_pred CCCCChHHhhcCCCCeeEEeCc-hHHHHH--HhhhCC--------------------CccCcccCCCHHHHHHHhhcCCC
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNS-FARNYL--VDELNI--------------------DESRLVPLNSPEEYAKALKDGPH 646 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s-~~~~~l--~~~~~~--------------------~~~~~~~~~~~~~~~~~l~~~~~ 646 (848)
..|+|++||.. |++|++.... .....+ .+..+. ...++++. ...+...++.+
T Consensus 119 ~~i~si~DL~~-Gk~IAip~d~~n~~r~L~lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~-~~~~~~~al~~--- 193 (271)
T PRK11063 119 KKIKSLDELQD-GSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVEL-EAPQLPRSLDD--- 193 (271)
T ss_pred cCCCCHHHhcC-CCEEEecCCCccHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEEC-cHHHHHHhccc---
Confidence 57999999963 7889988522 111111 122111 11233333 45566777777
Q ss_pred CCceEEEEccHHHHHHHHhcC-CcEEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccCchHHHHHh
Q 003093 647 KGGVAAVVDDRAYAELFLSTR-CEFSIVGQVFTKNGWGFAFPRDSPLAVDISTAILKLSENGDLQRIHDK 715 (848)
Q Consensus 647 ~~~~~a~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~G~~~~~~~k 715 (848)
|.+|+.+...++..-...+. .+-......-.++--.+++++...=.+.+...+.-++....-+.|.++
T Consensus 194 -g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~~~~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~~ 262 (271)
T PRK11063 194 -AQIALAVINTTYASQIGLTPAKDGIFVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANKV 262 (271)
T ss_pred -ccccEEEEChHHHHHcCCCCCCCeeEECCCCCCeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence 88999998888776432222 122222221112223456665533334444444434433333344444
No 309
>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=81.38 E-value=7.4 Score=42.87 Aligned_cols=85 Identities=6% Similarity=-0.015 Sum_probs=62.5
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCC-ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDH-GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~-g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
..+.++++.+| +++.+|+....+ .....+.+.+.|++.|+++.....+.+..+.+++...+..+++.++|+||-.+.+
T Consensus 15 ~~l~~~~~~~g-~r~livt~~~~~~~~g~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiavGGG 93 (380)
T cd08185 15 NELGEEALKPG-KKALIVTGNGSSKKTGYLDRVIELLKQAGVEVVVFDKVEPNPTTTTVMEGAALAREEGCDFVVGLGGG 93 (380)
T ss_pred HHHHHHHHhcC-CeEEEEeCCCchhhccHHHHHHHHHHHcCCeEEEeCCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCc
Confidence 45666777788 899888855442 4567788999999999987655556555666888888899999999999977654
Q ss_pred --CcHHHHH
Q 003093 140 --NRGPVVF 146 (848)
Q Consensus 140 --~~~~~~~ 146 (848)
-++.+.+
T Consensus 94 S~iD~aK~i 102 (380)
T cd08185 94 SSMDTAKAI 102 (380)
T ss_pred cHHHHHHHH
Confidence 3444444
No 310
>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=80.67 E-value=44 Score=34.72 Aligned_cols=133 Identities=10% Similarity=0.032 Sum_probs=68.6
Q ss_pred HhhccCCccEEecccCCCCCCCCCCC-ceEeccCChHHHHHHHHHHHHHc--CcEEEEEEEEcCC-Ccc---chHHHHHH
Q 003093 22 HVANELQVPLLSFSATDPTLSSLQFP-YFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDDD-HGR---NGIAALGD 94 (848)
Q Consensus 22 ~i~~~~~vP~Is~~at~p~ls~~~~p-~f~r~~p~d~~q~~ai~~~~~~~--~w~~vaii~~dd~-~g~---~~~~~l~~ 94 (848)
..+.+.++|+|.+....+. .....+ .+-.+..++...+..+++++... |-++++++...+. ... ...+.+.+
T Consensus 75 ~~~~~~~iPvV~~d~~~~~-~~~~~~~~~~~v~~D~~~~~~~~~~~L~~~~~G~~~i~~i~~~~~~~~~~r~~~~~~~~~ 153 (280)
T cd06315 75 ELAQKAGIPVVGWHAGPEP-GPIEEPGIFYNVTTDPLAVAEVAALYAIANSGGKAGVVIFTDSRFSIAKAKANAMKEIIE 153 (280)
T ss_pred HHHHHCCCCEEEecCCCCC-CcccCCceeEEecCCHHHHHHHHHHHHHHHcCCCceEEEEeCCCCccHHHHHHHHHHHHH
Confidence 3345689999987553211 000011 13345566777778888887665 8899998863321 111 23344444
Q ss_pred HHhccCcEEEEeeecCCCCChHHHHHHHHHHhc---CCCeEEEEEccCCcHHHHHHHHHHcCCCCCC
Q 003093 95 TLAAKRCRISFKAPLSVEATEDEITDLLVKVAL---TESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 158 (848)
Q Consensus 95 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~---~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~ 158 (848)
++++.++ ..................++++.+ ..+++|+ +++...+..+++.+++.|+..++
T Consensus 154 a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~-~~~D~~A~g~~~~l~~~g~~~p~ 217 (280)
T cd06315 154 ACKGCTV--LSIEDVPISRTATRMPALTARLLQRYGDKWTHSL-AINDLYFDYMAPPLASAGRKADE 217 (280)
T ss_pred hCCCCEE--EEecccCcchhhhhhHHHHHHHHHhcCcccceec-ccchhhhHHhHHHHHHhcccCCC
Confidence 4443343 111111111111111133344432 2356544 44555677789999999986543
No 311
>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=80.46 E-value=4 Score=44.72 Aligned_cols=89 Identities=8% Similarity=0.037 Sum_probs=67.3
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
+.+.+.++.+| ++.+|+...-......+.+.+.|++.|+++.....+....+..++...+..++..++|+||..+.+
T Consensus 12 ~~l~~~l~~~g--r~lvVt~~~~~~~~~~~~v~~~L~~~~i~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 89 (366)
T PF00465_consen 12 EELGEELKRLG--RVLVVTDPSLSKSGLVDRVLDALEEAGIEVQVFDGVGPNPTLEDVDEAAEQARKFGADCIIAIGGGS 89 (366)
T ss_dssp GGHHHHHHCTT--EEEEEEEHHHHHHTHHHHHHHHHHHTTCEEEEEEEESSS-BHHHHHHHHHHHHHTTSSEEEEEESHH
T ss_pred HHHHHHHHhcC--CEEEEECchHHhCccHHHHHHHHhhCceEEEEEecCCCCCcHHHHHHHHHHHHhcCCCEEEEcCCCC
Confidence 45667788887 999998663333447899999999999999777777777778999999999999999999988664
Q ss_pred -CcHHHHHHHHHH
Q 003093 140 -NRGPVVFHVAQY 151 (848)
Q Consensus 140 -~~~~~~~~~a~~ 151 (848)
-++.+++..+..
T Consensus 90 ~~D~aK~va~~~~ 102 (366)
T PF00465_consen 90 VMDAAKAVALLLA 102 (366)
T ss_dssp HHHHHHHHHHHHT
T ss_pred cCcHHHHHHhhcc
Confidence 344455544443
No 312
>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=80.38 E-value=7.9 Score=42.55 Aligned_cols=80 Identities=8% Similarity=0.010 Sum_probs=59.7
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
...+.++++.+|.+++.+++.....-....+.+.+.|++.|+.+.....+....+..++...+..++..++|+||..+.+
T Consensus 16 l~~l~~~l~~~g~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 95 (377)
T cd08188 16 LKLAGRYARRLGAKKVLLVSDPGVIKAGWVDRVIESLEEAGLEYVVFSDVSPNPRDEEVMAGAELYLENGCDVIIAVGGG 95 (377)
T ss_pred HHHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 35567778888989999887544333346788999999999877654445445556778888889998999999987654
No 313
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=79.86 E-value=43 Score=35.27 Aligned_cols=86 Identities=12% Similarity=0.181 Sum_probs=50.8
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..||||+... . ..++-.+++..+.+..+ .+++.... ++...+..+|.+|++|+++....
T Consensus 93 g~l~i~~~~~--~-----------~~~~l~~~l~~f~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~ 151 (296)
T PRK11062 93 LLFDVGVADA--L-----------SKRLVSRVLLTAVPEDE-SIHLRCFE-------STHEMLLEQLSQHKLDMILSDCP 151 (296)
T ss_pred eEEEEEecch--h-----------hHhhHHHHHHHHHhcCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEecCC
Confidence 4689888631 1 23566677777766553 33344432 45788999999999999986322
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
........+ ...|+....++++++.+.
T Consensus 152 ~~~~~~~~l-~~~~l~~~~~~~~~~~~~ 178 (296)
T PRK11062 152 VDSTQQEGL-FSKKLGECGVSFFCTNPL 178 (296)
T ss_pred Cccccccch-hhhhhhccCcceEecCCC
Confidence 111111222 245666777777665543
No 314
>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=79.86 E-value=22 Score=37.50 Aligned_cols=127 Identities=11% Similarity=0.195 Sum_probs=69.2
Q ss_pred CeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC----CCCC--ceEeccCChHHHHHHHHHHHHHc--CcEEE
Q 003093 4 QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS----LQFP--YFVRTTQSDQYQMAAIAEIVDHY--GWREV 75 (848)
Q Consensus 4 ~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~----~~~p--~f~r~~p~d~~q~~ai~~~~~~~--~w~~v 75 (848)
+.+.|+-- .+..+.+++...... +|++-.+-++|.-.. ...| ++.=+. +........++++++ +-+++
T Consensus 59 ~~DlIi~~-gt~aa~~~~~~~~~~-iPVVf~~V~dp~~~~l~~~~~~~~~nvTGv~--~~~~~~~~l~l~~~l~P~~k~i 134 (294)
T PF04392_consen 59 KPDLIIAI-GTPAAQALAKHLKDD-IPVVFCGVSDPVGAGLVDSLDRPGKNVTGVS--ERPPIEKQLELIKKLFPDAKRI 134 (294)
T ss_dssp S-SEEEEE-SHHHHHHHHHH-SS--S-EEEECES-TTTTTS-S-SSS--SSEEEEE--E---HHHHHHHHHHHSTT--EE
T ss_pred CCCEEEEe-CcHHHHHHHHhcCCC-cEEEEEeccChhhhhccccccCCCCCEEEEE--CCcCHHHHHHHHHHhCCCCCEE
Confidence 44444432 234456555555443 999877776765432 2222 443333 444455566666554 57999
Q ss_pred EEEEEcCCC-ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 76 IAIYVDDDH-GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 76 aii~~dd~~-g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
+++|.++.- +....+.+.+.+++.|+++... .++ +..++...+..+. .+.|++++..+.
T Consensus 135 gvl~~~~~~~~~~~~~~~~~~a~~~g~~l~~~-~v~---~~~~~~~~~~~l~-~~~da~~~~~~~ 194 (294)
T PF04392_consen 135 GVLYDPSEPNSVAQIEQLRKAAKKLGIELVEI-PVP---SSEDLEQALEALA-EKVDALYLLPDN 194 (294)
T ss_dssp EEEEETT-HHHHHHHHHHHHHHHHTT-EEEEE-EES---SGGGHHHHHHHHC-TT-SEEEE-S-H
T ss_pred EEEecCCCccHHHHHHHHHHHHHHcCCEEEEE-ecC---cHhHHHHHHHHhh-ccCCEEEEECCc
Confidence 999976643 4566788888889999997654 333 3467888888875 467888876543
No 315
>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=79.84 E-value=11 Score=38.04 Aligned_cols=194 Identities=18% Similarity=0.102 Sum_probs=112.3
Q ss_pred eeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcC-eeeEEeeceeeecCc---eeeee--ecccccccc
Q 003093 401 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAG-VYDAAVGDIAIITNR---TKMAD--FTQPYIESG 474 (848)
Q Consensus 401 ~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g-~~D~~~~~~~~t~~R---~~~~d--fs~p~~~~~ 474 (848)
.+..-++.+...++-++++++.... -..+...|..| ++|+.+..-....++ ...+. -..|+..+.
T Consensus 10 ~~~~~~l~~~f~~~~g~~v~v~~~~---------s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~ 80 (230)
T PF13531_consen 10 APALEELAEAFEKQPGIKVEVSFGG---------SGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLARSP 80 (230)
T ss_dssp HHHHHHHHHHHHHHHCEEEEEEEEC---------HHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEEEE
T ss_pred HHHHHHHHHHHHhccCCeEEEEECC---------hHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCcccccccCc
Confidence 3455678888888888886666543 56788888877 699988754221111 12233 567888888
Q ss_pred eEEEEeccCCCCCcccccccCchhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcchhhhhHHHHhhhcCcccccc
Q 003093 475 LVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMFFAHKEKTVS 554 (848)
Q Consensus 475 ~~~v~~~~~~~~~~~~fl~PF~~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~s 554 (848)
+++++++..+
T Consensus 81 ~vl~~~~~~~---------------------------------------------------------------------- 90 (230)
T PF13531_consen 81 LVLAVPKGNP---------------------------------------------------------------------- 90 (230)
T ss_dssp EEEEEETTST----------------------------------------------------------------------
T ss_pred eEEEeccCcc----------------------------------------------------------------------
Confidence 9999987761
Q ss_pred chhHHHHHHHHhhhhhhhccccceeeeeeeeccccCCCCChHHhhcCCCCeeEEeCc------hHHHHHHhhhC---C--
Q 003093 555 ALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNS------FARNYLVDELN---I-- 623 (848)
Q Consensus 555 ~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~s~~~i~~~~~s------~~~~~l~~~~~---~-- 623 (848)
..+.+++||.+.+.+|++.... .....+.+ .+ .
T Consensus 91 -----------------------------------~~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~-~g~~~~~~ 134 (230)
T PF13531_consen 91 -----------------------------------KGIRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAA-AGGQELLD 134 (230)
T ss_dssp -----------------------------------TSTTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHH-HTHCHHHH
T ss_pred -----------------------------------cccCCHHHHhhccCEEEecCcccChhhHHHHHHHHH-cccHHHHH
Confidence 3677888888766678877521 12222221 11 0
Q ss_pred -CccCcc-cCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcE--EEeCCccc--cCCceeeecCCCCchHHHH
Q 003093 624 -DESRLV-PLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEF--SIVGQVFT--KNGWGFAFPRDSPLAVDIS 697 (848)
Q Consensus 624 -~~~~~~-~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l--~~~~~~~~--~~~~~~~~~k~spl~~~in 697 (848)
-..++. ..++..+....+.+ |+.++.+.......+. .+...+ ..+++... ...+.+++.++++-.+.-.
T Consensus 135 ~l~~~~~~~~~~~~~~~~~v~~----g~~d~~~~~~s~~~~~-~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~a~ 209 (230)
T PF13531_consen 135 ALQKNIVQYVPSTSQVLSAVAS----GEADAGIVYESQAIFA-RQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPEAAR 209 (230)
T ss_dssp HHHHTEEEEESSHHHHHHHHHT----TSSSEEEEEHHHHHHC-TSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHHHHH
T ss_pred HHHHhCcccccchHHHHHHHHc----CCCcceeeHHHHHHHh-hcCCCeEEEECCchhcCCCEEEEEEEecCCCCHHHHH
Confidence 012333 35677888888888 7888888766555322 222233 34444444 2457788888876555555
Q ss_pred HHHHhhhccCchHHHHHh
Q 003093 698 TAILKLSENGDLQRIHDK 715 (848)
Q Consensus 698 ~~i~~l~e~G~~~~~~~k 715 (848)
..+..|... .-+++..+
T Consensus 210 ~f~~~L~s~-~~q~~l~~ 226 (230)
T PF13531_consen 210 AFIDFLLSP-EGQQILAK 226 (230)
T ss_dssp HHHHHHTSH-HHHHHHHH
T ss_pred HHHHHHCCH-HHHHHHHH
Confidence 555544433 34444433
No 316
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=79.79 E-value=2.8 Score=46.25 Aligned_cols=89 Identities=13% Similarity=0.190 Sum_probs=71.5
Q ss_pred hhhHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCCcchhhhhHHHHhhhc--CccccccchhHHHHHHHHhhhhhhhcc
Q 003093 497 PMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMFFA--HKEKTVSALGRLVLIIWLFVVLIINSS 574 (848)
Q Consensus 497 ~~vW~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~p~s~~~R~~~~~w~~~~lil~~~ 574 (848)
...|..-++.+++.++++|+.|.....+-.+....+.-.++|+...++... |...|..+.+|++...+.++++-+-+.
T Consensus 234 iTt~YIGFL~LIfsSflVYLaEKd~~~e~~n~~F~TyADALWWG~ITltTIGYGDk~P~TWlGr~laa~fsligiSFFAL 313 (654)
T KOG1419|consen 234 ITTWYIGFLVLIFSSFLVYLAEKDAQGEGTNDEFPTYADALWWGVITLTTIGYGDKTPQTWLGRLLAACFSLIGISFFAL 313 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccccccccccchhHHHHHHhhheeEEeeccCCcCcccchhHHHHHHHHHHHHHHHhc
Confidence 367999999999999999999988544433344567889999999988855 577999999999999999998877777
Q ss_pred ccceeeeeeee
Q 003093 575 YTASLTSILTV 585 (848)
Q Consensus 575 Yta~L~s~Lt~ 585 (848)
=.+.|-|=++.
T Consensus 314 PAGILGSGfAL 324 (654)
T KOG1419|consen 314 PAGILGSGFAL 324 (654)
T ss_pred ccccccchhhh
Confidence 77777766654
No 317
>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=79.40 E-value=26 Score=33.54 Aligned_cols=101 Identities=13% Similarity=0.061 Sum_probs=66.3
Q ss_pred hHHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhcc--CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEE
Q 003093 56 DQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK--RCRISFKAPLSVEATEDEITDLLVKVALTESRII 133 (848)
Q Consensus 56 d~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~vi 133 (848)
.......+.+.+...+ .+|.++....+ ..+.+.+.+++. |++|+....-+. ...+-..++.+|++.+||+|
T Consensus 31 g~dl~~~ll~~~~~~~-~~v~llG~~~~----~~~~~~~~l~~~yp~l~i~g~~~g~~--~~~~~~~i~~~I~~~~pdiv 103 (171)
T cd06533 31 GSDLMPALLELAAQKG-LRVFLLGAKPE----VLEKAAERLRARYPGLKIVGYHHGYF--GPEEEEEIIERINASGADIL 103 (171)
T ss_pred cHHHHHHHHHHHHHcC-CeEEEECCCHH----HHHHHHHHHHHHCCCcEEEEecCCCC--ChhhHHHHHHHHHHcCCCEE
Confidence 3445666677666655 67888875554 455555555554 777776322222 22444558999999999999
Q ss_pred EEEccCCcHHHHHHHHHHcCCCCCCeEEEecCc
Q 003093 134 VVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSW 166 (848)
Q Consensus 134 v~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 166 (848)
++.+..+....++.+.++.. +.-+++..++
T Consensus 104 ~vglG~PkQE~~~~~~~~~l---~~~v~~~vG~ 133 (171)
T cd06533 104 FVGLGAPKQELWIARHKDRL---PVPVAIGVGG 133 (171)
T ss_pred EEECCCCHHHHHHHHHHHHC---CCCEEEEece
Confidence 99999988888887777654 2335666554
No 318
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=79.36 E-value=54 Score=34.96 Aligned_cols=69 Identities=9% Similarity=0.030 Sum_probs=44.4
Q ss_pred eeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEecc
Q 003093 403 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 403 ~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
+-.+++..+.+..+ .+.+.... +.-.++...|.+|++|+++..-. .....+. ..++....++++++..
T Consensus 103 ~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~L~~g~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~lv~~~~ 170 (317)
T PRK15421 103 WLTPALENFHKNWP-QVEMDFKS-------GVTFDPQPALQQGELDLVMTSDI---LPRSGLH-YSPMFDYEVRLVLAPD 170 (317)
T ss_pred HHHHHHHHHHHHCC-CceEEEEe-------CccHHHHHHHHCCCcCEEEecCc---ccCCCce-EEEeccceEEEEEcCC
Confidence 34566777776653 23344433 33567899999999999986322 1122333 3677788888888766
Q ss_pred C
Q 003093 483 K 483 (848)
Q Consensus 483 ~ 483 (848)
.
T Consensus 171 h 171 (317)
T PRK15421 171 H 171 (317)
T ss_pred C
Confidence 5
No 319
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=79.32 E-value=81 Score=32.53 Aligned_cols=69 Identities=13% Similarity=0.101 Sum_probs=45.0
Q ss_pred eeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEecc
Q 003093 403 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 403 ~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
+-.+++..+.+..+ .+++.... ++..+++..|.+|++|+++..-.... ..+ -..|+....++++++++
T Consensus 98 ~~~~~l~~~~~~~p-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~lv~s~~ 165 (279)
T TIGR03339 98 YVLDLVARFRQRYP-GIEVSVRI-------GNSQEVLQALQSYRVDVAVSSEVVDD---PRL-DRVVLGNDPLVAVVHRQ 165 (279)
T ss_pred HHHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEecccCC---Cce-EEEEcCCceEEEEECCC
Confidence 45567777777664 23344443 35778999999999999986332222 122 24667778888888766
Q ss_pred C
Q 003093 483 K 483 (848)
Q Consensus 483 ~ 483 (848)
.
T Consensus 166 ~ 166 (279)
T TIGR03339 166 H 166 (279)
T ss_pred C
Confidence 5
No 320
>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=78.94 E-value=9.2 Score=41.67 Aligned_cols=78 Identities=5% Similarity=0.037 Sum_probs=58.6
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCc-cchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHG-RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g-~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
+.+.++++.+| +++.+|+....+- .+..+.+.+.|++.|+++.....+....+.+++...+..+++.++|+||..+.+
T Consensus 15 ~~l~~~~~~~g-~r~lvVt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 93 (357)
T cd08181 15 EKHGEELAALG-KRALIVTGKSSAKKNGSLDDVTKALEELGIEYEIFDEVEENPSLETIMEAVEIAKKFNADFVIGIGGG 93 (357)
T ss_pred HHHHHHHHHcC-CEEEEEeCCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 44566788888 8888887544433 345678999999999887655555555566888999999999999999988765
No 321
>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=78.59 E-value=62 Score=30.76 Aligned_cols=70 Identities=19% Similarity=0.240 Sum_probs=46.3
Q ss_pred eeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEecc
Q 003093 403 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 403 ~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
+..+++..+.++.+ .+++.... ++..+++..+.+|++|+++...... ....+ .+.+.....++++++..
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~~ 83 (199)
T cd08451 15 LVPGLIRRFREAYP-DVELTLEE-------ANTAELLEALREGRLDAAFVRPPVA--RSDGL-VLELLLEEPMLVALPAG 83 (199)
T ss_pred ccHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHCCCccEEEEecCCC--CCCce-eEEEeecccEEEEecCC
Confidence 55677888888764 23344443 4577899999999999998633221 11122 35677788888888765
Q ss_pred C
Q 003093 483 K 483 (848)
Q Consensus 483 ~ 483 (848)
.
T Consensus 84 ~ 84 (199)
T cd08451 84 H 84 (199)
T ss_pred C
Confidence 4
No 322
>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=78.59 E-value=19 Score=37.20 Aligned_cols=144 Identities=17% Similarity=0.102 Sum_probs=73.6
Q ss_pred CCCeEEEEccCCchhHHHHHHhhccC-CccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEE
Q 003093 2 EGQTVAIIGPQDAVTSHVVSHVANEL-QVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYV 80 (848)
Q Consensus 2 ~~~V~aiIGp~~S~~~~ava~i~~~~-~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~ 80 (848)
++++..||+ .+.....++..++.++ ++.++...+..+. +.-..+.|+.. ...+.+-.+|.++..- .+|++|..
T Consensus 55 ~~g~dlIi~-~g~~~~~~~~~vA~~~p~~~F~~~d~~~~~--~Nv~~~~~~~~-e~~ylaG~~Aa~~t~t--~kVG~I~g 128 (258)
T cd06353 55 AQGYDLIFG-TSFGFMDAALKVAKEYPDVKFEHCSGYKTA--PNVGSYFARIY-EGRYLAGVVAGKMTKT--NKVGYVAA 128 (258)
T ss_pred HcCCCEEEE-CchhhhHHHHHHHHHCCCCEEEECCCCCCC--CCeeeEechhh-HHHHHHHHHHHHhhcC--CcEEEEcC
Confidence 357788888 4445566666666665 3333332221110 11112333332 1223444455554432 58999874
Q ss_pred cC-CCccchHHHHHHHHhccCcEEEEeeecCCCC-ChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 81 DD-DHGRNGIAALGDTLAAKRCRISFKAPLSVEA-TEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 81 dd-~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~-~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.+ +........|.+-++..+-.+.....+.-.- +...-......+.+.++|+|+..+ ....++++|++.|.
T Consensus 129 ~~~~~~~~~~~gF~~G~~~~~p~~~v~~~~~g~~~D~~~a~~~a~~l~~~G~DvI~~~~---~~~g~~~aa~~~g~ 201 (258)
T cd06353 129 FPIPEVVRGINAFALGARSVNPDATVKVIWTGSWFDPAKEKEAALALIDQGADVIYQHT---DSPGVIQAAEEKGV 201 (258)
T ss_pred cccHHHHHHHHHHHHHHHHHCCCcEEEEEEecCCCCcHHHHHHHHHHHHCCCcEEEecC---CChHHHHHHHHhCC
Confidence 33 2233445667666654433332222232211 222234445566678999888887 23458889988774
No 323
>PF13685 Fe-ADH_2: Iron-containing alcohol dehydrogenase; PDB: 3CE9_C.
Probab=78.21 E-value=9.4 Score=38.99 Aligned_cols=103 Identities=15% Similarity=0.213 Sum_probs=59.6
Q ss_pred HHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc
Q 003093 62 AIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR 141 (848)
Q Consensus 62 ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~ 141 (848)
.+.++++.++.+++.+|...+.| ....+.+.+.++..|+++..........+..++.....+++..++|+|+-.+.+.-
T Consensus 9 ~l~~~l~~~~~~~~lvv~d~~t~-~~~g~~v~~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ii~vGgG~i 87 (250)
T PF13685_consen 9 KLPEILSELGLKKVLVVTDENTY-KAAGEKVEESLKSAGIEVAVIEEFVGDADEDEVEKLVEALRPKDADLIIGVGGGTI 87 (250)
T ss_dssp GHHHHHGGGT-SEEEEEEETTHH-HHHHHHHHHHHHTTT-EEEEEE-EE---BHHHHHHHHTTS--TT--EEEEEESHHH
T ss_pred HHHHHHHhcCCCcEEEEEcCCHH-HHHHHHHHHHHHHcCCeEEEEecCCCCCCHHHHHHHHHHhcccCCCEEEEeCCcHH
Confidence 45677888888999999866644 34557788899999999874433333344466667777776678998888877643
Q ss_pred HHHHHHHHHHcCCCCCCeEEEecCccc
Q 003093 142 GPVVFHVAQYLGMLGTGYVWIATSWLS 168 (848)
Q Consensus 142 ~~~~~~~a~~~g~~~~~~~wi~~~~~~ 168 (848)
.-..=..|.++|. .|+-+.|..-.
T Consensus 88 ~D~~K~~A~~~~~---p~isVPTa~S~ 111 (250)
T PF13685_consen 88 IDIAKYAAFELGI---PFISVPTAASH 111 (250)
T ss_dssp HHHHHHHHHHHT-----EEEEES--SS
T ss_pred HHHHHHHHHhcCC---CEEEecccccc
Confidence 3222233455664 67777765433
No 324
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=77.89 E-value=78 Score=33.50 Aligned_cols=70 Identities=13% Similarity=0.143 Sum_probs=42.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+ .+++.... .+-..+...|.+|++|+++...... ...+ ...+......+++++.
T Consensus 107 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 174 (309)
T PRK11013 107 SLLPGLCQPFLARYP-DVSLNIVP-------QESPLLEEWLSAQRHDLGLTETLHT---PAGT-ERTELLTLDEVCVLPA 174 (309)
T ss_pred hhHHHHHHHHHHHCC-CCeEEEEe-------CCHHHHHHHHHcCCCCEEEEcCCCC---CCCc-eeeeecceeEEEEEcC
Confidence 456677777887763 23354443 2356788999999999998632211 1122 2345556667777776
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 175 ~~ 176 (309)
T PRK11013 175 GH 176 (309)
T ss_pred CC
Confidence 54
No 325
>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=77.56 E-value=8.7 Score=42.26 Aligned_cols=79 Identities=10% Similarity=0.076 Sum_probs=59.2
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
..+.+.++.+|-+++.+++....+-....+.+.+.|++.|+++.....+....+.+.+...+..+++.++|+||-.+.+
T Consensus 17 ~~l~~~l~~~g~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 95 (377)
T cd08176 17 KEIGDELKNLGFKKALIVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVKPNPTITNVKDGLAVFKKEGCDFIISIGGG 95 (377)
T ss_pred HHHHHHHHHhCCCeEEEECCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4566778888888888887443333356788999999999887655455555566788888999999999999977654
No 326
>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=77.33 E-value=8.1 Score=42.04 Aligned_cols=76 Identities=17% Similarity=0.117 Sum_probs=57.3
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
..+.++++.++ +++.+|+....+. ...+.+.+.|++.|+.+.+. .+....+.+++...++.+++.++|+||..+.+
T Consensus 12 ~~l~~~~~~~~-~r~livt~~~~~~-~~~~~v~~~L~~~~i~~~~~-~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 87 (351)
T cd08170 12 DELGEYLARLG-KRALIIADEFVLD-LVGAKIEESLAAAGIDARFE-VFGGECTRAEIERLAEIARDNGADVVIGIGGG 87 (351)
T ss_pred HHHHHHHHHhC-CeEEEEECHHHHH-HHHHHHHHHHHhCCCeEEEE-EeCCcCCHHHHHHHHHHHhhcCCCEEEEecCc
Confidence 44666777776 8888888444443 67788999999999987643 35555566788888889998999999988765
No 327
>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=77.26 E-value=11 Score=41.48 Aligned_cols=86 Identities=13% Similarity=0.087 Sum_probs=59.3
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
..+.++++.+| +++.+|+....+.....+.+.+.|++.|+++.....+.+..+..+....+...++.++|+||-.+.+
T Consensus 12 ~~l~~~~~~~g-~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~~~~~~v~~~~~~~~~~~~D~IIaiGGGS 90 (386)
T cd08191 12 RQLPRLAARLG-SRALIVTDERMAGTPVFAELVQALAAAGVEVEVFDGVLPDLPRSELCDAASAAARAGPDVIIGLGGGS 90 (386)
T ss_pred HHHHHHHHHcC-CeEEEEECcchhhcchHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 45667788889 8888888444333467788999999999887554444433344667777777888899999987654
Q ss_pred -CcHHHHHH
Q 003093 140 -NRGPVVFH 147 (848)
Q Consensus 140 -~~~~~~~~ 147 (848)
-++.+++.
