Query 003633
Match_columns 806
No_of_seqs 518 out of 3759
Neff 9.4
Searched_HMMs 46136
Date Fri Mar 29 03:06:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003633.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003633hhsearch_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 8.9E-89 1.9E-93 700.1 44.3 701 2-752 106-846 (897)
2 KOG4440 NMDA selective glutama 100.0 3.5E-79 7.6E-84 631.8 33.4 669 3-751 117-857 (993)
3 KOG1053 Glutamate-gated NMDA-t 100.0 2.7E-71 5.8E-76 594.0 47.6 670 5-748 122-853 (1258)
4 KOG1052 Glutamate-gated kainat 100.0 5E-70 1.1E-74 638.4 52.5 600 102-751 4-624 (656)
5 cd06390 PBP1_iGluR_AMPA_GluR1 100.0 2.1E-41 4.6E-46 365.4 29.4 286 2-311 72-363 (364)
6 cd06392 PBP1_iGluR_delta_1 N-t 100.0 4.2E-41 9.1E-46 362.7 26.7 288 1-312 77-399 (400)
7 cd06387 PBP1_iGluR_AMPA_GluR3 100.0 8.3E-39 1.8E-43 344.1 29.2 287 2-311 79-371 (372)
8 cd06391 PBP1_iGluR_delta_2 N-t 100.0 3.3E-38 7.1E-43 344.2 28.8 291 2-312 78-399 (400)
9 cd06379 PBP1_iGluR_NMDA_NR1 N- 100.0 3E-38 6.6E-43 346.8 28.5 258 2-308 101-364 (377)
10 cd06365 PBP1_Pheromone_recepto 100.0 4.9E-38 1.1E-42 352.5 28.3 285 2-307 119-452 (469)
11 cd06367 PBP1_iGluR_NMDA N-term 100.0 6.6E-38 1.4E-42 342.5 26.5 262 2-307 82-351 (362)
12 cd06375 PBP1_mGluR_groupII Lig 100.0 1.8E-37 3.8E-42 346.6 29.5 285 2-307 121-454 (458)
13 cd06374 PBP1_mGluR_groupI Liga 100.0 2.8E-37 6.1E-42 348.1 28.7 291 2-312 133-468 (472)
14 cd06376 PBP1_mGluR_groupIII Li 100.0 4.6E-37 9.9E-42 345.8 29.3 287 2-307 119-452 (463)
15 cd06361 PBP1_GPC6A_like Ligand 100.0 5.1E-37 1.1E-41 337.1 28.0 268 2-310 119-396 (403)
16 cd06393 PBP1_iGluR_Kainate_Glu 100.0 7.8E-37 1.7E-41 335.8 27.5 287 2-312 88-382 (384)
17 cd06389 PBP1_iGluR_AMPA_GluR2 100.0 2.2E-36 4.7E-41 328.9 29.3 289 2-312 73-369 (370)
18 cd06362 PBP1_mGluR Ligand bind 100.0 1.9E-36 4.1E-41 340.9 29.1 291 2-312 119-451 (452)
19 cd06388 PBP1_iGluR_AMPA_GluR4 100.0 3.3E-36 7.1E-41 326.6 29.3 287 2-312 79-370 (371)
20 cd06364 PBP1_CaSR Ligand-bindi 100.0 4.9E-36 1.1E-40 338.4 29.2 289 2-308 134-494 (510)
21 cd06380 PBP1_iGluR_AMPA N-term 100.0 7.7E-36 1.7E-40 328.7 30.1 296 2-311 78-381 (382)
22 cd06378 PBP1_iGluR_NMDA_NR2 N- 100.0 5.4E-36 1.2E-40 322.7 24.1 268 1-312 80-354 (362)
23 cd06386 PBP1_NPR_C_like Ligand 100.0 9.6E-35 2.1E-39 319.1 27.0 278 2-309 83-380 (387)
24 KOG1056 Glutamate-gated metabo 100.0 9.2E-35 2E-39 325.4 25.7 310 2-350 141-494 (878)
25 cd06385 PBP1_NPR_A Ligand-bind 100.0 1.8E-33 3.9E-38 312.1 27.9 281 2-309 90-392 (405)
26 cd06384 PBP1_NPR_B Ligand-bind 100.0 1.1E-32 2.3E-37 304.8 27.7 281 2-309 89-393 (399)
27 cd06363 PBP1_Taste_receptor Li 100.0 1.1E-32 2.3E-37 305.8 27.6 268 2-308 123-396 (410)
28 cd06373 PBP1_NPR_like Ligand b 100.0 1.6E-32 3.5E-37 303.7 25.4 282 2-309 89-390 (396)
29 cd06371 PBP1_sensory_GC_DEF_li 100.0 3.8E-32 8.2E-37 297.8 27.5 274 2-305 82-369 (382)
30 cd06370 PBP1_Speract_GC_like L 100.0 4.1E-32 9E-37 300.5 26.7 277 2-304 83-391 (404)
31 cd06372 PBP1_GC_G_like Ligand- 100.0 1.5E-31 3.3E-36 295.3 27.6 281 2-309 84-387 (391)
32 cd06366 PBP1_GABAb_receptor Li 100.0 2.3E-31 4.9E-36 289.9 26.0 263 2-313 82-348 (350)
33 PF01094 ANF_receptor: Recepto 100.0 3.4E-31 7.3E-36 288.6 24.9 272 2-295 67-348 (348)
34 cd06394 PBP1_iGluR_Kainate_KA1 100.0 1.1E-31 2.4E-36 284.4 17.6 245 2-312 82-332 (333)
35 cd06352 PBP1_NPR_GC_like Ligan 100.0 2.4E-30 5.2E-35 286.2 28.0 284 2-310 84-384 (389)
36 cd06382 PBP1_iGluR_Kainate N-t 100.0 1E-29 2.2E-34 274.0 20.7 242 2-311 79-326 (327)
37 cd06381 PBP1_iGluR_delta_like 100.0 7.6E-28 1.6E-32 259.9 26.4 260 2-312 78-363 (363)
38 cd06383 PBP1_iGluR_AMPA_Like N 100.0 3E-29 6.5E-34 271.3 15.4 265 2-287 83-353 (368)
39 cd06368 PBP1_iGluR_non_NMDA_li 100.0 2.5E-27 5.4E-32 255.3 21.8 243 2-311 78-323 (324)
40 cd06350 PBP1_GPCR_family_C_lik 99.9 4.4E-26 9.5E-31 248.3 21.6 229 2-308 107-340 (348)
41 cd06342 PBP1_ABC_LIVBP_like Ty 99.9 1.3E-25 2.7E-30 243.3 23.7 250 2-294 82-334 (334)
42 PRK15404 leucine ABC transport 99.9 1E-24 2.2E-29 237.9 23.8 256 2-300 108-365 (369)
43 cd06338 PBP1_ABC_ligand_bindin 99.9 7.6E-25 1.6E-29 238.2 22.1 250 2-294 87-345 (345)
44 cd06351 PBP1_iGluR_N_LIVBP_lik 99.9 2.7E-24 5.8E-29 232.2 21.9 241 2-307 79-322 (328)
45 cd06345 PBP1_ABC_ligand_bindin 99.9 2.9E-24 6.2E-29 233.3 21.9 244 2-287 83-339 (344)
46 cd06346 PBP1_ABC_ligand_bindin 99.9 4.8E-24 1E-28 228.1 21.2 224 3-290 85-309 (312)
47 cd06377 PBP1_iGluR_NMDA_NR3 N- 99.9 2.1E-23 4.5E-28 221.1 25.2 260 2-311 98-374 (382)
48 cd06348 PBP1_ABC_ligand_bindin 99.9 4.5E-23 9.8E-28 224.0 22.6 256 2-291 83-343 (344)
49 KOG1055 GABA-B ion channel rec 99.9 2.7E-24 5.8E-29 233.2 12.4 290 2-309 128-431 (865)
50 cd06340 PBP1_ABC_ligand_bindin 99.9 5E-23 1.1E-27 223.6 19.5 245 2-287 86-342 (347)
51 cd06360 PBP1_alkylbenzenes_lik 99.9 2.8E-22 6E-27 217.2 23.2 247 3-288 82-331 (336)
52 cd06344 PBP1_ABC_ligand_bindin 99.9 1.3E-22 2.8E-27 219.2 19.7 242 2-287 82-327 (332)
53 cd06347 PBP1_ABC_ligand_bindin 99.9 1.2E-21 2.6E-26 212.1 22.9 242 2-287 83-329 (334)
54 cd06355 PBP1_FmdD_like Peripla 99.9 1.6E-21 3.5E-26 211.7 23.9 259 2-302 83-345 (348)
55 cd06336 PBP1_ABC_ligand_bindin 99.9 6.5E-22 1.4E-26 214.9 20.1 245 3-289 87-344 (347)
56 COG0683 LivK ABC-type branched 99.9 2.1E-21 4.6E-26 211.4 23.6 257 2-298 94-356 (366)
57 cd06327 PBP1_SBP_like_1 Peripl 99.9 8.1E-22 1.8E-26 213.2 19.6 244 2-287 82-330 (334)
58 cd06329 PBP1_SBP_like_3 Peripl 99.9 1.4E-21 2.9E-26 212.0 21.2 234 3-280 90-330 (342)
59 cd06343 PBP1_ABC_ligand_bindin 99.9 4.2E-21 9E-26 210.2 23.9 260 2-299 90-362 (362)
60 cd06349 PBP1_ABC_ligand_bindin 99.9 4.8E-21 1E-25 207.8 23.9 252 2-298 83-339 (340)
61 cd06359 PBP1_Nba_like Type I p 99.9 2.7E-21 5.9E-26 208.9 21.7 248 2-292 81-331 (333)
62 PRK10797 glutamate and asparta 99.9 3.2E-21 7E-26 203.5 21.3 224 355-701 39-273 (302)
63 cd06330 PBP1_Arsenic_SBP_like 99.9 1.8E-21 3.8E-26 211.8 19.5 242 2-281 83-333 (346)
64 PRK09495 glnH glutamine ABC tr 99.9 9E-21 1.9E-25 195.5 21.5 220 354-700 23-244 (247)
65 cd06331 PBP1_AmiC_like Type I 99.9 6.1E-21 1.3E-25 206.2 20.7 242 2-285 83-326 (333)
66 cd06332 PBP1_aromatic_compound 99.9 1.6E-20 3.4E-25 203.2 22.4 243 3-287 82-327 (333)
67 TIGR03669 urea_ABC_arch urea A 99.9 3.6E-20 7.7E-25 201.7 23.4 261 2-306 84-349 (374)
68 PRK11917 bifunctional adhesin/ 99.9 3.4E-20 7.4E-25 191.7 21.3 218 354-697 36-257 (259)
69 cd06357 PBP1_AmiC Periplasmic 99.9 1E-19 2.2E-24 198.5 25.3 262 2-303 83-347 (360)
70 TIGR03407 urea_ABC_UrtA urea A 99.9 7.7E-20 1.7E-24 199.3 24.2 252 2-295 84-338 (359)
71 PF00497 SBP_bac_3: Bacterial 99.8 1.4E-20 3.1E-25 191.0 15.6 221 358-699 1-224 (225)
72 cd06328 PBP1_SBP_like_2 Peripl 99.8 5.6E-20 1.2E-24 198.4 20.8 239 2-284 84-326 (333)
73 PRK15010 ABC transporter lysin 99.8 1.1E-19 2.4E-24 188.8 22.1 223 354-700 24-255 (260)
74 cd06269 PBP1_glutamate_recepto 99.8 3.3E-20 7.1E-25 197.0 18.5 148 2-152 87-235 (298)
75 PF13458 Peripla_BP_6: Peripla 99.8 4.7E-20 1E-24 200.4 20.0 254 2-297 85-342 (343)
76 PRK11260 cystine transporter s 99.8 1.1E-19 2.4E-24 189.4 20.8 222 354-700 39-262 (266)
77 TIGR01096 3A0103s03R lysine-ar 99.8 1.8E-19 3.9E-24 186.4 20.6 218 356-698 24-250 (250)
78 cd06337 PBP1_ABC_ligand_bindin 99.8 1.3E-19 2.9E-24 197.4 20.6 253 2-299 85-357 (357)
79 PRK15007 putative ABC transpor 99.8 2.5E-19 5.4E-24 184.5 21.4 217 355-699 20-242 (243)
80 cd06334 PBP1_ABC_ligand_bindin 99.8 2.9E-19 6.2E-24 193.7 22.0 248 2-280 82-344 (351)
81 cd06335 PBP1_ABC_ligand_bindin 99.8 2.4E-19 5.1E-24 194.8 20.5 241 2-280 83-334 (347)
82 cd06358 PBP1_NHase Type I peri 99.8 3.2E-19 6.8E-24 192.8 21.3 238 2-283 83-324 (333)
83 PRK15437 histidine ABC transpo 99.8 4E-19 8.6E-24 184.5 19.2 223 354-700 24-255 (259)
84 cd06356 PBP1_Amide_Urea_BP_lik 99.8 1.3E-18 2.7E-23 188.0 21.5 240 2-283 83-325 (334)
85 TIGR02995 ectoine_ehuB ectoine 99.8 7.2E-19 1.6E-23 184.2 18.4 223 354-698 31-260 (275)
86 cd06369 PBP1_GC_C_enterotoxin_ 99.8 5.3E-18 1.2E-22 175.0 21.1 258 2-309 97-366 (380)
87 cd06339 PBP1_YraM_LppC_lipopro 99.8 1.4E-18 2.9E-23 187.6 17.5 231 2-284 75-329 (336)
88 PRK10859 membrane-bound lytic 99.8 2.7E-18 5.8E-23 192.9 18.2 222 354-700 41-267 (482)
89 PF00060 Lig_chan: Ligand-gate 99.7 2E-19 4.3E-24 169.7 -0.5 107 477-583 1-115 (148)
90 TIGR03863 PQQ_ABC_bind ABC tra 99.7 5E-17 1.1E-21 174.5 16.7 233 2-294 75-315 (347)
91 PRK09959 hybrid sensory histid 99.7 1.9E-16 4.2E-21 200.1 23.8 217 355-700 301-521 (1197)
92 cd06326 PBP1_STKc_like Type I 99.7 2.7E-16 5.8E-21 170.4 21.5 237 3-280 85-326 (336)
93 TIGR03870 ABC_MoxJ methanol ox 99.7 1.3E-16 2.8E-21 164.0 16.6 208 357-697 1-241 (246)
94 TIGR02285 conserved hypothetic 99.7 2.1E-16 4.6E-21 164.8 16.5 226 355-699 17-261 (268)
95 cd04509 PBP1_ABC_transporter_G 99.7 3.3E-16 7.2E-21 166.2 16.8 202 2-216 83-290 (299)
96 COG0834 HisJ ABC-type amino ac 99.7 9.3E-16 2E-20 161.0 19.3 226 354-700 32-265 (275)
97 cd00134 PBPb Bacterial peripla 99.7 2.8E-15 6.1E-20 150.5 20.3 214 358-698 1-218 (218)
98 smart00062 PBPb Bacterial peri 99.7 3E-15 6.5E-20 150.2 19.6 215 357-698 1-219 (219)
99 PRK09959 hybrid sensory histid 99.7 1E-15 2.2E-20 193.5 19.5 221 354-700 54-278 (1197)
100 cd06341 PBP1_ABC_ligand_bindin 99.6 6.3E-15 1.4E-19 160.0 19.7 230 4-274 84-318 (341)
101 cd06333 PBP1_ABC-type_HAAT_lik 99.6 6.3E-15 1.4E-19 157.8 18.8 201 3-218 83-293 (312)
102 TIGR03871 ABC_peri_MoxJ_2 quin 99.6 7.4E-15 1.6E-19 150.0 18.2 211 357-698 1-228 (232)
103 cd06268 PBP1_ABC_transporter_L 99.6 2.8E-14 6.1E-19 151.3 18.3 202 2-218 82-287 (298)
104 PF13433 Peripla_BP_5: Peripla 99.5 7E-13 1.5E-17 138.0 19.5 228 28-294 107-337 (363)
105 smart00079 PBPe Eukaryotic hom 99.4 1.1E-12 2.3E-17 121.4 10.9 123 572-699 1-133 (134)
106 COG4623 Predicted soluble lyti 99.3 2.1E-11 4.6E-16 123.0 12.7 223 354-701 21-249 (473)
107 TIGR01098 3A0109s03R phosphate 98.9 9.7E-09 2.1E-13 106.3 13.5 198 356-684 32-254 (254)
108 cd01391 Periplasmic_Binding_Pr 98.9 2.8E-08 6.2E-13 102.9 15.0 145 3-151 75-221 (269)
109 PRK00489 hisG ATP phosphoribos 98.8 1.6E-08 3.4E-13 105.9 11.1 164 415-700 52-220 (287)
110 PF10613 Lig_chan-Glu_bd: Liga 98.7 9.1E-09 2E-13 79.1 3.2 47 377-425 14-65 (65)
111 TIGR03431 PhnD phosphonate ABC 98.1 2.6E-05 5.7E-10 82.3 13.6 116 572-693 126-258 (288)
112 PF04348 LppC: LppC putative l 97.9 0.00043 9.2E-09 78.7 17.1 228 10-295 304-534 (536)
113 PRK11553 alkanesulfonate trans 97.3 0.0025 5.5E-08 68.1 12.5 70 572-647 120-193 (314)
114 PF12974 Phosphonate-bd: ABC t 97.2 0.002 4.2E-08 66.1 9.9 121 571-697 95-230 (243)
115 cd01537 PBP1_Repressors_Sugar_ 97.1 0.0047 1E-07 63.7 12.1 135 4-146 73-212 (264)
116 cd01536 PBP1_ABC_sugar_binding 97.0 0.01 2.2E-07 61.3 13.5 134 5-146 75-214 (267)
117 cd06267 PBP1_LacI_sugar_bindin 96.8 0.0095 2.1E-07 61.4 11.4 135 5-146 73-211 (264)
118 TIGR01729 taurine_ABC_bnd taur 96.5 0.031 6.6E-07 59.3 12.8 70 571-647 90-164 (300)
119 PF13379 NMT1_2: NMT1-like fam 96.1 0.012 2.6E-07 60.7 6.7 74 571-649 104-189 (252)
120 cd06282 PBP1_GntR_like_2 Ligan 95.9 0.091 2E-06 54.3 12.5 131 5-145 74-209 (266)
121 TIGR03427 ABC_peri_uca ABC tra 95.9 0.04 8.8E-07 58.7 9.5 68 573-647 98-170 (328)
122 cd06300 PBP1_ABC_sugar_binding 95.8 0.083 1.8E-06 54.9 11.7 124 5-137 80-209 (272)
123 cd06273 PBP1_GntR_like_1 This 95.7 0.089 1.9E-06 54.5 11.6 134 5-145 73-211 (268)
124 COG3107 LppC Putative lipoprot 95.5 0.25 5.5E-06 53.8 13.6 175 9-192 341-539 (604)
125 cd06325 PBP1_ABC_uncharacteriz 95.1 0.2 4.3E-06 52.2 11.9 125 6-136 77-208 (281)
126 cd06320 PBP1_allose_binding Pe 94.9 0.45 9.7E-06 49.4 13.8 125 5-137 77-207 (275)
127 cd08468 PBP2_Pa0477 The C-term 94.9 1.1 2.4E-05 43.5 15.9 73 383-464 13-85 (202)
128 cd05466 PBP2_LTTR_substrate Th 94.8 0.91 2E-05 43.2 14.8 70 383-464 13-82 (197)
129 PF09084 NMT1: NMT1/THI5 like; 94.8 0.13 2.7E-06 51.5 8.7 62 571-638 83-148 (216)
130 COG3221 PhnD ABC-type phosphat 94.7 0.51 1.1E-05 49.3 13.0 110 571-686 134-260 (299)
131 TIGR01481 ccpA catabolite cont 94.7 0.35 7.6E-06 51.8 12.5 130 6-142 134-266 (329)
132 cd06298 PBP1_CcpA_like Ligand- 94.6 0.33 7.2E-06 50.1 11.8 135 6-147 74-213 (268)
133 cd06323 PBP1_ribose_binding Pe 94.5 0.55 1.2E-05 48.4 13.1 123 6-136 76-205 (268)
134 cd08459 PBP2_DntR_NahR_LinR_li 94.4 0.79 1.7E-05 44.5 13.4 70 383-464 13-82 (201)
135 TIGR01728 SsuA_fam ABC transpo 94.4 0.38 8.3E-06 50.3 11.8 71 571-647 91-165 (288)
136 cd06319 PBP1_ABC_sugar_binding 94.4 0.62 1.3E-05 48.4 13.3 127 5-137 75-210 (277)
137 cd01545 PBP1_SalR Ligand-bindi 94.3 0.4 8.7E-06 49.6 11.6 129 5-140 75-207 (270)
138 cd06317 PBP1_ABC_sugar_binding 94.2 0.62 1.3E-05 48.3 12.8 128 6-137 77-212 (275)
139 cd08421 PBP2_LTTR_like_1 The C 94.1 2.6 5.7E-05 40.5 16.4 70 383-464 13-82 (198)
140 cd06295 PBP1_CelR Ligand bindi 94.1 0.41 8.8E-06 49.8 11.1 134 6-146 83-220 (275)
141 cd06271 PBP1_AglR_RafR_like Li 94.0 0.51 1.1E-05 48.7 11.7 134 6-146 78-215 (268)
142 cd08442 PBP2_YofA_SoxR_like Th 93.9 3 6.6E-05 39.8 16.4 70 383-464 13-82 (193)
143 PRK11151 DNA-binding transcrip 93.9 2.1 4.5E-05 45.3 16.3 83 356-464 91-173 (305)
144 cd06288 PBP1_sucrose_transcrip 93.9 0.4 8.6E-06 49.6 10.5 134 7-147 75-212 (269)
145 TIGR02122 TRAP_TAXI TRAP trans 93.9 0.23 5E-06 53.0 8.9 61 571-637 131-197 (320)
146 cd06312 PBP1_ABC_sugar_binding 93.7 0.98 2.1E-05 46.8 13.0 132 6-145 78-214 (271)
147 PF03466 LysR_substrate: LysR 93.6 1.9 4E-05 42.0 14.4 196 356-686 6-206 (209)
148 cd08418 PBP2_TdcA The C-termin 93.5 3.8 8.2E-05 39.4 16.4 72 383-464 13-84 (201)
149 cd06305 PBP1_methylthioribose_ 93.5 0.83 1.8E-05 47.3 12.1 126 6-137 76-208 (273)
150 cd08440 PBP2_LTTR_like_4 TThe 93.5 4.3 9.3E-05 38.7 16.5 70 383-464 13-82 (197)
151 TIGR00363 lipoprotein, YaeC fa 93.4 2.4 5.3E-05 43.4 14.8 121 571-697 106-250 (258)
152 PRK12684 transcriptional regul 93.2 3.5 7.5E-05 43.9 16.5 208 355-698 92-304 (313)
153 cd06310 PBP1_ABC_sugar_binding 93.2 2.1 4.6E-05 44.2 14.6 132 7-147 79-217 (273)
154 cd08420 PBP2_CysL_like C-termi 93.1 4.7 0.0001 38.6 16.1 70 383-464 13-82 (201)
155 cd08438 PBP2_CidR The C-termin 93.0 5.1 0.00011 38.2 16.4 70 383-464 13-82 (197)
156 cd06301 PBP1_rhizopine_binding 93.0 1.8 3.9E-05 44.7 13.8 135 6-147 77-218 (272)
157 cd06313 PBP1_ABC_sugar_binding 93.0 2 4.2E-05 44.6 13.9 125 6-136 76-207 (272)
158 cd08463 PBP2_DntR_like_4 The C 92.8 5.3 0.00012 38.9 16.2 71 383-464 13-83 (203)
159 COG1609 PurR Transcriptional r 92.8 1.2 2.6E-05 47.8 12.2 127 5-140 132-265 (333)
160 CHL00180 rbcR LysR transcripti 92.7 5 0.00011 42.4 16.9 86 356-464 95-180 (305)
161 cd06309 PBP1_YtfQ_like Peripla 92.7 2.3 5E-05 44.0 14.1 136 6-146 76-219 (273)
162 cd08412 PBP2_PAO1_like The C-t 92.6 7.6 0.00016 37.1 16.9 71 382-464 12-82 (198)
163 cd01575 PBP1_GntR Ligand-bindi 92.5 1.3 2.9E-05 45.5 11.9 134 6-146 74-211 (268)
164 cd08433 PBP2_Nac The C-teminal 92.4 8.8 0.00019 36.7 17.1 70 383-464 13-82 (198)
165 cd06284 PBP1_LacI_like_6 Ligan 92.4 1.2 2.6E-05 45.7 11.4 123 9-138 76-202 (267)
166 cd06283 PBP1_RegR_EndR_KdgR_li 92.3 1.5 3.3E-05 45.0 12.0 134 6-146 74-212 (267)
167 TIGR02990 ectoine_eutA ectoine 92.2 1.5 3.3E-05 44.3 11.2 127 5-135 66-206 (239)
168 cd06294 PBP1_ycjW_transcriptio 92.2 1.2 2.7E-05 45.8 11.2 131 6-142 79-213 (270)
169 cd06285 PBP1_LacI_like_7 Ligan 92.1 1.3 2.7E-05 45.7 11.1 125 7-140 75-203 (265)
170 TIGR00787 dctP tripartite ATP- 91.9 0.82 1.8E-05 47.1 9.3 102 571-684 126-230 (257)
171 cd06299 PBP1_LacI_like_13 Liga 91.9 1.5 3.3E-05 45.0 11.4 134 6-146 74-209 (265)
172 cd06297 PBP1_LacI_like_12 Liga 91.9 1.4 3E-05 45.6 11.1 131 6-146 74-214 (269)
173 PRK11242 DNA-binding transcrip 91.9 6.5 0.00014 41.2 16.4 83 356-464 91-173 (296)
174 cd08435 PBP2_GbpR The C-termin 91.8 9.1 0.0002 36.6 16.5 72 383-464 13-84 (201)
175 PF07885 Ion_trans_2: Ion chan 91.8 0.23 4.9E-06 40.6 4.0 55 511-565 22-78 (79)