T Consensus 91 ~iD~aK~ia 99 (386)
T cd08191 91 CIDLAKIAG 99 (386)
T ss_pred HHHHHHHHH
Confidence 34444443
No 328
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=76.93 E-value=9.9 Score=40.77 Aligned_cols=65 Identities=11% Similarity=0.168 Sum_probs=45.6
Q ss_pred HHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCcee-eeeecccccc
Q 003093 405 IDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTK-MADFTQPYIE 472 (848)
Q Consensus 405 ~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~-~~dfs~p~~~ 472 (848)
..+-+++.++.|-++++...|.+. -|.=..++++|..|.+|+.+.+......+.. .--|+.||..
T Consensus 47 ~~fa~~v~ekt~G~l~i~vfP~~q---LG~~~~~ie~l~~G~id~~~~s~~~l~~~~P~~~v~~lPflf 112 (332)
T COG1638 47 KKFAELVEEKTGGRLKIEVFPNSQ---LGGEAEMIEQLRSGTLDIGVVSLGFLAGLVPEFGVFDLPFLF 112 (332)
T ss_pred HHHHHHHHHHhCCeEEEEECCCcc---cCcHHHHHHHHhcCCeeEEeccchhhcccCCcceeecCCeee
Confidence 345677889999998877776322 1346789999999999999987766555542 2345666654
No 329
>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=76.81 E-value=71 Score=30.50 Aligned_cols=73 Identities=15% Similarity=0.128 Sum_probs=45.6
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+ .+++.... +....+..+|.+|++|+++............+ -+.|.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~~ 83 (200)
T cd08453 13 SVLPELVRRFREAYP-DVELQLRE-------ATSDVQLEALLAGEIDAGIVIPPPGASAPPAL-AYRPLLSEPLVLAVPA 83 (200)
T ss_pred HHHHHHHHHHHHhCC-CceEEEEe-------CCHHHHHHHHHcCCCCEEEEecCcccCCCcce-eEEEeeeCceEEEEEC
Confidence 355677777877663 23354443 34678999999999999986322111011222 2566777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 84 ~h 85 (200)
T cd08453 84 AW 85 (200)
T ss_pred CC
Confidence 54
No 330
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=76.55 E-value=60 Score=34.05 Aligned_cols=82 Identities=15% Similarity=0.085 Sum_probs=51.5
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..|+||+... . ...+-..++..+.++- .++++... +.-..++..+.+|++|+++..-.
T Consensus 90 g~l~I~~~~~--~-----------~~~~l~~~l~~f~~~~--~i~i~l~~-------~~~~~~~~~l~~~~~d~~i~~~~ 147 (294)
T PRK03635 90 LTLSIAVNAD--S-----------LATWFLPALAPVLARS--GVLLDLVV-------EDQDHTAELLRRGEVVGAVTTEP 147 (294)
T ss_pred eEEEEeecch--h-----------HHHHHHHHHHHHHhCC--CcEEEEEe-------cCcHHHHHHHhCCCceEEEeccC
Confidence 4689988631 1 1123345667777653 44455543 33567899999999999986322
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
. ....+ .+.|+.+..++++++...
T Consensus 148 ~---~~~~l-~~~~l~~~~~~lv~~~~~ 171 (294)
T PRK03635 148 Q---PVQGC-RVDPLGAMRYLAVASPAF 171 (294)
T ss_pred C---CCCCc-eeeecccceEEEEEcchH
Confidence 1 22222 467888899999887653
No 331
>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=76.20 E-value=22 Score=36.29 Aligned_cols=122 Identities=7% Similarity=0.026 Sum_probs=77.1
Q ss_pred HHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHH--cCcEEEEEEEEcC-CCccchHHHHHHHH
Q 003093 20 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH--YGWREVIAIYVDD-DHGRNGIAALGDTL 96 (848)
Q Consensus 20 va~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~--~~w~~vaii~~dd-~~g~~~~~~l~~~l 96 (848)
.....++.++|++......+. ...+++ +..++..-+..+++.+.. .|-+++++|.... ..+....+.+.+.+
T Consensus 68 ~~~~~~~~~~PvV~i~~~~~~--~~~~~~---V~~D~~~~~~~a~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l 142 (247)
T cd06276 68 YFLLKKIPKEKLLILDHSIPE--GGEYSS---VAQDFEKAIYNALQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFC 142 (247)
T ss_pred HHHHhccCCCCEEEEcCcCCC--CCCCCe---EEEccHHHHHHHHHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHH
Confidence 344555578898876543221 112332 445666777788888877 8999999997443 34556678999999
Q ss_pred hccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCCCCCeE
Q 003093 97 AAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 160 (848)
Q Consensus 97 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~~~~~~ 160 (848)
++.|+.... .. .. .+ ... .++++ |++++...+..+++.+++.|+..++-+
T Consensus 143 ~~~g~~~~~---~~-~~--~~------~~~-~~~~a-i~~~~d~~A~g~~~~l~~~g~~iP~di 192 (247)
T cd06276 143 KDYNIETEI---IN-DY--EN------REI-EKGDL-YIILSDTDLVFLIKKARESGLLLGKDI 192 (247)
T ss_pred HHcCCCccc---cc-cc--ch------hhc-cCCcE-EEEeCHHHHHHHHHHHHHcCCcCCcee
Confidence 999986431 11 00 11 000 12454 555566778889999999998655433
No 332
>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=75.52 E-value=13 Score=40.79 Aligned_cols=85 Identities=7% Similarity=0.017 Sum_probs=61.1
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
..+.++++.+|.+++.+|+....+ ..+.+.+.+++.|+.+.....+....+.+.+...+..+++.++|+||..+.+
T Consensus 12 ~~l~~~~~~~g~~~~livtd~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGGs 88 (367)
T cd08182 12 AKLPSLLKGLGGKRVLLVTGPRSA---IASGLTDILKPLGTLVVVFDDVQPNPDLEDLAAGIRLLREFGPDAVLAVGGGS 88 (367)
T ss_pred HHHHHHHHhcCCCeEEEEeCchHH---HHHHHHHHHHHcCCeEEEEcCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCcH
Confidence 456677888888999998755444 4566788888888876655555555566778888888888899999977654
Q ss_pred -CcHHHHHHH
Q 003093 140 -NRGPVVFHV 148 (848)
Q Consensus 140 -~~~~~~~~~ 148 (848)
-++.+++..
T Consensus 89 ~~D~aK~ia~ 98 (367)
T cd08182 89 VLDTAKALAA 98 (367)
T ss_pred HHHHHHHHHH
Confidence 344444443
No 333
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=75.25 E-value=13 Score=39.96 Aligned_cols=72 Identities=24% Similarity=0.263 Sum_probs=49.4
Q ss_pred CCCCChHHhhcCCCCeeEEeCch-HHHHHH---hhhCCCcc--CcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHH
Q 003093 590 SPIKGIDSLRSSNYPIGYQVNSF-ARNYLV---DELNIDES--RLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELF 663 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~~s~-~~~~l~---~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~ 663 (848)
.+|++++||. |+++|+..++. ....+. ...+.... .++.+ .+.+...++.. |.+||++...++....
T Consensus 126 ~~i~~~adlk--Gk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~----g~vda~~~~ep~~~~~ 198 (335)
T COG0715 126 SGIKSVADLK--GKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNL-PPADAVAALAA----GQVDAFVVWEPWNAAA 198 (335)
T ss_pred CCcccccCCC--CceEEEeCCCchHHHHHHHHHHHcCCCcccceEEee-CcHHHHHHHhc----CCcceEEecCCchhhh
Confidence 6888999997 99999998874 333332 22333333 33333 45588888888 8999988888887766
Q ss_pred HhcCC
Q 003093 664 LSTRC 668 (848)
Q Consensus 664 ~~~~~ 668 (848)
..+..
T Consensus 199 ~~~~~ 203 (335)
T COG0715 199 EGEGG 203 (335)
T ss_pred hccCC
Confidence 66653
No 334
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=74.79 E-value=82 Score=32.23 Aligned_cols=83 Identities=18% Similarity=0.128 Sum_probs=51.1
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..++||+... . ...+..+++..+.+..+ .+++.... ++-.+++.+|.+|++|+++....
T Consensus 67 ~~l~I~~~~~--~-----------~~~~~~~~l~~~~~~~p-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~ 125 (269)
T PRK11716 67 GELSLFCSVT--A-----------AYSHLPPILDRFRAEHP-LVEIKLTT-------GDAADAVEKVQSGEADLAIAAKP 125 (269)
T ss_pred ceEEEEecch--H-----------HHHHHHHHHHHHHHHCC-CeEEEEEE-------CCHHHHHHHHHCCCccEEEEecC
Confidence 4688887631 1 12355677888888764 23344443 44678999999999999986322
Q ss_pred eecCceeeeeecccccccceEEEEecc
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
.. . ...+. ..+.....++++++..
T Consensus 126 ~~-~-~~~~~-~~~l~~~~~~~v~~~~ 149 (269)
T PRK11716 126 ET-L-PASVA-FSPIDEIPLVLIAPAL 149 (269)
T ss_pred CC-C-CcceE-EEEcccceEEEEEcCC
Confidence 11 1 11122 3566777788877655
No 335
>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=74.36 E-value=12 Score=41.17 Aligned_cols=78 Identities=8% Similarity=0.087 Sum_probs=57.5
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCC-ccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDH-GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~-g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
+.+.++++.++ +++.+|.....+ ..+..+.+.+.|++.|+++.....+....+.+++...+..++..++|+||-.+.+
T Consensus 18 ~~l~~~~~~~~-~r~livt~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 96 (382)
T cd08187 18 SELGKELKKYG-KKVLLVYGGGSIKKNGLYDRVIASLKEAGIEVVELGGVEPNPRLETVREGIELCKEEKVDFILAVGGG 96 (382)
T ss_pred HHHHHHHHHhC-CEEEEEeCCcHHHhcCcHHHHHHHHHHcCCeEEEECCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCh
Confidence 45666777775 888888644333 2345788999999999987655555555566788888999999999999977654
No 336
>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=74.00 E-value=83 Score=29.92 Aligned_cols=70 Identities=14% Similarity=0.115 Sum_probs=45.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
++-.+++..+.++.+ .+++.... +.+..+..+|.+|++|+++..... ....+ -+.+.....+++++++
T Consensus 14 ~~l~~~i~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~v~~~ 81 (198)
T cd08446 14 DTVPRLLRAFLTARP-DVTVSLHN-------MTKDEQIEALRAGRIHIGFGRFYP---VEPDI-AVENVAQERLYLAVPK 81 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEee-------CCHHHHHHHHHCCCccEEEEecCC---CCCCc-eeEEeeeccEEEEEeC
Confidence 345677788877764 33455443 457889999999999999863222 11222 2456677888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~~ 83 (198)
T cd08446 82 SH 83 (198)
T ss_pred CC
Confidence 55
No 337
>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=73.65 E-value=15 Score=40.47 Aligned_cols=87 Identities=9% Similarity=0.042 Sum_probs=61.2
Q ss_pred HHHHHHHHHc---CcEEEEEEEEcCCCc-cchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEE
Q 003093 61 AAIAEIVDHY---GWREVIAIYVDDDHG-RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVH 136 (848)
Q Consensus 61 ~ai~~~~~~~---~w~~vaii~~dd~~g-~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~ 136 (848)
+.+.++++.+ |.+++.+|+....+. .+..+.+.+.|++.|+++.....+.+..+.+++...+..++..++|+||..
T Consensus 12 ~~l~~~l~~~~~~g~kr~livtd~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIai 91 (383)
T cd08186 12 EKIGEILKDLKSKGISKVLLVTGKSAYKKSGAWDKVEPALDEHGIEYVLYNKVTPNPTVDQVDEAAKLGREFGAQAVIAI 91 (383)
T ss_pred HHHHHHHHHhcccCCCEEEEEcCccHHhhcChHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence 4456667776 778998887544333 344678899999999877655455555566888889999999999999977
Q ss_pred ccC--CcHHHHHH
Q 003093 137 THY--NRGPVVFH 147 (848)
Q Consensus 137 ~~~--~~~~~~~~ 147 (848)
+.+ -+...++.
T Consensus 92 GGGS~iD~aK~ia 104 (383)
T cd08186 92 GGGSPIDSAKSAA 104 (383)
T ss_pred CCccHHHHHHHHH
Confidence 654 34444443
No 338
>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=73.50 E-value=43 Score=32.24 Aligned_cols=99 Identities=14% Similarity=0.056 Sum_probs=64.5
Q ss_pred HHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhcc--CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEE
Q 003093 57 QYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK--RCRISFKAPLSVEATEDEITDLLVKVALTESRIIV 134 (848)
Q Consensus 57 ~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv 134 (848)
.+.+..+.+.....+ .+|.++....+ ..+.+.+.+++. |++|+....+ .++.+-..++.+|.+++||+++
T Consensus 34 ~dl~~~l~~~~~~~~-~~vfllG~~~~----v~~~~~~~l~~~yP~l~i~g~~g~---f~~~~~~~i~~~I~~s~~dil~ 105 (177)
T TIGR00696 34 PDLMEELCQRAGKEK-LPIFLYGGKPD----VLQQLKVKLIKEYPKLKIVGAFGP---LEPEERKAALAKIARSGAGIVF 105 (177)
T ss_pred HHHHHHHHHHHHHcC-CeEEEECCCHH----HHHHHHHHHHHHCCCCEEEEECCC---CChHHHHHHHHHHHHcCCCEEE
Confidence 455666777666667 47777765543 556666666654 7777765222 2334556789999999999999
Q ss_pred EEccCCcHHHHHHHHHHcCCCCCCeEEEecCc
Q 003093 135 VHTHYNRGPVVFHVAQYLGMLGTGYVWIATSW 166 (848)
Q Consensus 135 ~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 166 (848)
+.+..+....++.+.++.- +.-++++.++
T Consensus 106 VglG~PkQE~~~~~~~~~~---~~~v~~gvGg 134 (177)
T TIGR00696 106 VGLGCPKQEIWMRNHRHLK---PDAVMIGVGG 134 (177)
T ss_pred EEcCCcHhHHHHHHhHHhC---CCcEEEEece
Confidence 9998887777776654432 1234555443
No 339
>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=73.34 E-value=14 Score=37.56 Aligned_cols=78 Identities=9% Similarity=0.137 Sum_probs=55.1
Q ss_pred EEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHH
Q 003093 74 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQY 151 (848)
Q Consensus 74 ~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~ 151 (848)
+++++... +.++......+++++++.|+++..... ..+.......++++.+.++|.||+..........+..+.+
T Consensus 1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~~---~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~l~~ 77 (264)
T cd01537 1 TIGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLANS---QNDAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARK 77 (264)
T ss_pred CeEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEecCCCcchhHHHHhhh
Confidence 36777754 678888899999999999998765432 2233556777788887889999887654444335677766
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|.
T Consensus 78 ~~i 80 (264)
T cd01537 78 AGI 80 (264)
T ss_pred cCC
Confidence 665
No 340
>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=72.89 E-value=14 Score=39.97 Aligned_cols=77 Identities=18% Similarity=0.176 Sum_probs=55.9
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
..+.+.++.++ +++.+|+....+ ....+.+.+.+++.|+.+.....+....+.+++.......++.++|+||-.+.+
T Consensus 12 ~~l~~~~~~~~-~r~liv~d~~~~-~~~~~~v~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~iiavGGG 88 (345)
T cd08171 12 KKIPEVCEKYG-KKVVVIGGKTAL-AAAKDKIKAALEQSGIEITDFIWYGGESTYENVERLKKNPAVQEADMIFAVGGG 88 (345)
T ss_pred HHHHHHHHhcC-CEEEEEeCHHHH-HHHHHHHHHHHHHCCCeEEEEEecCCCCCHHHHHHHHHHHhhcCCCEEEEeCCc
Confidence 44666777777 888888754444 345677888899999887644455555566778888888888899999987654
No 341
>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=72.75 E-value=15 Score=37.87 Aligned_cols=77 Identities=9% Similarity=0.046 Sum_probs=54.4
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-CcHHHHHHHHHH
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQY 151 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~-~~~~~~~~~a~~ 151 (848)
|+++.. ++.|.......+.+++++.|.++..... ..+.......+..+...++|.|++.... ......++++++
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~~~i~~~~~ 78 (273)
T cd06305 2 IAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYDA---GGDDAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRALD 78 (273)
T ss_pred eEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEecCChhhhHHHHHHHHH
Confidence 566664 5778888899999999999999876422 2233445566777777799999987533 334567788888
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|+
T Consensus 79 ~~i 81 (273)
T cd06305 79 AGI 81 (273)
T ss_pred cCC
Confidence 776
No 342
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=72.61 E-value=88 Score=29.61 Aligned_cols=70 Identities=19% Similarity=0.165 Sum_probs=45.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.++++.+.++.+ .+++.... ++...++..|.+|++|+++...... ...+ ...+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 80 (196)
T cd08450 13 QWLPEVLPILREEHP-DLDVELSS-------LFSPQLAEALMRGKLDVAFMRPEIQ---SDGI-DYQLLLKEPLIVVLPA 80 (196)
T ss_pred hhHHHHHHHHHhhCC-CcEEEEEe-------cChHHHHHHHhcCCccEEEEeCCCC---CCCc-EEEEEEccceEEEecC
Confidence 455677888887764 23344443 3467899999999999998632211 1222 2466777888888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (196)
T cd08450 81 DH 82 (196)
T ss_pred CC
Confidence 54
No 343
>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=72.53 E-value=24 Score=36.47 Aligned_cols=85 Identities=13% Similarity=0.074 Sum_probs=57.5
Q ss_pred EEEEEEE----cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHH
Q 003093 74 EVIAIYV----DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 149 (848)
Q Consensus 74 ~vaii~~----dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a 149 (848)
+|+++++ |..|.....+.+.+.-++.|+++.+.+..+ +..++...++++.+.++|+|+.++.. ....+.+.|
T Consensus 1 kva~l~~g~~~D~~~n~~~~~G~~~~~~~~gv~~~~~e~~~---~~~~~~~~i~~~~~~g~dlIi~~g~~-~~~~~~~vA 76 (258)
T cd06353 1 KVAFVYVGPIGDQGWNYAHDEGRKAAEKALGVEVTYVENVP---EGADAERVLRELAAQGYDLIFGTSFG-FMDAALKVA 76 (258)
T ss_pred CEEEEEeCCCCccchhHHHHHHHHHHHHhcCCeEEEEecCC---chHhHHHHHHHHHHcCCCEEEECchh-hhHHHHHHH
Confidence 4777774 444555667888888788899988877654 23788999999988899999985443 223355556
Q ss_pred HHcCCCCCCeEEEecCc
Q 003093 150 QYLGMLGTGYVWIATSW 166 (848)
Q Consensus 150 ~~~g~~~~~~~wi~~~~ 166 (848)
++. |+..|+..+.
T Consensus 77 ~~~----p~~~F~~~d~ 89 (258)
T cd06353 77 KEY----PDVKFEHCSG 89 (258)
T ss_pred HHC----CCCEEEECCC
Confidence 553 3445565443
No 344
>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=72.52 E-value=14 Score=37.62 Aligned_cols=76 Identities=8% Similarity=0.053 Sum_probs=56.0
Q ss_pred EEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
++++..+ ++|.......+++++++.|+.+.... ...+.......++++.+.++|.|++......... ++.+.+.
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~---~~~~~~~~~~~~~~~~~~~~d~iii~~~~~~~~~-~~~~~~~ 77 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSVLLCN---SDEDPEKEREALELLLSRRVDGIILAPSRLDDEL-LEELAAL 77 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEEEEEc---CCCCHHHHHHHHHHHHHcCcCEEEEecCCcchHH-HHHHHHc
Confidence 5666644 78888999999999999998877542 2223345566777888889999998877666555 7778877
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (264)
T cd06267 78 GI 79 (264)
T ss_pred CC
Confidence 76
No 345
>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=72.50 E-value=17 Score=39.12 Aligned_cols=86 Identities=9% Similarity=0.072 Sum_probs=59.3
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
..+.+.++.++.+++.+|+....+- ...+.+.+.+++. +++..........+.+++...+..+++.++|+||..+.+
T Consensus 12 ~~l~~~~~~~g~~~~liv~~~~~~~-~~~~~v~~~l~~~-~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs 89 (332)
T cd07766 12 EKIGEEIKRGGFDRALVVSDEGVVK-GVGEKVADSLKKL-IAVHIFDGVGPNPTFEEVKEAVERARAAEVDAVIAVGGGS 89 (332)
T ss_pred HHHHHHHHhcCCCeEEEEeCCchhh-hHHHHHHHHHHhc-CcEEEeCCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCch
Confidence 3456677888989999998544433 6777888888887 665544334433466788888899998899999977654
Q ss_pred -CcHHHHHHH
Q 003093 140 -NRGPVVFHV 148 (848)
Q Consensus 140 -~~~~~~~~~ 148 (848)
-+...++..
T Consensus 90 ~~D~aK~ia~ 99 (332)
T cd07766 90 TLDTAKAVAA 99 (332)
T ss_pred HHHHHHHHHH
Confidence 344444433
No 346
>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=72.44 E-value=90 Score=29.62 Aligned_cols=71 Identities=14% Similarity=0.068 Sum_probs=45.6
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+ .+++.... ++.+.++.+|.+|++|+++...... ....+ .+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~ 81 (195)
T cd08431 13 QPLYPLIAEFYQLNK-ATRIRLSE-------EVLGGTWDALASGRADLVIGATGEL--PPGGV-KTRPLGEVEFVFAVAP 81 (195)
T ss_pred HHHHHHHHHHHHHCC-CCceEEEE-------eccchHHHHHhCCCCCEEEEecCCC--CCCce-EEEecccceEEEEEcC
Confidence 456788888888874 23344443 3466889999999999998632111 11122 3566677788888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~h 83 (195)
T cd08431 82 NH 83 (195)
T ss_pred CC
Confidence 54
No 347
>PLN02245 ATP phosphoribosyl transferase
Probab=72.39 E-value=26 Score=38.11 Aligned_cols=104 Identities=10% Similarity=0.073 Sum_probs=56.9
Q ss_pred CCCChHHhhc-------CCCCeeEEeCchHHHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHH
Q 003093 591 PIKGIDSLRS-------SNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELF 663 (848)
Q Consensus 591 ~i~sl~dL~~-------s~~~i~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~ 663 (848)
.+++++||.. ..++|+..--.....||. +.+....+++...-.-|.. -.- |-.|++++-.....-+
T Consensus 178 ~~~s~~dL~g~~~~~~~~~~RIATkYp~ltr~ff~-~~Gv~~v~Iv~l~GAvE~A--P~l----GlADaIvDIVsTGtTL 250 (403)
T PLN02245 178 NINSLKELAQMPQWTEERPLRVVTGFTYLGPKFMK-DNGFKHVTFSTADGALEAA--PAM----GIADAILDLVSSGTTL 250 (403)
T ss_pred ccCCHHHhcccccccccCceEEEeCCHHHHHHHHH-HcCCCeEEEEECcCceecc--ccc----CchhhhcchhccHHHH
Confidence 5788999973 115677776667788884 3454333455443333332 222 5667777655555444
Q ss_pred HhcCCcEEEeC-CccccCCceeeecCCCC-----chHHHHHHHHhh
Q 003093 664 LSTRCEFSIVG-QVFTKNGWGFAFPRDSP-----LAVDISTAILKL 703 (848)
Q Consensus 664 ~~~~~~l~~~~-~~~~~~~~~~~~~k~sp-----l~~~in~~i~~l 703 (848)
..+ +|++++ +.+....-.+...+++. -++.++..+.+|
T Consensus 251 raN--gLk~i~~~~Il~S~A~LIan~~sl~~~~~~~~~i~~ll~rl 294 (403)
T PLN02245 251 REN--NLKEIEGGVVLESQAVLVASRRALLERKGALEVVHEILERL 294 (403)
T ss_pred HHC--CCEEccCceEEEEEEEEEEecchhhcchhHHHHHHHHHHHH
Confidence 444 578885 44444444555566643 223444444444
No 348
>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=72.35 E-value=14 Score=38.23 Aligned_cols=78 Identities=9% Similarity=0.049 Sum_probs=56.3
Q ss_pred EEEEEEEc--CCCccchHHHHHHHHhc-cCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCC-cHHHHHHHH
Q 003093 74 EVIAIYVD--DDHGRNGIAALGDTLAA-KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVA 149 (848)
Q Consensus 74 ~vaii~~d--d~~g~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~-~~~~~~~~a 149 (848)
+|++|..+ ++|.......+.+++++ .|.++..... ..+.......+.++.+.++|.+++..... ....++.++
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~l 77 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFEDA---KNDVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVKAA 77 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEeCC---CCCHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHHHH
Confidence 46777744 67888888999999999 8998876432 12335566778888888999998875443 345677778
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
.+.|.
T Consensus 78 ~~~~i 82 (272)
T cd06301 78 NAAGI 82 (272)
T ss_pred HHCCC
Confidence 77775
No 349
>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=72.24 E-value=91 Score=29.61 Aligned_cols=66 Identities=9% Similarity=0.051 Sum_probs=40.2
Q ss_pred eHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEecc
Q 003093 404 CIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 404 ~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
...++..+.++. .+++.... ++...+.+++.+|++|+++..- ......+ .+.+......+++++..
T Consensus 15 l~~~l~~f~~~~--~v~l~l~~-------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~~ 80 (195)
T cd08428 15 FLPALAPVLKRE--RILLDLIV-------DDEDRTHDLLRDGEVVGCISTQ---AQPMQGC-RSDYLGSMDYLLVASPD 80 (195)
T ss_pred hHHHHHHHHhCc--CeEEEEEe-------CCchhHHHHHHcCcceEEEEec---CCCCCCc-eeEEeeeeeEEEEECCc
Confidence 345677777763 44455543 3467889999999999877521 1111222 34566667777776543
No 350
>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=72.08 E-value=92 Score=29.58 Aligned_cols=72 Identities=14% Similarity=0.122 Sum_probs=45.4
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
++-.+++..+.++.+ .+++.... +....+..++.+|++|+++..... +.....+ -+.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~l-~~~~l~~~~~~~v~~~ 82 (199)
T cd08416 13 NTVPRIIMGLKLRRP-ELDIELTL-------GSNKDLLKKLKDGELDAILVATPE-GLNDPDF-EVVPLFEDDIFLAVPA 82 (199)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEEE-------cCcHHHHHHHhCCCCCEEEEecCC-cCCCCCe-EEEEeecceEEEEECC
Confidence 456677888887774 22344433 346678999999999999873221 0011222 2556777788888876
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 83 ~h 84 (199)
T cd08416 83 TS 84 (199)
T ss_pred CC
Confidence 54
No 351
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=71.37 E-value=42 Score=34.15 Aligned_cols=90 Identities=11% Similarity=0.095 Sum_probs=58.7
Q ss_pred hHHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhc-cCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEE
Q 003093 56 DQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAA-KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIV 134 (848)
Q Consensus 56 d~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv 134 (848)
..+....+.+.....| .+|.++..+.+ .++.+.+.+++ .|+.|+.... .+ .+.++...++.+|.+++||+++
T Consensus 90 G~dl~~~ll~~~~~~~-~~v~llG~~~~----v~~~a~~~l~~~y~l~i~g~~~-Gy-f~~~e~~~i~~~I~~s~~dil~ 162 (243)
T PRK03692 90 GADLWEALMARAGKEG-TPVFLVGGKPE----VLAQTEAKLRTQWNVNIVGSQD-GY-FTPEQRQALFERIHASGAKIVT 162 (243)
T ss_pred hHHHHHHHHHHHHhcC-CeEEEECCCHH----HHHHHHHHHHHHhCCEEEEEeC-CC-CCHHHHHHHHHHHHhcCCCEEE
Confidence 3445666666666667 67888865544 44444454433 3777764321 11 1335567789999999999999
Q ss_pred EEccCCcHHHHHHHHHHc
Q 003093 135 VHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 135 ~~~~~~~~~~~~~~a~~~ 152 (848)
+.+..+....++...++.
T Consensus 163 VglG~PkQE~~~~~~~~~ 180 (243)
T PRK03692 163 VAMGSPKQEIFMRDCRLV 180 (243)
T ss_pred EECCCcHHHHHHHHHHHh
Confidence 999988777777665553
No 352
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=71.35 E-value=63 Score=33.68 Aligned_cols=121 Identities=22% Similarity=0.247 Sum_probs=71.9
Q ss_pred CCCCChHHhhc----CCC--CeeEE-eCch---HHHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHH
Q 003093 590 SPIKGIDSLRS----SNY--PIGYQ-VNSF---ARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAY 659 (848)
Q Consensus 590 ~~i~sl~dL~~----s~~--~i~~~-~~s~---~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~ 659 (848)
.+++|++||++ +.. .+|.. .|+. ....+.+..+.. .+.++|+...+.+.+|.. |.+++.+.....