176 cd01540 PBP1_arabinose_binding 91.8 2.7 5.8E-05 43.9 13.3 141 5-145 74-227 (289)
177 cd06272 PBP1_hexuronate_repres 91.8 1.3 2.8E-05 45.5 10.7 131 7-145 71-205 (261)
178 cd08461 PBP2_DntR_like_3 The C 91.8 5.5 0.00012 38.2 14.7 70 383-464 13-82 (198)
179 PRK12679 cbl transcriptional r 91.7 8.9 0.00019 40.8 17.3 207 356-699 93-306 (316)
180 cd06270 PBP1_GalS_like Ligand 91.7 2.1 4.6E-05 44.1 12.2 128 6-140 74-205 (268)
181 cd08415 PBP2_LysR_opines_like 91.6 7.7 0.00017 37.0 15.6 71 382-464 12-82 (196)
182 cd06275 PBP1_PurR Ligand-bindi 91.6 1.7 3.6E-05 44.8 11.4 133 7-146 76-212 (269)
183 cd06296 PBP1_CatR_like Ligand- 91.6 1.5 3.3E-05 45.2 11.0 131 6-142 74-208 (270)
184 cd06308 PBP1_sensor_kinase_lik 91.5 3.7 7.9E-05 42.4 13.9 132 7-147 78-216 (270)
185 PRK10014 DNA-binding transcrip 91.5 2.5 5.5E-05 45.5 13.1 127 6-139 140-270 (342)
186 cd08411 PBP2_OxyR The C-termin 91.5 6.2 0.00013 37.9 14.8 70 383-464 14-83 (200)
187 cd06291 PBP1_Qymf_like Ligand 91.5 2 4.4E-05 44.1 11.8 130 7-145 72-206 (265)
188 cd06293 PBP1_LacI_like_11 Liga 91.4 2.5 5.3E-05 43.6 12.4 131 9-146 77-211 (269)
189 cd06274 PBP1_FruR Ligand bindi 91.3 2.7 5.8E-05 43.2 12.5 133 7-146 75-212 (264)
190 cd08462 PBP2_NodD The C-termin 91.3 5.4 0.00012 38.6 14.1 68 384-464 14-81 (200)
191 cd08434 PBP2_GltC_like The sub 91.3 10 0.00022 36.0 16.0 70 383-464 13-82 (195)
192 cd01542 PBP1_TreR_like Ligand- 91.3 1.9 4.1E-05 44.1 11.3 130 6-147 74-208 (259)
193 cd06292 PBP1_LacI_like_10 Liga 91.2 2.2 4.7E-05 44.1 11.8 134 7-146 80-215 (273)
194 cd08466 PBP2_LeuO The C-termin 91.2 4.7 0.0001 38.8 13.6 70 383-464 13-82 (200)
195 cd06278 PBP1_LacI_like_2 Ligan 91.2 2 4.3E-05 44.1 11.4 121 6-135 73-197 (266)
196 cd08413 PBP2_CysB_like The C-t 91.2 8.5 0.00018 37.1 15.4 71 383-464 13-83 (198)
197 cd06289 PBP1_MalI_like Ligand- 91.0 1.5 3.3E-05 45.0 10.3 129 6-141 75-207 (268)
198 cd06324 PBP1_ABC_sugar_binding 90.9 3 6.5E-05 44.1 12.7 137 6-145 78-235 (305)
199 cd08417 PBP2_Nitroaromatics_li 90.9 6.1 0.00013 37.9 14.1 70 383-464 13-82 (200)
200 PRK10653 D-ribose transporter 90.8 4.5 9.7E-05 42.5 13.8 125 5-136 102-231 (295)
201 cd06316 PBP1_ABC_sugar_binding 90.6 4.8 0.00011 42.2 13.9 137 6-147 77-219 (294)
202 cd06311 PBP1_ABC_sugar_binding 90.5 5 0.00011 41.5 13.7 125 6-137 81-210 (274)
203 PRK12682 transcriptional regul 90.5 7.6 0.00016 41.1 15.3 84 356-464 93-176 (309)
204 PRK12681 cysB transcriptional 90.5 7.2 0.00016 41.7 15.1 85 355-464 92-176 (324)
205 PRK12683 transcriptional regul 90.5 14 0.0003 39.2 17.2 84 356-464 93-176 (309)
206 PRK10703 DNA-binding transcrip 90.4 2.2 4.8E-05 45.9 11.3 132 9-146 138-273 (341)
207 PRK11480 tauA taurine transpor 90.4 1.6 3.6E-05 46.5 10.1 68 572-645 113-184 (320)
208 cd08444 PBP2_Cbl The C-termina 90.3 14 0.0003 35.6 16.0 71 383-464 13-83 (198)
209 cd06307 PBP1_uncharacterized_s 90.3 3.6 7.8E-05 42.6 12.4 125 6-137 79-210 (275)
210 cd08465 PBP2_ToxR The C-termin 90.3 5.6 0.00012 38.5 13.2 70 383-464 13-82 (200)
211 PRK10837 putative DNA-binding 90.0 13 0.00029 38.7 16.6 83 356-464 89-171 (290)
212 PRK09791 putative DNA-binding 90.0 9.9 0.00021 40.0 15.7 86 355-464 94-179 (302)
213 cd06303 PBP1_LuxPQ_Quorum_Sens 90.0 6 0.00013 41.1 13.8 110 34-147 109-224 (280)
214 PRK10423 transcriptional repre 90.0 3.2 7E-05 44.3 12.0 131 9-146 135-269 (327)
215 cd08464 PBP2_DntR_like_2 The C 89.9 11 0.00023 36.1 14.8 70 383-464 13-82 (200)
216 cd08437 PBP2_MleR The substrat 89.8 16 0.00035 34.9 16.0 72 383-464 13-84 (198)
217 cd01574 PBP1_LacI Ligand-bindi 89.8 5.4 0.00012 40.9 13.2 130 7-146 76-208 (264)
218 cd08441 PBP2_MetR The C-termin 89.8 13 0.00029 35.5 15.4 69 384-464 14-82 (198)
219 cd08426 PBP2_LTTR_like_5 The C 89.7 18 0.00038 34.5 16.2 70 383-464 13-82 (199)
220 cd06322 PBP1_ABC_sugar_binding 89.7 6.2 0.00014 40.5 13.6 129 6-146 76-210 (267)
221 TIGR02424 TF_pcaQ pca operon t 89.6 11 0.00024 39.5 15.7 86 355-464 92-177 (300)
222 cd08460 PBP2_DntR_like_1 The C 89.6 5.4 0.00012 38.5 12.4 70 382-464 12-81 (200)
223 cd08436 PBP2_LTTR_like_3 The C 89.5 16 0.00034 34.7 15.6 71 383-464 13-83 (194)
224 cd06290 PBP1_LacI_like_9 Ligan 89.4 3.6 7.8E-05 42.2 11.5 126 9-141 76-205 (265)
225 cd06287 PBP1_LacI_like_8 Ligan 89.2 5 0.00011 41.5 12.3 133 7-146 76-212 (269)
226 cd01544 PBP1_GalR Ligand-bindi 89.1 4.4 9.6E-05 41.8 12.0 132 6-146 70-213 (270)
227 cd08419 PBP2_CbbR_RubisCO_like 89.0 21 0.00045 33.8 16.7 70 383-464 12-81 (197)
228 PRK11303 DNA-binding transcrip 89.0 6.8 0.00015 41.8 13.7 131 7-146 138-272 (328)
229 PRK09860 putative alcohol dehy 88.7 2.8 6E-05 46.0 10.4 88 43-130 20-109 (383)
230 cd06279 PBP1_LacI_like_3 Ligan 88.6 4.2 9.2E-05 42.3 11.5 127 6-140 75-223 (283)
231 cd08456 PBP2_LysR The C-termin 88.4 13 0.00029 35.3 14.3 70 383-464 13-82 (196)
232 PF00532 Peripla_BP_1: Peripla 88.4 3.7 8E-05 42.8 10.7 127 10-142 79-211 (279)
233 PF13377 Peripla_BP_3: Peripla 88.4 1.4 3E-05 41.3 6.9 99 46-146 1-102 (160)
234 cd08425 PBP2_CynR The C-termin 88.2 21 0.00046 34.0 15.6 70 383-464 14-83 (197)
235 cd01541 PBP1_AraR Ligand-bindi 88.1 4.8 0.0001 41.6 11.4 133 7-146 80-217 (273)
236 cd06306 PBP1_TorT-like TorT-li 88.0 7.7 0.00017 40.0 12.9 122 6-136 77-207 (268)
237 cd06280 PBP1_LacI_like_4 Ligan 87.9 7.1 0.00015 40.0 12.5 129 8-146 75-206 (263)
238 cd08467 PBP2_SyrM The C-termin 87.5 17 0.00036 35.1 14.4 70 383-464 13-82 (200)
239 cd08443 PBP2_CysB The C-termin 87.4 28 0.00061 33.4 16.8 72 382-464 12-83 (198)
240 PF03808 Glyco_tran_WecB: Glyc 87.2 7.8 0.00017 37.1 11.3 107 32-150 29-137 (172)
241 cd06321 PBP1_ABC_sugar_binding 87.2 9.9 0.00022 39.1 13.2 130 7-147 79-214 (271)
242 PF13407 Peripla_BP_4: Peripla 87.0 4.6 0.0001 41.2 10.5 134 6-146 76-214 (257)
243 cd01543 PBP1_XylR Ligand-bindi 87.0 6.4 0.00014 40.4 11.5 135 6-147 67-207 (265)
244 PRK15454 ethanol dehydrogenase 86.7 4.1 9E-05 44.8 10.2 88 43-130 38-127 (395)
245 TIGR02417 fruct_sucro_rep D-fr 86.7 7.5 0.00016 41.4 12.2 130 7-146 137-271 (327)
246 PRK10341 DNA-binding transcrip 86.5 18 0.00039 38.3 15.0 71 384-464 111-181 (312)
247 cd01539 PBP1_GGBP Periplasmic 86.4 13 0.00029 39.1 13.8 133 6-139 78-228 (303)
248 PRK12680 transcriptional regul 86.4 27 0.00058 37.3 16.2 84 356-464 93-176 (327)
249 cd06318 PBP1_ABC_sugar_binding 86.4 16 0.00035 37.8 14.3 134 6-146 76-222 (282)
250 cd08192 Fe-ADH7 Iron-containin 86.2 5.2 0.00011 43.7 10.7 89 43-131 13-103 (370)
251 COG1454 EutG Alcohol dehydroge 86.2 6.3 0.00014 42.6 10.9 91 43-133 18-110 (377)
252 cd08427 PBP2_LTTR_like_2 The C 86.1 28 0.00061 32.9 15.0 72 383-464 13-84 (195)
253 cd06281 PBP1_LacI_like_5 Ligan 86.0 5.5 0.00012 41.0 10.5 128 6-142 75-206 (269)
254 cd08423 PBP2_LTTR_like_6 The C 85.9 27 0.00059 33.1 14.9 73 383-464 13-87 (200)
255 cd08458 PBP2_NocR The C-termin 85.9 33 0.00071 32.7 16.7 70 383-464 13-82 (196)
256 cd06354 PBP1_BmpA_PnrA_like Pe 85.8 7.5 0.00016 40.1 11.3 124 6-135 76-206 (265)
257 PF03480 SBP_bac_7: Bacterial 85.2 1.6 3.5E-05 45.8 5.9 210 386-683 16-229 (286)
258 cd08190 HOT Hydroxyacid-oxoaci 85.2 6.1 0.00013 43.8 10.7 87 43-129 12-100 (414)
259 cd08449 PBP2_XapR The C-termin 85.1 35 0.00076 32.3 16.6 72 383-464 13-84 (197)
260 cd06302 PBP1_LsrB_Quorum_Sensi 85.0 17 0.00036 38.2 13.6 127 6-137 77-210 (298)
261 PRK09701 D-allose transporter 84.9 18 0.00039 38.3 14.0 128 7-137 104-241 (311)
262 cd08469 PBP2_PnbR The C-termin 84.8 24 0.00053 34.5 14.2 70 383-464 13-82 (221)
263 PRK11063 metQ DL-methionine tr 84.8 16 0.00034 37.9 12.8 121 571-697 119-263 (271)
264 cd08486 PBP2_CbnR The C-termin 84.6 33 0.00071 32.9 14.8 70 383-464 14-83 (198)
265 PRK11013 DNA-binding transcrip 84.6 35 0.00075 36.1 16.0 83 356-464 94-176 (309)
266 PRK09526 lacI lac repressor; R 84.6 16 0.00034 39.3 13.5 128 9-146 143-274 (342)
267 cd06277 PBP1_LacI_like_1 Ligan 84.6 9.2 0.0002 39.3 11.3 127 6-140 76-205 (268)
268 PRK09492 treR trehalose repres 84.4 11 0.00024 39.8 12.2 99 34-136 155-256 (315)
269 PRK10624 L-1,2-propanediol oxi 84.4 6.5 0.00014 43.1 10.4 87 43-129 19-107 (382)
270 cd08551 Fe-ADH iron-containing 84.3 6.7 0.00014 42.8 10.5 89 43-131 12-102 (370)
271 cd08189 Fe-ADH5 Iron-containin 84.3 7 0.00015 42.8 10.6 89 43-131 15-105 (374)
272 PRK11233 nitrogen assimilation 84.2 19 0.00041 38.0 13.7 69 383-463 105-173 (305)
273 PRK14987 gluconate operon tran 84.1 10 0.00022 40.5 11.8 133 6-146 138-273 (331)
274 cd08429 PBP2_NhaR The C-termin 84.0 43 0.00093 32.5 16.4 71 383-462 13-83 (204)
275 cd08457 PBP2_OccR The C-termin 83.9 40 0.00086 32.0 17.1 70 383-464 13-82 (196)
276 cd08193 HVD 5-hydroxyvalerate 83.9 7.3 0.00016 42.6 10.6 88 43-130 15-104 (376)
277 PRK10727 DNA-binding transcrip 83.7 6.2 0.00013 42.5 9.9 112 34-146 156-271 (343)
278 PF13685 Fe-ADH_2: Iron-contai 83.6 7.8 0.00017 39.4 9.7 99 44-147 9-108 (250)
279 COG3473 Maleate cis-trans isom 83.6 28 0.00061 33.7 12.5 130 3-135 60-204 (238)
280 cd08428 PBP2_IciA_ArgP The C-t 83.3 42 0.00092 31.8 14.9 66 385-463 15-80 (195)
281 COG0715 TauA ABC-type nitrate/ 83.2 5.3 0.00011 42.9 9.1 73 571-649 126-203 (335)
282 PRK10339 DNA-binding transcrip 83.1 10 0.00022 40.5 11.2 132 6-145 132-267 (327)
283 cd06286 PBP1_CcpB_like Ligand- 82.8 7.4 0.00016 39.7 9.7 109 34-143 94-206 (260)
284 PRK11074 putative DNA-binding 82.8 40 0.00086 35.4 15.5 86 355-464 91-176 (300)
285 cd08194 Fe-ADH6 Iron-containin 82.6 9.3 0.0002 41.8 10.7 87 43-129 12-100 (375)
286 TIGR01256 modA molybdenum ABC 82.6 16 0.00034 36.3 11.6 70 610-684 133-203 (216)
287 cd08414 PBP2_LTTR_aromatics_li 82.5 44 0.00096 31.5 16.1 70 383-464 13-82 (197)
288 PRK09508 leuO leucine transcri 82.4 16 0.00035 38.7 12.3 84 355-464 111-194 (314)
289 PRK11482 putative DNA-binding 82.3 36 0.00078 36.1 14.9 82 355-464 116-197 (317)
290 PRK11041 DNA-binding transcrip 82.1 8 0.00017 40.8 9.9 112 34-146 132-247 (309)
291 cd08453 PBP2_IlvR The C-termin 81.8 49 0.0011 31.5 16.7 73 383-464 13-85 (200)
292 cd06304 PBP1_BmpA_like Peripla 81.4 12 0.00026 38.3 10.7 120 10-135 80-202 (260)
293 cd08185 Fe-ADH1 Iron-containin 81.3 11 0.00023 41.4 10.6 87 43-130 15-104 (380)
294 COG1638 DctP TRAP-type C4-dica 81.2 4.4 9.6E-05 43.2 7.3 65 386-453 47-112 (332)
295 PF00465 Fe-ADH: Iron-containi 81.1 4.4 9.5E-05 44.2 7.4 89 43-133 12-102 (366)
296 TIGR02638 lactal_redase lactal 80.7 10 0.00022 41.5 10.2 87 43-129 18-106 (379)
297 TIGR02405 trehalos_R_Ecol treh 80.6 22 0.00047 37.6 12.5 118 7-136 133-253 (311)
298 cd08445 PBP2_BenM_CatM_CatR Th 80.5 55 0.0012 31.3 15.5 70 383-464 14-83 (203)
299 PRK10401 DNA-binding transcrip 80.5 12 0.00027 40.2 10.8 111 35-146 157-271 (346)
300 PRK10936 TMAO reductase system 80.5 20 0.00044 38.6 12.4 130 6-146 124-262 (343)
301 cd08188 Fe-ADH4 Iron-containin 79.8 14 0.00029 40.5 10.7 87 43-129 17-105 (377)
302 cd08448 PBP2_LTTR_aromatics_li 79.8 55 0.0012 30.8 16.0 70 383-464 13-82 (197)
303 cd08430 PBP2_IlvY The C-termin 79.0 59 0.0013 30.7 17.1 71 383-464 13-83 (199)
304 cd01538 PBP1_ABC_xylose_bindin 78.8 37 0.0008 35.3 13.5 126 6-138 76-216 (288)
305 cd08181 PPD-like 1,3-propanedi 78.6 16 0.00034 39.7 10.7 86 43-129 15-103 (357)
306 PRK09861 cytoplasmic membrane 78.5 37 0.00079 35.2 12.8 122 570-697 119-264 (272)
307 PRK11062 nhaR transcriptional 78.3 46 0.001 34.8 14.0 86 356-464 93-178 (296)
308 PRK10094 DNA-binding transcrip 78.3 82 0.0018 33.2 16.0 70 385-464 108-177 (308)
309 cd06314 PBP1_tmGBP Periplasmic 78.0 56 0.0012 33.5 14.5 120 10-137 79-204 (271)
310 KOG3857 Alcohol dehydrogenase, 77.8 20 0.00043 37.4 10.1 96 27-122 39-138 (465)
311 cd08191 HHD 6-hydroxyhexanoate 77.7 17 0.00036 40.0 10.7 87 43-130 12-100 (386)
312 PRK15421 DNA-binding transcrip 77.1 62 0.0013 34.3 14.7 69 384-464 103-171 (317)
313 cd08451 PBP2_BudR The C-termin 77.1 67 0.0014 30.3 18.3 70 384-464 15-84 (199)
314 COG2984 ABC-type uncharacteriz 76.8 33 0.00072 35.8 11.6 122 10-136 109-240 (322)
315 PRK11716 DNA-binding transcrip 76.5 67 0.0015 32.7 14.5 83 356-463 67-149 (269)
316 PF14503 YhfZ_C: YhfZ C-termin 76.1 8.9 0.00019 38.2 7.1 104 582-698 113-224 (232)
317 PF12727 PBP_like: PBP superfa 76.1 36 0.00079 33.2 11.4 103 571-683 81-191 (193)
318 cd08182 HEPD Hydroxyethylphosp 76.1 19 0.00042 39.2 10.6 86 43-131 12-99 (367)
319 cd08176 LPO Lactadehyde:propan 76.0 16 0.00035 40.0 9.9 87 43-129 17-105 (377)
320 cd08170 GlyDH Glycerol dehydro 75.2 9.6 0.00021 41.3 7.9 84 43-129 12-97 (351)
321 TIGR02955 TMAO_TorT TMAO reduc 74.4 37 0.0008 35.5 12.0 127 9-146 80-215 (295)
322 PRK15395 methyl-galactoside AB 74.1 49 0.0011 35.3 13.1 129 6-136 102-249 (330)
323 PF13531 SBP_bac_11: Bacterial 74.0 23 0.00051 35.4 10.0 194 382-696 10-226 (230)
324 TIGR03339 phn_lysR aminoethylp 73.6 1.1E+02 0.0024 31.3 16.0 69 384-464 98-166 (279)
325 PF07302 AroM: AroM protein; 73.1 39 0.00085 33.5 10.6 111 9-131 86-200 (221)
326 PRK03635 chromosome replicatio 73.1 67 0.0014 33.5 13.6 82 356-464 90-171 (294)
327 cd08186 Fe-ADH8 Iron-containin 72.3 25 0.00055 38.5 10.4 88 43-130 12-105 (383)
328 PF13407 Peripla_BP_4: Peripla 72.1 7.9 0.00017 39.5 6.1 78 57-136 1-81 (257)
329 cd08187 BDH Butanol dehydrogen 71.9 14 0.0003 40.5 8.2 86 43-129 18-106 (382)
330 cd07766 DHQ_Fe-ADH Dehydroquin 71.7 25 0.00055 37.6 10.1 100 43-147 12-113 (332)
331 cd08416 PBP2_MdcR The C-termin 70.5 97 0.0021 29.2 15.4 72 383-464 13-84 (199)
332 cd06533 Glyco_transf_WecG_TagA 70.4 57 0.0012 31.1 11.1 100 39-148 32-133 (171)
333 TIGR00696 wecB_tagA_cpsF bacte 70.3 68 0.0015 30.8 11.4 86 39-132 34-121 (177)
334 PRK10537 voltage-gated potassi 70.1 6.6 0.00014 43.0 5.1 54 509-562 164-219 (393)
335 cd08171 GlyDH-like2 Glycerol d 69.9 17 0.00037 39.2 8.2 86 43-130 12-99 (345)
336 COG0725 ModA ABC-type molybdat 69.8 70 0.0015 32.8 12.1 112 575-697 126-252 (258)
337 cd08431 PBP2_HupR The C-termin 67.6 1.1E+02 0.0024 28.8 14.4 71 383-464 13-83 (195)
338 cd08183 Fe-ADH2 Iron-containin 67.1 36 0.00078 37.2 10.1 83 43-130 12-96 (374)
339 cd08450 PBP2_HcaR The C-termin 66.9 1.1E+02 0.0025 28.6 15.7 70 383-464 13-82 (196)
340 PRK09906 DNA-binding transcrip 66.9 1.6E+02 0.0036 30.5 15.5 70 383-464 103-172 (296)
341 PF03401 TctC: Tripartite tric 66.5 1.1E+02 0.0023 31.8 13.1 121 571-696 88-241 (274)
342 PLN03192 Voltage-dependent pot 66.2 5.6 0.00012 48.6 3.9 55 512-566 249-305 (823)
343 PLN02245 ATP phosphoribosyl tr 66.0 39 0.00086 36.6 9.7 104 572-684 178-294 (403)
344 PRK09423 gldA glycerol dehydro 64.8 22 0.00048 38.7 7.9 84 43-129 19-104 (366)
345 cd08485 PBP2_ClcR The C-termin 64.8 1.3E+02 0.0028 28.6 15.7 70 383-464 14-83 (198)
346 cd06305 PBP1_methylthioribose_ 64.5 24 0.00053 36.1 8.0 77 57-136 2-81 (273)
347 cd06276 PBP1_FucR_like Ligand- 63.3 62 0.0013 32.8 10.5 120 7-145 73-195 (247)
348 cd08178 AAD_C C-terminal alcoh 63.2 44 0.00096 36.8 10.0 80 51-130 18-99 (398)
349 KOG1419 Voltage-gated K+ chann 62.4 15 0.00033 40.7 5.8 89 478-566 234-324 (654)
350 cd06267 PBP1_LacI_sugar_bindin 62.3 29 0.00063 35.1 8.0 76 57-136 2-79 (264)
351 TIGR02634 xylF D-xylose ABC tr 62.0 1.2E+02 0.0026 31.7 12.8 125 6-137 75-209 (302)
352 PF14981 FAM165: FAM165 family 61.6 19 0.00041 25.2 4.0 33 718-750 3-35 (51)
353 cd06301 PBP1_rhizopine_binding 61.1 26 0.00057 35.8 7.5 78 56-136 1-82 (272)
354 PRK03601 transcriptional regul 61.0 1.3E+02 0.0027 31.1 12.6 84 355-464 88-171 (275)
355 cd01537 PBP1_Repressors_Sugar_ 61.0 27 0.00059 35.2 7.5 77 57-136 2-80 (264)
356 PRK15408 autoinducer 2-binding 61.0 1.2E+02 0.0025 32.6 12.5 125 6-136 101-233 (336)
357 cd06353 PBP1_BmpA_Med_like Per 60.8 55 0.0012 33.6 9.6 85 56-148 1-89 (258)
358 cd08550 GlyDH-like Glycerol_de 59.2 33 0.00072 37.0 8.0 84 43-129 12-97 (349)
359 PF01634 HisG: ATP phosphoribo 58.4 16 0.00034 34.5 4.5 101 572-684 57-159 (163)
360 PRK09986 DNA-binding transcrip 57.9 2.3E+02 0.005 29.2 16.6 85 356-464 97-181 (294)
361 cd06303 PBP1_LuxPQ_Quorum_Sens 57.6 28 0.00061 36.0 7.0 79 57-135 2-84 (280)