T Consensus 88 sp~~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~G~~~~~~allg----G~vd~~~~~~~~ 162 (274)
T PF03401_consen 88 SPYKTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYDGGAEALTALLG----GHVDAAFGSPGE 162 (274)
T ss_dssp SS-SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-SSHHHHHHHHHT----TSSSEEEEEHHH
T ss_pred CccccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeCCccHHHHHHhC----CeeeEEeecHHH
Confidence 58899999864 222 35544 2332 223344455543 567899999999999999 899998877554
Q ss_pred H-HHHHhcCC---------------cEEEeCCc-----cccCCceeeecCCCC--chHHHHHHHHhhhccCchHHHHHh
Q 003093 660 A-ELFLSTRC---------------EFSIVGQV-----FTKNGWGFAFPRDSP--LAVDISTAILKLSENGDLQRIHDK 715 (848)
Q Consensus 660 ~-~~~~~~~~---------------~l~~~~~~-----~~~~~~~~~~~k~sp--l~~~in~~i~~l~e~G~~~~~~~k 715 (848)
. .+..+..- ++-.+.+. ......+++.|||-| ..+.+..++.+..++-.+++..++
T Consensus 163 ~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~ 241 (274)
T PF03401_consen 163 ALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEK 241 (274)
T ss_dssp HHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHH
T ss_pred HHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 4 44332211 11111221 112235888999998 899999999999998776655444
No 353
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=70.67 E-value=1.3e+02 Score=31.49 Aligned_cols=70 Identities=19% Similarity=0.170 Sum_probs=47.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+..+++..+.++.+ .+.+.... .+..+++..|.+|++|+++..... ....+. +.|.....+++++++
T Consensus 103 ~~l~~~~~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~ 170 (296)
T PRK09906 103 NLLPKVLPMFRLRHP-DTLIELVS-------LITTQQEEKLRRGELDVGFMRHPV---YSDEID-YLELLDEPLVVVLPV 170 (296)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe-------CCcHHHHHHHHcCCeeEEEecCCC---CCCCce-EEEEecccEEEEecC
Confidence 345567777777764 34455543 346789999999999999874432 223344 468888899999886
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 171 ~~ 172 (296)
T PRK09906 171 DH 172 (296)
T ss_pred CC
Confidence 65
No 354
>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2.7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....
Probab=70.10 E-value=69 Score=30.90 Aligned_cols=131 Identities=13% Similarity=0.150 Sum_probs=68.4
Q ss_pred CCeEEEEccCCchhHHHHHHhhccCC--ccE-EecccCCCCCCC-CCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEE
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANELQ--VPL-LSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAI 78 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~~--vP~-Is~~at~p~ls~-~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii 78 (848)
.++++++||.+|+-...+..+.+... +.. +++..-.|.-.+ .+-.|.|-+ .. .+-+.++.-..=...-
T Consensus 2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~~~~~~v~~TTR~~r~~E~~g~~y~fvs---~~----~f~~~~~~~~fie~~~- 73 (183)
T PF00625_consen 2 RRPIVLVGPSGSGKSTLAKRLIQEFPDKFGRVVSHTTRPPRPGEVDGVDYHFVS---KE----EFERMIKAGEFIEYGE- 73 (183)
T ss_dssp SSEEEEESSTTSSHHHHHHHHHHHSTTTEEEEEEEESS-GGTTS-TTTSEEE-----HH----HHHHHHHTTHEEEEEE-
T ss_pred CCEEEEECCCCCCHHHHHHHHHHhcccccccceeecccCCcccccCCcceEEEe---ec----hhhhhhccccEEEEee-
Confidence 57899999999998888888877653 433 343333344333 344566642 11 1222222211111222
Q ss_pred EEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcC
Q 003093 79 YVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLG 153 (848)
Q Consensus 79 ~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g 153 (848)
|.++.||.. .+.+.+.+++...++.... . .-+..|+....+.++++..++....+-+.+++.|
T Consensus 74 ~~g~~YGt~-~~~i~~~~~~gk~~il~~~--------~---~g~~~L~~~~~~~~~IfI~~~s~~~l~~~l~~r~ 136 (183)
T PF00625_consen 74 YDGNYYGTS-KSAIDKVLEEGKHCILDVD--------P---EGVKQLKKAGFNPIVIFIKPPSPEVLKRRLRRRG 136 (183)
T ss_dssp ETTEEEEEE-HHHHHHHHHTTTEEEEEET--------H---HHHHHHHHCTTTEEEEEEEESSHHHHHHHHHTTT
T ss_pred ecchhhhhc-cchhhHhhhcCCcEEEEcc--------H---HHHHHHHhcccCceEEEEEccchHHHHHHHhccc
Confidence 445667754 5677788887777665421 1 1234455545555555554444444555544433
No 355
>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=68.94 E-value=18 Score=37.39 Aligned_cols=80 Identities=8% Similarity=-0.054 Sum_probs=54.1
Q ss_pred EEEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHH
Q 003093 74 EVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQY 151 (848)
Q Consensus 74 ~vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~ 151 (848)
+|++++. ++.|.......+.+++++.|.++.....-.. .+..+-...++.+.+.++|.|++.....+....+.++++
T Consensus 1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~-~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~ 79 (268)
T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGGY-PNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVA 79 (268)
T ss_pred CeEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCCCC-CCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHH
Confidence 3677774 3678888889999999999998876432111 122344566777778899999987644333225677777
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|+
T Consensus 80 ~gi 82 (268)
T cd06306 80 ASI 82 (268)
T ss_pred CCC
Confidence 776
No 356
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=68.78 E-value=18 Score=39.51 Aligned_cols=76 Identities=13% Similarity=0.126 Sum_probs=56.1
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
..+.+.++.+| +++.+|+....+ ....+.+.+.+++.|+++.+. .+....+.+.+...+..+++.++|+||..+.+
T Consensus 19 ~~l~~~l~~~g-~~~livtd~~~~-~~~~~~v~~~l~~~~~~~~~~-~~~~ep~~~~v~~~~~~~~~~~~d~IIavGGG 94 (366)
T PRK09423 19 ARLGEYLKPLG-KRALVIADEFVL-GIVGDRVEASLKEAGLTVVFE-VFNGECSDNEIDRLVAIAEENGCDVVIGIGGG 94 (366)
T ss_pred HHHHHHHHHcC-CEEEEEEChhHH-HHHHHHHHHHHHhCCCeEEEE-EeCCCCCHHHHHHHHHHHHhcCCCEEEEecCh
Confidence 45666788888 898888744433 346778888899999887543 34555566778888888888899999987655
No 357
>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=68.46 E-value=22 Score=39.07 Aligned_cols=82 Identities=10% Similarity=0.101 Sum_probs=58.2
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
..+.++++.++ +++.+|+..... ..+.+.+.|++.|+.+.... +....+.+++...+..++..++|+||-.+.+
T Consensus 12 ~~l~~~l~~~~-~r~livtd~~~~---~~~~v~~~L~~~g~~~~~~~-~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 86 (374)
T cd08183 12 KELPALAAELG-RRVLLVTGASSL---RAAWLIEALRAAGIEVTHVV-VAGEPSVELVDAAVAEARNAGCDVVIAIGGGS 86 (374)
T ss_pred HHHHHHHHHcC-CcEEEEECCchH---HHHHHHHHHHHcCCeEEEec-CCCCcCHHHHHHHHHHHHhcCCCEEEEecCch
Confidence 44666777775 888888754433 67778889999998875443 3444556778888888988999999988655
Q ss_pred -CcHHHHHH
Q 003093 140 -NRGPVVFH 147 (848)
Q Consensus 140 -~~~~~~~~ 147 (848)
-++.+++.
T Consensus 87 ~~D~aK~ia 95 (374)
T cd08183 87 VIDAGKAIA 95 (374)
T ss_pred HHHHHHHHH
Confidence 34444443
No 358
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=68.34 E-value=54 Score=32.85 Aligned_cols=48 Identities=21% Similarity=0.216 Sum_probs=32.5
Q ss_pred hhHHHHHHhcCeeeEEeeceeeecCce------eeeeecccccccceEEEEecc
Q 003093 435 CTELVRLITAGVYDAAVGDIAIITNRT------KMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 435 ~~~~i~~l~~g~~D~~~~~~~~t~~R~------~~~dfs~p~~~~~~~~v~~~~ 482 (848)
-.++-..+..|.+|+++.+..+-.|.. -+.-.-..|-...+++.+|..
T Consensus 54 ~~DIp~yV~~G~~DlGI~G~D~l~E~~~~~~~~v~elldLgfG~crl~vA~p~~ 107 (228)
T PRK13583 54 ASEIPRELGAGRVDLGVTGEDLVREKLADWDKRVEIVARLGFGHADLVVAVPEI 107 (228)
T ss_pred HHHHHHHHhCCCCcEEEeeeeeeecccccCCCCeEEEecCCCCceEEEEEEECc
Confidence 457889999999999999887776632 112223455556667776654
No 359
>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=67.60 E-value=28 Score=35.66 Aligned_cols=77 Identities=4% Similarity=0.002 Sum_probs=53.9
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. +++|.......+.+++++.|..+..... ..+.......++++.+.++|.|++..........+..+.+.
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATT---DYDAEREADAVETLLRQRVDGLILTVADAATSPALDLLDAE 78 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeC---CCCHHHHHHHHHHHHhcCCCEEEEecCCCCchHHHHHHhhC
Confidence 455653 4567788889999999999999876432 22334556677788778999999864433334477888887
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 79 ~i 80 (266)
T cd06282 79 RV 80 (266)
T ss_pred CC
Confidence 76
No 360
>TIGR00035 asp_race aspartate racemase.
Probab=67.35 E-value=26 Score=35.37 Aligned_cols=41 Identities=12% Similarity=0.035 Sum_probs=25.4
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEE
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRIS 104 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~ 104 (848)
++.++.++..+.++|+++....- -....+++.+++.|++++
T Consensus 106 ~~~~~~~~~~~~~~VgvLaT~~T---~~s~~y~~~l~~~g~~v~ 146 (229)
T TIGR00035 106 EETAEAVKEDGVKKAGLLGTKGT---MKDGVYEREMKKHGIEIV 146 (229)
T ss_pred HHHHHHHHHcCCCEEEEEecHHH---HHhHHHHHHHHHCCCEEE
Confidence 34444455567888998864432 123447778888887655
No 361
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=67.06 E-value=74 Score=33.08 Aligned_cols=121 Identities=10% Similarity=0.123 Sum_probs=59.7
Q ss_pred cCCCCChHHhhcCCCCeeEEe--CchHHH-HHHhhhC---------C-----------CccCcccCCCHHHHHHHhhcCC
Q 003093 589 SSPIKGIDSLRSSNYPIGYQV--NSFARN-YLVDELN---------I-----------DESRLVPLNSPEEYAKALKDGP 645 (848)
Q Consensus 589 ~~~i~sl~dL~~s~~~i~~~~--~s~~~~-~l~~~~~---------~-----------~~~~~~~~~~~~~~~~~l~~~~ 645 (848)
..+++|++||.+ |.+|++.. +...+- .+.+..+ . ...+++++ ...+...++.+
T Consensus 119 s~~iksl~DL~~-Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~-~~~q~~~al~d-- 194 (272)
T PRK09861 119 SKKIKTVAQIKE-GATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMEL-EGAQLPRVLDD-- 194 (272)
T ss_pred ccCCCCHHHcCC-CCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEc-CHHHhHhhccC--
Confidence 468999999964 77899986 222222 2222211 1 11122223 44556777777
Q ss_pred CCCceEEEEccHHHHHHHHhcCC--cEEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccCchHHHHHhh
Q 003093 646 HKGGVAAVVDDRAYAELFLSTRC--EFSIVGQVFTKNGWGFAFPRDSPLAVDISTAILKLSENGDLQRIHDKW 716 (848)
Q Consensus 646 ~~~~~~a~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~G~~~~~~~kw 716 (848)
|.+|+.+...++..- ..-.+ +-........++--.++++.+..=.+.+...+..++....-+.|.++|
T Consensus 195 --g~vD~a~i~~~~~~~-ag~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 264 (272)
T PRK09861 195 --PKVDVAIISTTYIQQ-TGLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETIF 264 (272)
T ss_pred --cccCEEEEchhHHHH-cCCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 788888887776542 11111 111222111122234555554334455555555555444444444443
No 362
>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=66.59 E-value=29 Score=35.56 Aligned_cols=77 Identities=10% Similarity=0.061 Sum_probs=53.6
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
+++|.. .+.|.......+.+++++.|.++... ....+...-...++++.+.++|.|++..........++++.+.
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 456664 46788888899999999999887543 2122234456677888888999998876544444577788877
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 79 ~i 80 (268)
T cd06289 79 GI 80 (268)
T ss_pred CC
Confidence 76
No 363
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=66.55 E-value=20 Score=37.28 Aligned_cols=81 Identities=12% Similarity=0.059 Sum_probs=52.5
Q ss_pred EEEEEEEc---CCCccchHHHHHHHHhccCcEEEEeeecCCC-CChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHH
Q 003093 74 EVIAIYVD---DDHGRNGIAALGDTLAAKRCRISFKAPLSVE-ATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 149 (848)
Q Consensus 74 ~vaii~~d---d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~-~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a 149 (848)
+|++|..+ ++|.......+.+++++.|..+......+.. .+...-...+..+...++|.|++..........++.+
T Consensus 1 ~Igvi~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIv~~~~~~~~~~~~~l 80 (280)
T cd06303 1 KIAVIYPGQQISDYWVRNIASFTARLEELNIPYELTQFSSRPGIDHRLQSQQLNEALQSKPDYLIFTLDSLRHRKLIERV 80 (280)
T ss_pred CeeEEecCccHHHHHHHHHHHHHHHHHHcCCcEEEEEeccCcccCHHHHHHHHHHHHHcCCCEEEEcCCchhhHHHHHHH
Confidence 36777764 4677888899999999999877654222111 1223445567777788999998875433334556666
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
.+.+.
T Consensus 81 ~~~~~ 85 (280)
T cd06303 81 LASGK 85 (280)
T ss_pred HhCCC
Confidence 66553
No 364
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=66.14 E-value=22 Score=38.33 Aligned_cols=82 Identities=11% Similarity=0.024 Sum_probs=58.4
Q ss_pred CcEEEEEEE--EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHH
Q 003093 71 GWREVIAIY--VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFH 147 (848)
Q Consensus 71 ~w~~vaii~--~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~ 147 (848)
.-.+++++. .+++|.......+.+++++.|.++.... +...+...-...+..+.+.++|.|++...... ....++
T Consensus 22 ~~~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~G~~v~~~~--~~~~d~~~q~~~i~~li~~~vdgIiv~~~d~~al~~~l~ 99 (336)
T PRK15408 22 AAERIAFIPKLVGVGFFTSGGNGAKEAGKELGVDVTYDG--PTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALK 99 (336)
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHHHHHHhCCEEEEEC--CCCCCHHHHHHHHHHHHHcCCCEEEEecCCHHHHHHHHH
Confidence 446788887 3578888889999999999999987532 22222233345677777889999999754333 356888
Q ss_pred HHHHcCC
Q 003093 148 VAQYLGM 154 (848)
Q Consensus 148 ~a~~~g~ 154 (848)
+|++.|.
T Consensus 100 ~a~~~gI 106 (336)
T PRK15408 100 RAMQRGV 106 (336)
T ss_pred HHHHCCC
Confidence 9998886
No 365
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=65.34 E-value=1.3e+02 Score=31.27 Aligned_cols=84 Identities=12% Similarity=0.017 Sum_probs=54.9
Q ss_pred CceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece
Q 003093 375 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 454 (848)
Q Consensus 375 g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~ 454 (848)
+..++||+... ....+-.+++..+.+... .+++.... +...++++.|.+|++|+++...
T Consensus 88 ~~~l~Ig~~~~-------------~~~~~l~~~l~~f~~~~P-~v~v~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 146 (275)
T PRK03601 88 HNELSIGASAS-------------LWECMLTPWLGRLYQNQE-ALQFEARI-------AQRQSLVKQLHERQLDLLITTE 146 (275)
T ss_pred CceEEEeccHH-------------HHHHHHHHHHHHHHHhCC-CcEEEEEE-------CChHHHHHHHHcCCCCEEEEcC
Confidence 35688888631 123556677777776653 23344433 4577899999999999999743
Q ss_pred eeecCceeeeeecccccccceEEEEeccC
Q 003093 455 AIITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 455 ~~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.... ..+ ...|.....+++++++..
T Consensus 147 ~~~~---~~l-~~~~l~~~~~~~v~~~~~ 171 (275)
T PRK03601 147 APKM---DEF-SSQLLGHFTLALYTSAPS 171 (275)
T ss_pred CCcc---CCc-cEEEecceeEEEEecCch
Confidence 3221 223 356888889999987654
No 366
>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=65.31 E-value=1.3e+02 Score=28.74 Aligned_cols=70 Identities=13% Similarity=0.104 Sum_probs=43.2
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .+++.... ++-++++.+|.+|++|+++...... ...+. +.++.+..++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~~~~~ 81 (198)
T cd08485 14 HTLPLLLRQLLSVAP-SATVSLTQ-------MSKNRQIEALDAGTIDIGFGRFYPY---QEGVV-VRNVTNERLFLGAQK 81 (198)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEE-------CCHHHHHHHHHcCCccEEEecCCCC---CCCeE-EEEeeccceEEEeCC
Confidence 345667777776653 33444443 3467899999999999998632221 12222 456677777777655
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 82 ~~ 83 (198)
T cd08485 82 SR 83 (198)
T ss_pred CC
Confidence 43
No 367
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=65.17 E-value=1.8e+02 Score=30.28 Aligned_cols=85 Identities=16% Similarity=0.115 Sum_probs=52.8
Q ss_pred ceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeecee
Q 003093 376 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 455 (848)
Q Consensus 376 ~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~ 455 (848)
..++||+... . ...+..+++..+.++.+ .+.+.... .+-++++.+|.+|++|+++....
T Consensus 97 ~~l~I~~~~~--~-----------~~~~l~~~l~~f~~~~p-~i~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~~ 155 (294)
T PRK09986 97 GRIEIGIVGT--A-----------LWGRLRPAMRHFLKENP-NVEWLLRE-------LSPSMQMAALERRELDAGIWRMA 155 (294)
T ss_pred ceEEEEEehH--H-----------hHHHHHHHHHHHHHhCC-CeEEEEEe-------CCHHHHHHHHHcCCCCEEEecCC
Confidence 4689987631 1 12344667777777765 23344443 33578899999999999985211
Q ss_pred eecCceeeeeecccccccceEEEEeccC
Q 003093 456 IITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 456 ~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
.......+. ..|.....+++++++..
T Consensus 156 -~~~~~~~l~-~~~l~~~~~~~v~~~~~ 181 (294)
T PRK09986 156 -DLEPNPGFT-SRRLHESAFAVAVPEEH 181 (294)
T ss_pred -ccCCCCCeE-EEEeecccEEEEEcCCC
Confidence 111223343 36777788888888765
No 368
>PF15179 Myc_target_1: Myc target protein 1
Probab=65.10 E-value=20 Score=33.76 Aligned_cols=38 Identities=5% Similarity=0.175 Sum_probs=26.5
Q ss_pred ccceecccchhHHHH-HHHHHHHHHHHHHHHHHHHhhcc
Q 003093 731 VDRLQLKSFSGLYLL-CGLACLLALFIYLMQIVHQFSRH 768 (848)
Q Consensus 731 ~~~l~l~~~~g~f~i-l~~g~~la~~vf~~e~~~~~~~~ 768 (848)
.+.++++++...|.+ +++|++++.+|+++-.+-.++|.
T Consensus 13 ~~~f~~~~lIlaF~vSm~iGLviG~li~~LltwlSRRRA 51 (197)
T PF15179_consen 13 LENFDWEDLILAFCVSMAIGLVIGALIWALLTWLSRRRA 51 (197)
T ss_pred hhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 345667888888855 67888888888877655555544
No 369
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=64.98 E-value=1.3e+02 Score=28.63 Aligned_cols=70 Identities=16% Similarity=0.121 Sum_probs=45.1
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.++.+ .++++... ++..++..+|.+|++|+++..- ......+. +.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~lv~~~ 80 (197)
T cd08452 13 EFLPPIVREYRKKFP-SVKVELRE-------LSSPDQVEELLKGRIDIGFLHP---PIQHTALH-IETVQSSPCVLALPK 80 (197)
T ss_pred hHHHHHHHHHHHHCC-CcEEEEEe-------cChHHHHHHHHCCCccEEEeeC---CCCCCCee-EEEeeeccEEEEEeC
Confidence 344677888877764 23454443 4577899999999999998622 11222333 456677778888776
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~h 82 (197)
T cd08452 81 QH 82 (197)
T ss_pred CC
Confidence 54
No 370
>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=64.72 E-value=38 Score=34.80 Aligned_cols=75 Identities=12% Similarity=0.003 Sum_probs=51.4
Q ss_pred EEEEEEc-----CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHH
Q 003093 75 VIAIYVD-----DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 149 (848)
Q Consensus 75 vaii~~d-----d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a 149 (848)
|+++.++ +.|.......+.+++++.|.++..... .. ...+....+..+...++|.|++...... ..+..+
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~~--~~~~~~~~~~~l~~~~vdgiii~~~~~~--~~~~~l 76 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKFV-SD--EDEEEFELPSFLEDGKVDGIILLGGIST--EYIKEI 76 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEeC-CC--ChHHHHHHHHHHHHCCCCEEEEeCCCCh--HHHHHH
Confidence 5666655 778888899999999999988765432 21 2233444556677788999998764433 247777
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
.+.|.
T Consensus 77 ~~~~i 81 (268)
T cd06277 77 KELGI 81 (268)
T ss_pred hhcCC
Confidence 77775
No 371
>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=64.72 E-value=52 Score=33.66 Aligned_cols=76 Identities=12% Similarity=0.026 Sum_probs=54.6
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. +++|.......+.+++++.|..+..... ..+.......+..+.+.++|.|++....... ..++++++.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~-~~~~~l~~~ 77 (265)
T cd06299 2 IGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNS---DENPETENRYLDNLLSQRVDGIIVVPHEQSA-EQLEDLLKR 77 (265)
T ss_pred EEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeC---CCCHHHHHHHHHHHHhcCCCEEEEcCCCCCh-HHHHHHHhC
Confidence 566664 4678888889999999999998876532 1233455667788888899999987654333 457888887
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (265)
T cd06299 78 GI 79 (265)
T ss_pred CC
Confidence 75
No 372
>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=64.37 E-value=1.3e+02 Score=28.43 Aligned_cols=70 Identities=21% Similarity=0.220 Sum_probs=44.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
.+-.+++..+.+..+ .+++.... ++...+..++.+|++|+++.... .....+ ...+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~-------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~ 80 (198)
T cd08447 13 SFLPRLLAAARAALP-DVDLVLRE-------MVTTDQIEALESGRIDLGLLRPP---FARPGL-ETRPLVREPLVAAVPA 80 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHcCCceEEEecCC---CCCCCe-eEEEeecCceEEEecC
Confidence 455677888877764 23344432 45788999999999999986321 111222 2356677778877765
Q ss_pred cC
Q 003093 482 RK 483 (848)
Q Consensus 482 ~~ 483 (848)
..
T Consensus 81 ~~ 82 (198)
T cd08447 81 GH 82 (198)
T ss_pred CC
Confidence 44
No 373
>cd08550 GlyDH-like Glycerol_dehydrogenase-like. Families of proteins related to glycerol dehydrogenases. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site. Some subfamilies have not been characterized till now.
Probab=64.25 E-value=26 Score=38.08 Aligned_cols=76 Identities=16% Similarity=0.178 Sum_probs=52.9
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
..+.++++.+| +++.+|+....+ ....+.+.+.|++.|+.+.... +....+.+.+...+..+++.++|+||..+.+
T Consensus 12 ~~l~~~~~~~g-~~~liv~~~~~~-~~~~~~v~~~l~~~~i~~~~~~-~~~~p~~~~v~~~~~~~~~~~~d~IIavGGG 87 (349)
T cd08550 12 KEIAAILSTFG-SKVAVVGGKTVL-KKSRPRFEAALAKSIIVVDVIV-FGGECSTEEVVKALCGAEEQEADVIIGVGGG 87 (349)
T ss_pred HHHHHHHHHcC-CeEEEEEChHHH-HHHHHHHHHHHHhcCCeeEEEE-cCCCCCHHHHHHHHHHHHhcCCCEEEEecCc
Confidence 45667788888 888777643333 3556788888988887654332 4333355677888888888899999977654
No 374
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=64.09 E-value=65 Score=30.48 Aligned_cols=65 Identities=12% Similarity=0.016 Sum_probs=38.9
Q ss_pred eeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEecc
Q 003093 403 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 403 ~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
+...++..+.+..+ .+++.... .+ .+.++.+|++|+++.... .....+ .+.+.....+++++++.
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~---------~~-~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~~ 78 (194)
T cd08432 14 WLIPRLARFQARHP-DIDLRLST---------SD-RLVDFAREGIDLAIRYGD---GDWPGL-EAERLMDEELVPVCSPA 78 (194)
T ss_pred HHHHHhHHHHHHCC-CeEEEEEe---------cC-CccccccccccEEEEecC---CCCCCc-ceEEccCCcEEEecCHH
Confidence 44566677777664 34455543 11 456788999999986221 111222 35667778888887654
No 375
>PRK10537 voltage-gated potassium channel; Provisional
Probab=63.80 E-value=5.9 Score=43.56 Aligned_cols=56 Identities=23% Similarity=0.307 Sum_probs=42.7
Q ss_pred CCCCCcchhhhhHHHHhhhcC--ccccccchhHHHHHHHHhhhhhhhccccceeeeee
Q 003093 528 PPKRQVVTIFWFSFSTMFFAH--KEKTVSALGRLVLIIWLFVVLIINSSYTASLTSIL 583 (848)
Q Consensus 528 ~~~~~~~~~~~~~~~~l~~~~--~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~L 583 (848)
+...++.+++|+++.++...| ...|.+..+|++.+++.++++.+..+..+.++..+
T Consensus 164 ~~~~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~p~ 221 (393)
T PRK10537 164 PPIESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFGPV 221 (393)
T ss_pred cCCCCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445689999999999888554 55789999999999999998776655555544433
No 376
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=63.70 E-value=24 Score=36.40 Aligned_cols=79 Identities=11% Similarity=0.058 Sum_probs=55.0
Q ss_pred EEEEEEE---cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHH
Q 003093 74 EVIAIYV---DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVA 149 (848)
Q Consensus 74 ~vaii~~---dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a 149 (848)
+|+++.. ++.|.....+.+.+++++.|..+..... ...+.......+.++...++|.+++...... ....++.+
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~~--~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~l~~~ 78 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRGP--ETFDVADMARLIEAAIAAKPDGIVVTIPDPDALDPAIKRA 78 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEECC--CCCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHHHH
Confidence 4667764 4578888999999999999998875432 1113345566777787789999988754332 34567777
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
++.|.
T Consensus 79 ~~~~i 83 (271)
T cd06312 79 VAAGI 83 (271)
T ss_pred HHCCC
Confidence 77775
No 377
>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=63.60 E-value=27 Score=36.02 Aligned_cols=80 Identities=14% Similarity=0.147 Sum_probs=53.6
Q ss_pred EEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcH-HHHHHHHH
Q 003093 74 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRG-PVVFHVAQ 150 (848)
Q Consensus 74 ~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~-~~~~~~a~ 150 (848)
||++|..+ ++|.......+.++++++|.++.....-. ..+.......+.++...++|.|++....... ...+..+.
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 46777744 66778888999999999999887653211 1133445566777777889999886543332 34667777
Q ss_pred HcCC
Q 003093 151 YLGM 154 (848)
Q Consensus 151 ~~g~ 154 (848)
+.|.
T Consensus 80 ~~~i 83 (273)
T cd06310 80 DAGI 83 (273)
T ss_pred HCCC
Confidence 7665
No 378
>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=63.48 E-value=35 Score=35.69 Aligned_cols=77 Identities=5% Similarity=0.015 Sum_probs=55.4
Q ss_pred EEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-CcHHHHHHHHHH
Q 003093 75 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQY 151 (848)
Q Consensus 75 vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~-~~~~~~~~~a~~ 151 (848)
|+++..+ +.|.......+.+++++.|.++..... ..+.......++.+.+.++|.|++.... ......++++++
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 5677743 667788889999999999999876432 2233455677777888899999887543 334567888888
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|.
T Consensus 79 ~~i 81 (288)
T cd01538 79 AGI 81 (288)
T ss_pred CCC
Confidence 775
No 379
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=62.92 E-value=25 Score=37.76 Aligned_cols=62 Identities=18% Similarity=0.182 Sum_probs=43.9
Q ss_pred cCCCceEEEEecCCCCccceEEeCCCcceeeeeHHHHHHHHHhCCCCc-ceEEeeCCCCCCCCChhHHHHHHhcCeeeEE
Q 003093 372 PNNGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAV-PYKLIPFGDGHNNPSCTELVRLITAGVYDAA 450 (848)
Q Consensus 372 ~~~g~~lrv~v~~~~~~~p~~~~~~~~~~~G~~~dll~~i~~~l~~~~-~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~ 450 (848)
|..|+++++++. +|.. .-+.-.|++.+.+.+|+++ ++... +-.-+...|.+|++|+.
T Consensus 25 ~~~~~~V~~~~~---~W~~----------~~~~t~v~~~iLe~~GY~V~e~~~~---------~~~~~~~ala~GdiDv~ 82 (331)
T PRK11119 25 PGKGITVQPAQS---TIAE----------ETFQTLLVSRALEKLGYDVNKPKEV---------DYNVFYTSIANGDATFT 82 (331)
T ss_pred CCCCeEEEEeec---CccH----------HHHHHHHHHHHHHHcCCceeeeccc---------CcHHHHHHHHcCCCeEe
Confidence 567899999887 3322 1244567888888899986 55443 23677889999999998
Q ss_pred eecee
Q 003093 451 VGDIA 455 (848)
Q Consensus 451 ~~~~~ 455 (848)
.....
T Consensus 83 ~~~W~ 87 (331)
T PRK11119 83 AVNWF 87 (331)
T ss_pred hhhcc
Confidence 86443
No 380
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=62.87 E-value=1.2e+02 Score=29.15 Aligned_cols=108 Identities=21% Similarity=0.247 Sum_probs=61.0
Q ss_pred EEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecC
Q 003093 31 LLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLS 110 (848)
Q Consensus 31 ~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~ 110 (848)
+||-++|...|...-.--.+...++..+..+++.... .++ ++++++.-.+.. .....+.+.+ |..+... .+.