362 PRK10355 xylF D-xylose transpo 56.7 1.6E+02 0.0034 31.4 12.7 132 6-146 102-243 (330)
363 TIGR02637 RhaS rhamnose ABC tr 56.6 2E+02 0.0044 29.9 13.5 131 6-146 77-217 (302)
364 cd08471 PBP2_CrgA_like_2 The C 56.1 1.1E+02 0.0025 28.7 10.7 65 383-462 14-78 (201)
365 PRK03692 putative UDP-N-acetyl 55.8 1.2E+02 0.0027 30.7 10.8 88 39-133 91-179 (243)
366 PF13380 CoA_binding_2: CoA bi 55.6 17 0.00037 32.1 4.1 86 55-147 1-88 (116)
367 cd08446 PBP2_Chlorocatechol Th 55.6 1.8E+02 0.0039 27.3 16.2 70 383-464 14-83 (198)
368 PRK00002 aroB 3-dehydroquinate 54.9 83 0.0018 34.1 10.2 101 43-147 20-127 (358)
369 PRK13348 chromosome replicatio 54.4 2.6E+02 0.0056 28.9 13.8 65 387-464 107-171 (294)
370 cd06306 PBP1_TorT-like TorT-li 54.3 43 0.00093 34.3 7.6 79 57-136 2-82 (268)
371 cd08179 NADPH_BDH NADPH-depend 54.0 45 0.00099 36.4 8.0 79 52-130 21-102 (375)
372 cd06289 PBP1_MalI_like Ligand- 53.8 46 0.001 33.8 7.8 77 57-136 2-80 (268)
373 cd06277 PBP1_LacI_like_1 Ligan 53.6 52 0.0011 33.6 8.1 75 57-136 2-81 (268)
374 PRK13583 hisG ATP phosphoribos 53.5 94 0.002 31.1 9.2 92 572-672 110-212 (228)
375 PF04392 ABC_sub_bind: ABC tra 53.5 1.4E+02 0.0031 31.2 11.5 104 11-121 82-194 (294)
376 cd08432 PBP2_GcdR_TrpI_HvrB_Am 53.4 1.6E+02 0.0034 27.5 11.1 65 384-463 14-78 (194)
377 cd08175 G1PDH Glycerol-1-phosp 53.4 50 0.0011 35.6 8.2 85 43-129 12-100 (348)
378 TIGR00070 hisG ATP phosphoribo 53.4 64 0.0014 31.0 7.8 74 572-657 100-173 (182)
379 PRK15408 autoinducer 2-binding 53.1 59 0.0013 34.9 8.6 82 53-136 22-106 (336)
380 cd06312 PBP1_ABC_sugar_binding 53.1 45 0.00098 34.2 7.6 79 56-136 1-83 (271)
381 COG1910 Periplasmic molybdate- 53.0 1.2E+02 0.0025 30.0 9.4 108 571-689 87-202 (223)
382 PRK10677 modA molybdate transp 52.6 99 0.0022 31.7 9.8 70 386-464 42-117 (257)
383 COG1879 RbsB ABC-type sugar tr 52.4 2.2E+02 0.0048 30.0 13.0 136 5-146 111-251 (322)
384 cd06282 PBP1_GntR_like_2 Ligan 52.4 57 0.0012 33.1 8.2 77 57-136 2-80 (266)
385 cd01391 Periplasmic_Binding_Pr 52.2 48 0.001 33.2 7.6 78 56-136 1-83 (269)
386 COG2358 Imp TRAP-type uncharac 52.2 69 0.0015 33.8 8.5 79 571-655 127-214 (321)
387 PRK14498 putative molybdopteri 52.1 1.7E+02 0.0037 34.5 13.0 67 52-121 184-262 (633)
388 cd06167 LabA_like LabA_like pr 52.0 1.9E+02 0.0041 26.4 12.6 99 45-148 29-132 (149)
389 cd06322 PBP1_ABC_sugar_binding 51.8 53 0.0012 33.4 7.9 77 57-136 2-81 (267)
390 cd08447 PBP2_LTTR_aromatics_li 50.9 2.1E+02 0.0046 26.7 15.3 70 383-464 13-82 (198)
391 PF04273 DUF442: Putative phos 50.3 1.7E+02 0.0038 25.5 10.4 79 49-128 23-103 (110)
392 cd08422 PBP2_CrgA_like The C-t 50.3 82 0.0018 29.5 8.6 66 383-463 14-79 (197)
393 cd01536 PBP1_ABC_sugar_binding 50.1 55 0.0012 33.1 7.7 77 56-135 1-80 (267)
394 cd08177 MAR Maleylacetate redu 49.9 63 0.0014 34.7 8.2 97 43-147 12-110 (337)
395 cd08180 PDD 1,3-propanediol de 49.7 76 0.0016 34.0 8.8 78 50-128 18-97 (332)
396 cd01545 PBP1_SalR Ligand-bindi 49.5 70 0.0015 32.5 8.4 78 57-136 2-81 (270)
397 cd08452 PBP2_AlsR The C-termin 49.2 2.3E+02 0.0051 26.6 17.0 70 383-464 13-82 (197)
398 PRK09189 uroporphyrinogen-III 48.3 52 0.0011 33.3 7.0 88 39-132 101-190 (240)
399 cd01538 PBP1_ABC_xylose_bindin 47.9 77 0.0017 32.8 8.5 77 57-136 2-81 (288)
400 PRK11119 proX glycine betaine 47.9 57 0.0012 34.9 7.3 63 352-436 25-87 (331)
401 cd06299 PBP1_LacI_like_13 Liga 47.5 84 0.0018 31.9 8.6 76 57-136 2-79 (265)
402 cd08197 DOIS 2-deoxy-scyllo-in 47.4 1.5E+02 0.0033 32.0 10.6 101 43-147 12-119 (355)
403 cd08184 Fe-ADH3 Iron-containin 47.4 1.3E+02 0.0028 32.4 10.1 84 43-130 12-102 (347)
404 cd08549 G1PDH_related Glycerol 47.3 74 0.0016 34.1 8.2 98 43-147 12-113 (332)
405 cd08479 PBP2_CrgA_like_9 The C 47.0 1.9E+02 0.0042 27.0 10.7 65 383-462 14-78 (198)
406 cd06318 PBP1_ABC_sugar_binding 46.6 64 0.0014 33.2 7.6 77 57-136 2-81 (282)
407 cd00757 ThiF_MoeB_HesA_family 46.6 2E+02 0.0043 28.8 10.8 89 41-135 32-136 (228)
408 PRK11139 DNA-binding transcrip 46.1 3.1E+02 0.0067 28.4 12.8 104 573-684 180-288 (297)
409 cd06310 PBP1_ABC_sugar_binding 46.1 68 0.0015 32.8 7.6 80 56-136 1-83 (273)
410 cd06295 PBP1_CelR Ligand bindi 45.9 1E+02 0.0022 31.5 8.9 78 53-136 2-88 (275)
411 cd03364 TOPRIM_DnaG_primases T 45.7 53 0.0011 26.5 5.3 42 44-86 34-75 (79)
412 cd01540 PBP1_arabinose_binding 45.3 60 0.0013 33.6 7.1 76 57-136 2-80 (289)
413 TIGR00249 sixA phosphohistidin 45.1 92 0.002 28.9 7.5 98 34-132 23-120 (152)
414 PF02602 HEM4: Uroporphyrinoge 44.4 26 0.00055 35.2 4.0 92 35-133 97-189 (231)
415 PF02608 Bmp: Basic membrane p 44.2 72 0.0016 33.7 7.5 87 56-149 3-94 (306)
416 cd06315 PBP1_ABC_sugar_binding 44.1 3.3E+02 0.0071 27.9 12.5 132 6-139 77-216 (280)
417 cd01324 cbb3_Oxidase_CcoQ Cyto 44.0 25 0.00054 25.5 2.7 25 479-503 12-36 (48)
418 TIGR02667 moaB_proteo molybden 43.3 1.2E+02 0.0025 28.7 8.0 66 53-120 3-72 (163)
419 PF02310 B12-binding: B12 bind 43.3 2.2E+02 0.0049 24.7 10.0 45 69-119 15-59 (121)
420 cd06271 PBP1_AglR_RafR_like Li 42.9 2.4E+02 0.0052 28.4 11.1 69 64-136 15-83 (268)
421 PF13362 Toprim_3: Toprim doma 42.9 72 0.0016 26.8 5.9 52 52-106 39-92 (96)
422 PRK07377 hypothetical protein; 42.7 57 0.0012 31.0 5.4 61 356-433 75-135 (184)
423 PF01936 NYN: NYN domain; Int 42.6 1.8E+02 0.004 26.2 9.2 99 42-146 22-126 (146)
424 cd06285 PBP1_LacI_like_7 Ligan 42.3 3.2E+02 0.007 27.5 12.0 75 57-135 2-78 (265)
425 cd06302 PBP1_LsrB_Quorum_Sensi 41.9 90 0.002 32.6 7.9 78 57-136 2-82 (298)
426 cd06273 PBP1_GntR_like_1 This 41.9 1.1E+02 0.0024 31.0 8.4 76 57-136 2-79 (268)
427 PRK10355 xylF D-xylose transpo 41.8 1E+02 0.0022 32.9 8.3 79 54-135 25-106 (330)
428 cd06281 PBP1_LacI_like_5 Ligan 41.5 1.1E+02 0.0025 31.0 8.4 76 57-135 2-79 (269)
429 cd02071 MM_CoA_mut_B12_BD meth 41.3 1.6E+02 0.0034 26.1 8.1 62 69-136 14-79 (122)
430 COG1810 Uncharacterized protei 41.1 3E+02 0.0064 27.2 10.1 75 56-135 3-80 (224)
431 COG4521 TauA ABC-type taurine 41.0 1.1E+02 0.0023 30.6 7.2 106 571-683 120-238 (334)
432 cd08173 Gro1PDH Sn-glycerol-1- 41.0 1E+02 0.0022 33.1 8.1 95 44-147 14-111 (339)
433 PRK10936 TMAO reductase system 40.8 1E+02 0.0023 33.0 8.3 81 54-136 46-129 (343)
434 cd08481 PBP2_GcdR_like The C-t 40.5 1.9E+02 0.004 27.0 9.3 65 610-680 124-190 (194)
435 cd06316 PBP1_ABC_sugar_binding 40.2 88 0.0019 32.5 7.5 79 56-136 1-82 (294)
436 PRK10014 DNA-binding transcrip 40.1 1.4E+02 0.003 31.7 9.2 79 55-136 65-145 (342)
437 cd00886 MogA_MoaB MogA_MoaB fa 39.9 1.3E+02 0.0027 28.0 7.6 64 56-121 2-71 (152)
438 PRK01686 hisG ATP phosphoribos 39.6 3.4E+02 0.0073 27.0 10.7 92 582-684 114-207 (215)
439 cd06296 PBP1_CatR_like Ligand- 39.3 1.2E+02 0.0025 30.9 8.1 75 57-135 2-78 (270)
440 cd01539 PBP1_GGBP Periplasmic 39.2 1.1E+02 0.0025 31.9 8.2 78 56-136 1-83 (303)
441 TIGR03414 ABC_choline_bnd chol 38.8 2.6E+02 0.0056 29.2 10.5 41 385-434 23-63 (290)
442 cd06317 PBP1_ABC_sugar_binding 38.6 1.1E+02 0.0023 31.2 7.8 77 57-136 2-82 (275)
443 cd06323 PBP1_ribose_binding Pe 38.6 1.1E+02 0.0023 31.0 7.7 77 57-136 2-81 (268)
444 PRK11303 DNA-binding transcrip 38.5 1.7E+02 0.0036 31.0 9.4 80 54-136 61-142 (328)
445 cd01575 PBP1_GntR Ligand-bindi 38.4 1.2E+02 0.0025 30.8 7.9 76 57-136 2-79 (268)
446 cd06315 PBP1_ABC_sugar_binding 38.3 1.4E+02 0.003 30.8 8.5 79 55-136 1-82 (280)
447 cd06320 PBP1_allose_binding Pe 37.9 1.1E+02 0.0024 31.2 7.8 79 57-136 2-83 (275)
448 cd06319 PBP1_ABC_sugar_binding 37.5 1E+02 0.0022 31.5 7.3 77 57-136 2-81 (277)
449 cd06300 PBP1_ABC_sugar_binding 37.5 1.2E+02 0.0025 31.0 7.8 80 56-136 1-86 (272)
450 cd06275 PBP1_PurR Ligand-bindi 37.3 3.5E+02 0.0077 27.2 11.4 62 57-121 2-65 (269)
451 TIGR00854 pts-sorbose PTS syst 37.2 2.2E+02 0.0047 26.5 8.5 81 41-129 13-93 (151)
452 cd06324 PBP1_ABC_sugar_binding 37.1 1.1E+02 0.0024 32.0 7.7 77 57-136 2-83 (305)
453 cd06293 PBP1_LacI_like_11 Liga 36.8 4.2E+02 0.0091 26.7 11.9 62 57-121 2-65 (269)
454 cd00758 MoCF_BD MoCF_BD: molyb 36.6 1.4E+02 0.003 26.9 7.1 61 57-120 2-67 (133)
455 cd06270 PBP1_GalS_like Ligand 36.5 1.6E+02 0.0034 29.9 8.6 76 57-136 2-79 (268)
456 PRK00843 egsA NAD(P)-dependent 36.5 1.4E+02 0.0031 32.1 8.4 96 43-147 22-120 (350)
457 cd00001 PTS_IIB_man PTS_IIB, P 36.5 2.2E+02 0.0048 26.5 8.4 82 41-130 12-93 (151)
458 cd00338 Ser_Recombinase Serine 36.2 3.1E+02 0.0068 24.4 10.2 25 39-64 17-41 (137)
459 PRK09756 PTS system N-acetylga 35.9 2.1E+02 0.0046 26.8 8.3 81 41-130 17-98 (158)
460 PRK09701 D-allose transporter 35.6 1.5E+02 0.0033 31.2 8.4 85 51-136 21-108 (311)
461 cd08169 DHQ-like Dehydroquinat 35.5 2.4E+02 0.0053 30.3 9.9 101 43-147 12-118 (344)
462 PF13155 Toprim_2: Toprim-like 35.2 52 0.0011 27.6 3.9 41 42-82 35-75 (96)
463 cd01542 PBP1_TreR_like Ligand- 35.1 1.3E+02 0.0029 30.2 7.7 75 57-135 2-78 (259)
464 TIGR03298 argP transcriptional 34.9 5.2E+02 0.011 26.6 15.2 64 387-463 107-170 (292)
465 PF08659 KR: KR domain; Inter 34.8 3.3E+02 0.0071 26.0 9.9 79 39-120 10-89 (181)
466 PRK10653 D-ribose transporter 34.6 1.9E+02 0.0041 30.0 8.9 80 54-136 26-108 (295)
467 PF12273 RCR: Chitin synthesis 34.4 40 0.00086 30.5 3.1 29 722-750 2-30 (130)
468 PF01102 Glycophorin_A: Glycop 34.2 61 0.0013 28.8 4.0 28 723-750 66-93 (122)
469 cd06278 PBP1_LacI_like_2 Ligan 34.0 1.5E+02 0.0033 29.9 7.9 75 57-136 2-78 (266)
470 PLN02727 NAD kinase 34.0 4.5E+02 0.0097 32.1 12.1 108 21-132 253-362 (986)
471 cd06274 PBP1_FruR Ligand bindi 33.9 1.7E+02 0.0038 29.5 8.4 76 57-136 2-79 (264)
472 PLN02428 lipoic acid synthase 33.7 3E+02 0.0065 29.6 10.0 100 36-138 129-249 (349)
473 PRK10481 hypothetical protein; 33.5 2.8E+02 0.006 27.7 9.0 75 46-124 120-195 (224)
474 PRK11425 PTS system N-acetylga 33.1 2.6E+02 0.0056 26.2 8.4 80 41-129 15-94 (157)
475 PF00072 Response_reg: Respons 32.8 2.7E+02 0.0058 23.4 8.2 76 58-147 1-79 (112)
476 cd06309 PBP1_YtfQ_like Peripla 32.8 94 0.002 31.7 6.2 71 63-136 10-81 (273)
477 PF00218 IGPS: Indole-3-glycer 32.7 1.6E+02 0.0035 30.1 7.4 89 41-137 69-160 (254)
478 TIGR00177 molyb_syn molybdenum 32.7 1.8E+02 0.004 26.6 7.4 48 71-121 29-76 (144)
479 TIGR02634 xylF D-xylose ABC tr 32.5 1.3E+02 0.0029 31.4 7.3 72 62-136 8-80 (302)
480 PF00731 AIRC: AIR carboxylase 32.4 4E+02 0.0086 24.8 9.2 71 56-128 2-72 (150)
481 PRK05752 uroporphyrinogen-III 32.4 1.1E+02 0.0025 31.1 6.6 89 36-130 107-200 (255)
482 cd03770 SR_TndX_transposase Se 32.3 3.9E+02 0.0084 24.3 10.3 26 97-122 54-79 (140)
483 cd06321 PBP1_ABC_sugar_binding 32.3 1.7E+02 0.0037 29.7 8.0 77 57-136 2-83 (271)
484 cd02067 B12-binding B12 bindin 32.3 2.9E+02 0.0062 24.1 8.3 62 68-135 13-78 (119)
485 PRK15138 aldehyde reductase; P 31.9 2.1E+02 0.0045 31.4 8.8 84 43-130 20-106 (387)
486 cd06307 PBP1_uncharacterized_s 31.9 1.6E+02 0.0034 30.1 7.7 80 56-136 1-84 (275)
487 cd03522 MoeA_like MoeA_like. T 31.9 2.3E+02 0.0051 29.9 8.7 69 51-121 156-229 (312)
488 cd08475 PBP2_CrgA_like_6 The C 31.7 4.2E+02 0.0092 24.5 10.9 68 608-681 127-196 (199)
489 PF03830 PTSIIB_sorb: PTS syst 31.6 1E+02 0.0022 28.7 5.4 82 42-131 14-95 (151)
490 cd01574 PBP1_LacI Ligand-bindi 31.4 2.2E+02 0.0047 28.7 8.6 76 57-135 2-79 (264)
491 TIGR02637 RhaS rhamnose ABC tr 31.2 1.5E+02 0.0032 31.0 7.4 72 63-136 9-82 (302)
492 PF02310 B12-binding: B12 bind 30.9 1.6E+02 0.0034 25.7 6.5 71 42-120 17-88 (121)
493 COG0134 TrpC Indole-3-glycerol 30.8 81 0.0018 32.0 4.8 87 43-137 69-158 (254)
494 PF09651 Cas_APE2256: CRISPR-a 30.8 1.9E+02 0.0042 26.3 7.0 50 40-89 5-57 (136)
495 PF01054 MMTV_SAg: Mouse mamma 30.5 48 0.001 32.0 3.0 60 691-750 2-72 (313)
496 cd00885 cinA Competence-damage 30.3 1.8E+02 0.004 27.6 7.1 46 71-119 21-66 (170)
497 cd08483 PBP2_HvrB The C-termin 30.3 4.4E+02 0.0095 24.3 10.5 64 384-462 14-77 (190)
498 PF15179 Myc_target_1: Myc tar 30.1 68 0.0015 30.3 3.8 38 713-750 13-51 (197)
499 TIGR00288 conserved hypothetic 30.0 3.3E+02 0.0072 25.6 8.4 81 43-131 69-149 (160)
500 PRK13805 bifunctional acetalde 30.0 2.8E+02 0.006 34.2 10.3 92 44-135 469-565 (862)
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=8.9e-89 Score=700.10 Aligned_cols=701 Identities=20% Similarity=0.332 Sum_probs=571.4
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
+..+|..+++|.|+++. |. +...++.+.+.|+- ..|+++++.||+|.+++++| |.+.|...++++.+.+.++
T Consensus 106 ltsfc~aLh~~~vtpsf--p~--~~~~~Fviq~RP~l---~~al~s~i~hy~W~~fv~ly-D~~rg~s~Lqai~~~a~~~ 177 (897)
T KOG1054|consen 106 LTSFCGALHVSFVTPSF--PT--DGDNQFVIQMRPAL---KGALLSLIDHYKWEKFVYLY-DTDRGLSILQAIMEAAAQN 177 (897)
T ss_pred hhhhccceeeeeecccC--Cc--CCCceEEEEeCchH---HHHHHHHHHhcccceEEEEE-cccchHHHHHHHHHHHHhc
Confidence 45678999999999866 32 23346788888764 48999999999999999999 8889999999999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
+++|.....-.+ .+..+++.+++.+...+.+.|++.|..+...+++.++.++|-...+|++|+.+..-...+. .
T Consensus 178 nw~VtA~~v~~~-~d~~~yr~~f~~l~~r~e~rv~iDce~~~~~~il~q~i~~~k~~~~YHYvlaNl~f~d~dl-----~ 251 (897)
T KOG1054|consen 178 NWQVTAINVGNI-NDVKEYRMLFEMLDRRQENRVLIDCESERRNRILLQVIELGKHVKGYHYVLANLGFTDIDL-----E 251 (897)
T ss_pred CceEEEEEcCCc-ccHHHHHHHHHHHhccccceEEEEcccHHHHHHHHHHHHHhhhccceEEEEeeCCCchhhH-----H
Confidence 999987664443 3556699999999999999999999999999999999999988899999999854433332 2
Q ss_pred hhhhhccceEEEEEeCCCChhhHHHHHHHhhhcc---CCCCCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccCCCC
Q 003633 162 TSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQ---KGLVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSASHE 237 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~---~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~~~ 237 (806)
.......++.|++....++|..++|.++|++... ++.+...+..-++.+|||+.++++|+..+.++. .+..
T Consensus 252 ~f~~g~aNitgFqivn~~~~~~~k~~~~~~~l~~~~~~g~~~~~~k~tsAlthDailV~~eaf~~~~~q~~~~~r----- 326 (897)
T KOG1054|consen 252 RFQHGGANITGFQIVNKNNPMVKKFIQRWKELDEREYPGASNDPIKYTSALTHDAILVMAEAFRSLRRQRIDISR----- 326 (897)
T ss_pred HHhcCCcceeEEEEecCCChHHHHHHHHHhhhcccccCCCCCCCcchhhhhhhhHHHHHHHHHHHHHHhhhchhc-----
Confidence 3344556789999999999999999999987654 222334566668899999999999999998876 3331
Q ss_pred CCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCccccCcc
Q 003633 238 LPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGFSVLPPE 317 (806)
Q Consensus 238 l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl~~~~~~ 317 (806)
+...|+++. .+..+|.+|..+-.+++++.++|+||+|+||..|.|.+...+|++++.++.++||+|....|+......
T Consensus 327 -RG~~GD~~a-n~~~p~~qG~~I~ralk~v~~eGLTGniqFd~~G~R~Nyt~~i~elk~~~~rk~~~W~e~~~fv~~~t~ 404 (897)
T KOG1054|consen 327 -RGNAGDCLA-NPAVPWEQGIDIERALKQVQVEGLTGNIQFDKYGRRTNYTIDIVELKSNGSRKVGYWNEGEGFVPGSTV 404 (897)
T ss_pred -cCCCccccC-CCCCchhcchhHHHHHHheeecccccceeecccCccccceEEEEEeccCCcceeeeecccCceeecccc
Confidence 112232222 136689999999999999999999999999999999999999999999999999999999998643211
Q ss_pred cccCCCCCCCccccccceeeeCCCCccCCCceeecCCCCCeEEeeeccCCccceEEe---ecCCceeEeeeHHHHHHHHH
Q 003633 318 TLKGKNVSHSQLDWKLQNITWPGGKTETPRGWVIADNARPLRIGVPRRASFVGFVTE---EHDSHKVQGYCIDILLEALK 394 (806)
Q Consensus 318 ~~~~~~~~~~~~~~~l~~i~Wpg~~~~~P~~~~~~~~g~~lrv~v~~~~~~~~f~~~---~~~~~~~~G~~idl~~~i~~ 394 (806)
.. .. +... ..+.++..|.+....||..+... -.|+.+++|||+||+.+||+
T Consensus 405 a~-~~---~d~~----------------------~~~n~tvvvttiL~spyvm~kkn~~~~egn~ryEGyCvdLa~~iAk 458 (897)
T KOG1054|consen 405 AQ-SR---NDQA----------------------SKENRTVVVTTILESPYVMLKKNHEQLEGNERYEGYCVDLAAEIAK 458 (897)
T ss_pred cc-cc---cccc----------------------ccccceEEEEEecCCchhHHHhhHHHhcCCcccceeHHHHHHHHHH
Confidence 10 00 0000 01234555555554455433221 14678999999999999999
Q ss_pred hCCCCcceEEEEcC-CC--CCCCC-HHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEeccC-CCCCc
Q 003633 395 LVPYDVPYKFELFG-DG--LSNPS-YDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPINN-HKASA 469 (806)
Q Consensus 395 ~l~~~~~~~~~~~~-~~--~~n~s-~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~~-~~~~~ 469 (806)
+.++.+++.++..| +| ...++ |+||++.|..|++|++++++|||..|++.+|||.|||+.|+++|+++|. ..+..