T Consensus 38 iIsRG~ta~~lr~~~~iPVV~I~~s~~Dil~al~~a~-~~~-~~Iavv~~~~~~--~~~~~~~~ll---~~~i~~~-~~~ 109 (176)
T PF06506_consen 38 IISRGGTAELLRKHVSIPVVEIPISGFDILRALAKAK-KYG-PKIAVVGYPNII--PGLESIEELL---GVDIKIY-PYD 109 (176)
T ss_dssp EEEEHHHHHHHHCC-SS-EEEE---HHHHHHHHHHCC-CCT-SEEEEEEESS-S--CCHHHHHHHH---T-EEEEE-EES
T ss_pred EEECCHHHHHHHHhCCCCEEEECCCHhHHHHHHHHHH-hcC-CcEEEEeccccc--HHHHHHHHHh---CCceEEE-EEC
Confidence 4454555444433111223445556666666666643 444 899998765554 2255555555 5555533 222
Q ss_pred CCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 111 VEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 111 ~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
+..++...+.+++..+.++|+-.. ...+.|++.|+.
T Consensus 110 ---~~~e~~~~i~~~~~~G~~viVGg~------~~~~~A~~~gl~ 145 (176)
T PF06506_consen 110 ---SEEEIEAAIKQAKAEGVDVIVGGG------VVCRLARKLGLP 145 (176)
T ss_dssp ---SHHHHHHHHHHHHHTT--EEEESH------HHHHHHHHTTSE
T ss_pred ---CHHHHHHHHHHHHHcCCcEEECCH------HHHHHHHHcCCc
Confidence 458999999999999999988543 356788888983
No 381
>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=62.76 E-value=96 Score=32.91 Aligned_cols=147 Identities=13% Similarity=0.034 Sum_probs=75.3
Q ss_pred CCeEEEEccCCchhHHHHHHhhccC-CccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEE--
Q 003093 3 GQTVAIIGPQDAVTSHVVSHVANEL-QVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIY-- 79 (848)
Q Consensus 3 ~~V~aiIGp~~S~~~~ava~i~~~~-~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~-- 79 (848)
++...||++. .....++..++.++ ++-++...+..+.-...-..+.||..- ..+.+-.+|.++..- .+++.+.
T Consensus 60 ~g~dlIi~~g-~~~~~~~~~vA~~yPd~~F~~~d~~~~~~~~Nv~~~~f~~~e-~~fLaG~~Aa~~tkt--~~vg~ig~i 135 (306)
T PF02608_consen 60 QGYDLIIGHG-FEYSDALQEVAKEYPDTKFIIIDGYIDAPEPNVISITFREEE-ASFLAGYLAALMTKT--GKVGFIGDI 135 (306)
T ss_dssp TT-SEEEEES-GGGHHHHHHHHTC-TTSEEEEESS---ST-TTEEEEEE-HHH-HHHHHHHHHHHHHSS--TEEEEEEEE
T ss_pred cCCCEEEEcc-HHHHHHHHHHHHHCCCCEEEEEecCcCCCCCcEEEEEccccc-hhHHHHHHHHHHhcc--Ccccccccc
Confidence 4666777733 44556777788777 455554443322111112234444422 334455555555443 3677776
Q ss_pred --EcCCCccchHHHHHHHHhccCcEEEEeeecCCCC-ChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 80 --VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEA-TEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 80 --~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~-~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
.+.+--......|..-++..+-.+.....+...- +...-......+-..++|||+..+.. ....++++|++.|.
T Consensus 136 ~G~~~p~~~~~~~gF~~Ga~~~np~i~v~~~~~gs~~D~~~~~~~a~~li~~GaDvI~~~ag~-~~~gv~~aa~e~g~ 212 (306)
T PF02608_consen 136 GGMDIPPVNRFINGFIAGAKYVNPDIKVNVSYTGSFNDPAKAKEAAEALIDQGADVIFPVAGG-SGQGVIQAAKEAGV 212 (306)
T ss_dssp ES--SCTTHHHHHHHHHHHHHTTTT-EEEEEE-SSSS-HHHHHHHHHHHHHTT-SEEEEE-CC-CHHHHHHHHHHHTH
T ss_pred cCCCcHhHHHHHHHHHHHHHHhCcCceEEEEEcCCcCchHHHHHHHHHHhhcCCeEEEECCCC-CchHHHHHHHHcCC
Confidence 3444444566677777766544433333333322 22333444456666899999986664 44568999999885
No 382
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=62.45 E-value=1.3e+02 Score=27.71 Aligned_cols=92 Identities=13% Similarity=-0.018 Sum_probs=56.0
Q ss_pred HHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecC--CCCChHHH---HHHHHHHhcCCCeEEEEE
Q 003093 62 AIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLS--VEATEDEI---TDLLVKVALTESRIIVVH 136 (848)
Q Consensus 62 ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~--~~~~~~d~---~~~l~~i~~~~~~viv~~ 136 (848)
.+.+.+...+-....-+|.+.... .....+.++|+..|.++....... ...+..|. ...+..+...+.|.|++.
T Consensus 28 ~l~~~~~~~~~~~~~r~y~~~~~~-~~~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLv 106 (149)
T cd06167 28 KLLEFLRDGGEIVLARAYGNWTSP-ERQRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLV 106 (149)
T ss_pred HHHHHHHhCCeEEEEEEEEecCCc-hhHHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEE
Confidence 334444433323344444443221 456789999999999987665321 11122232 233444444578999998
Q ss_pred ccCCcHHHHHHHHHHcCC
Q 003093 137 THYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 137 ~~~~~~~~~~~~a~~~g~ 154 (848)
+...+-..+++.+++.|.
T Consensus 107 SgD~Df~~~i~~lr~~G~ 124 (149)
T cd06167 107 SGDSDFVPLVERLRELGK 124 (149)
T ss_pred ECCccHHHHHHHHHHcCC
Confidence 888889999999999875
No 383
>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=62.31 E-value=34 Score=34.91 Aligned_cols=78 Identities=4% Similarity=-0.069 Sum_probs=53.7
Q ss_pred EEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCC-cHHHHHHHHH
Q 003093 74 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVAQ 150 (848)
Q Consensus 74 ~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~-~~~~~~~~a~ 150 (848)
+|++|..+ +.|.......+.+++++.|+++.....- .+.......++++...++|.|++..... .....+..++
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~---~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~~~~~~l~ 77 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDAQ---NDVSKQIQQIEDLIAQGVDGIIISPVDSAALTPALKKAN 77 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECCC---CCHHHHHHHHHHHHHcCCCEEEEeCCCchhHHHHHHHHH
Confidence 46777754 5788888999999999999887654322 1334455677777777999998875433 3234667777
Q ss_pred HcCC
Q 003093 151 YLGM 154 (848)
Q Consensus 151 ~~g~ 154 (848)
+.+.
T Consensus 78 ~~~i 81 (267)
T cd01536 78 AAGI 81 (267)
T ss_pred HCCC
Confidence 6664
No 384
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=61.65 E-value=34 Score=35.12 Aligned_cols=77 Identities=8% Similarity=0.014 Sum_probs=53.1
Q ss_pred EEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHHHH
Q 003093 75 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQY 151 (848)
Q Consensus 75 vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a~~ 151 (848)
|+++..+ +.|.....+.+.+++++.|.++..... ..+.......+.++.+.++|.+++...... ....+.++++
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~~---~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSIA---NQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKK 78 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHH
Confidence 4555544 667888889999999999988865321 123344566777777789999998654332 3456778877
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|+
T Consensus 79 ~~i 81 (267)
T cd06322 79 AGI 81 (267)
T ss_pred CCC
Confidence 775
No 385
>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=61.61 E-value=30 Score=38.30 Aligned_cols=78 Identities=6% Similarity=-0.028 Sum_probs=56.1
Q ss_pred cCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC--CcHHHHHH
Q 003093 70 YGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY--NRGPVVFH 147 (848)
Q Consensus 70 ~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~--~~~~~~~~ 147 (848)
.+.+++.+|+.......+..+.+.+.|++.|+++.....+.+..+.+.+...+..++..++|+||-.+.+ -+...++.
T Consensus 19 ~~~~k~liVtd~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS~iD~AK~iA 98 (398)
T cd08178 19 KGKKRAFIVTDRFMVKLGYVDKVIDVLKRRGVETEVFSDVEPDPSLETVRKGLELMNSFKPDTIIALGGGSPMDAAKIMW 98 (398)
T ss_pred cCCCeEEEEcChhHHhCccHHHHHHHHHHCCCeEEEecCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHHHH
Confidence 4568888887443333447788999999999887655556656666788888899999999999977654 34444443
No 386
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=61.60 E-value=2.1e+02 Score=29.85 Aligned_cols=47 Identities=13% Similarity=-0.001 Sum_probs=33.0
Q ss_pred CChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEeccC
Q 003093 433 PSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVRK 483 (848)
Q Consensus 433 ~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~~ 483 (848)
+...+++.+|.+|++|+++..... ....+. +.|.....++++++...
T Consensus 125 ~~~~~~~~~L~~~~~d~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~~ 171 (294)
T PRK13348 125 DDQDHTFALLERGEVVGCVSTQPK---PMRGCL-AEPLGTMRYRCVASPAF 171 (294)
T ss_pred cchHHHHHHHhcCCeEEEEecCCc---ccCCcc-cccccccceEEEEccch
Confidence 347789999999999998753222 223343 67788888888887553
No 387
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=61.39 E-value=2.1e+02 Score=29.79 Aligned_cols=64 Identities=16% Similarity=0.088 Sum_probs=40.4
Q ss_pred HHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEecc
Q 003093 406 DVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 482 (848)
Q Consensus 406 dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~~ 482 (848)
.++..+.++. .+++.... ++-..+++.|.+|++|+++...... ...+. +.|+.+..++++++++
T Consensus 107 ~~l~~~~~~~--~i~i~l~~-------~~~~~~~~~l~~g~~d~~i~~~~~~---~~~l~-~~~l~~~~~~~v~~~~ 170 (292)
T TIGR03298 107 PALAPVLAQE--GVLLDLVV-------EDQDHTAELLRSGEVLGAVTTQAKP---VQGCR-VVPLGAMRYLAVASPA 170 (292)
T ss_pred HHHHHHHhCC--CceEEEEe-------CcchhHHHHHhCCCceEEEecCCCC---CCCce-EEecCCceEEEEECch
Confidence 4556666653 33454443 3355789999999999998643221 22333 4677888888887654
No 388
>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=61.19 E-value=1.2e+02 Score=30.14 Aligned_cols=113 Identities=17% Similarity=0.160 Sum_probs=69.2
Q ss_pred ccCCccEEecccC--CCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcE
Q 003093 25 NELQVPLLSFSAT--DPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCR 102 (848)
Q Consensus 25 ~~~~vP~Is~~at--~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~ 102 (848)
+..++..|-.-|| .|.|...+ + + .-++......++.++.. .++++|....+ -.+...+..+..+..
T Consensus 84 e~~G~d~illlCTG~F~~l~~~~-~-l---leP~ril~~lV~al~~~---~~vGVivP~~e----Q~~~~~~kW~~l~~~ 151 (221)
T PF07302_consen 84 EAQGYDVILLLCTGEFPGLTARN-P-L---LEPDRILPPLVAALVGG---HQVGVIVPLPE----QIAQQAEKWQPLGNP 151 (221)
T ss_pred HHCCCCEEEEeccCCCCCCCCCc-c-e---eehHHhHHHHHHHhcCC---CeEEEEecCHH----HHHHHHHHHHhcCCC
Confidence 3345555544444 34444322 3 2 22333334444444433 79999997764 344455566666666
Q ss_pred EEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC--CcHHHHHHHH
Q 003093 103 ISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY--NRGPVVFHVA 149 (848)
Q Consensus 103 v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~--~~~~~~~~~a 149 (848)
+.+...-|+..+..++...-+++++.++|+|+++|-+ ...+.+++++
T Consensus 152 ~~~a~asPy~~~~~~l~~Aa~~L~~~gadlIvLDCmGYt~~~r~~~~~~ 200 (221)
T PF07302_consen 152 VVVAAASPYEGDEEELAAAARELAEQGADLIVLDCMGYTQEMRDIVQRA 200 (221)
T ss_pred eEEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEECCCCCHHHHHHHHHH
Confidence 6666666664567889999999999999999998754 4555565554
No 389
>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=60.89 E-value=31 Score=34.87 Aligned_cols=78 Identities=9% Similarity=0.080 Sum_probs=55.5
Q ss_pred EEEEEEEc---CCCccchHHHHHHHHhc--cCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHH
Q 003093 74 EVIAIYVD---DDHGRNGIAALGDTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHV 148 (848)
Q Consensus 74 ~vaii~~d---d~~g~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~ 148 (848)
+|++|..+ +.|+......+.+++++ .++++..... ..+..+....+.++...+++.|+..........+...
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~ 77 (269)
T cd01391 1 KIGVLLPLSGSAPFGAQLLAGIELAAEEIGRGLEVILADS---QSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVEL 77 (269)
T ss_pred CceEEeecCCCcHHHHHHHHHHHHHHHHhCCceEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEecCCCHHHHHHHHH
Confidence 36777753 57788888999999999 7777765432 2233466777788887889999988776555547777
Q ss_pred HHHcCC
Q 003093 149 AQYLGM 154 (848)
Q Consensus 149 a~~~g~ 154 (848)
+.+.|.
T Consensus 78 ~~~~~i 83 (269)
T cd01391 78 AAAAGI 83 (269)
T ss_pred HHHcCC
Confidence 777665
No 390
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=60.79 E-value=21 Score=35.73 Aligned_cols=78 Identities=13% Similarity=0.116 Sum_probs=44.0
Q ss_pred CcceeeeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeece-------eeecCceeeeeeccc
Q 003093 397 SEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI-------AIITNRTKMADFTQP 469 (848)
Q Consensus 397 ~~~~~G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~-------~~t~~R~~~~dfs~p 469 (848)
..++.|+.--|.+.+.+ .++++.+-+.. | -..-++.|.+|++|+++.+- .-..+..-.++|..-
T Consensus 23 Sr~YEGLATGl~~~f~~-~~ip~~~aymR-------G-a~~Rie~l~~g~yDfaVvS~lAA~~~i~~~~~l~i~~~fG~~ 93 (232)
T PF14503_consen 23 SRRYEGLATGLYEQFEE-SGIPLNFAYMR-------G-AENRIEALKNGRYDFAVVSKLAAEHYIEEGEDLEIVLEFGPG 93 (232)
T ss_dssp SHHHHHHHHHHHCTTT---TS-EEEEE-S---------HHHHHHHHHTTS-SEEEEEHHHHCCCCCC-SSEEEEEE--TT
T ss_pred hhhhHHHHHHHHHHhcc-CCCceEEEeec-------c-chHHHHHHHhCCcceEeehHHHHHHHHhhccCeEEEEeeCCC
Confidence 55788888888777776 77776677664 3 44568999999999999752 112233445666655
Q ss_pred ccccceEEEEeccC
Q 003093 470 YIESGLVVVAPVRK 483 (848)
Q Consensus 470 ~~~~~~~~v~~~~~ 483 (848)
-+.+.-+++.+.+.
T Consensus 94 sYvs~Hvli~~~~~ 107 (232)
T PF14503_consen 94 SYVSEHVLIFRDGE 107 (232)
T ss_dssp SSS--EEEEEETT-
T ss_pred CcccceEEEEecCC
Confidence 55555556655443
No 391
>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=60.64 E-value=74 Score=28.37 Aligned_cols=71 Identities=13% Similarity=0.125 Sum_probs=45.7
Q ss_pred EEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC----CcHHHHHHHHHHcC
Q 003093 78 IYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY----NRGPVVFHVAQYLG 153 (848)
Q Consensus 78 i~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~----~~~~~~~~~a~~~g 153 (848)
....++.-.-+..-+...++..|.+|.+..... . ....+..+.+.+|++|++++.. +.+..+++++++.|
T Consensus 5 ~~~~gd~H~lG~~~~~~~l~~~G~~vi~lG~~v---p---~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~ 78 (122)
T cd02071 5 AKPGLDGHDRGAKVIARALRDAGFEVIYTGLRQ---T---PEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELG 78 (122)
T ss_pred EecCCChhHHHHHHHHHHHHHCCCEEEECCCCC---C---HHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcC
Confidence 333444444456667778899999988754432 1 2345566667889999998754 34455677777776
Q ss_pred C
Q 003093 154 M 154 (848)
Q Consensus 154 ~ 154 (848)
.
T Consensus 79 ~ 79 (122)
T cd02071 79 A 79 (122)
T ss_pred C
Confidence 5
No 392
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=60.60 E-value=1.8e+02 Score=28.76 Aligned_cols=107 Identities=20% Similarity=0.191 Sum_probs=62.4
Q ss_pred CCCCChHHhhcCCCC-eeEEeCchHHHHHHhh---hCCCccCcccC----CCHHHHHHHhhcCCCCCceEEEEccHHHHH
Q 003093 590 SPIKGIDSLRSSNYP-IGYQVNSFARNYLVDE---LNIDESRLVPL----NSPEEYAKALKDGPHKGGVAAVVDDRAYAE 661 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~-i~~~~~s~~~~~l~~~---~~~~~~~~~~~----~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~ 661 (848)
..|++++||.+.+.+ |-=.+||-....+... .+.....+.-| .+-.....++.. |+.|+=+.-+..++
T Consensus 87 k~i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~----G~AD~GvGlr~~A~ 162 (223)
T COG1910 87 KNISSLEDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVAS----GRADAGVGLRHAAE 162 (223)
T ss_pred CccccHHHHhhcCcEEEecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHc----CCCCccccHHHHHH
Confidence 458999999954444 2234677666555432 23333444444 345566777888 89998888554433
Q ss_pred HHHhcC-CcEEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccCc
Q 003093 662 LFLSTR-CEFSIVGQVFTKNGWGFAFPRDSPLAVDISTAILKLSENGD 708 (848)
Q Consensus 662 ~~~~~~-~~l~~~~~~~~~~~~~~~~~k~spl~~~in~~i~~l~e~G~ 708 (848)
+. -+|.-+ ....|-|+++|+.--.+.+...+..|...++
T Consensus 163 ----~~gL~Fipl----~~E~YD~virke~~~~~~vr~fi~~L~s~~~ 202 (223)
T COG1910 163 ----KYGLDFIPL----GDEEYDFVIRKERLDKPVVRAFIKALKSEGF 202 (223)
T ss_pred ----HcCCceEEc----ccceEEEEEehhHccCHHHHHHHHHhccccc
Confidence 32 234433 3456888898876544555555555554433
No 393
>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=60.50 E-value=49 Score=34.01 Aligned_cols=77 Identities=10% Similarity=0.085 Sum_probs=53.2
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. ++.|.......+.+.+++.|..+..... ..+.......+..+...++|.|++.........+++++++.
T Consensus 2 Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~ 78 (269)
T cd06281 2 IGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIANS---LNDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALASL 78 (269)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEeC---CCChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhC
Confidence 566664 4677788889999999999998765432 11234456677778878899998865443444567777776
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 79 ~i 80 (269)
T cd06281 79 DL 80 (269)
T ss_pred CC
Confidence 64
No 394
>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=60.41 E-value=45 Score=34.18 Aligned_cols=78 Identities=6% Similarity=0.026 Sum_probs=51.8
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. ++.|.......+.+++++.|.++.....- . ..+......++.+...++|.|++..........+..+.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~-~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 79 (270)
T cd01545 2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCD-S-GSPDLAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEA 79 (270)
T ss_pred EEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCC-C-CchHHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHHhc
Confidence 456663 46788889999999999999887654322 1 1122455566667778899888864433334567777776
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 80 ~i 81 (270)
T cd01545 80 GV 81 (270)
T ss_pred CC
Confidence 65
No 395
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=60.28 E-value=1.2e+02 Score=31.28 Aligned_cols=69 Identities=16% Similarity=0.130 Sum_probs=45.7
Q ss_pred HHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCe-eeEEeeceeeecCc---e--eeeeecccccccceEEEE
Q 003093 406 DVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGV-YDAAVGDIAIITNR---T--KMADFTQPYIESGLVVVA 479 (848)
Q Consensus 406 dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~-~D~~~~~~~~t~~R---~--~~~dfs~p~~~~~~~~v~ 479 (848)
+|.+.+.+..|.++++.+- .-..+.+++.+|. +|+.+..=...... . -.-+...+|....+++++
T Consensus 46 ~i~~~F~~~~~~~V~~~f~---------gS~~l~~qIe~Ga~~D~fiSa~~~~~~~l~~~g~~~~~~~~~fa~n~lvl~~ 116 (258)
T COG0725 46 EIAKQFEKETGVKVEVEFG---------GSGALARQIEQGAPADLFISADDAYMDKLEDKGLIYADSRIVFAGNRLVLAV 116 (258)
T ss_pred HHHHHHHHHHCCeEEEEec---------chHHHHHHHHcCCCcCEEEECCHHHHHHHHhcCCccCCceEEeeCCeEEEEE
Confidence 6677777777777666653 3567888888876 88877633222111 1 123367788888999999
Q ss_pred eccC
Q 003093 480 PVRK 483 (848)
Q Consensus 480 ~~~~ 483 (848)
+...
T Consensus 117 ~~~~ 120 (258)
T COG0725 117 PKGS 120 (258)
T ss_pred eCCC
Confidence 8765
No 396
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=59.32 E-value=51 Score=31.24 Aligned_cols=65 Identities=15% Similarity=0.018 Sum_probs=36.7
Q ss_pred cccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEEEeCC--ccccCCceeeecCCCCchHHHHH
Q 003093 628 LVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQ--VFTKNGWGFAFPRDSPLAVDIST 698 (848)
Q Consensus 628 ~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~k~spl~~~in~ 698 (848)
....++.+...+++.. |...+++.+.. ....... ..+..+.. ......++++.+|+.+....+..
T Consensus 126 ~~~~~~~~~~~~~v~~----g~gi~~~p~~~-~~~~~~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 192 (197)
T cd08422 126 RLVVNDGEALRAAALA----GLGIALLPDFL-VAEDLAS-GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRA 192 (197)
T ss_pred cEEEccHHHHHHHHHc----CCcEEEecHHH-HhhhccC-CeEEEecCcccCCCceEEEEEcccccCCHHHHH
Confidence 3456888899999988 55556665433 3222222 23333322 23346678888877665444443
No 397
>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=59.28 E-value=39 Score=35.02 Aligned_cols=77 Identities=5% Similarity=-0.092 Sum_probs=53.2
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHHHH
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQY 151 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a~~ 151 (848)
|+++.. .+.|.......+.+++++.|.++..... ..+...-...+..+...++|.|++...... ....++.+.+
T Consensus 2 igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~~---~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~ 78 (282)
T cd06318 2 IGFSQYTLNSPFFAALTEAAKAHAKALGYELISTDA---QGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKA 78 (282)
T ss_pred eeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEcC---CCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHH
Confidence 566653 3677788889999999999998865422 123344456777888889999998754333 2456778877
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|.
T Consensus 79 ~~i 81 (282)
T cd06318 79 AGV 81 (282)
T ss_pred CCC
Confidence 775
No 398
>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=58.51 E-value=1.3e+02 Score=26.39 Aligned_cols=81 Identities=12% Similarity=0.140 Sum_probs=42.3
Q ss_pred HHHcCcEEEEEEEEcCC-CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHH
Q 003093 67 VDHYGWREVIAIYVDDD-HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVV 145 (848)
Q Consensus 67 ~~~~~w~~vaii~~dd~-~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~ 145 (848)
+...|.+.|.=+-.|++ -+......+.+++++.|+..++.-......+..++....+.+.....-|.+.|.++..+..+
T Consensus 23 la~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y~~iPv~~~~~~~~~v~~f~~~l~~~~~Pvl~hC~sG~Ra~~l 102 (110)
T PF04273_consen 23 LAAQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQYVHIPVDGGAITEEDVEAFADALESLPKPVLAHCRSGTRASAL 102 (110)
T ss_dssp HHHCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EEEE----TTT--HHHHHHHHHHHHTTTTSEEEE-SCSHHHHHH
T ss_pred HHHCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeEEEeecCCCCCCHHHHHHHHHHHHhCCCCEEEECCCChhHHHH
Confidence 44589999988877754 35556677889999999997765333333455666666666665443454444445444444
Q ss_pred HH
Q 003093 146 FH 147 (848)
Q Consensus 146 ~~ 147 (848)
..
T Consensus 103 ~~ 104 (110)
T PF04273_consen 103 WA 104 (110)
T ss_dssp HH
T ss_pred HH
Confidence 33
No 399
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=58.39 E-value=6.2 Score=48.47 Aligned_cols=53 Identities=13% Similarity=0.319 Sum_probs=45.9
Q ss_pred cchhhhhHHHHhhhcC--ccccccchhHHHHHHHHhhhhhhhccccceeeeeeee
Q 003093 533 VVTIFWFSFSTMFFAH--KEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTV 585 (848)
Q Consensus 533 ~~~~~~~~~~~l~~~~--~~~p~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~ 585 (848)
...++|+++.++...| .-.|.+...|++.++|.++++++.++..+++++++..
T Consensus 251 Yi~slYwai~TmtTVGYGDi~p~t~~E~i~~i~~ml~g~~~~a~~ig~i~~li~~ 305 (823)
T PLN03192 251 YISAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE 305 (823)
T ss_pred HHHHHHHHHHHHhhccCCCcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4558999999998665 5589999999999999999999999999999987754
No 400
>cd08175 G1PDH Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner. Glycerol-1-phosphate dehydrogenase (G1PDH) plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires a Ni++ ion. In Bacillus subtilis, it has been described as AraM gene in L-arabinose (ara) operon. AraM protein forms homodimer. This family is bacteria specific.
Probab=57.93 E-value=38 Score=36.74 Aligned_cols=84 Identities=11% Similarity=0.167 Sum_probs=55.4
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCC--CChHHHHHHHHHHhcCCCeEEEEEcc
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVE--ATEDEITDLLVKVALTESRIIVVHTH 138 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~--~~~~d~~~~l~~i~~~~~~viv~~~~ 138 (848)
+.+.++++.++.+++.+|+....+ ....+.+.+.|++.|+.+......... .+.+.+...+..+++ ++|+||..+.
T Consensus 12 ~~l~~~~~~~~~~~~livtd~~~~-~~~~~~v~~~l~~~~i~~~~~~~~~~~~~pt~~~v~~~~~~~~~-~~d~IIaIGG 89 (348)
T cd08175 12 ERLPEILKEFGYKKALIVADENTY-AAAGKKVEALLKRAGVVVLLIVLPAGDLIADEKAVGRVLKELER-DTDLIIAVGS 89 (348)
T ss_pred HHHHHHHHhcCCCcEEEEECCcHH-HHHHHHHHHHHHHCCCeeEEeecCCCcccCCHHHHHHHHHHhhc-cCCEEEEECC
Confidence 456677888888998888743332 223577888999999876443333332 455677777777777 8999998765
Q ss_pred C--CcHHHHH
Q 003093 139 Y--NRGPVVF 146 (848)
Q Consensus 139 ~--~~~~~~~ 146 (848)
+ -+...++
T Consensus 90 Gs~~D~aK~v 99 (348)
T cd08175 90 GTINDITKYV 99 (348)
T ss_pred cHHHHHHHHH
Confidence 4 3444444
No 401
>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=57.66 E-value=58 Score=33.34 Aligned_cols=76 Identities=18% Similarity=0.081 Sum_probs=52.6
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. ++.|.......+.+++++.|..+... ....+.......++++.+.++|.+++..... ....++.+++.
T Consensus 2 i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~---~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06273 2 IGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVA---SSGYDLDREYAQARKLLERGVDGLALIGLDH-SPALLDLLARR 77 (268)
T ss_pred eEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEe---cCCCCHHHHHHHHHHHHhcCCCEEEEeCCCC-CHHHHHHHHhC
Confidence 566664 46777888899999999999888753 2222334456677788878899888765432 23556677776
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (268)
T cd06273 78 GV 79 (268)
T ss_pred CC
Confidence 65
No 402
>KOG3713 consensus Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism]
Probab=57.32 E-value=12 Score=41.27 Aligned_cols=61 Identities=18% Similarity=0.319 Sum_probs=46.4
Q ss_pred HHHHHhhhhhcccCCCCCCCCCCCcchhhhhHHHHhhhcC--ccccccchhHHHHHHHHhhhhhhhc
Q 003093 509 AVGAVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMFFAH--KEKTVSALGRLVLIIWLFVVLIINS 573 (848)
Q Consensus 509 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~p~s~~~R~~~~~w~~~~lil~~ 573 (848)
+.+.+++.+|+-.+ +++..++--++|++..+|..-| .-.|++..+|++....++.++++.+
T Consensus 358 iFStlvY~~Ek~~~----~~~FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gklvas~cil~GVLvlA 420 (477)
T KOG3713|consen 358 IFSTLVYFAEKDEP----DTKFTSIPAGFWWAVVTMTTVGYGDMVPVTVLGKLVASLCILCGVLVLA 420 (477)
T ss_pred HHHHHHHHhhhcCC----CCCCccccchhheeeEEEeeecccCccccccchHHHHHHHHHHhHHHhh
Confidence 44445667776543 3346778899999999988665 5589999999999999999887765
No 403
>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=57.00 E-value=43 Score=35.54 Aligned_cols=87 Identities=13% Similarity=0.118 Sum_probs=59.6
Q ss_pred EEEEEEE----EcCCCccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHH
Q 003093 73 REVIAIY----VDDDHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFH 147 (848)
Q Consensus 73 ~~vaii~----~dd~~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~ 147 (848)
++++++. .|..|.+...+.+.+.-++. |+++.+.+..+. +..++...+.++.+.+.|+|+.++..-. ..+..