T Consensus 459 hi~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REeviDFSKPfMslGISIMIKKPqKsk~gV 538 (897)
T KOG1054|consen 459 HIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGV 538 (897)
T ss_pred hcCceEEEEEecCCcccccCCCcccccchhHHHhcCccceEEeeeeeehhhhhhhccccchhhcCeEEEEeCcccCCCCe
Confidence 99987444444433 22 24455 9999999999999999999999999999999999999999999999988 78899
Q ss_pred ceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCC------C-------CccchhhHHHHHHHhhhccCcc-cccc
Q 003633 470 WVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRG------P-------PRRQIATMFLFSFSTLFKTNQE-ATVS 535 (806)
Q Consensus 470 ~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~------~-------~~~~~~~~~~~~~~~l~~~~~~-~~~s 535 (806)
++|+.|+..++|+|++..++.|++++++..|++|.+|+- + ....+.|++||+++++++|+.+ .|+|
T Consensus 539 FSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~rg~~t~~~~~NeFgifNsLWFsLgAFMQQG~DI~PRs 618 (897)
T KOG1054|consen 539 FSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTPSDPPNEFGIFNSLWFSLGAFMQQGCDISPRS 618 (897)
T ss_pred eeecchhHHHHHHHHHHHHhcceEEEEEEeccCchheeccccccCCCCCCCCCccchhhHHHHHHHHHHHhcCCCCCccc
Confidence 999999999999999999999999999999999877652 1 1235899999999999999988 8999
Q ss_pred cchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCC-ceeEEeCchhHHHhhhhc--------cccc
Q 003633 536 SLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDW-PIGYQVGSFAYSYLSDSL--------RIQK 606 (806)
Q Consensus 536 ~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~-~ig~~~gs~~~~~l~~~~--------~~~~ 606 (806)
.++|++-.+||||.|||.++|||||++|||++++.+||+|.+||.++.+ ..|+..+....+++++.. ....
T Consensus 619 lSGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeFFr~Skiavy~kMW~yM~ 698 (897)
T KOG1054|consen 619 LSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMK 698 (897)
T ss_pred cccceeccchhhhhhhhhhhhhhHHHHHHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHHHhhhhHHHHHHHHHHHh
Confidence 9999999999999999999999999999999999999999999998877 367777777777775321 0000
Q ss_pred c-cc-eeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhC-CCCeEEeCCccccCCceeeecCCCCchHHHHHHHHh
Q 003633 607 S-RL-ISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSN-QTDFGIIGQPFTRSGWGFAFQRDSPLAVGMSTAILK 683 (806)
Q Consensus 607 ~-~~-~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~-~~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~il~ 683 (806)
+ .. +-..+..|.++.+++. .+.+|++.|...-+|.-++ .|+.+.+|..+.+.+||+|.||||.|+..+|.++++
T Consensus 699 SaepsVFv~t~aeGv~rVRks---KGkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGiATp~Gsslr~~vNLAvLk 775 (897)
T KOG1054|consen 699 SAEPSVFVRTTAEGVARVRKS---KGKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLK 775 (897)
T ss_pred cCCcceeeehhhhHHHHHHhc---CCceEeehHhhhhhhhhccCCccceecccccCCcceeecCCCCcccccchhhhhhh
Confidence 0 11 2234566777777664 7889999999888887654 799999999999999999999999999999999999
Q ss_pred hhccchhHHHHHhhc-CCCCCCCcCcCCC-CccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 003633 684 LSENGMLQKLHEKWF-CKEGCPEERRQHS-EPHQLRLISFWGLYLLCGTITFTAFLVFLLRMVCQYVRYKQ 752 (806)
Q Consensus 684 l~e~G~~~~i~~kw~-~~~~c~~~~~~~~-~~~~L~l~~~~g~F~il~~g~~lal~vf~~E~~~~~~~~~~ 752 (806)
|.|.|+++++++||| .+++|.....+.+ ..+.|+|.+++|+||||..|+++|+++.++|++|+.+...+
T Consensus 776 L~E~G~LdKLkNKWWYDkGeC~sg~~ds~~ktsaLsLSnVAGvFYIL~gGl~laMlvALiEF~yksr~Eak 846 (897)
T KOG1054|consen 776 LNEQGLLDKLKNKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAK 846 (897)
T ss_pred hcccchHHHhhhhhcccccccCCCCCCCCcchhhcchhhccceeeeehhhHHHHHHHHHHHHHHHhhHHHH
Confidence 999999999999999 4899998866653 44799999999999999999999999999999998876654
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=3.5e-79 Score=631.85 Aligned_cols=669 Identities=23% Similarity=0.425 Sum_probs=561.2
Q ss_pred hcccccCCCcEEecccCCCCcccCC-CCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 3 SEVANGLKVPLVSFAATDPTLSALQ-FPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~~~-~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
+--+..+++|+|..+..+..+|++. ++.|+|++|+.+.|+....+++.+|.|++|+++.+||.-|+.....++..+++.
T Consensus 117 SYT~gFY~iPV~G~~~Rda~fSdKnIh~sFlRtvpPyshqa~VwleMl~~~~y~~vi~l~s~d~~gra~~~r~qt~~e~~ 196 (993)
T KOG4440|consen 117 SYTAGFYRIPVLGLTTRDAIFSDKNIHLSFLRTVPPYSHQASVWLEMLRVYSYNHVILLVSDDHEGRAAQKRLQTLLEER 196 (993)
T ss_pred eeeccceeeeeeeeeehhhhhccCceeeeEeecCCCccchhHHHHHHHHHhhcceEEEEEcccccchhHHhHHHHHHHHH
Confidence 4456778999999988899999876 999999999999999999999999999999999999999998888888888877
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
..++.....+.|+ ..+++..|-++|..++||+++....++|..|++.|-+++|++.|||||+++....
T Consensus 197 ~~~~e~v~~f~p~--~~~~t~~l~~~k~~~~rv~~~~as~dDA~~ifr~Ag~lnmTG~G~VWiV~E~a~~---------- 264 (993)
T KOG4440|consen 197 ESKAEKVLQFDPG--TKNVTALLMEAKELEARVIILSASEDDAATIFRAAGMLNMTGSGYVWIVGERAIS---------- 264 (993)
T ss_pred hhhhhhheecCcc--cchHHHHHhhhhhhhheeEEeecccchHHHHHHhhhhhcccCceEEEEEeccccc----------
Confidence 7776655566655 4689999999999999999999999999999999999999999999999984322
Q ss_pred hhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCCC
Q 003633 162 TSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELPDS 241 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~ 241 (806)
.....+|++|++.....+. .+..-|+|.++|.|++.+++..++.-
T Consensus 265 -~nn~PdG~LGlqL~~~~~~-------------------------~~hirDsv~vlasAv~e~~~~e~I~~--------- 309 (993)
T KOG4440|consen 265 -GNNLPDGILGLQLINGKNE-------------------------SAHIRDSVGVLASAVHELLEKENITD--------- 309 (993)
T ss_pred -cCCCCCceeeeEeecCccc-------------------------cceehhhHHHHHHHHHHHHhhccCCC---------
Confidence 1234689999887543221 12456999999999999998763321
Q ss_pred cccccccccccccCchHHHHHHHHccc-cCCceeeEEEecCCCeecccEEEEEee-cCceEEEEEeeCCCCccccCcccc
Q 003633 242 KATRVQLEQLKVFDGGTFLLRKLLQTN-FTGLSGQVQFNQDRNIVSRGYDVINID-KMEIHRVGYWFDGSGFSVLPPETL 319 (806)
Q Consensus 242 ~~~~~~~~~~~~~~~g~~l~~~l~~~~-f~G~tG~i~Fd~~G~~~~~~~~I~~~~-~~~~~~VG~w~~~~gl~~~~~~~~ 319 (806)
.+..+|++...|..|..|...+...+ -.|.||++.||++|||....|+|+|+. ..+.+.+|.++. +.+
T Consensus 310 -~P~~c~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~Fnd~gdRi~a~YdiiN~hq~rk~Vg~~~yd~---~r~------ 379 (993)
T KOG4440|consen 310 -PPRGCVDNTNIWKTGPLLKRVLMSSKYADGVTGRVEFNDDGDRIFANYDIINLHQNRKLVGVGIYDG---TRV------ 379 (993)
T ss_pred -CCCcccCccchhcccHHHHHHHhhhcccCCcceeEEEcCCCceeeccceeEehhhhhhhhhhccccc---eee------
Confidence 11236677788998999999888755 579999999999999999999999994 555566665543 221
Q ss_pred cCCCCCCCccccccceeeeCCCCccCCCceeecCCCCCeEEeeeccCCccceEEeec-----------------------
Q 003633 320 KGKNVSHSQLDWKLQNITWPGGKTETPRGWVIADNARPLRIGVPRRASFVGFVTEEH----------------------- 376 (806)
Q Consensus 320 ~~~~~~~~~~~~~l~~i~Wpg~~~~~P~~~~~~~~g~~lrv~v~~~~~~~~f~~~~~----------------------- 376 (806)
..+...|+|||+-+.+|+|..+| ++|||.+...+| |+|..+
T Consensus 380 ----------~~nd~~IiWpGg~~~KP~gi~~p---thLrivTi~~~P---FVYv~p~~sd~~c~eef~~~~d~~~k~~c 443 (993)
T KOG4440|consen 380 ----------IPNDRKIIWPGGETEKPRGIQMP---THLRIVTIHQEP---FVYVKPTLSDGTCKEEFTVNGDPVKKVIC 443 (993)
T ss_pred ----------ccCCceeecCCCCcCCCcccccc---ceeEEEEeccCC---eEEEecCCCCcchhhhccccCCcccceee
Confidence 12346899999999999999998 679999987665 444320
Q ss_pred -C-------------CceeEeeeHHHHHHHHHhCCCCcceEEEEcCC-CC---------CCC-CHHHHHHHHHcCcccEE
Q 003633 377 -D-------------SHKVQGYCIDILLEALKLVPYDVPYKFELFGD-GL---------SNP-SYDGLVKMVANDVFDAA 431 (806)
Q Consensus 377 -~-------------~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~-~~---------~n~-s~~~l~~~l~~g~~D~~ 431 (806)
+ .-|+.||||||+-.+++.+||+++..+++.+. |. .|+ +|+|++++|.++.+||+
T Consensus 444 ~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMi 523 (993)
T KOG4440|consen 444 TGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMI 523 (993)
T ss_pred cCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhCCccceE
Confidence 0 11789999999999999999997666776442 11 122 79999999999999999
Q ss_pred EeeEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCC-CCCC-
Q 003633 432 VGDIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDD-FRGP- 509 (806)
Q Consensus 432 ~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~-~~~~- 509 (806)
+++++|+++|.++++||.||...|+.++.+++.+.+....||+||+..+|+++.++..+++++++++.|+++.+ |...
T Consensus 524 vaplTINpERa~yieFskPfkYqGitILeKk~~r~Stl~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPFgRFk~~d 603 (993)
T KOG4440|consen 524 VAPLTINPERAQYIEFSKPFKYQGITILEKKEIRRSTLDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPFGRFKVND 603 (993)
T ss_pred eeceeeChhhhhheeccCcccccceEEEeeCCCCCchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccceeecc
Confidence 99999999999999999999999999999999899999999999999999999999999999999999998743 3322
Q ss_pred ------CccchhhHHHHHHHhhhccCc--ccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhh
Q 003633 510 ------PRRQIATMFLFSFSTLFKTNQ--EATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLIT 581 (806)
Q Consensus 510 ------~~~~~~~~~~~~~~~l~~~~~--~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~ 581 (806)
..-.++..+||+|+.|+..+- ..|+|.+.|++-++|+-|++||.++|||||++||...+.+..++++.|-.-
T Consensus 604 s~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLdrPe~~ltGinDpRL 683 (993)
T KOG4440|consen 604 SEEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLDRPEERLTGINDPRL 683 (993)
T ss_pred CccchhhhcchhhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhhhhhheeecCccccccCCCCccc
Confidence 123589999999999998763 489999999999999999999999999999999999999999999999432
Q ss_pred CC----CceeEEeCchhHHHhhhhccccc----ccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEE
Q 003633 582 ND----WPIGYQVGSFAYSYLSDSLRIQK----SRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGI 653 (806)
Q Consensus 582 ~~----~~ig~~~gs~~~~~l~~~~~~~~----~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~ 653 (806)
.+ ...+.+.+|.+..|++++..... -.-..|.+.+|.++++.+ |..+|++-|...+++..+++|++..