T Consensus 2 ~~v~~~~~g~~~D~g~n~~~~~G~~~~~~~~~~i~~~~~e~~~~--~~~~~~~~~~~~~~~g~dlIi~~g~~~~-~~~~~ 78 (306)
T PF02608_consen 2 KKVALLDPGGINDKGFNQSAYEGLKRAEKELDGIEIIYVENVPE--TDADYEEAIRQLADQGYDLIIGHGFEYS-DALQE 78 (306)
T ss_dssp EEEEEESSS-CCCSSHHHHHHHHHHHHHHHCTTEEEEEEES-S---TCHHHHHHHHHHHHTT-SEEEEESGGGH-HHHHH
T ss_pred eEEEEEECCCCCCccHHHHHHHHHHHHHHHcCCceEEEEecCCc--cHHHHHHHHHHHHHcCCCEEEEccHHHH-HHHHH
Confidence 4566665 45567777788888888888 999988877663 2378999999999999999999875432 33445
Q ss_pred HHHHcCCCCCCeEEEecCc
Q 003093 148 VAQYLGMLGTGYVWIATSW 166 (848)
Q Consensus 148 ~a~~~g~~~~~~~wi~~~~ 166 (848)
.|++ . |+..|+..++
T Consensus 79 vA~~--y--Pd~~F~~~d~ 93 (306)
T PF02608_consen 79 VAKE--Y--PDTKFIIIDG 93 (306)
T ss_dssp HHTC-----TTSEEEEESS
T ss_pred HHHH--C--CCCEEEEEec
Confidence 5544 2 4555666554
No 404
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=56.89 E-value=73 Score=33.92 Aligned_cols=80 Identities=10% Similarity=0.027 Sum_probs=53.6
Q ss_pred cEEEEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHH
Q 003093 72 WREVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 149 (848)
Q Consensus 72 w~~vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a 149 (848)
-+.|+++.. ++.|.......+.+++++.|..+...... .+...-...+..+...++|.|++..........++++
T Consensus 61 ~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~---~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 137 (328)
T PRK11303 61 TRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSD---DQPDNEMRCAEHLLQRQVDALIVSTSLPPEHPFYQRL 137 (328)
T ss_pred CceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEcCCCCCChHHHHHH
Confidence 356888874 35677778889999999999988764321 1223334566777778899998865433234566777
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
.+.|.
T Consensus 138 ~~~~i 142 (328)
T PRK11303 138 QNDGL 142 (328)
T ss_pred HhcCC
Confidence 77665
No 405
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=56.66 E-value=1.7e+02 Score=30.58 Aligned_cols=101 Identities=11% Similarity=0.055 Sum_probs=51.0
Q ss_pred CCChHHhhcCCCCeeE-EeCchHHHHHHhhhCCCc---cCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcC
Q 003093 592 IKGIDSLRSSNYPIGY-QVNSFARNYLVDELNIDE---SRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR 667 (848)
Q Consensus 592 i~sl~dL~~s~~~i~~-~~~s~~~~~l~~~~~~~~---~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~ 667 (848)
.-+++||. +.++.. ..+.....++.+ .+... .....+++.+...+++.. |...+++... .........
T Consensus 180 ~i~~~dL~--~~p~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~v~~----g~gi~~lp~~-~~~~~~~~~ 251 (297)
T PRK11139 180 LKTPEDLA--RHTLLHDDSREDWRAWFRA-AGLDDLNVQQGPIFSHSSMALQAAIH----GQGVALGNRV-LAQPEIEAG 251 (297)
T ss_pred CCCHHHhh--cCceEeecCcccHHHHHHH-hCCCCcCcccceeeCCHHHHHHHHHh----CCCeEecchh-hhHHHHHCC
Confidence 34788888 555433 222334445533 23211 112346788888888888 5555665543 333333332
Q ss_pred CcEEEeCCcc-ccCCceeeecCCCCchHHHHHHH
Q 003093 668 CEFSIVGQVF-TKNGWGFAFPRDSPLAVDISTAI 700 (848)
Q Consensus 668 ~~l~~~~~~~-~~~~~~~~~~k~spl~~~in~~i 700 (848)
.-...+.+.. ....+.++++|+.+....+...+
T Consensus 252 ~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~ 285 (297)
T PRK11139 252 RLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFR 285 (297)
T ss_pred ceecccccCcCCCccEEEEeccccccChhHHHHH
Confidence 2122233322 23567888888766555444433
No 406
>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=56.47 E-value=64 Score=33.07 Aligned_cols=76 Identities=4% Similarity=-0.062 Sum_probs=52.2
Q ss_pred EEEEE--EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIY--VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~--~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
+++|. .++.|.......+.+++++.|..+.....- .+...-...+..+.+.++|.|++....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~~~---~~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~~~ 77 (268)
T cd06270 2 IGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITAGH---HSAEKEREAIEFLLERRCDALILHSKALSD-DELIELAAQ 77 (268)
T ss_pred EEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEeCC---CchHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhC
Confidence 45555 357788888999999999999988754321 122334566777778899999987653333 237778777
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (268)
T cd06270 78 VP 79 (268)
T ss_pred CC
Confidence 75
No 407
>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=56.47 E-value=36 Score=35.66 Aligned_cols=79 Identities=8% Similarity=0.056 Sum_probs=52.4
Q ss_pred EEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHHH
Q 003093 74 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQ 150 (848)
Q Consensus 74 ~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a~ 150 (848)
||++|..+ +.|.......+.+++++.|..+.... ....+.......+..+...++|.|++...... ....++++.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~--~~~~~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~~~i~~~~ 78 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVATT--DAQFDPAKQVADIETTISQKPDIIISIPVDPVSTAAAYKKVA 78 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHHcCCEEEEec--CCCCCHHHHHHHHHHHHHhCCCEEEEcCCCchhhhHHHHHHH
Confidence 46666633 45666778889999999999876431 22223344456677777788999888643322 356778888
Q ss_pred HcCC
Q 003093 151 YLGM 154 (848)
Q Consensus 151 ~~g~ 154 (848)
+.|.
T Consensus 79 ~~~i 82 (294)
T cd06316 79 EAGI 82 (294)
T ss_pred HcCC
Confidence 8776
No 408
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=56.43 E-value=49 Score=35.76 Aligned_cols=81 Identities=9% Similarity=-0.052 Sum_probs=55.3
Q ss_pred cEEEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcH-HHHHHH
Q 003093 72 WREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRG-PVVFHV 148 (848)
Q Consensus 72 w~~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~-~~~~~~ 148 (848)
-+.|+++..+ +.|.....+.+.+++++.|..+.....-.. .+.......++.+.+.++|.|++.....+. ...+ +
T Consensus 46 t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~~-~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l-~ 123 (343)
T PRK10936 46 AWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGGY-YNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDL-E 123 (343)
T ss_pred CeEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCCC-CCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHH-H
Confidence 3788888854 667778889999999999998876533211 122344566777778899999887644333 2445 6
Q ss_pred HHHcCC
Q 003093 149 AQYLGM 154 (848)
Q Consensus 149 a~~~g~ 154 (848)
+++.|.
T Consensus 124 ~~~~gi 129 (343)
T PRK10936 124 LQAANI 129 (343)
T ss_pred HHHCCC
Confidence 777775
No 409
>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=56.10 E-value=69 Score=33.01 Aligned_cols=77 Identities=10% Similarity=0.040 Sum_probs=50.5
Q ss_pred cEEEEEEEE---------cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcH
Q 003093 72 WREVIAIYV---------DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRG 142 (848)
Q Consensus 72 w~~vaii~~---------dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~ 142 (848)
.+.|++|.+ ++.|.....+.+.+.+++.|..+..... . . .+.......+.+.++|.|++......
T Consensus 3 s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~~-~--~--~~~~~~~~~l~~~~~dgiii~~~~~~- 76 (275)
T cd06295 3 TDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSFV-S--S--PDRDWLARYLASGRADGVILIGQHDQ- 76 (275)
T ss_pred ceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEeC-C--c--hhHHHHHHHHHhCCCCEEEEeCCCCC-
Confidence 467888885 3456777788899999999998765421 1 1 12233444555678999988654333
Q ss_pred HHHHHHHHHcCC
Q 003093 143 PVVFHVAQYLGM 154 (848)
Q Consensus 143 ~~~~~~a~~~g~ 154 (848)
...++++.+.|.
T Consensus 77 ~~~~~~~~~~~i 88 (275)
T cd06295 77 DPLPERLAETGL 88 (275)
T ss_pred hHHHHHHHhCCC
Confidence 245777877776
No 410
>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=55.52 E-value=41 Score=35.07 Aligned_cols=76 Identities=11% Similarity=0.079 Sum_probs=53.8
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-CcHHHHHHHHHH
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQY 151 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~-~~~~~~~~~a~~ 151 (848)
|++|.. .+.|.......+.+++++.|..+.... .. +.......+.++...++|.|++.... .....+++++++
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~-~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~~~~ 77 (289)
T cd01540 2 IGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKID---VP-DGEKVLSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAKA 77 (289)
T ss_pred eeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEcc---CC-CHHHHHHHHHHHHHcCCCEEEEccCchhhhHHHHHHHHh
Confidence 566664 356788888999999999998876532 22 23444567777888899999987543 334567888888
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|.
T Consensus 78 ~~i 80 (289)
T cd01540 78 YNM 80 (289)
T ss_pred CCC
Confidence 775
No 411
>TIGR00249 sixA phosphohistidine phosphatase SixA.
Probab=55.20 E-value=74 Score=29.68 Aligned_cols=98 Identities=10% Similarity=0.000 Sum_probs=60.3
Q ss_pred ccCChHHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCe
Q 003093 52 TTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESR 131 (848)
Q Consensus 52 ~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~ 131 (848)
.++.-..|++.+++.++..+..--.++.+.-.-....++.+.+.+.. -..+.....+.+..+..++...+.++...+.+
T Consensus 23 Lt~~G~~qa~~~~~~l~~~~~~~d~i~sSp~~Ra~qTa~~l~~~~~~-~~~~~~~~~l~p~~~~~~~~~~l~~~~~~~~~ 101 (152)
T TIGR00249 23 LTTNGCDESRLVAQWLKGQGVEIERILVSPFVRAEQTAEIVGDCLNL-PSSAEVLEGLTPCGDIGLVSDYLEALTNEGVA 101 (152)
T ss_pred cCHHHHHHHHHHHHHHHhCCCCCCEEEECCcHHHHHHHHHHHHHcCC-CcceEEccCcCCCCCHHHHHHHHHHHHhcCCC
Confidence 34455678999999988765433344445544455555555444321 12333333444344456677777777655567
Q ss_pred EEEEEccCCcHHHHHHHHH
Q 003093 132 IIVVHTHYNRGPVVFHVAQ 150 (848)
Q Consensus 132 viv~~~~~~~~~~~~~~a~ 150 (848)
.++++++.+....++..+-
T Consensus 102 ~vliVgH~P~i~~l~~~l~ 120 (152)
T TIGR00249 102 SVLLVSHLPLVGYLVAELC 120 (152)
T ss_pred EEEEEeCCCCHHHHHHHHh
Confidence 8888899988888888874
No 412
>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=55.20 E-value=1.1e+02 Score=33.40 Aligned_cols=101 Identities=11% Similarity=0.047 Sum_probs=62.8
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEee--ecCCCCChHHHHHHHHHHhcCCCe---EEEE
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKA--PLSVEATEDEITDLLVKVALTESR---IIVV 135 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~--~~~~~~~~~d~~~~l~~i~~~~~~---viv~ 135 (848)
..+.++++.++-+++.++++...+ ....+.+.+.+++.|+.+.... ......+.+.+...+..+++.++| +|+.
T Consensus 12 ~~l~~~l~~~g~~rvlvVtd~~v~-~~~~~~l~~~L~~~g~~~~~~~~~~~e~~k~~~~v~~~~~~~~~~~~dr~~~IIA 90 (355)
T cd08197 12 DSVLGYLPELNADKYLLVTDSNVE-DLYGHRLLEYLREAGAPVELLSVPSGEEHKTLSTLSDLVERALALGATRRSVIVA 90 (355)
T ss_pred HHHHHHHHhcCCCeEEEEECccHH-HHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEE
Confidence 345566777777899888855544 3466788899999887653221 222223446788888888888887 7777
Q ss_pred EccC--CcHHHHHHHHHHcCCCCCCeEEEecC
Q 003093 136 HTHY--NRGPVVFHVAQYLGMLGTGYVWIATS 165 (848)
Q Consensus 136 ~~~~--~~~~~~~~~a~~~g~~~~~~~wi~~~ 165 (848)
.+.+ -+...++......| ..++.|-|.
T Consensus 91 vGGGsv~D~ak~~A~~~~rg---ip~I~IPTT 119 (355)
T cd08197 91 LGGGVVGNIAGLLAALLFRG---IRLVHIPTT 119 (355)
T ss_pred ECCcHHHHHHHHHHHHhccC---CCEEEecCc
Confidence 6654 34444444333233 355666554
No 413
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=55.06 E-value=76 Score=34.03 Aligned_cols=79 Identities=11% Similarity=0.029 Sum_probs=55.8
Q ss_pred EEEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHH
Q 003093 73 REVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQ 150 (848)
Q Consensus 73 ~~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~ 150 (848)
+.++++..+ +.|.......+.+++++.|..+.... ...+.......+..+.+.++|.|++..........+..++
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 67888888999999999998765432 1223345567777888889999998754433445677777
Q ss_pred HcCC
Q 003093 151 YLGM 154 (848)
Q Consensus 151 ~~g~ 154 (848)
+.|.
T Consensus 142 ~~~i 145 (342)
T PRK10014 142 EKGI 145 (342)
T ss_pred hcCC
Confidence 7665
No 414
>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=54.93 E-value=62 Score=33.16 Aligned_cols=76 Identities=7% Similarity=0.066 Sum_probs=52.3
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
++++.. +++|.......+.+.+++.|.++.....- .+.......++.+.+.++|.|++....... ..++.+.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (270)
T cd06296 2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSESG---RRTSPERQWVERLSARRTDGVILVTPELTS-AQRAALRRT 77 (270)
T ss_pred eEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecCC---CchHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHhcC
Confidence 456653 47888899999999999999988654322 122445567777888889988876544333 457777776
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (270)
T cd06296 78 GI 79 (270)
T ss_pred CC
Confidence 64
No 415
>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=54.77 E-value=27 Score=38.39 Aligned_cols=77 Identities=4% Similarity=-0.073 Sum_probs=54.0
Q ss_pred cCcEEEEEEEEcCCCc-cchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC--CcHHHHH
Q 003093 70 YGWREVIAIYVDDDHG-RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY--NRGPVVF 146 (848)
Q Consensus 70 ~~w~~vaii~~dd~~g-~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~--~~~~~~~ 146 (848)
++-+++.+|+....+- .+..+.+.+.|++.|+++.....+....+.+.+...+..+++.++|+||-.+.+ -++.+.+
T Consensus 21 ~~~~r~livt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGGSviD~AK~i 100 (375)
T cd08179 21 LKGKKAFIVTGGGSMKKFGFLDKVEAYLKEAGIEVEVFEGVEPDPSVETVLKGAEAMREFEPDWIIALGGGSPIDAAKAM 100 (375)
T ss_pred hcCCeEEEEeCchHHHhCChHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHHH
Confidence 3447888887443332 345678889999999887655455555566788889999999999999987655 3444443
No 416
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=54.77 E-value=42 Score=35.32 Aligned_cols=78 Identities=8% Similarity=-0.033 Sum_probs=53.6
Q ss_pred EEEEE--EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHHHH
Q 003093 75 VIAIY--VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQY 151 (848)
Q Consensus 75 vaii~--~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a~~ 151 (848)
|+++. .++.|.......+.+++++.|..+.... +...+.......++.+...++|.|++...... ...+++++++
T Consensus 2 I~vi~~~~~~~f~~~i~~gi~~~a~~~g~~v~~~~--~~~~d~~~~~~~i~~~~~~~~DgiIi~~~~~~~~~~~~~~~~~ 79 (298)
T cd06302 2 IAFVPKVTGIPYFNRMEEGAKEAAKELGVDAIYVG--PTTADAAGQVQIIEDLIAQGVDAIAVVPNDPDALEPVLKKARE 79 (298)
T ss_pred EEEEEcCCCChHHHHHHHHHHHHHHHhCCeEEEEC--CCCCCHHHHHHHHHHHHhcCCCEEEEecCCHHHHHHHHHHHHH
Confidence 55555 3567888888999999999999876431 11123345566777777788999998753322 3567788887
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|+
T Consensus 80 ~~i 82 (298)
T cd06302 80 AGI 82 (298)
T ss_pred CCC
Confidence 776
No 417
>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=53.88 E-value=1.3e+02 Score=26.37 Aligned_cols=46 Identities=9% Similarity=0.103 Sum_probs=23.1
Q ss_pred cchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEc
Q 003093 86 RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT 137 (848)
Q Consensus 86 ~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~ 137 (848)
.-+...+...+++.|.+|...... . +.....+.+++.++|+|.+.+
T Consensus 14 ~lGl~~la~~l~~~G~~v~~~d~~---~---~~~~l~~~~~~~~pd~V~iS~ 59 (121)
T PF02310_consen 14 PLGLLYLAAYLRKAGHEVDILDAN---V---PPEELVEALRAERPDVVGISV 59 (121)
T ss_dssp SHHHHHHHHHHHHTTBEEEEEESS---B----HHHHHHHHHHTTCSEEEEEE
T ss_pred hHHHHHHHHHHHHCCCeEEEECCC---C---CHHHHHHHHhcCCCcEEEEEc
Confidence 334555566666666665543211 1 113344455555666666665
No 418
>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=53.83 E-value=72 Score=32.61 Aligned_cols=76 Identities=7% Similarity=0.041 Sum_probs=51.6
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. ++.|.......+.+++++.|.++...... .+.......+..+...++|.|++.....+.. .++++.+.
T Consensus 2 igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~-~~~~~~~~ 77 (264)
T cd06274 2 IGLIIPDLENRSFARIAKRLEALARERGYQLLIACSD---DDPETERETVETLIARQVDALIVAGSLPPDD-PYYLCQKA 77 (264)
T ss_pred EEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEcCCCCchH-HHHHHHhc
Confidence 455553 46777788889999999999987764332 1234455677788888999999876543333 26667776
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (264)
T cd06274 78 GL 79 (264)
T ss_pred CC
Confidence 65
No 419
>PF06084 Cytomega_TRL10: Cytomegalovirus TRL10 protein; InterPro: IPR009284 This family consists of several Cytomegalovirus TRL10 proteins. TRL10 represents a structural component of the virus particle and like the other HCMV envelope glycoproteins, is present in a disulphide-linked complex [].
Probab=53.70 E-value=23 Score=30.20 Aligned_cols=79 Identities=22% Similarity=0.296 Sum_probs=42.6
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCCCchhhhhHHHHhccccccchhhhhhccccccccccccC
Q 003093 738 SFSGLYLLCGLACLLALFIYLMQIVHQFSRHYPGDTESNGGSSRSARLQTFLSFVNEKEDEVKSRSKRRHVERTSYRSED 817 (848)
Q Consensus 738 ~~~g~f~il~~g~~la~~vf~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 817 (848)
.+.|++-.+|.|.++|.++.++-+++-.+. |++.+.......... --.+.+-.|+-+.+.+.|+...++..++++.
T Consensus 52 s~lg~ysawgagsfiatliillviffviy~--re~~~~~~gt~~d~~--layr~ltrkkl~~ha~kkqniyeripyrp~r 127 (150)
T PF06084_consen 52 SMLGIYSAWGAGSFIATLIILLVIFFVIYS--REEEKNNNGTEVDQC--LAYRSLTRKKLEQHASKKQNIYERIPYRPCR 127 (150)
T ss_pred hhhhhhhhcccchHHHHHHHHHHHhheeEe--ccccccCCCceechh--hHHHHHHHHHHHHHHHhhcchhhhcCCCccc
Confidence 456788888888888777665544432222 222221211111111 1122233455566777788888888888885
Q ss_pred CCC
Q 003093 818 EMS 820 (848)
Q Consensus 818 ~~~ 820 (848)
|..
T Consensus 128 q~d 130 (150)
T PF06084_consen 128 QND 130 (150)
T ss_pred ccC
Confidence 433
No 420
>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=53.33 E-value=64 Score=32.93 Aligned_cols=76 Identities=9% Similarity=0.100 Sum_probs=51.9
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
+++|.. ++.|.......+.+++++.|.++..... ..+..+....+.++...++|.|++...... ...+..+.+.
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 456663 3566777888999999999998765332 223345667788888889999988764433 3456666666
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (268)
T cd01575 78 GI 79 (268)
T ss_pred CC
Confidence 65
No 421
>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=53.29 E-value=61 Score=33.32 Aligned_cols=77 Identities=5% Similarity=-0.079 Sum_probs=53.1
Q ss_pred EEEEEE---cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCC-cHHHHHHHHH
Q 003093 75 VIAIYV---DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVAQ 150 (848)
Q Consensus 75 vaii~~---dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~-~~~~~~~~a~ 150 (848)
|++|.. +++|+......+.+++++.|..+..... ..+.......++.+...++|.|++..... .....++.++
T Consensus 2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~l~~~~ 78 (275)
T cd06317 2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVLDA---NGDVARQAAQVEDLIAQKVDGIILWPTDGQAYIPGLRKAK 78 (275)
T ss_pred eEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEEcC---CcCHHHHHHHHHHHHHcCCCEEEEecCCccccHHHHHHHH
Confidence 456663 4678888899999999999998775422 22334445567777778899998875433 2345677787
Q ss_pred HcCC
Q 003093 151 YLGM 154 (848)
Q Consensus 151 ~~g~ 154 (848)
+.|.
T Consensus 79 ~~~i 82 (275)
T cd06317 79 QAGI 82 (275)
T ss_pred HCCC
Confidence 7775
No 422
>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=52.92 E-value=59 Score=33.44 Aligned_cols=80 Identities=8% Similarity=-0.020 Sum_probs=52.3
Q ss_pred EEEEEE--EcCCCccchHHHHHHHHhcc---CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHH
Q 003093 74 EVIAIY--VDDDHGRNGIAALGDTLAAK---RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFH 147 (848)
Q Consensus 74 ~vaii~--~dd~~g~~~~~~l~~~l~~~---g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~ 147 (848)
||+++. .++.|.......+.+++++. |.++.... +....+.......++++...++|.|++...... ....+.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i-~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~ 79 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIV-TSADGDVAQQIADIRNLIAQGVDAIIINPASPTALNPVIE 79 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEE-ecCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHH
Confidence 456665 34557777888999999998 87432211 122223455677888888889999999764433 344677
Q ss_pred HHHHcCC
Q 003093 148 VAQYLGM 154 (848)
Q Consensus 148 ~a~~~g~ 154 (848)
.+++.|.
T Consensus 80 ~~~~~~i 86 (272)
T cd06300 80 EACEAGI 86 (272)
T ss_pred HHHHCCC
Confidence 7877775
No 423
>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=52.88 E-value=30 Score=37.31 Aligned_cols=71 Identities=7% Similarity=0.009 Sum_probs=48.6
Q ss_pred HHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 68 DHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 68 ~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
+.++.+++.+|+....+-.+..+.+.+.+++. +.+.....+....+.+.+...+..+++.++|+||-.+.+
T Consensus 18 ~~~~~~~~lvv~~~~~~~~g~~~~v~~~l~~~-~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IiaiGGG 88 (332)
T cd08180 18 KELKNKRVLIVTDPFMVKSGMLDKVTDHLDSS-IEVEIFSDVVPDPPIEVVAKGIKKFLDFKPDIVIALGGG 88 (332)
T ss_pred HHhCCCeEEEEeCchhhhCccHHHHHHHHHhc-CcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEECCc
Confidence 44556898888744333334677788888876 555443344444456778888888988999999977654
No 424
>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=52.49 E-value=15 Score=26.68 Aligned_cols=27 Identities=22% Similarity=0.560 Sum_probs=22.0
Q ss_pred hhhHHHHHHHHHHHHHHhhhhhcccCC
Q 003093 497 PMMWGVTAIFFLAVGAVVWILEHRLND 523 (848)
Q Consensus 497 ~~vW~~~~~~~~~~~~v~~~~~~~~~~ 523 (848)
.++|.+++.+++++++++|.+..+..+
T Consensus 11 a~~~~l~~~~~~Figiv~wa~~p~~k~ 37 (48)
T cd01324 11 ADSWGLLYLALFFLGVVVWAFRPGRKK 37 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcch
Confidence 368999999999999999999655443
No 425
>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=52.48 E-value=54 Score=33.81 Aligned_cols=80 Identities=6% Similarity=-0.020 Sum_probs=51.8
Q ss_pred EEEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-CcHHHHHHHHH
Q 003093 74 EVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQ 150 (848)
Q Consensus 74 ~vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~-~~~~~~~~~a~ 150 (848)
++++|.. ++.|.......+.+++++.|..+.....- ...+...-...+.++...++|.|++.... ......++.++
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~ 79 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAP-SEGDQQGQLSIAENMINKGYKGLLFSPISDVNLVPAVERAK 79 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEccC-CCCCHHHHHHHHHHHHHhCCCEEEECCCChHHhHHHHHHHH
Confidence 3566663 46677788889999999999887654221 11122334556777777889998876432 22234567777
Q ss_pred HcCC
Q 003093 151 YLGM 154 (848)
Q Consensus 151 ~~g~ 154 (848)
+.|.
T Consensus 80 ~~~i 83 (275)
T cd06320 80 KKGI 83 (275)
T ss_pred HCCC
Confidence 7665
No 426
>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=52.38 E-value=12 Score=33.16 Aligned_cols=86 Identities=16% Similarity=0.147 Sum_probs=46.2
Q ss_pred EEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHh--cCCCeEEEEEccCCcHHHHHHHHH
Q 003093 73 REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVA--LTESRIIVVHTHYNRGPVVFHVAQ 150 (848)
Q Consensus 73 ~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~--~~~~~viv~~~~~~~~~~~~~~a~ 150 (848)
|+++++...++-+.- ...+.+.+.+.|.+|... .+....-+=......+. -..+|+++++..+.....+++++.
T Consensus 1 ksiAVvGaS~~~~~~-g~~v~~~l~~~G~~v~~V---np~~~~i~G~~~y~sl~e~p~~iDlavv~~~~~~~~~~v~~~~ 76 (116)
T PF13380_consen 1 KSIAVVGASDNPGKF-GYRVLRNLKAAGYEVYPV---NPKGGEILGIKCYPSLAEIPEPIDLAVVCVPPDKVPEIVDEAA 76 (116)
T ss_dssp -EEEEET--SSTTSH-HHHHHHHHHHTT-EEEEE---STTCSEETTEE-BSSGGGCSST-SEEEE-S-HHHHHHHHHHHH
T ss_pred CEEEEEcccCCCCCh-HHHHHHHHHhCCCEEEEE---CCCceEECcEEeeccccCCCCCCCEEEEEcCHHHHHHHHHHHH
Confidence 577888755443332 333445555577676532 22211100001222333 358999999999999999999999
Q ss_pred HcCCCCCCeEEEecC
Q 003093 151 YLGMLGTGYVWIATS 165 (848)
Q Consensus 151 ~~g~~~~~~~wi~~~ 165 (848)
++|. +.+|+.++
T Consensus 77 ~~g~---~~v~~~~g 88 (116)
T PF13380_consen 77 ALGV---KAVWLQPG 88 (116)
T ss_dssp HHT----SEEEE-TT
T ss_pred HcCC---CEEEEEcc
Confidence 9984 68899887
No 427
>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=52.13 E-value=69 Score=33.24 Aligned_cols=79 Identities=13% Similarity=0.043 Sum_probs=54.1
Q ss_pred EEEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHH
Q 003093 73 REVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVA 149 (848)
Q Consensus 73 ~~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a 149 (848)
|+|+++..+ +.|.......+.+++++.|..+..... ..+.+.-...+..+...++|.|++...... ....++.+
T Consensus 1 ~~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~~~~~~~ 77 (280)
T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRILDG---RGSEAGQAAALNQAIALKPDGIVLGGVDAAELQAELELA 77 (280)
T ss_pred CeEEEEecccCCcHHHHHHHHHHHHHHHcCcEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHHHHHHH
Confidence 467777743 567778889999999999988765422 123344566778888889999998754322 23456667
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
++.|.
T Consensus 78 ~~~~i 82 (280)
T cd06315 78 QKAGI 82 (280)
T ss_pred HHCCC
Confidence 77665
No 428
>COG4213 XylF ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=52.10 E-value=3.1e+02 Score=28.85 Aligned_cols=145 Identities=9% Similarity=0.110 Sum_probs=80.3
Q ss_pred EEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEecc--CChHHHHHHHHHHHHHcC---cEEEEEEE-
Q 003093 6 VAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTT--QSDQYQMAAIAEIVDHYG---WREVIAIY- 79 (848)
Q Consensus 6 ~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~--p~d~~q~~ai~~~~~~~~---w~~vaii~- 79 (848)
+.||+|..|.+...+...+...+||+|+|. ..+.+..+.|+...- ---..|+.++.+-++.-. -..+.++.
T Consensus 84 vlvi~a~d~~~l~~~i~~A~~~gikViaYD---RlI~n~dvd~YvsFDN~~VG~lQa~~l~~~lk~k~~~~~gn~~l~~G 160 (341)
T COG4213 84 VLVIGAIDGGVLSNAVEKAKSEGIKVIAYD---RLINNADVDFYVSFDNEKVGELQAKALVKGLKLKPLTSEGNYVLLGG 160 (341)
T ss_pred EEEEEeccchhHHHHHHHHHHcCCeEEEee---cccccCCccEEEEecchhHHHHHHHHHHHHhccCCCCCCCCEEEecC
Confidence 457799999999999999999999999873 333333444443221 122356666655554333 23344554
Q ss_pred -EcCC----CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc---CCCeEEEEEccCCcHHHHHHHHHH
Q 003093 80 -VDDD----HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL---TESRIIVVHTHYNRGPVVFHVAQY 151 (848)
Q Consensus 80 -~dd~----~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~---~~~~viv~~~~~~~~~~~~~~a~~ 151 (848)
++|. +-.+.++.|+..+..-.+.++.....+ .-....-...+..+-. .+.|.|+..-+ ..+...+..++.
T Consensus 161 Sp~DnNA~lf~~G~m~VLkp~idsGkik~~Ge~~~d-~W~ps~Aq~~men~lta~~~~vdaVvA~nD-gtagGaI~aL~a 238 (341)
T COG4213 161 SPDDNNAKLFFAGAMKVLKPLIDSGKIKVVGEQWTD-GWLPSNAQQIMENLLTANYNDIDAVVAPND-GTAGGAIAALKA 238 (341)
T ss_pred CCCCcchHHHHhcHHHHHHHHhhCCceEEeeecccc-ccCHHHHHHHHHHHHhcccCceeEEEcCCC-chhHHHHHHHHh
Confidence 2222 122334555555555556665444333 2222222333333222 34555544433 566678888999
Q ss_pred cCCC
Q 003093 152 LGML 155 (848)
Q Consensus 152 ~g~~ 155 (848)
.|+-
T Consensus 239 ~Gl~ 242 (341)
T COG4213 239 QGLA 242 (341)
T ss_pred cccC
Confidence 9985
No 429
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=51.98 E-value=1.1e+02 Score=33.46 Aligned_cols=101 Identities=7% Similarity=0.035 Sum_probs=62.2
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEe--eecCCCCChHHHHHHHHHHhcCCC---eEEEE
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFK--APLSVEATEDEITDLLVKVALTES---RIIVV 135 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~--~~~~~~~~~~d~~~~l~~i~~~~~---~viv~ 135 (848)
..+.++++.++.+++.+++.... .....+.+.+.+++.|+.+... .......+.+.+...+..+++.++ |+||.
T Consensus 20 ~~l~~~l~~~~~~~~livtd~~~-~~~~~~~v~~~L~~~gi~~~~~~~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~IIa 98 (358)
T PRK00002 20 SELGELLAPLKGKKVAIVTDETV-APLYLEKLRASLEAAGFEVDVVVLPDGEQYKSLETLEKIYDALLEAGLDRSDTLIA 98 (358)
T ss_pred HHHHHHHHhcCCCeEEEEECCch-HHHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCCEEEE
Confidence 45666777778899988885443 3457778888899888876522 122223345777788888877654 88887
Q ss_pred EccC--CcHHHHHHHHHHcCCCCCCeEEEecC
Q 003093 136 HTHY--NRGPVVFHVAQYLGMLGTGYVWIATS 165 (848)
Q Consensus 136 ~~~~--~~~~~~~~~a~~~g~~~~~~~wi~~~ 165 (848)
.+.+ -++..++......|. .++-|-|.
T Consensus 99 vGGGsv~D~aK~iA~~~~~gi---p~i~IPTT 127 (358)
T PRK00002 99 LGGGVIGDLAGFAAATYMRGI---RFIQVPTT 127 (358)
T ss_pred EcCcHHHHHHHHHHHHhcCCC---CEEEcCch
Confidence 7654 344444443333343 34444443
No 430
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=51.65 E-value=60 Score=31.32 Aligned_cols=74 Identities=23% Similarity=0.322 Sum_probs=45.1
Q ss_pred CCCChHHhhcCCCCeeEEeCchHHHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcE
Q 003093 591 PIKGIDSLRSSNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEF 670 (848)
Q Consensus 591 ~i~sl~dL~~s~~~i~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l 670 (848)
++++.+||. +++|+..-......||.+ .+.. -+++...-.-|..-. . |-.|++++-.....-+..+ +|
T Consensus 100 ~~~~~~~l~--~~rIATkyp~i~~~~f~~-~Gi~-v~ii~l~GsvE~aP~--~----GlaD~IvDiv~TG~TL~~N--gL 167 (182)
T TIGR00070 100 DISSVEDLK--GKRIATKYPNLARRYFEK-KGID-VEIIKLNGSVELAPL--L----GLADAIVDIVSTGTTLREN--GL 167 (182)
T ss_pred CCCChHHhC--CCEEEECCHHHHHHHHHH-cCCe-EEEEECcceeecccC--C----CceeEEEEEeCCHHHHHHC--CC
Confidence 567889987 888988777778888843 4442 344444333332221 2 7788888876666555554 35
Q ss_pred EEeCCc
Q 003093 671 SIVGQV 676 (848)
Q Consensus 671 ~~~~~~ 676 (848)
.++.+.
T Consensus 168 ~~ie~i 173 (182)
T TIGR00070 168 RIIEVI 173 (182)
T ss_pred EEeeEE
Confidence 555443
No 431
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=51.53 E-value=1.1e+02 Score=29.91 Aligned_cols=88 Identities=10% Similarity=-0.005 Sum_probs=60.1
Q ss_pred EEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC----CcHHHHHHH
Q 003093 73 REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY----NRGPVVFHV 148 (848)
Q Consensus 73 ~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~----~~~~~~~~~ 148 (848)
.+|.+....++.-.-+..-+...++..|.+|.+-- .+. .....+..+++.+||+|.+.+.. .....++++
T Consensus 85 ~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG---~~v---p~e~~v~~~~~~~pd~v~lS~~~~~~~~~~~~~i~~ 158 (197)
T TIGR02370 85 GKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLG---RDV---PIDTVVEKVKKEKPLMLTGSALMTTTMYGQKDINDK 158 (197)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECC---CCC---CHHHHHHHHHHcCCCEEEEccccccCHHHHHHHHHH
Confidence 46666666666666677788889999999988643 222 23455666777899999987653 456667888
Q ss_pred HHHcCCCCCCeEEEecCc
Q 003093 149 AQYLGMLGTGYVWIATSW 166 (848)
Q Consensus 149 a~~~g~~~~~~~wi~~~~ 166 (848)
+++.|....-.+|+++..
T Consensus 159 l~~~~~~~~v~i~vGG~~ 176 (197)
T TIGR02370 159 LKEEGYRDSVKFMVGGAP 176 (197)
T ss_pred HHHcCCCCCCEEEEEChh
Confidence 888887544456666543
No 432
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=51.34 E-value=70 Score=34.34 Aligned_cols=79 Identities=6% Similarity=0.043 Sum_probs=57.4
Q ss_pred EEEEEEE--EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHH
Q 003093 73 REVIAIY--VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVA 149 (848)
Q Consensus 73 ~~vaii~--~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a 149 (848)
.+|+++. .+++|.....+.+.+++++.|..+..... ..+..+....+..+.+.++|.|++...... ....+..+
T Consensus 26 ~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~~---~~~~~~~~~~i~~l~~~~vDGiIi~~~~~~~~~~~l~~~ 102 (330)
T PRK10355 26 VKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSA---NGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVIKEA 102 (330)
T ss_pred ceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHHHHH
Confidence 5677776 45788999999999999999999876422 223355667788888889999998764322 24566777
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
.+.|.
T Consensus 103 ~~~~i 107 (330)
T PRK10355 103 KQEGI 107 (330)
T ss_pred HHCCC
Confidence 77674
No 433
>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=51.21 E-value=51 Score=33.99 Aligned_cols=72 Identities=8% Similarity=0.134 Sum_probs=52.4
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHHHHcCC
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a~~~g~ 154 (848)
.++.|.......+.+++++.|.++.....- .+.......++.+...++|.|++...... ....++++.+.|.
T Consensus 9 ~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~i~~~~~~~i 81 (273)
T cd06309 9 AESPWRTAETKSIKDAAEKRGFDLKFADAQ---QKQENQISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAAGI 81 (273)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCEEEEeCCC---CCHHHHHHHHHHHHHcCCCEEEEcCCccccchHHHHHHHHCCC
Confidence 356788889999999999999998864321 23345567788888889999988654333 2457788888775
No 434
>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=51.12 E-value=43 Score=36.14 Aligned_cols=77 Identities=10% Similarity=0.070 Sum_probs=53.5
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
...+.+.++.+|.+++.+++....+-. ..+.+.+.+++.+..+ + ..+....+.+.+...+..++..++|.||..+.+
T Consensus 11 l~~l~~~l~~~g~~~~livt~~~~~~~-~~~~v~~~l~~~~~~~-~-~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 87 (337)
T cd08177 11 LAALAAELERLGASRALVLTTPSLATK-LAERVASALGDRVAGT-F-DGAVMHTPVEVTEAAVAAAREAGADGIVAIGGG 87 (337)
T ss_pred HHHHHHHHHHcCCCeEEEEcChHHHHH-HHHHHHHHhccCCcEE-e-CCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 355677888999999988875443333 6667788887765432 2 234344455778888888888899999987654
No 435
>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=51.01 E-value=58 Score=34.37 Aligned_cols=77 Identities=8% Similarity=0.059 Sum_probs=52.4
Q ss_pred EEEEEE---cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC--CCeEEEEEccCCcHHHHHHHH
Q 003093 75 VIAIYV---DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVA 149 (848)
Q Consensus 75 vaii~~---dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~--~~~viv~~~~~~~~~~~~~~a 149 (848)
|+++.. ++.|.......+.+++++.|..+..... ..+...-...+..+.+. ++|.|++.........+++.+
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~~---~~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~ 78 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLYA---ERDRFLMLQQARTILQRPDKPDALIFTNEKSVAPELLRLA 78 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHHHhccCCCEEEEcCCccchHHHHHHH
Confidence 556652 4567788888999999999998765422 12233445667777777 899999865433345567788
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
++.|.
T Consensus 79 ~~~gi 83 (305)
T cd06324 79 EGAGV 83 (305)
T ss_pred HhCCC
Confidence 77775
No 436
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=50.99 E-value=3.2e+02 Score=28.71 Aligned_cols=90 Identities=11% Similarity=0.109 Sum_probs=58.2
Q ss_pred CeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEecc-----CC---hHHHHHHHHHHHHHcC----
Q 003093 4 QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTT-----QS---DQYQMAAIAEIVDHYG---- 71 (848)
Q Consensus 4 ~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~-----p~---d~~q~~ai~~~~~~~~---- 71 (848)
-|.-|+||-..+....++.+..+.++=.+..+.... ...-.||.|+. |. -...-.++.++.+.+|
T Consensus 10 ~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d---~~~~~ffm~i~~~~~~~~~~~~~~l~~~l~~l~~~l~l~~~ 86 (289)
T PRK13010 10 YVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDD---DESGRFFMRVSFHAQSAEAASVDTFRQEFQPVAEKFDMQWA 86 (289)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHCCCCEEecccccc---cccCcEEEEEEEEcCCCCCCCHHHHHHHHHHHHHHhCCeEE
Confidence 378899999999999999999999988886544321 12224676622 22 2344556666666653
Q ss_pred ------cEEEEEEEEcCCCccchHHHHHHHHhcc
Q 003093 72 ------WREVIAIYVDDDHGRNGIAALGDTLAAK 99 (848)
Q Consensus 72 ------w~~vaii~~dd~~g~~~~~~l~~~l~~~ 99 (848)
.++++++.+... ...+++.++.++.
T Consensus 87 i~~~~~~~kiavl~Sg~g---~nl~al~~~~~~~ 117 (289)
T PRK13010 87 IHPDGQRPKVVIMVSKFD---HCLNDLLYRWRMG 117 (289)
T ss_pred EecCCCCeEEEEEEeCCC---ccHHHHHHHHHCC
Confidence 568888886653 2345555555544
No 437
>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=50.80 E-value=93 Score=31.76 Aligned_cols=76 Identities=5% Similarity=-0.024 Sum_probs=52.6
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. +++|.......+.+.+++.|.++.... ...+.......++.+...++|.|++....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~---~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (265)
T cd06285 2 IGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVAN---TGDNPDAQRRAIEMLLDRRVDGLILGDARSDD-HFLDELTRR 77 (265)
T ss_pred EEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEe---CCCCHHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHHHc
Confidence 566664 467888888999999999999875432 22233445567778888899988887544333 356777777
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (265)
T cd06285 78 GV 79 (265)
T ss_pred CC
Confidence 65
No 438
>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=50.58 E-value=65 Score=33.99 Aligned_cols=78 Identities=9% Similarity=0.067 Sum_probs=52.7
Q ss_pred EEEEEEEc--CCCccchHHHHHHHHhc--cCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEcc-CCcHHHHHHH
Q 003093 74 EVIAIYVD--DDHGRNGIAALGDTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNRGPVVFHV 148 (848)
Q Consensus 74 ~vaii~~d--d~~g~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~-~~~~~~~~~~ 148 (848)
+|+++..+ +.|.......+.+++++ .|.++.... ...+...-...+..+...++|.|++... +......+++
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~~---~~~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~ 77 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFYD---AKNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINK 77 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEec---CCCCHHHHHHHHHHHHHcCCCEEEEecCchhhHHHHHHH
Confidence 35666643 56777788899999999 787766542 2223344456677888889999888643 3333567788
Q ss_pred HHHcCC
Q 003093 149 AQYLGM 154 (848)
Q Consensus 149 a~~~g~ 154 (848)
+++.|.
T Consensus 78 ~~~~gi 83 (303)
T cd01539 78 AKQKNI 83 (303)
T ss_pred HHHCCC
Confidence 887776
No 439
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=50.32 E-value=85 Score=32.33 Aligned_cols=71 Identities=23% Similarity=0.171 Sum_probs=41.8
Q ss_pred eHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCe-eeEEeeceeeecCc---eeeee-ec-ccccccceEE
Q 003093 404 CIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGV-YDAAVGDIAIITNR---TKMAD-FT-QPYIESGLVV 477 (848)
Q Consensus 404 ~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~-~D~~~~~~~~t~~R---~~~~d-fs-~p~~~~~~~~ 477 (848)
.-++.+.+.++.|.++.+.+- + -..+..++.+|. +|+.+.+-....++ ...+. .+ .+|....+++
T Consensus 41 ~~~l~~~Fe~~~g~~v~~~~~--------~-Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~n~lvl 111 (257)
T PRK10677 41 LQDIAAQYKKEKGVDVVSSFA--------S-SSTLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLGNSLVV 111 (257)
T ss_pred HHHHHHHHHhhhCCeEEEEec--------c-cHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeecCEEEE
Confidence 345666666666777555442 2 346778888877 99988754221111 11221 11 3577788888
Q ss_pred EEeccC
Q 003093 478 VAPVRK 483 (848)
Q Consensus 478 v~~~~~ 483 (848)
+++++.
T Consensus 112 ~~~~~~ 117 (257)
T PRK10677 112 VAPKAS 117 (257)
T ss_pred EEECCC
Confidence 888764
No 440
>PF14981 FAM165: FAM165 family
Probab=50.23 E-value=36 Score=23.94 Aligned_cols=33 Identities=15% Similarity=0.094 Sum_probs=27.5
Q ss_pred cccchhHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 003093 736 LKSFSGLYLLCGLACLLALFIYLMQIVHQFSRH 768 (848)
Q Consensus 736 l~~~~g~f~il~~g~~la~~vf~~e~~~~~~~~ 768 (848)
++++-.++||++.-.++.++.|..--+|+++|.
T Consensus 3 L~~vPlLlYILaaKtlilClaFAgvK~yQ~krl 35 (51)
T PF14981_consen 3 LDNVPLLLYILAAKTLILCLAFAGVKMYQRKRL 35 (51)
T ss_pred hhhchHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 567778899999998999999988888887664
No 441
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=50.22 E-value=17 Score=34.14 Aligned_cols=31 Identities=10% Similarity=0.118 Sum_probs=22.7
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 003093 739 FSGLYLLCGLACLLALFIYLMQIVHQFSRHY 769 (848)
Q Consensus 739 ~~g~f~il~~g~~la~~vf~~e~~~~~~~~~ 769 (848)
+.-.||++++..+++++.|++..++.+++.+
T Consensus 94 l~R~~~Vl~g~s~l~i~yfvir~~R~r~~~r 124 (163)
T PF06679_consen 94 LKRALYVLVGLSALAILYFVIRTFRLRRRNR 124 (163)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHhhccccc
Confidence 4556778777778888888888887666443
No 442
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=49.76 E-value=2e+02 Score=32.67 Aligned_cols=139 Identities=12% Similarity=0.126 Sum_probs=72.0
Q ss_pred EEccCCchhHHHHHHhhc-cCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcCCCc-
Q 003093 8 IIGPQDAVTSHVVSHVAN-ELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHG- 85 (848)
Q Consensus 8 iIGp~~S~~~~ava~i~~-~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~~g- 85 (848)
|+||++..+-.++..+.+ ...+=+|.++- --++|- +.....+...+..+...=+++.|+|. +.||
T Consensus 198 i~~p~~~~v~~~l~~~~~l~l~~~~i~p~H----------G~i~r~--~~~~~l~~Y~~~~~~~~~~kv~IvY~-S~~Gn 264 (479)
T PRK05452 198 ILTPFSRLVTPKITEILGFNLPVDMIATSH----------GVVWRD--NPTQIVELYLKWAADYQEDRITIFYD-TMSNN 264 (479)
T ss_pred hhhhhHHHHHHHHHHHhhcCCCCCEEECCC----------CceEeC--CHHHHHHHHHHHhhccCcCcEEEEEE-CCccH
Confidence 678887766666666654 23344443221 123552 22222233333343323478999983 3344
Q ss_pred -cchHHHHHHHHhcc--CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC------CcHHHHHHHHHHcCCCC
Q 003093 86 -RNGIAALGDTLAAK--RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY------NRGPVVFHVAQYLGMLG 156 (848)
Q Consensus 86 -~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~------~~~~~~~~~a~~~g~~~ 156 (848)
+..++.+.+.+++. |+.|.... +.. .+...++..+. ++|.|++.++. +....++.......+.+
T Consensus 265 Te~mA~~ia~gl~~~g~gv~v~~~~-v~~----~~~~~i~~~~~--~ad~vilGspT~~~~~~p~~~~fl~~l~~~~l~g 337 (479)
T PRK05452 265 TRMMADAIAQGIAEVDPRVAVKIFN-VAR----SDKNEILTNVF--RSKGVLVGSSTMNNVMMPKIAGLLEEITGLRFRN 337 (479)
T ss_pred HHHHHHHHHHHHHhhCCCceEEEEE-CCC----CCHHHHHhHHh--hCCEEEEECCccCCcchHHHHHHHHHhhccCcCC
Confidence 56678888999876 45544322 221 23444555553 56788877654 22444555555555544
Q ss_pred CCeEEEecCc
Q 003093 157 TGYVWIATSW 166 (848)
Q Consensus 157 ~~~~wi~~~~ 166 (848)
+...-+++-+
T Consensus 338 K~~~vFGSyg 347 (479)
T PRK05452 338 KRASAFGSHG 347 (479)
T ss_pred CEEEEEECCC
Confidence 3333344433
No 443
>COG3340 PepE Peptidase E [Amino acid transport and metabolism]
Probab=49.67 E-value=1.7e+02 Score=28.86 Aligned_cols=96 Identities=16% Similarity=0.068 Sum_probs=57.6
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCC--CccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEcc
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH 138 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~--~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~ 138 (848)
.-+.+.++.. -++|+.|=.-.. -.....+.++++|++.|..+......... ..++.. ++ .++|+|++.+.
T Consensus 22 ~~i~n~l~g~-~~~i~FIPtAs~~~~~~~Yv~k~~~~l~~lg~~v~~L~l~~~~--~~~Ie~---~l--~~~d~IyVgGG 93 (224)
T COG3340 22 PFIANFLQGK-RKTIAFIPTASVDSEDDFYVEKVRNALAKLGLEVSELHLSKPP--LAAIEN---KL--MKADIIYVGGG 93 (224)
T ss_pred HHHHHHhcCC-CceEEEEecCccccchHHHHHHHHHHHHHcCCeeeeeeccCCC--HHHHHH---hh--hhccEEEECCc
Confidence 3444445444 367877742111 11346889999999999998865444322 233333 33 34688887654
Q ss_pred CCcHHHHHHHHHHcCCCC-------CCeEEEecCc
Q 003093 139 YNRGPVVFHVAQYLGMLG-------TGYVWIATSW 166 (848)
Q Consensus 139 ~~~~~~~~~~a~~~g~~~-------~~~~wi~~~~ 166 (848)
....+++++++-|+.. .|.++|+.++
T Consensus 94 --NTF~LL~~lke~gld~iIr~~vk~G~~YiG~SA 126 (224)
T COG3340 94 --NTFNLLQELKETGLDDIIRERVKAGTPYIGWSA 126 (224)
T ss_pred --hHHHHHHHHHHhCcHHHHHHHHHcCCceEEecc
Confidence 4567888888888643 4445665543
No 444
>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=49.24 E-value=85 Score=31.97 Aligned_cols=75 Identities=11% Similarity=0.111 Sum_probs=51.7
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. ++.|.......+.+.+++.|..+..... ..+ .+....+.++...++|.|++....... ..++.+.+.
T Consensus 2 I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~-~~~~~~i~~~~~~~vdgiii~~~~~~~-~~~~~~~~~ 76 (266)
T cd06278 2 IGVVVADLDNPFYSELLEALSRALQARGYQPLLINT---DDD-EDLDAALRQLLQYRVDGVIVTSGTLSS-ELAEECRRN 76 (266)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcC---CCC-HHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhc
Confidence 455553 4678888889999999999998765422 122 256677778888899998886543332 457777777
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 77 ~i 78 (266)
T cd06278 77 GI 78 (266)
T ss_pred CC
Confidence 75
No 445
>PRK09701 D-allose transporter subunit; Provisional
Probab=49.20 E-value=1.4e+02 Score=31.65 Aligned_cols=85 Identities=9% Similarity=-0.009 Sum_probs=58.0
Q ss_pred HcCcEEEEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHH
Q 003093 69 HYGWREVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVV 145 (848)
Q Consensus 69 ~~~w~~vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~ 145 (848)
.+.-.++++++. ++.|.......+.+++++.|..+..... +...+..+-...+..+...++|.|++...... ....
T Consensus 21 ~~~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~v~~~~~-~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~~ 99 (311)
T PRK09701 21 AFAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFAS-PSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMP 99 (311)
T ss_pred hccCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCeEEEecC-CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHH
Confidence 455678999984 4678888899999999999988765321 11122234456677777788999998764432 2344
Q ss_pred HHHHHHcCC
Q 003093 146 FHVAQYLGM 154 (848)
Q Consensus 146 ~~~a~~~g~ 154 (848)
+.++.+.|+
T Consensus 100 l~~~~~~gi 108 (311)
T PRK09701 100 VARAWKKGI 108 (311)
T ss_pred HHHHHHCCC
Confidence 667777775
No 446
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=49.17 E-value=90 Score=32.67 Aligned_cols=80 Identities=3% Similarity=-0.022 Sum_probs=54.9
Q ss_pred cEEEEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHH
Q 003093 72 WREVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHV 148 (848)
Q Consensus 72 w~~vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~ 148 (848)
-+.++++.. ++.|.......+.++++++|..+..... ..+.......++++...++|.+++...... ....++.
T Consensus 26 ~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~~---~~d~~~~~~~~~~l~~~~~dgiii~~~~~~~~~~~l~~ 102 (295)
T PRK10653 26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDS---QNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKM 102 (295)
T ss_pred CCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEecC---CCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHH
Confidence 567888874 4567788889999999999998875422 112344556677777778998887654332 2356777
Q ss_pred HHHcCC
Q 003093 149 AQYLGM 154 (848)
Q Consensus 149 a~~~g~ 154 (848)
+++.|.
T Consensus 103 ~~~~~i 108 (295)
T PRK10653 103 ANQANI 108 (295)
T ss_pred HHHCCC
Confidence 777665
No 447
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=49.14 E-value=1e+02 Score=32.60 Aligned_cols=79 Identities=24% Similarity=0.204 Sum_probs=44.5
Q ss_pred CCCCChHHhhcCCCCeeEEe-CchHHHHH---HhhhCCCccCccc--CCCHHHHHHHhhcCCCCCceEEEEccHHH---H
Q 003093 590 SPIKGIDSLRSSNYPIGYQV-NSFARNYL---VDELNIDESRLVP--LNSPEEYAKALKDGPHKGGVAAVVDDRAY---A 660 (848)
Q Consensus 590 ~~i~sl~dL~~s~~~i~~~~-~s~~~~~l---~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~a~~~~~~~---~ 660 (848)
..|++++||. |++|++-. ||-.+-.. .+..+.....+.. .-...+..+++++ |.+||.+.-... .
T Consensus 127 ~~Ikti~DL~--GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~~~~~~a~~~~~l~~----g~iDA~~~~~G~p~~a 200 (321)
T COG2358 127 AGIKTIADLK--GKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAESADALKN----GTIDAAFYVAGVPNPA 200 (321)
T ss_pred CCcceehhcC--CCEEeecCCCCccHHHHHHHHHHcCCCCcchhhhhhcCchhhHHHhhC----CcccEEEEecCCCCcc
Confidence 4799999999 99988853 44333222 2334443322221 1123345777777 899988764321 1
Q ss_pred HHHHhcCCcEEEeC
Q 003093 661 ELFLSTRCEFSIVG 674 (848)
Q Consensus 661 ~~~~~~~~~l~~~~ 674 (848)
-..+...|++.+++
T Consensus 201 i~el~~~~~i~lv~ 214 (321)
T COG2358 201 ISELATTCDIVLVP 214 (321)
T ss_pred HHHHHhhCCeEEEe
Confidence 23444556666664
No 448
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=49.03 E-value=1.3e+02 Score=25.69 Aligned_cols=58 Identities=9% Similarity=0.060 Sum_probs=38.8
Q ss_pred chHHHHHHHHhccCc-EEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEc--cCCcHHHHHHHHHHcC
Q 003093 87 NGIAALGDTLAAKRC-RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT--HYNRGPVVFHVAQYLG 153 (848)
Q Consensus 87 ~~~~~l~~~l~~~g~-~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~--~~~~~~~~~~~a~~~g 153 (848)
.....+.+.++..|. .+.. . .+....+..++...+|++++.. ....+..++++.++.+
T Consensus 9 ~~~~~l~~~l~~~~~~~v~~---~------~~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~~ 69 (112)
T PF00072_consen 9 EIRELLEKLLERAGYEEVTT---A------SSGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIRQIN 69 (112)
T ss_dssp HHHHHHHHHHHHTTEEEEEE---E------SSHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCCEEEE---E------CCHHHHHHHhcccCceEEEEEeeecccccccccccccccc
Confidence 456677777777787 4432 1 1234455666667799999874 4467777888888877
No 449
>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=48.82 E-value=66 Score=33.11 Aligned_cols=77 Identities=9% Similarity=-0.065 Sum_probs=51.7
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHHHH
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQY 151 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a~~ 151 (848)
+++|.. ++.|.......+.+.+++.|.++... ....+...-...++++.+.++|.|++...... ....+..+.+
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 556653 46788888899999999999887643 22223333456677777789999987654332 3356777777
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|.
T Consensus 79 ~~i 81 (277)
T cd06319 79 AKI 81 (277)
T ss_pred CCC
Confidence 775
No 450
>PRK00945 acetyl-CoA decarbonylase/synthase complex subunit epsilon; Provisional
Probab=48.64 E-value=81 Score=30.08 Aligned_cols=114 Identities=14% Similarity=0.191 Sum_probs=62.2
Q ss_pred CCeEEEEccCCch---hHHHHHHhhccCCccEEecccCCCCCCCCCCCceEeccCChHHHHHHHHHHHHHcCcE------
Q 003093 3 GQTVAIIGPQDAV---TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWR------ 73 (848)
Q Consensus 3 ~~V~aiIGp~~S~---~~~ava~i~~~~~vP~Is~~at~p~ls~~~~p~f~r~~p~d~~q~~ai~~~~~~~~w~------ 73 (848)
++.+.++|..... ....+..+++++++|+++...+...|.+.+ ..|. ......+..++..-+|.
T Consensus 35 KrPlIivG~ga~~~~ea~e~l~elaEkl~iPVvtT~~~~~~~~~kg------v~~~-~~~lg~lg~~~~~p~~e~~~g~~ 107 (171)
T PRK00945 35 KRPLLVVGSLLLDDEELLDRAVKIAKKANIPVAATGGSYKGLIDKG------VDAK-YINLHELTNYLKDPNWKGLDGNG 107 (171)
T ss_pred CCcEEEECcCccccchHHHHHHHHHHHHCCCEEEccccccccccCC------ccCC-cccHHHHHhhccCchhhhhcCCC
Confidence 4678899987754 677899999999999997554444444422 1111 22234455555444443
Q ss_pred ---EEEEEEEcCCCccchHHHHHHHHhccCcE-EEEeeecCCCC-------ChHHHHHHHHHHh
Q 003093 74 ---EVIAIYVDDDHGRNGIAALGDTLAAKRCR-ISFKAPLSVEA-------TEDEITDLLVKVA 126 (848)
Q Consensus 74 ---~vaii~~dd~~g~~~~~~l~~~l~~~g~~-v~~~~~~~~~~-------~~~d~~~~l~~i~ 126 (848)
-|..+..+..|....+..++.... ++ |+....+.+.+ +.+++...|.+|.
T Consensus 108 ~~DlvlfvG~~~~~~~~~l~~lk~f~~---~~~~~~~~~y~~~a~~s~~~~~~~~~~~~l~~li 168 (171)
T PRK00945 108 NYDLVIFIGVTYYYASQGLSALKHFSP---LKTITIDRYYHPNADMSFPNLSKEEYLEYLDELI 168 (171)
T ss_pred CcCEEEEecCCchhHHHHHHHHhhcCC---ceEEEecCCcCCCCceecCCCCHHHHHHHHHHHH
Confidence 334444666665555555543322 32 22223333322 3456666666653
No 451
>cd08184 Fe-ADH3 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the iron-containing alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron or zinc ions. Members of this family are mainly found in bacteria.
Probab=48.58 E-value=79 Score=34.22 Aligned_cols=75 Identities=15% Similarity=0.046 Sum_probs=51.0
Q ss_pred HHHHHHHHHcCc--EEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcC---CCeEEEE
Q 003093 61 AAIAEIVDHYGW--REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVV 135 (848)
Q Consensus 61 ~ai~~~~~~~~w--~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~---~~~viv~ 135 (848)
..+.++++.+|. +++.+++ |...-. ..+.+.|++.|+.+.....+....+.+++....+..++. ++|+||-
T Consensus 12 ~~l~~~~~~~g~~~~~~lvvt-d~~~~~---~~v~~~L~~~g~~~~~f~~v~~nPt~~~v~~~~~~~~~~~~~~~D~IIa 87 (347)
T cd08184 12 DQLNDLLAPKRKNKDPAVFFV-DDVFQG---KDLISRLPVESEDMIIWVDATEEPKTDQIDALTAQVKSFDGKLPCAIVG 87 (347)
T ss_pred HHHHHHHHHcCCCCCeEEEEE-Ccchhh---hHHHHHHHhcCCcEEEEcCCCCCcCHHHHHHHHHHHHhhCCCCCCEEEE
Confidence 456667777764 5566656 432211 567788888888765544566666667788888888876 8999997
Q ss_pred EccC
Q 003093 136 HTHY 139 (848)
Q Consensus 136 ~~~~ 139 (848)
.+.+
T Consensus 88 iGGG 91 (347)
T cd08184 88 IGGG 91 (347)
T ss_pred eCCc
Confidence 7654
No 452
>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=48.22 E-value=71 Score=34.36 Aligned_cols=84 Identities=10% Similarity=0.089 Sum_probs=54.0
Q ss_pred HHHHHHHHHcCc-EEEEEEEEcCCCccchHHHHHHHHhccCcEEEEee-ecCCCCChHHHHHHHHHHhcCCCeEEEEEcc
Q 003093 61 AAIAEIVDHYGW-REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKA-PLSVEATEDEITDLLVKVALTESRIIVVHTH 138 (848)
Q Consensus 61 ~ai~~~~~~~~w-~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~-~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~ 138 (848)
..+.++++.++. +++.+|.....+-. ..+.+.+.|++.|+++.... ......+.+.+...+..++. ++|+||..+.
T Consensus 12 ~~l~~~~~~~~~~~kvlivtd~~~~~~-~~~~i~~~L~~~~~~~~i~~~~~~~~p~~~~v~~~~~~~~~-~~d~IIaiGG 89 (332)
T cd08549 12 NDIGPIINKIGVNSKIMIVCGNNTYKV-AGKEIIERLESNNFTKEVLERDSLLIPDEYELGEVLIKLDK-DTEFLLGIGS 89 (332)
T ss_pred HHHHHHHHHcCCCCcEEEEECCcHHHH-HHHHHHHHHHHcCCeEEEEecCCCCCCCHHHHHHHHHHhhc-CCCEEEEECC
Confidence 445667777776 78888875544333 34788888988887654321 22222345777888888887 8999998765
Q ss_pred C--CcHHHHH
Q 003093 139 Y--NRGPVVF 146 (848)
Q Consensus 139 ~--~~~~~~~ 146 (848)
+ -+...++
T Consensus 90 Gsv~D~aK~i 99 (332)
T cd08549 90 GTIIDLVKFV 99 (332)
T ss_pred cHHHHHHHHH
Confidence 5 3444444
No 453
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=48.05 E-value=63 Score=36.22 Aligned_cols=141 Identities=9% Similarity=0.059 Sum_probs=89.1
Q ss_pred CeEEEEccCCchhHHHHHHhhccCCccEEecccCCCCCCC-CC-CCceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEc
Q 003093 4 QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQ-FPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 81 (848)
Q Consensus 4 ~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~at~p~ls~-~~-~p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~d 81 (848)
+-+.++|.+.+.....+.++.++.+|-+..+.. +..+.+ .. .+. ...++-....++++..+.+.++-..+.+-+
T Consensus 194 ~~vnl~G~~~~~~~~~i~~lL~~lGI~v~~~lp-~~~~~eL~~~~~~-~~~c~~~P~ls~aa~~Le~~~gvp~~~~P~-- 269 (457)
T CHL00073 194 PPLVLFGSLPSTVASQLTLELKRQGIKVSGWLP-SQRYTDLPSLGEG-VYVCGVNPFLSRTATTLMRRRKCKLIGAPF-- 269 (457)
T ss_pred CcEEEEEecCcccHHHHHHHHHHcCCeEeEEeC-CCCHHHHHhhCcc-cEEEEcCcchHHHHHHHHHHhCCceeecCC--
Confidence 457899999999999999999999999886544 444443 11 122 222333333345555555788877666544
Q ss_pred CCCccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhc--CCCeEEEEEccCCcHHHHHHHHHHcCCC
Q 003093 82 DDHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGML 155 (848)
Q Consensus 82 d~~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~--~~~~viv~~~~~~~~~~~~~~a~~~g~~ 155 (848)
.+|....+.+..++.+. |.. .+.+.. ....+.+.+...+. .+-++. +.+.+.....+.+.+.++||.
T Consensus 270 -PiGi~~Td~fLr~Ia~~~G~~---pe~l~~--Er~rl~dal~d~~~~L~GKrva-i~Gdp~~~i~LarfL~elGme 339 (457)
T CHL00073 270 -PIGPDGTRAWIEKICSVFGIE---PQGLEE--REEQIWESLKDYLDLVRGKSVF-FMGDNLLEISLARFLIRCGMI 339 (457)
T ss_pred -cCcHHHHHHHHHHHHHHhCcC---HHHHHH--HHHHHHHHHHHHHHHHCCCEEE-EECCCcHHHHHHHHHHHCCCE
Confidence 48888888777777764 532 222211 11223333333222 355665 788888999999999999984
No 454
>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=47.91 E-value=1.4e+02 Score=31.79 Aligned_cols=80 Identities=8% Similarity=0.060 Sum_probs=54.2
Q ss_pred cEEEEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHH
Q 003093 72 WREVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 149 (848)
Q Consensus 72 w~~vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a 149 (848)
-+.++++.. ++.|.......+.+.+++.|..+..... . .+.......+..+...++|.|++..........+.++
T Consensus 60 ~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~-~--~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 136 (327)
T TIGR02417 60 SRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACS-D--DNPDQEKVVIENLLARQVDALIVASCMPPEDAYYQKL 136 (327)
T ss_pred CceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeC-C--CCHHHHHHHHHHHHHcCCCEEEEeCCCCCChHHHHHH
Confidence 357888875 3667788889999999999998865432 1 1223445567777778899988875433233556677
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
.+.|.
T Consensus 137 ~~~~i 141 (327)
T TIGR02417 137 QNEGL 141 (327)
T ss_pred HhcCC
Confidence 66664
No 455
>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=47.63 E-value=91 Score=31.77 Aligned_cols=76 Identities=11% Similarity=0.015 Sum_probs=46.4
Q ss_pred EEEEEEc------CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHH
Q 003093 75 VIAIYVD------DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHV 148 (848)
Q Consensus 75 vaii~~d------d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~ 148 (848)
|+++..+ +.|.......+.+.+++.|+.+.....-. .........+.+...++|.|++....... ..+..
T Consensus 2 igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~vdgiii~~~~~~~-~~~~~ 77 (268)
T cd06271 2 IGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYDLVLLPVDP---DEDPLEVYRRLVESGLVDGVIISRTRPDD-PRVAL 77 (268)
T ss_pred eEEEeCCcccccCCccHHHHHHHHHHHHHHCCceEEEecCCC---cHHHHHHHHHHHHcCCCCEEEEecCCCCC-hHHHH
Confidence 4556544 78888889999999999999877653211 11222233333445679998886543222 23456
Q ss_pred HHHcCC
Q 003093 149 AQYLGM 154 (848)
Q Consensus 149 a~~~g~ 154 (848)
+.+.|.
T Consensus 78 ~~~~~i 83 (268)
T cd06271 78 LLERGF 83 (268)
T ss_pred HHhcCC
Confidence 666664
No 456
>PRK10481 hypothetical protein; Provisional
Probab=47.42 E-value=2e+02 Score=28.83 Aligned_cols=68 Identities=15% Similarity=0.099 Sum_probs=45.4
Q ss_pred CcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcH
Q 003093 71 GWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRG 142 (848)
Q Consensus 71 ~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~ 142 (848)
+-++++++....+ ..+.-.+.+.+.|..+.....-|...+...+....++++..++|+||+.|-+-..
T Consensus 128 ~g~riGVitP~~~----qi~~~~~kw~~~G~~v~~~~aspy~~~~~~l~~aa~~L~~~gaD~Ivl~C~G~~~ 195 (224)
T PRK10481 128 GGHQVGVIVPVEE----QLAQQAQKWQVLQKPPVFALASPYHGSEEELIDAGKELLDQGADVIVLDCLGYHQ 195 (224)
T ss_pred CCCeEEEEEeCHH----HHHHHHHHHHhcCCceeEeecCCCCCCHHHHHHHHHHhhcCCCCEEEEeCCCcCH
Confidence 3489999986544 2333334444558887765544433444577788888888999999999876544
No 457
>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=47.35 E-value=1e+02 Score=31.39 Aligned_cols=76 Identities=9% Similarity=0.082 Sum_probs=51.3
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. ++.|.......+.+++++.|..+.... ...+.......++++...++|.|++....... ..++++++.
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 445553 466888889999999999998876432 12233445567778888899999887654333 346677766
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (267)
T cd06283 78 GK 79 (267)
T ss_pred CC
Confidence 64
No 458
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=47.17 E-value=1.4e+02 Score=35.44 Aligned_cols=68 Identities=16% Similarity=0.105 Sum_probs=48.4
Q ss_pred HcCcEEEEEEEEcCCC---------c---cchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEE
Q 003093 69 HYGWREVIAIYVDDDH---------G---RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVH 136 (848)
Q Consensus 69 ~~~w~~vaii~~dd~~---------g---~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~ 136 (848)
-|..-+|++|...|+- | ......+...+++.|.++.....++. +...+...+.++.+ ++|+|+..
T Consensus 183 v~~~prv~vi~tG~El~~~~~~~~~g~i~dsn~~~l~~~l~~~g~~~~~~~~v~D--d~~~i~~~l~~~~~-~~D~iItt 259 (633)
T PRK14498 183 VYKKPRVGIISTGDELVEPGEPLKPGKIYDVNSYTLAAAVEEAGGEPVRYGIVPD--DEEELEAALRKALK-ECDLVLLS 259 (633)
T ss_pred EecCcEEEEEecCccccCCCCCCCCCEEEEChHHHHHHHHHHCCCEEEEEEEeCC--CHHHHHHHHHHHHh-cCCEEEEC
Confidence 3455688888765541 2 23456788889999999988777764 33677888877754 79999988
Q ss_pred ccC
Q 003093 137 THY 139 (848)
Q Consensus 137 ~~~ 139 (848)
+..
T Consensus 260 GG~ 262 (633)
T PRK14498 260 GGT 262 (633)
T ss_pred CCC
Confidence 654
No 459
>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=47.15 E-value=69 Score=33.01 Aligned_cols=80 Identities=11% Similarity=-0.060 Sum_probs=51.6
Q ss_pred EEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeec-CCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHH
Q 003093 74 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPL-SVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVA 149 (848)
Q Consensus 74 ~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~-~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a 149 (848)
+|++++.+ +.|.......+.+++++.|..+...... ....+.......+..+.. ++|.+++...... ....++++
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 46777744 5677788899999999998654433221 111223445566777777 8999988654333 34677888
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
.+.|.
T Consensus 80 ~~~~i 84 (275)
T cd06307 80 AAAGV 84 (275)
T ss_pred HHCCC
Confidence 88775
No 460
>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=46.96 E-value=1e+02 Score=31.28 Aligned_cols=76 Identities=8% Similarity=-0.019 Sum_probs=51.8
Q ss_pred EEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++..+ +.|.....+.+.+++++.|.++..... ..+.......++++...++|.+++...... ..++..+++.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~~dgii~~~~~~~-~~~~~~~~~~ 77 (259)
T cd01542 2 IGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMNT---NFSIEKEIEALELLARQKVDGIILLATTIT-DEHREAIKKL 77 (259)
T ss_pred eEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEeC---CCCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHhcC
Confidence 4556543 556677889999999999998865422 223345566778888889999999765432 3466667666
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 78 ~i 79 (259)
T cd01542 78 NV 79 (259)
T ss_pred CC
Confidence 64
No 461
>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=46.85 E-value=74 Score=32.46 Aligned_cols=77 Identities=4% Similarity=-0.057 Sum_probs=52.1
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHHHH
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQY 151 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a~~ 151 (848)
+++|.. ++.|.......+.+++++.|..+.... ...+..+....+.++...++|.|++...... ....+.++++
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~---~~~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~~~l~~l~~ 78 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKELGYELTVLD---AQNDAAKQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAANE 78 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHcCceEEecC---CCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHH
Confidence 455553 566888888999999999998886532 2223355667788888788999887643322 2346777777
Q ss_pred cCC
Q 003093 152 LGM 154 (848)
Q Consensus 152 ~g~ 154 (848)
.|.
T Consensus 79 ~~i 81 (268)
T cd06323 79 AGI 81 (268)
T ss_pred CCC
Confidence 665
No 462
>KOG0025 consensus Zn2+-binding dehydrogenase (nuclear receptor binding factor-1) [Transcription; Energy production and conversion]
Probab=46.53 E-value=3.6e+02 Score=28.09 Aligned_cols=97 Identities=8% Similarity=0.040 Sum_probs=69.6
Q ss_pred CceEeccCChHHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHh
Q 003093 47 PYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVA 126 (848)
Q Consensus 47 p~f~r~~p~d~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~ 126 (848)
.++++...+ +.-++++.++.+.+|.+.+.+|-+.+ .++.+.+.|+..|.+-+..+.--.+ .++.. .+..
T Consensus 162 D~vIQNgan-S~VG~~ViQlaka~GiktinvVRdR~-----~ieel~~~Lk~lGA~~ViTeeel~~---~~~~k--~~~~ 230 (354)
T KOG0025|consen 162 DSVIQNGAN-SGVGQAVIQLAKALGIKTINVVRDRP-----NIEELKKQLKSLGATEVITEEELRD---RKMKK--FKGD 230 (354)
T ss_pred CeeeecCcc-cHHHHHHHHHHHHhCcceEEEeecCc-----cHHHHHHHHHHcCCceEecHHHhcc---hhhhh--hhcc
Confidence 477776544 55789999999999999999997544 5888999999999886654332211 22211 1224
Q ss_pred cCCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 127 LTESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 127 ~~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
..+++.-+-+..+..+..+.+.+.+-|.
T Consensus 231 ~~~prLalNcVGGksa~~iar~L~~Ggt 258 (354)
T KOG0025|consen 231 NPRPRLALNCVGGKSATEIARYLERGGT 258 (354)
T ss_pred CCCceEEEeccCchhHHHHHHHHhcCce
Confidence 4678888888888888888888877664
No 463
>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=46.50 E-value=1.3e+02 Score=30.88 Aligned_cols=77 Identities=10% Similarity=-0.040 Sum_probs=51.7
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEcc-CCc---HHHHHHH
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNR---GPVVFHV 148 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~-~~~---~~~~~~~ 148 (848)
+++|.. ++.|.......+.+++++.|..+.... ...+.+.....++.+...++|.+++... ..+ ....+.+
T Consensus 2 Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~i~~ 78 (273)
T cd06292 2 VGLLVPELSNPIFPAFAEAIEAALAQYGYTVLLCN---TYRGGVSEADYVEDLLARGVRGVVFISSLHADTHADHSHYER 78 (273)
T ss_pred EEEEeCCCcCchHHHHHHHHHHHHHHCCCEEEEEe---CCCChHHHHHHHHHHHHcCCCEEEEeCCCCCcccchhHHHHH
Confidence 455553 567888888999999999999876432 2223345567788888889999888643 222 2234666
Q ss_pred HHHcCC
Q 003093 149 AQYLGM 154 (848)
Q Consensus 149 a~~~g~ 154 (848)
+.+.|+
T Consensus 79 ~~~~~i 84 (273)
T cd06292 79 LAERGL 84 (273)
T ss_pred HHhCCC
Confidence 777665
No 464
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=46.27 E-value=53 Score=31.66 Aligned_cols=28 Identities=32% Similarity=0.568 Sum_probs=26.3
Q ss_pred EEEEccCCchhHHHHHHhhccCCccEEe
Q 003093 6 VAIIGPQDAVTSHVVSHVANELQVPLLS 33 (848)
Q Consensus 6 ~aiIGp~~S~~~~ava~i~~~~~vP~Is 33 (848)
+.|+||..|+=+-....+++++++|+|+
T Consensus 3 iiilG~pGaGK~T~A~~La~~~~i~hls 30 (178)
T COG0563 3 ILILGPPGAGKSTLAKKLAKKLGLPHLD 30 (178)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCcEEc
Confidence 6899999999999999999999999997
No 465
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial. This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA.
Probab=46.16 E-value=1.1e+02 Score=29.06 Aligned_cols=66 Identities=12% Similarity=0.083 Sum_probs=45.9
Q ss_pred cEEEEEEEEcCCCcc---chHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc-CCCeEEEEEccC
Q 003093 72 WREVIAIYVDDDHGR---NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTHY 139 (848)
Q Consensus 72 w~~vaii~~dd~~g~---~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~-~~~~viv~~~~~ 139 (848)
.-++++|...|+-+. .....+...+++.|+++.....++.+ ...+...+++..+ .++|+|+..+..
T Consensus 4 ~~rv~vit~~d~~~~~~d~n~~~l~~~L~~~G~~v~~~~iv~Dd--~~~i~~~l~~~~~~~~~DlVIttGGt 73 (163)
T TIGR02667 4 PLRIAILTVSDTRTEEDDTSGQYLVERLTEAGHRLADRAIVKDD--IYQIRAQVSAWIADPDVQVILITGGT 73 (163)
T ss_pred ccEEEEEEEeCcCCccCCCcHHHHHHHHHHCCCeEEEEEEcCCC--HHHHHHHHHHHHhcCCCCEEEECCCc
Confidence 457888775553322 23457788899999998887777743 4778888877653 579999987643
No 466
>cd08173 Gro1PDH Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate using either NADH or NADPH as a coenzyme. Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH, EC 1.1.1.261) plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids. It catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate using either NADH or NADPH as a coenzyme. The activity is zinc-dependent. One characteristic feature of archaea is that their cellular membrane has an ether linkage between the glycerol backbone and the hydrocarbon residues. The polar lipids of the members of Archaea consist of di- and tetraethers of glycerol with isoprenoid alcohols bound at the sn-2 and sn-3 positions of the glycerol moiety. The archaeal polar lipids have the enantiomeric configuration of a glycerophosph
Probab=46.07 E-value=81 Score=34.07 Aligned_cols=81 Identities=9% Similarity=-0.018 Sum_probs=54.4
Q ss_pred HHHHHHH-HcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-
Q 003093 62 AIAEIVD-HYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 139 (848)
Q Consensus 62 ai~~~~~-~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~- 139 (848)
.+.++++ ..+.+++.+|+.... .....+.+.+.|++.| .+... +....+.+.+...+..+++.++|+||..+.+
T Consensus 14 ~l~~~l~~~~~~~~~liv~d~~~-~~~~~~~v~~~l~~~~-~~~~~--~~~~~~~~~v~~~~~~~~~~~~d~iIaiGGGs 89 (339)
T cd08173 14 KIPNVLRDLLLGGRVLVVTGPTT-KSIAGKKVEALLEDEG-EVDVV--IVEDATYEEVEKVESSARDIGADFVIGVGGGR 89 (339)
T ss_pred HHHHHHHHhCCCCeEEEEECCch-HHHHHHHHHHHHHhcC-CeEEE--EeCCCCHHHHHHHHHHhhhcCCCEEEEeCCch
Confidence 3556666 456789988874443 3356778888898888 54332 2233466788888888888899999977654
Q ss_pred -CcHHHHH
Q 003093 140 -NRGPVVF 146 (848)
Q Consensus 140 -~~~~~~~ 146 (848)
-+...++
T Consensus 90 ~~D~aK~~ 97 (339)
T cd08173 90 VIDVAKVA 97 (339)
T ss_pred HHHHHHHH
Confidence 3444444
No 467
>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=45.84 E-value=75 Score=32.62 Aligned_cols=77 Identities=5% Similarity=-0.018 Sum_probs=51.2
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhc--cCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHH
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVA 149 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a 149 (848)
|++++. ++.|.......+.+++++ .|.++..... ..+.......+..+...++|.|++...... ....++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~ 78 (271)
T cd06321 2 IGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVVSA---DYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRA 78 (271)
T ss_pred eEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEccC---CCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHH
Confidence 566663 467888889999999999 7766654321 223344556677777788999988653322 34567777
Q ss_pred HHcCC
Q 003093 150 QYLGM 154 (848)
Q Consensus 150 ~~~g~ 154 (848)
++.|.
T Consensus 79 ~~~~i 83 (271)
T cd06321 79 QAAGI 83 (271)
T ss_pred HHCCC
Confidence 77664
No 468
>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=45.72 E-value=75 Score=33.50 Aligned_cols=72 Identities=6% Similarity=0.045 Sum_probs=52.1
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCC-cHHHHHHHHHHcCC
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVAQYLGM 154 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~-~~~~~~~~a~~~g~ 154 (848)
.+++|.....+.+.+++++.|..+..... ..+...-...+..+.+.++|.|++..... .....++.+++.|.
T Consensus 8 ~~~~~~~~~~~~i~~~a~~~g~~v~~~~~---~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~~~i 80 (302)
T TIGR02634 8 LRLERWQKDRDIFVAAAESLGAKVFVQSA---NGNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKDEGI 80 (302)
T ss_pred cchhhHHHHHHHHHHHHHhcCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHHCCC
Confidence 46778888899999999999998865422 22334455677888888999998875433 34567788888775
No 469
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=45.48 E-value=2.7e+02 Score=26.27 Aligned_cols=66 Identities=15% Similarity=0.046 Sum_probs=37.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeeceeeecCceeeeeecccccccceEEEEec
Q 003093 402 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 481 (848)
Q Consensus 402 G~~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~~~~t~~R~~~~dfs~p~~~~~~~~v~~~ 481 (848)
++..+++..+.++.+ .+++.... .+.+...+ .+++|+++..- +.....+ -+.++....++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~v~~~~---------~~~~~~~l-~~~~D~~i~~~---~~~~~~l-~~~~l~~~~~~~v~~~ 78 (202)
T cd08472 14 LLLIPALPDFLARYP-DIELDLGV---------SDRPVDLI-REGVDCVIRVG---ELADSSL-VARRLGELRMVTCASP 78 (202)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEE---------CCCcchhh-cccccEEEEcC---CCCCccE-EEEEccceeEEEEECH
Confidence 455677788887764 23344322 22344444 46799998622 1112223 2557777778877764
Q ss_pred c
Q 003093 482 R 482 (848)
Q Consensus 482 ~ 482 (848)
.
T Consensus 79 ~ 79 (202)
T cd08472 79 A 79 (202)
T ss_pred H
Confidence 3
No 470
>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.
Probab=45.46 E-value=2.6e+02 Score=29.35 Aligned_cols=41 Identities=17% Similarity=0.152 Sum_probs=31.0
Q ss_pred eHHHHHHHHHhCCCCcceEEeeCCCCCCCCChhHHHHHHhcCeeeEEeec
Q 003093 404 CIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 453 (848)
Q Consensus 404 ~~dll~~i~~~l~~~~~~~~~~~~~~~~n~s~~~~i~~l~~g~~D~~~~~ 453 (848)
...|++.+.+.+|+++++.. ++-.-+...|.+|++|+.+..
T Consensus 23 ~~~i~~~iLE~~Gy~Ve~~~---------~~~~~~~~al~~GdiD~~~e~ 63 (290)
T TIGR03414 23 TTALASVLLEGLGYQPKVTL---------LSVPVTYAGLKDGDLDVFLGN 63 (290)
T ss_pred HHHHHHHHHHHcCCcceeEE---------ccHHHHHHHHHcCCceEeccc
Confidence 35677788888899877643 235677888999999998864
No 471
>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=45.40 E-value=1e+02 Score=28.68 Aligned_cols=64 Identities=19% Similarity=0.197 Sum_probs=43.3
Q ss_pred EEEEEEEcCCC--cc---chHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhc-CCCeEEEEEccC
Q 003093 74 EVIAIYVDDDH--GR---NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTHY 139 (848)
Q Consensus 74 ~vaii~~dd~~--g~---~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~-~~~~viv~~~~~ 139 (848)
++++|...|+- |+ .....+...+++.|.++.....++.+ .+++...+++..+ .++|+|+..+..
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 56777655532 21 23456888899999998887777653 3677777776654 378999987643
No 472
>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=45.39 E-value=1.2e+02 Score=30.94 Aligned_cols=77 Identities=9% Similarity=0.092 Sum_probs=49.6
Q ss_pred EEEEE--EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIY--VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~--~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|++|. .++.|.......+.+++++.|..+.....- ..+.......+..+.+.++|.+++........ .+.++.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~-~~~~~~~~ 78 (264)
T cd01574 2 IGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSMLA--EADEEALRAAVRRLLAQRVDGVIVNAPLDDAD-AALAAAPA 78 (264)
T ss_pred EEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEeCC--CCchHHHHHHHHHHHhcCCCEEEEeCCCCChH-HHHHHHhc
Confidence 45565 345677888899999999999887654221 11224455667777778899998875544333 34445555
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|.
T Consensus 79 ~i 80 (264)
T cd01574 79 DV 80 (264)
T ss_pred CC
Confidence 54
No 473
>PRK10200 putative racemase; Provisional
Probab=44.61 E-value=99 Score=31.23 Aligned_cols=40 Identities=10% Similarity=-0.017 Sum_probs=23.9
Q ss_pred HHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhcc-CcEEE
Q 003093 62 AIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK-RCRIS 104 (848)
Q Consensus 62 ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~-g~~v~ 104 (848)
++++.++..+-++|+++....- -....+++.+++. |+++.
T Consensus 107 ~~~~~~~~~~~~~VglLaT~~T---i~s~~Y~~~l~~~~g~~~~ 147 (230)
T PRK10200 107 ATGRAITGAGMTRVALLGTRYT---MEQDFYRGRLTEQFSINCL 147 (230)
T ss_pred HHHHHHHHcCCCeEEEeccHHH---HHHhHHHHHHHHhcCCeEe
Confidence 3444455557789999875432 2344566666655 87763
No 474
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=44.10 E-value=2.1e+02 Score=26.14 Aligned_cols=85 Identities=12% Similarity=0.097 Sum_probs=53.1
Q ss_pred EEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC----CcHHHHHHHH
Q 003093 74 EVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY----NRGPVVFHVA 149 (848)
Q Consensus 74 ~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~----~~~~~~~~~a 149 (848)
+|.+.....+.-.-+..-+...++..|.+|++--.- .. ...++..+.+.+||+|.+.+.. ..+..++.++
T Consensus 5 ~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~---vp---~e~i~~~a~~~~~d~V~lS~~~~~~~~~~~~~~~~L 78 (137)
T PRK02261 5 TVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVM---TS---QEEFIDAAIETDADAILVSSLYGHGEIDCRGLREKC 78 (137)
T ss_pred EEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCC---CC---HHHHHHHHHHcCCCEEEEcCccccCHHHHHHHHHHH
Confidence 444444444444455667788899999998875322 12 2345566666889999987643 4556677888
Q ss_pred HHcCCCCCCeEEEecC
Q 003093 150 QYLGMLGTGYVWIATS 165 (848)
Q Consensus 150 ~~~g~~~~~~~wi~~~ 165 (848)
++.|... -.+|+++.
T Consensus 79 ~~~~~~~-~~i~vGG~ 93 (137)
T PRK02261 79 IEAGLGD-ILLYVGGN 93 (137)
T ss_pred HhcCCCC-CeEEEECC
Confidence 8877642 23444443
No 475
>cd08475 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=43.92 E-value=2.2e+02 Score=26.74 Aligned_cols=67 Identities=18% Similarity=0.082 Sum_probs=38.6
Q ss_pred cccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcEEEeCC--ccccCCceeeecCCCCchHHHHHHH
Q 003093 628 LVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQ--VFTKNGWGFAFPRDSPLAVDISTAI 700 (848)
Q Consensus 628 ~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~k~spl~~~in~~i 700 (848)
...+++.+...+.+.. |...+++.+. ..+..... ..+..+.. ......+.++.+++......+...+
T Consensus 128 ~~~~~~~~~~~~~v~~----g~gi~~~p~~-~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (199)
T cd08475 128 RLQFDDGEAIADAALA----GLGIAQLPTW-LVADHLQR-GELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAV 196 (199)
T ss_pred cEEECCHHHHHHHHHh----CCCEEeeeHH-HHHhHhhc-CcEEEecCCCcCCCccEEEEeCCcccCCHHHHHHH
Confidence 3456888899999998 5555665543 33333322 23443322 2334567888888776555544433
No 476
>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=43.87 E-value=74 Score=33.43 Aligned_cols=72 Identities=7% Similarity=0.044 Sum_probs=46.9
Q ss_pred cCCCccchHHHHHHHHhccC-cEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-CcHHHHHHHHHHcCC
Q 003093 81 DDDHGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQYLGM 154 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~-~~~~~~~~~a~~~g~ 154 (848)
++.|.......+.+++++.| ..+.+.. +...+.......++.+.+.++|.|++.... +.....++++++.|.
T Consensus 9 ~~~f~~~~~~gi~~~a~~~g~~~~i~~~--~~~~d~~~q~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~~~~~gi 82 (302)
T TIGR02637 9 GNPFFEAANKGAEEAAKELGSVYIIYTG--PTGTTAEGQIEVVNSLIAQKVDAIAISANDPDALVPALKKAMKRGI 82 (302)
T ss_pred CCHHHHHHHHHHHHHHHHhCCeeEEEEC--CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHHCCC
Confidence 46677788889999999999 4443321 111223444567777777889998886543 233456778888775
No 477
>COG1922 WecG Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]
Probab=43.58 E-value=1.4e+02 Score=30.43 Aligned_cols=102 Identities=15% Similarity=0.065 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhcc--CcEEEEee-ecCCCCChHHHHHHHHHHhcCCCeEE
Q 003093 57 QYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK--RCRISFKA-PLSVEATEDEITDLLVKVALTESRII 133 (848)
Q Consensus 57 ~~q~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~--g~~v~~~~-~~~~~~~~~d~~~~l~~i~~~~~~vi 133 (848)
.+...++.+.+..-+ ++|.++....+ ..+.....+++. |..|+... .|-. ..++ ..++++|++++||++
T Consensus 94 ~Dl~~~Ll~~a~~~~-~~vfllGgkp~----V~~~a~~~l~~~~p~l~ivg~h~GYf~--~~e~-~~i~~~I~~s~pdil 165 (253)
T COG1922 94 TDLVEALLKRAAEEG-KRVFLLGGKPG----VAEQAAAKLRAKYPGLKIVGSHDGYFD--PEEE-EAIVERIAASGPDIL 165 (253)
T ss_pred HHHHHHHHHHhCccC-ceEEEecCCHH----HHHHHHHHHHHHCCCceEEEecCCCCC--hhhH-HHHHHHHHhcCCCEE
Confidence 345666666665544 56766654433 333344444443 34555433 2322 1233 689999999999999
Q ss_pred EEEccCCcHHHHHHHHHHcCCCCCCeEEEecCcccc
Q 003093 134 VVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLST 169 (848)
Q Consensus 134 v~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~ 169 (848)
++.+..+....++.+-++. + +.-++++.++..+
T Consensus 166 ~VgmG~P~QE~wi~~~~~~-~--~~~v~igVGg~fD 198 (253)
T COG1922 166 LVGMGVPRQEIWIARNRQQ-L--PVAVAIGVGGSFD 198 (253)
T ss_pred EEeCCCchhHHHHHHhHHh-c--CCceEEeccceEE
Confidence 9998887777776665543 2 2446777665443
No 478
>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=43.31 E-value=2e+02 Score=31.04 Aligned_cols=101 Identities=10% Similarity=0.024 Sum_probs=59.9
Q ss_pred HHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhc-cCcEEEEeeecCCCCChHHHHHHHHHHhcC---CCeEEEEE
Q 003093 61 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAA-KRCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVH 136 (848)
Q Consensus 61 ~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~---~~~viv~~ 136 (848)
..+.++++.++-+++.++.+...+ ....+.+.+.+++ .++.+..........+.+.+...+..+++. +.|+|+..
T Consensus 12 ~~l~~~~~~~~~~k~livtd~~v~-~~~~~~v~~~L~~~~~~~~~~~~~~e~~k~~~~v~~~~~~~~~~~~~r~d~IIai 90 (344)
T cd08169 12 ESVESYTTRDLFDQYFFISDSGVA-DLIAHYIAEYLSKILPVHILVIEGGEEYKTFETVTRILERAIALGANRRTAIVAV 90 (344)
T ss_pred HHHHHHHHhcCCCeEEEEECccHH-HHHHHHHHHHHHhhcCceEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEEE
Confidence 345566777777888888754433 3566778888877 676654333333333556677777777754 48999877
Q ss_pred ccC--CcHHHHHHHHHHcCCCCCCeEEEecC
Q 003093 137 THY--NRGPVVFHVAQYLGMLGTGYVWIATS 165 (848)
Q Consensus 137 ~~~--~~~~~~~~~a~~~g~~~~~~~wi~~~ 165 (848)
+.+ .+...++......|+ .++-|-|.
T Consensus 91 GGGsv~D~ak~vA~~~~rgi---p~i~VPTT 118 (344)
T cd08169 91 GGGATGDVAGFVASTLFRGI---AFIRVPTT 118 (344)
T ss_pred CCcHHHHHHHHHHHHhccCC---cEEEecCC
Confidence 654 344444443333343 44445443
No 479
>PF01177 Asp_Glu_race: Asp/Glu/Hydantoin racemase; InterPro: IPR015942 This entry represents a group of related proteins that includes aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase. Aspartate racemase (5.1.1.13 from EC) and glutamate racemase (5.1.1.3 from EC) are two evolutionary related bacterial enzymes that do not seem to require a cofactor for their activity []. Glutamate racemase, which interconverts L-glutamate into D-glutamate, is required for the biosynthesis of peptidoglycan and some peptide-based antibiotics such as gramicidin S. In addition to characterised aspartate and glutamate racemases, this family also includes a hypothetical protein from Erwinia carotovora and one from Escherichia coli (ygeA). Two conserved cysteines are present in the sequence of these enzymes. They are expected to play a role in catalytic activity by acting as bases in proton abstraction from the substrate.; PDB: 3S7Z_A 3S81_C 3OUT_A 3EIS_B 3IXL_A 3IP8_A 2VLB_D 3DTV_A 3IXM_A 3DG9_A ....
Probab=43.23 E-value=2.3e+02 Score=27.87 Aligned_cols=84 Identities=4% Similarity=-0.026 Sum_probs=50.8
Q ss_pred HHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhcc-Cc--EEEEee--e----cCCCC-ChH---HHHHHHHHH-hcCC
Q 003093 64 AEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK-RC--RISFKA--P----LSVEA-TED---EITDLLVKV-ALTE 129 (848)
Q Consensus 64 ~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~-g~--~v~~~~--~----~~~~~-~~~---d~~~~l~~i-~~~~ 129 (848)
++-+.. +-++++++.. ++......+.+.+++. |+ +++... . ...+. +.. .+...+.++ +..+
T Consensus 100 ~~~~~~-~~~ri~vl~t---~~~~~~~~~~~~~~~~~gi~~~~~~~i~~~~~~~~e~~~~~~~~~~~~~~~~~~l~~~~~ 175 (216)
T PF01177_consen 100 LEAAKA-GGKRIGVLTT---YTTEKSPLYEEFIEEAAGIDDEVVAGIHNAIYDVIELGDIPPEQIEILAEAARELIKEDG 175 (216)
T ss_dssp HHHHHH-TSSEEEEEES---HHHHHHTHHHHHHHHCTTEECEEEEEEEEEHTHHHHTTCTTHHHHHHHHHHHHHHHHCTT
T ss_pred HHHHHh-cCCEEEEEec---CcccchHHHHHHHHHhcCCcHHHHHHHHhhcHHHHhhhcCCHHHHHHHHHHHHHHhccCC
Confidence 333444 8899999984 5556677788888888 87 554421 1 11221 222 344555555 3789
Q ss_pred CeEEEEEccCCcHH-HHHHHHHH
Q 003093 130 SRIIVVHTHYNRGP-VVFHVAQY 151 (848)
Q Consensus 130 ~~viv~~~~~~~~~-~~~~~a~~ 151 (848)
+|+|++.|..-... .....+.+
T Consensus 176 ~d~iiLgCt~l~~~~~~~~~l~~ 198 (216)
T PF01177_consen 176 ADAIILGCTHLPLLLGAIEALEE 198 (216)
T ss_dssp SSEEEEESTTGGGGHHHHHHHHH
T ss_pred CCEEEECCCchHHHHHHHHhhcc
Confidence 99999987754433 55555544
No 480
>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=43.09 E-value=1.2e+02 Score=31.02 Aligned_cols=76 Identities=8% Similarity=-0.050 Sum_probs=50.9
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. ++.|.....+.+.+++++.|..+..... ..+...-...+.++...++|.|++..... ...++..+.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06298 2 VGVIIPDITNSYFAELARGIDDIATMYKYNIILSNS---DNDKEKELKVLNNLLAKQVDGIIFMGGKI-SEEHREEFKRS 77 (268)
T ss_pred EEEEECCCcchHHHHHHHHHHHHHHHcCCeEEEEeC---CCCHHHHHHHHHHHHHhcCCEEEEeCCCC-cHHHHHHHhcC
Confidence 456663 4677888889999999999988765432 12334456677777778999999865432 23466666665
Q ss_pred CC
Q 003093 153 GM 154 (848)
Q Consensus 153 g~ 154 (848)
|+
T Consensus 78 ~i 79 (268)
T cd06298 78 PT 79 (268)
T ss_pred CC
Confidence 54
No 481
>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=42.81 E-value=1.3e+02 Score=30.75 Aligned_cols=70 Identities=4% Similarity=0.001 Sum_probs=43.7
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHcCC
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 154 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~g~ 154 (848)
++.|.....+.+.+++++.|.++..... .. ...........+...++|.|++...... ...++.+.+.|.
T Consensus 15 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~--~~-~~~~~~~~~~~~~~~~~dgiii~~~~~~-~~~~~~~~~~~i 84 (270)
T cd06294 15 QNPFFIEVLRGISAVANENGYDISLATG--KN-EEELLEEVKKMIQQKRVDGFILLYSRED-DPIIDYLKEEKF 84 (270)
T ss_pred CCCCHHHHHHHHHHHHHHCCCEEEEecC--CC-cHHHHHHHHHHHHHcCcCEEEEecCcCC-cHHHHHHHhcCC
Confidence 3567778889999999999998765321 11 2222333333344567999888754322 356777777775
No 482
>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=42.64 E-value=56 Score=26.45 Aligned_cols=40 Identities=20% Similarity=0.271 Sum_probs=33.3
Q ss_pred HHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEE
Q 003093 64 AEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRIS 104 (848)
Q Consensus 64 ~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~ 104 (848)
.++++.+ -++|.+.+++|.-|......+.+.+.+.|..+.
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 4455554 589999999999999999999999999988764
No 483
>COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane]
Probab=42.61 E-value=92 Score=30.93 Aligned_cols=42 Identities=14% Similarity=0.052 Sum_probs=30.3
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEE
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRIS 104 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~ 104 (848)
.++.++-+++-|.++|+++....- -.....++.|+++|++++
T Consensus 105 idaTa~~ik~~g~kkvgLLgT~~T---m~~~fY~~~l~~~gievv 146 (230)
T COG1794 105 IDATAKAIKAAGAKKVGLLGTRFT---MEQGFYRKRLEEKGIEVV 146 (230)
T ss_pred HHHHHHHHHhcCCceeEEeeccch---HHhHHHHHHHHHCCceEe
Confidence 445555577889999999985432 233456889999998865
No 484
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=42.09 E-value=1.8e+02 Score=31.05 Aligned_cols=78 Identities=6% Similarity=0.046 Sum_probs=52.8
Q ss_pred EEEEEEEEc--CCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHH
Q 003093 73 REVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQ 150 (848)
Q Consensus 73 ~~vaii~~d--d~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~ 150 (848)
+.|+++..+ +.|.......+.+++++.|..+..... ..+.......+..+...++|.|++..... ....++.+.
T Consensus 64 ~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~~~~~~vdgiI~~~~~~-~~~~~~~l~ 139 (331)
T PRK14987 64 RAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHY---GYKPEMEQERLESMLSWNIDGLILTERTH-TPRTLKMIE 139 (331)
T ss_pred CEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEecC---CCCHHHHHHHHHHHHhcCCCEEEEcCCCC-CHHHHHHHH
Confidence 478888753 567788889999999999988765321 11223344566777778999999864322 234667777
Q ss_pred HcCC
Q 003093 151 YLGM 154 (848)
Q Consensus 151 ~~g~ 154 (848)
+.|+
T Consensus 140 ~~~i 143 (331)
T PRK14987 140 VAGI 143 (331)
T ss_pred hCCC
Confidence 7775
No 485
>PRK00843 egsA NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed
Probab=42.05 E-value=1e+02 Score=33.40 Aligned_cols=82 Identities=9% Similarity=0.028 Sum_probs=54.8
Q ss_pred HHHHHHHHHcCc-EEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 61 AAIAEIVDHYGW-REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 61 ~ai~~~~~~~~w-~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
..+.++++.++. +++.+|.+...+- ...+.+.+.+++.| .+... +....+.+.+...+.++++.++|+||..+.+
T Consensus 22 ~~l~~~l~~~~~~~~~livtd~~~~~-~~~~~l~~~l~~~~-~~~~~--~~~~~t~~~v~~~~~~~~~~~~d~IIaiGGG 97 (350)
T PRK00843 22 DDIGDVCSDLKLTGRALIVTGPTTKK-IAGDRVEENLEDAG-DVEVV--IVDEATMEEVEKVEEKAKDVNAGFLIGVGGG 97 (350)
T ss_pred HHHHHHHHHhCCCCeEEEEECCcHHH-HHHHHHHHHHHhcC-CeeEE--eCCCCCHHHHHHHHHHhhccCCCEEEEeCCc
Confidence 456667777775 7888887555443 34567888888877 54322 3334466778888889988889999977655
Q ss_pred --CcHHHHH
Q 003093 140 --NRGPVVF 146 (848)
Q Consensus 140 --~~~~~~~ 146 (848)
-+...++
T Consensus 98 sv~D~ak~v 106 (350)
T PRK00843 98 KVIDVAKLA 106 (350)
T ss_pred hHHHHHHHH
Confidence 3444444
No 486
>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=41.94 E-value=1e+02 Score=27.88 Aligned_cols=49 Identities=14% Similarity=0.255 Sum_probs=36.0
Q ss_pred chHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEcc
Q 003093 87 NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH 138 (848)
Q Consensus 87 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~ 138 (848)
.....+...+++.|.++.+...++. +...+...+.++.+. +|+|+..+.
T Consensus 19 ~n~~~l~~~l~~~G~~v~~~~~v~D--d~~~i~~~i~~~~~~-~DlvittGG 67 (133)
T cd00758 19 TNGPALEALLEDLGCEVIYAGVVPD--DADSIRAALIEASRE-ADLVLTTGG 67 (133)
T ss_pred chHHHHHHHHHHCCCEEEEeeecCC--CHHHHHHHHHHHHhc-CCEEEECCC
Confidence 3456788889999999887766654 347788888777544 899998754
No 487
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=41.73 E-value=1e+02 Score=32.75 Aligned_cols=82 Identities=4% Similarity=-0.021 Sum_probs=53.0
Q ss_pred EEEEEEE--EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEE-ccCCcHHHHHHHH
Q 003093 73 REVIAIY--VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVH-THYNRGPVVFHVA 149 (848)
Q Consensus 73 ~~vaii~--~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~-~~~~~~~~~~~~a 149 (848)
.++++++ .+++|.....+.+.++.++.|..... ...+...+...-...+..+...++|.|++. .++......+++|
T Consensus 34 ~~i~~~~~~~~~~f~~~~~~g~~~~a~~~g~~~~~-~~~~~~~d~~~Q~~~i~~~ia~~~daIiv~~~d~~~~~~~v~~a 112 (322)
T COG1879 34 KTIGVVVPTLGNPFFQAVRKGAEAAAKKLGVVVAV-VIADAQNDVAKQIAQIEDLIAQGVDAIIINPVDPDALTPAVKKA 112 (322)
T ss_pred ceEEEEeccCCChHHHHHHHHHHHHHHHcCCcEEE-EecccccChHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHH
Confidence 5666666 55778888889999999999962111 122211122222233444446789988886 5567777799999
Q ss_pred HHcCCC
Q 003093 150 QYLGML 155 (848)
Q Consensus 150 ~~~g~~ 155 (848)
.+.|.+
T Consensus 113 ~~aGIp 118 (322)
T COG1879 113 KAAGIP 118 (322)
T ss_pred HHCCCc
Confidence 999863
No 488
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=41.70 E-value=30 Score=31.59 Aligned_cols=32 Identities=19% Similarity=0.320 Sum_probs=27.9
Q ss_pred eEEEEccCCchhHHHHHHhhccCCccEEeccc
Q 003093 5 TVAIIGPQDAVTSHVVSHVANELQVPLLSFSA 36 (848)
Q Consensus 5 V~aiIGp~~S~~~~ava~i~~~~~vP~Is~~a 36 (848)
|+.++||..|+=+..+..++...+.++|+...
T Consensus 1 lii~~G~pgsGKSt~a~~l~~~~~~~~i~~D~ 32 (143)
T PF13671_consen 1 LIILCGPPGSGKSTLAKRLAKRLGAVVISQDE 32 (143)
T ss_dssp EEEEEESTTSSHHHHHHHHHHHSTEEEEEHHH
T ss_pred CEEEECCCCCCHHHHHHHHHHHCCCEEEeHHH
Confidence 57899999999999999999999988887544
No 489
>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].
Probab=41.59 E-value=40 Score=32.88 Aligned_cols=33 Identities=9% Similarity=0.085 Sum_probs=19.7
Q ss_pred eecccchhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 003093 734 LQLKSFSGLYLLCGLACLLALFIYLMQIVHQFS 766 (848)
Q Consensus 734 l~l~~~~g~f~il~~g~~la~~vf~~e~~~~~~ 766 (848)
.+-+.+.-++-+++..+++.|+||+.-++++.|
T Consensus 32 ~~~d~~~I~iaiVAG~~tVILVI~i~v~vR~CR 64 (221)
T PF08374_consen 32 RSKDYVKIMIAIVAGIMTVILVIFIVVLVRYCR 64 (221)
T ss_pred ccccceeeeeeeecchhhhHHHHHHHHHHHHHh
Confidence 334455556666666666677777766664333
No 490
>PRK09189 uroporphyrinogen-III synthase; Validated
Probab=41.20 E-value=72 Score=32.39 Aligned_cols=88 Identities=13% Similarity=0.045 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHHc--CcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEE
Q 003093 58 YQMAAIAEIVDHY--GWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVV 135 (848)
Q Consensus 58 ~q~~ai~~~~~~~--~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~ 135 (848)
..++.+++++... .-++|.++. |....+.+.+.|++.|..|.....|.......+-......+++.+.|+|++
T Consensus 102 ~~~e~L~~~~~~~~~~~~~vL~~r-----g~~~r~~l~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~l~~~~~d~i~f 176 (240)
T PRK09189 102 GDGVRLAETVAAALAPTARLLYLA-----GRPRAPVFEDRLAAAGIPFRVAECYDMLPVMYSPATLSAILGGAPFDAVLL 176 (240)
T ss_pred CCHHHHHHHHHHhcCCCCcEEEec-----cCcccchhHHHHHhCCCeeEEEEEEEeecCCCChHHHHHHHhcCCCCEEEE
Confidence 3467777776442 335666554 334457788999999988765554432211112223445556667777766
Q ss_pred EccCCcHHHHHHHHHH
Q 003093 136 HTHYNRGPVVFHVAQY 151 (848)
Q Consensus 136 ~~~~~~~~~~~~~a~~ 151 (848)
+. +..+..|++....
T Consensus 177 ~S-~~~~~~f~~~~~~ 191 (240)
T PRK09189 177 YS-RVAARRFFALMRL 191 (240)
T ss_pred eC-HHHHHHHHHHHhh
Confidence 65 4456777776643
No 491
>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=40.82 E-value=1.1e+02 Score=28.17 Aligned_cols=49 Identities=16% Similarity=0.166 Sum_probs=36.9
Q ss_pred hHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC
Q 003093 88 GIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 139 (848)
Q Consensus 88 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~ 139 (848)
....+...+++.|+++.....++.+ .+++...+.++.+ ++|+||..+..
T Consensus 28 n~~~l~~~l~~~G~~v~~~~~v~Dd--~~~i~~~l~~~~~-~~DliIttGG~ 76 (144)
T TIGR00177 28 NGPLLAALLEEAGFNVSRLGIVPDD--PEEIREILRKAVD-EADVVLTTGGT 76 (144)
T ss_pred cHHHHHHHHHHCCCeEEEEeecCCC--HHHHHHHHHHHHh-CCCEEEECCCC
Confidence 3557888899999999887777643 3677877777653 79999988643
No 492
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=40.47 E-value=43 Score=29.86 Aligned_cols=27 Identities=15% Similarity=0.178 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 003093 742 LYLLCGLACLLALFIYLMQIVHQFSRH 768 (848)
Q Consensus 742 ~f~il~~g~~la~~vf~~e~~~~~~~~ 768 (848)
+.+++|+.+++.++++++-++.+|+|+
T Consensus 67 ~~Ii~gv~aGvIg~Illi~y~irR~~K 93 (122)
T PF01102_consen 67 IGIIFGVMAGVIGIILLISYCIRRLRK 93 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHS-
T ss_pred eehhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 445555555555555544444443333
No 493
>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid [].; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.
Probab=40.45 E-value=19 Score=35.41 Aligned_cols=31 Identities=19% Similarity=0.413 Sum_probs=25.6
Q ss_pred CeEEEEccCCchhHHHHHHhhccCCccEEec
Q 003093 4 QTVAIIGPQDAVTSHVVSHVANELQVPLLSF 34 (848)
Q Consensus 4 ~V~aiIGp~~S~~~~ava~i~~~~~vP~Is~ 34 (848)
+|.+|+||.+++-+.....++++.+.|+|+-
T Consensus 2 ~v~~i~GpT~tGKt~~ai~lA~~~g~pvI~~ 32 (233)
T PF01745_consen 2 KVYLIVGPTGTGKTALAIALAQKTGAPVISL 32 (233)
T ss_dssp EEEEEE-STTSSHHHHHHHHHHHH--EEEEE
T ss_pred cEEEEECCCCCChhHHHHHHHHHhCCCEEEe
Confidence 5889999999999999999999999999974
No 494
>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=40.05 E-value=2.4e+02 Score=24.74 Aligned_cols=68 Identities=10% Similarity=0.028 Sum_probs=42.3
Q ss_pred EcCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC----CcHHHHHHHHHHcC
Q 003093 80 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY----NRGPVVFHVAQYLG 153 (848)
Q Consensus 80 ~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~----~~~~~~~~~a~~~g 153 (848)
..++.-.-+...+...++..|.+|.+... ..+ ....+..+.+.+||+|.+.+.. ..+..+++++++.+
T Consensus 7 ~~~e~H~lG~~~~~~~l~~~G~~V~~lg~---~~~---~~~l~~~~~~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~ 78 (119)
T cd02067 7 VGGDGHDIGKNIVARALRDAGFEVIDLGV---DVP---PEEIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELKEAG 78 (119)
T ss_pred eCCchhhHHHHHHHHHHHHCCCEEEECCC---CCC---HHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHHcC
Confidence 34444455566778888889988865431 122 2345556666789999888652 34455666666664
No 495
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=39.87 E-value=30 Score=32.74 Aligned_cols=101 Identities=18% Similarity=0.297 Sum_probs=55.6
Q ss_pred CCCChHHhhcCCCCeeEEeCchHHHHHHhhhCCCccCcccCCCHHHHHHHhhcCCCCCceEEEEccHHHHHHHHhcCCcE
Q 003093 591 PIKGIDSLRSSNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEF 670 (848)
Q Consensus 591 ~i~sl~dL~~s~~~i~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~~~l 670 (848)
++.+++||.. +++|+..--.....||.+ .+.+ .+++...-.-|..-.+ |-.|++++-.....-+.++ +|
T Consensus 57 ~~~~~~~l~~-~~rIATkyp~l~~~yf~~-~g~~-~~ii~l~GsvE~ap~~------glAD~IvDiv~TG~TLr~N--gL 125 (163)
T PF01634_consen 57 PYKSVEDLKA-GLRIATKYPNLTRRYFAE-KGIN-VEIIKLSGSVELAPPL------GLADAIVDIVETGTTLRAN--GL 125 (163)
T ss_dssp CGCCGGGGSS-TEEEEES-HHHHHHHHHH-CT-E-EEEEE-SS-TTHHHHT------TSSSEEEEEESSSHHHHHT--TE
T ss_pred CCCCHHHhcc-CCEEEECCHHHHHHHHHH-cCCc-EEEEEccCCccccCCC------CCCCEEEEeccCcHHHHHC--CC
Confidence 4678888864 667877766677888854 3333 4455544444444433 5678888866665554444 56
Q ss_pred EEeCCccccCCceeeecCCCC--chHHHHHHHHhh
Q 003093 671 SIVGQVFTKNGWGFAFPRDSP--LAVDISTAILKL 703 (848)
Q Consensus 671 ~~~~~~~~~~~~~~~~~k~sp--l~~~in~~i~~l 703 (848)
..++..+. ..-.+...+.+. -.+.++..+.+|
T Consensus 126 ~~i~~i~~-s~a~LI~n~~~~~~k~~~i~~l~~~l 159 (163)
T PF01634_consen 126 KEIETILE-SSARLIANKASLKEKEEKIDELVTRL 159 (163)
T ss_dssp EEEEEEEE-EEEEEEEEHHHHHHCHHHHHHHHHHH
T ss_pred EEeEEEEE-EEEEEEEcCccchhhHHHHHHHHHHH
Confidence 77754444 444444444442 233455555444
No 496
>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=39.72 E-value=93 Score=32.08 Aligned_cols=71 Identities=10% Similarity=-0.016 Sum_probs=50.1
Q ss_pred cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccC-CcHHHHHHHHHHcCC
Q 003093 81 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQYLGM 154 (848)
Q Consensus 81 dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~-~~~~~~~~~a~~~g~ 154 (848)
.+.|.......+.+++++.|.++.....- .+.......+..+...++|.|++.... ......++++.+.|.
T Consensus 10 ~~~f~~~~~~gi~~~~~~~G~~~~~~~~~---~d~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~i~~~~~~~i 81 (272)
T cd06313 10 QATWCAQGKQAADEAGKLLGVDVTWYGGA---LDAVKQVAAIENMASQGWDFIAVDPLGIGTLTEAVQKAIARGI 81 (272)
T ss_pred CChHHHHHHHHHHHHHHHcCCEEEEecCC---CCHHHHHHHHHHHHHcCCCEEEEcCCChHHhHHHHHHHHHCCC
Confidence 35677778889999999999988765322 133445567777778899999986543 334557788887775
No 497
>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=39.65 E-value=1.5e+02 Score=26.92 Aligned_cols=99 Identities=10% Similarity=0.041 Sum_probs=47.5
Q ss_pred HHHHHHHHHHcCcEEEEEEEEcCCCccchHHHHHHHHhccCcEEEEeeec-----CCCCChHHHHHHH-HHHhcCCCeEE
Q 003093 60 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPL-----SVEATEDEITDLL-VKVALTESRII 133 (848)
Q Consensus 60 ~~ai~~~~~~~~w~~vaii~~dd~~g~~~~~~l~~~l~~~g~~v~~~~~~-----~~~~~~~d~~~~l-~~i~~~~~~vi 133 (848)
...+.+.+...+--....+|.+ ........+.+.|...|+.+...... .....+..+..-+ ..+....++.+
T Consensus 22 ~~~l~~~i~~~~~~~~~~~y~~--~~~~~~~~~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~i 99 (146)
T PF01936_consen 22 FERLLEEIRKYGPLVRIRAYGN--WDDPNQKSFQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTI 99 (146)
T ss_dssp HHHHHHHHTTTEEEEEEEEEE------HHHHHHHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEE
T ss_pred HHHHHHHHHhcCCeEEEEEEee--ccccchhhHHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEE
Confidence 3455555555443323445544 22234577889999999977654331 1112122232222 22322346888
Q ss_pred EEEccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003093 134 VVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 164 (848)
Q Consensus 134 v~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 164 (848)
++.+...+...+++.+++.|. .+++..
T Consensus 100 vLvSgD~Df~~~v~~l~~~g~----~V~v~~ 126 (146)
T PF01936_consen 100 VLVSGDSDFAPLVRKLRERGK----RVIVVG 126 (146)
T ss_dssp EEE---GGGHHHHHHHHHH------EEEEEE
T ss_pred EEEECcHHHHHHHHHHHHcCC----EEEEEE
Confidence 888887888999999999885 245554
No 498
>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=39.60 E-value=1.3e+02 Score=30.80 Aligned_cols=77 Identities=5% Similarity=-0.014 Sum_probs=49.6
Q ss_pred EEEEEEc--CCCccchHHHHHHHHhcc-CcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCc-HHHHHHHHH
Q 003093 75 VIAIYVD--DDHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQ 150 (848)
Q Consensus 75 vaii~~d--d~~g~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~-~~~~~~~a~ 150 (848)
|+++..+ +.|.......+.+.+++. |.++..... . .+..+-...+..+...++|.|++...... ....+..+.
T Consensus 2 ig~~~~~~~~~~~~~~~~~i~~~~~~~~g~~~~~~~~-~--~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~ 78 (270)
T cd06308 2 IGFSQCNLADPWRAAMNDEIQREASNYPDVELIIADA-A--DDNSKQVADIENFIRQGVDLLIISPNEAAPLTPVVEEAY 78 (270)
T ss_pred EEEEeeCCCCHHHHHHHHHHHHHHHhcCCcEEEEEcC-C--CCHHHHHHHHHHHHHhCCCEEEEecCchhhchHHHHHHH
Confidence 5566643 456677788888888886 888765422 1 22344456677777788999988754322 245667777
Q ss_pred HcCC
Q 003093 151 YLGM 154 (848)
Q Consensus 151 ~~g~ 154 (848)
+.|.
T Consensus 79 ~~~i 82 (270)
T cd06308 79 RAGI 82 (270)
T ss_pred HCCC
Confidence 7775
No 499
>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=39.03 E-value=1.6e+02 Score=29.94 Aligned_cols=74 Identities=4% Similarity=-0.008 Sum_probs=49.5
Q ss_pred EEEEEE--cCCCccchHHHHHHHHhccCcEEEEeeecCCCCChHHHHHHHHHHhcCCCeEEEEEccCCcHHHHHHHHHHc
Q 003093 75 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 152 (848)
Q Consensus 75 vaii~~--dd~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~~viv~~~~~~~~~~~~~~a~~~ 152 (848)
|+++.. ++.|.....+.+.+++++.|.++..... ..+...-...+..+...++|.|++...... ...++.+.+.
T Consensus 2 i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~-~~~~~~~~~~ 77 (260)
T cd06286 2 IGVVLPYINHPYFSQLVDGIEKAALKHGYKVVLLQT---NYDKEKELEYLELLKTKQVDGLILCSREND-WEVIEPYTKY 77 (260)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeC---CCChHHHHHHHHHHHHcCCCEEEEeCCCCC-HHHHHHHhcC
Confidence 566664 4778888899999999999998876432 122244456677777788998888654333 2345555543
No 500
>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=38.75 E-value=2.9e+02 Score=24.73 Aligned_cols=87 Identities=17% Similarity=0.201 Sum_probs=0.0
Q ss_pred eEeccCChH-------HHHHHHHHHHHHcCcEEEEEEEEcCCCc-----cchHHHHHHHHhccCcEEEEeeecCCCC-Ch
Q 003093 49 FVRTTQSDQ-------YQMAAIAEIVDHYGWREVIAIYVDDDHG-----RNGIAALGDTLAAKRCRISFKAPLSVEA-TE 115 (848)
Q Consensus 49 f~r~~p~d~-------~q~~ai~~~~~~~~w~~vaii~~dd~~g-----~~~~~~l~~~l~~~g~~v~~~~~~~~~~-~~ 115 (848)
+.|+...+. .|-+.+-++....||.-+.++.+...-+ +.....+.+.++...+.++....+..-. +.
T Consensus 2 Y~RvSt~~q~~~~s~~~Q~~~~~~~a~~~g~~i~~~~~d~~~s~~~~~~R~~~~~ll~~~~~~~~d~ivv~~~~Rl~R~~ 81 (137)
T cd00338 2 YARVSTDKQEQGDSLERQREALREYAARNGLEVVGEYEDAGSSATSLVDRPGLQRLLADVKAGKIDVVLVEKLDRLSRNL 81 (137)
T ss_pred EEEEcchhhcccCCHHHHHHHHHHHHHHCCCEEEEEEEeCCCCcccccCCHHHHHHHHHHHcCCCCEEEEEecchhhCCH
Q ss_pred HHHHHHHHHHhcCCCeEEEE
Q 003093 116 DEITDLLVKVALTESRIIVV 135 (848)
Q Consensus 116 ~d~~~~l~~i~~~~~~viv~ 135 (848)
.+....+..+...+.+++++
T Consensus 82 ~~~~~~~~~l~~~gi~l~~~ 101 (137)
T cd00338 82 VDLLELLELLEAHGVRVVTA 101 (137)
T ss_pred HHHHHHHHHHHHCCCEEEEe
Done!