T Consensus 684 RNps~nf~~aTVk~SsVd~YFrRqVELS~MyR~ME~hNy~~A~eAiq~v~~----gkL~AFIWDS~rLEfEAs~~CeLvT 759 (993)
T KOG4440|consen 684 RNPSDNFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRD----GKLHAFIWDSARLEFEASQKCELVT 759 (993)
T ss_pred cCcccceeEEEecCccHHHHHHHHhHHHHHHHhhhhcchhhHHHHHHHHHc----CceeEEEeecceeeehhhcccceEe
Confidence 22 35788899999999976532211 111236678899999999 9999999999999999999999999
Q ss_pred eCCccccCCceeeecCCCCchHHHHHHHHhhhccchhHHHHHhhcCC---CCCCCcCcCCCCccccccccchhHHHHHHH
Q 003633 654 IGQPFTRSGWGFAFQRDSPLAVGMSTAILKLSENGMLQKLHEKWFCK---EGCPEERRQHSEPHQLRLISFWGLYLLCGT 730 (806)
Q Consensus 654 ~~~~~~~~~~~~~~~k~spl~~~~n~~il~l~e~G~~~~i~~kw~~~---~~c~~~~~~~~~~~~L~l~~~~g~F~il~~ 730 (806)
.|+.|...+||+.++|+||+...+..+|+++.|+|+|+++.++|... ..|..... .+..|+++++.|+|++.+.
T Consensus 760 ~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEkLDk~Wi~~Ggpq~c~~~~k---~PatLgl~NMagvFiLV~~ 836 (993)
T KOG4440|consen 760 TGELFGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEKLDKTWIRYGGPQECDSRSK---APATLGLENMAGVFILVAG 836 (993)
T ss_pred ccccccccccccccccCCCCcchhhHHHHHhhhcchHHHHHHHHHhcCCcchhhhhcc---CcccccccccccEEEEEec
Confidence 99999999999999999999999999999999999999999999963 34443322 6789999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhcc
Q 003633 731 ITFTAFLVFLLRMVCQYVRYK 751 (806)
Q Consensus 731 g~~lal~vf~~E~~~~~~~~~ 751 (806)
|+++++...++|+.|++++..
T Consensus 837 Gia~GifLifiEv~Ykrh~~~ 857 (993)
T KOG4440|consen 837 GIAAGIFLIFIEVAYKRHKDA 857 (993)
T ss_pred chhheeeEEEEeehhhhhhhh
Confidence 999999888999999887654
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=2.7e-71 Score=594.04 Aligned_cols=670 Identities=20% Similarity=0.354 Sum_probs=523.0
Q ss_pred ccccCCCcEEeccc-CCCCcccCC-CCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh--
Q 003633 5 VANGLKVPLVSFAA-TDPTLSALQ-FPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK-- 80 (806)
Q Consensus 5 i~~~~~vP~Is~~a-t~p~Ls~~~-~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~-- 80 (806)
++...+||+|+..+ .++-++++. -..|+++.||-.+|+.++.++++.|+|..++++..--+.-+..+..++.....
T Consensus 122 iSs~t~iPIisi~gg~a~~~~~kd~gs~flQlg~Sieqqa~Vml~iL~~ydW~~Fs~vtt~~pg~~~f~~~ir~~~d~s~ 201 (1258)
T KOG1053|consen 122 ISSQTHIPIISIHGGAAMVLTPKDLGSTFLQLGPSIEQQAQVMLKILEEYDWYNFSLVTTQFPGNRTFVSLIRQTNDNSH 201 (1258)
T ss_pred HHHhcCCcEEEEecCccceecCCCCcceEEEeCCcHHHHHHHHHHHHHHcCcceeEEEEeecCchHHHHHHHHHhhhhcc
Confidence 45678999999855 455555533 35789999999999999999999999999999998777555566666665553
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|+++.......+..+ +.......++|.-++.||+++|+.+++..||..|.++||++.+|+||++...... +
T Consensus 202 vgwe~i~v~~l~~s~~-d~~a~~q~qLkki~a~VillyC~~eea~~IF~~A~q~Gl~g~~y~Wi~pqlv~g~-~------ 273 (1258)
T KOG1053|consen 202 VGWEMINVLTLDPSTD-DLLAKLQAQLKKIQAPVILLYCSREEAERIFEEAEQAGLTGPGYVWIVPQLVEGL-E------ 273 (1258)
T ss_pred ccceeeeeeecCCCCC-chHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHhcCCcCCceEEEeehhccCC-C------
Confidence 4555554444443322 2223333445555689999999999999999999999999999999996533321 1
Q ss_pred hhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccCCCCCC
Q 003633 161 QTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSASHELP 239 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~~~l~ 239 (806)
..-.+..-|.+.+.... |+. ....+.-|+|-++|.|...++... .++ +++..
T Consensus 274 ~~pa~~P~GLisv~~~~------------w~~------------~l~~rVrdgvaiva~aa~s~~~~~~~lp---~~~~~ 326 (1258)
T KOG1053|consen 274 PRPAEFPLGLISVSYDT------------WRY------------SLEARVRDGVAIVARAASSMLRIHGFLP---EPKMD 326 (1258)
T ss_pred CCCccCccceeeeeccc------------hhh------------hHHHHHhhhHHHHHHHHHHHHhhcccCC---Ccccc
Confidence 11123445666654321 221 134567799999999999988765 221 11111
Q ss_pred CCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee-cCceEEEEEeeCCCCccccCccc
Q 003633 240 DSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID-KMEIHRVGYWFDGSGFSVLPPET 318 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~-~~~~~~VG~w~~~~gl~~~~~~~ 318 (806)
+..- .. .....++.|...|.|+.|+| ++++|+++|-..++...|+... +..|..||.|.+..
T Consensus 327 C~~~-----~~-~~~~~~~~l~r~l~NvT~~g--~~lsf~~~g~~v~p~lvvI~l~~~r~We~VG~We~~~--------- 389 (1258)
T KOG1053|consen 327 CREQ-----EE-TRLTSGETLHRFLANVTWDG--RDLSFNEDGYLVHPNLVVIDLNRDRTWERVGSWENGT--------- 389 (1258)
T ss_pred cccc-----cC-ccccchhhhhhhhheeeecc--cceeecCCceeeccceEEEecCCCcchheeceecCCe---------
Confidence 1111 11 12234889999999999999 7899999998888887777664 56799999998865
Q ss_pred ccCCCCCCCccccccceeeeCCCCccCCCceeecCCCCCeEEeeeccCCccceEEeec----------------------
Q 003633 319 LKGKNVSHSQLDWKLQNITWPGGKTETPRGWVIADNARPLRIGVPRRASFVGFVTEEH---------------------- 376 (806)
Q Consensus 319 ~~~~~~~~~~~~~~l~~i~Wpg~~~~~P~~~~~~~~g~~lrv~v~~~~~~~~f~~~~~---------------------- 376 (806)
..+...+||-.... ..+.| ...+|+|.+..++||......|.
T Consensus 390 ------------L~M~y~vWPr~~~~---~q~~~-d~~HL~VvTLeE~PFVive~vDP~t~~C~~ntvpc~s~~~~t~ss 453 (1258)
T KOG1053|consen 390 ------------LVMKYPVWPRYHKF---LQPVP-DKLHLTVVTLEERPFVIVEDVDPLTQTCVRNTVPCRSQLNSTFSS 453 (1258)
T ss_pred ------------EEEeccccccccCc---cCCCC-CcceeEEEEeccCCeEEEecCCCCcCcCCCCCCcchhhhhhccCC
Confidence 23556789833221 11111 23578888887766543322221
Q ss_pred ---C----CceeEeeeHHHHHHHHHhCCCCcceEEEEcC-CC-CCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEe
Q 003633 377 ---D----SHKVQGYCIDILLEALKLVPYDVPYKFELFG-DG-LSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDF 447 (806)
Q Consensus 377 ---~----~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~-~~-~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdf 447 (806)
. ..|++||||||++.|++.+||++...++..| .| +.|+.|+||+++|..+++||++++++|+++|.+.+||
T Consensus 454 ~~~~~~tvKkCCkGfCIDiLkKlA~~v~FtYDLYlVtnGKhGkk~ng~WnGmIGev~~~rA~MAVgSltINeeRSevVDF 533 (1258)
T KOG1053|consen 454 GDEANRTVKKCCKGFCIDILKKLARDVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEERSEVVDF 533 (1258)
T ss_pred CccCCchHHhhhhhhhHHHHHHHHhhcCcceEEEEecCCcccceecCcchhhHHHHHhhhhheeeeeeEechhhhccccc
Confidence 0 1289999999999999999999444444433 22 2689999999999999999999999999999999999
Q ss_pred cccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHH-HhhhhccccCCCCC---------CCCccchhhH
Q 003633 448 SQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAV-VIWILEHRVNDDFR---------GPPRRQIATM 517 (806)
Q Consensus 448 t~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~-v~~~~~~~~~~~~~---------~~~~~~~~~~ 517 (806)
|.||.++|+.+||.......+..+||.||++.+|+.+++++++++. .++++|+.++-.+- +.+...++.+
T Consensus 534 SvPFveTgIsVmV~rsngtvspsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp~Ftigka 613 (1258)
T KOG1053|consen 534 SVPFVETGISVMVARSNGTVSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGPSFTIGKA 613 (1258)
T ss_pred cccccccceEEEEEecCCccCchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcCcccccccccCCCCCCCcceehhhH
Confidence 9999999999999999988899999999999999999999998765 56688998754321 2335679999
Q ss_pred HHHHHHhhhccCc--ccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhC-------CCceeE
Q 003633 518 FLFSFSTLFKTNQ--EATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITN-------DWPIGY 588 (806)
Q Consensus 518 ~~~~~~~l~~~~~--~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~-------~~~ig~ 588 (806)
+|..|+.+|.... ++|+...+|+++.+|.||++|+.++|||||++||..+.+..++.++.|=.-+ ..+.|.
T Consensus 614 iwllwaLvFnnsVpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~vSGlsD~KfqrP~dq~PpFRFGT 693 (1258)
T KOG1053|consen 614 IWLLWALVFNNSVPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDTVSGLSDPKFQRPHDQYPPFRFGT 693 (1258)
T ss_pred HHHHHHHHhCCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccccCccccCCCccccc
Confidence 9999999887764 4899999999999999999999999999999999999999999999885422 346888
Q ss_pred EeCchhHHHhhhhcccccccceeC--CCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhC--CCCeEEeC--CccccCC
Q 003633 589 QVGSFAYSYLSDSLRIQKSRLISL--GSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSN--QTDFGIIG--QPFTRSG 662 (806)
Q Consensus 589 ~~gs~~~~~l~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~--~~~l~~~~--~~~~~~~ 662 (806)
+.++..++++++++......++.| ...++.++.|++ |+.||+|.|...++|...+ .|+|..+| ..|...+
T Consensus 694 VpngSTE~niR~Nyp~MHeYM~kyNq~~v~dal~sLK~----gKLDAFIyDaAVLnY~agkDegCKLvTIGsgKvFAttG 769 (1258)
T KOG1053|consen 694 VPNGSTERNIRSNYPEMHEYMVKYNQPGVEDALESLKN----GKLDAFIYDAAVLNYMAGKDEGCKLVTIGSGKVFATTG 769 (1258)
T ss_pred CCCCchhhhHHhccHHHHHHHHHhccCchHHHHHHHhc----ccchhHHHHHHHHHHhhccCCCceEEEecCCceeeecc
Confidence 888888888877654444555555 367899999999 9999999999999999887 59999998 8999999
Q ss_pred ceeeecCCCCchHHHHHHHHhhhccchhHHHHHhhcCCCCCCCcCcCCCCccccccccchhHHHHHHHHHHHHHHHHHHH
Q 003633 663 WGFAFQRDSPLAVGMSTAILKLSENGMLQKLHEKWFCKEGCPEERRQHSEPHQLRLISFWGLYLLCGTITFTAFLVFLLR 742 (806)
Q Consensus 663 ~~~~~~k~spl~~~~n~~il~l~e~G~~~~i~~kw~~~~~c~~~~~~~~~~~~L~l~~~~g~F~il~~g~~lal~vf~~E 742 (806)
||+++|||||++..++.+|++....|+++++++.|+. +.|.++..+. .+.+|++++|.|+||+|++|++|++++|++|
T Consensus 770 YGIal~k~Spwkr~IdlallQy~gdGeme~Le~~Wlt-gic~n~k~ev-mSsqLdIdnmaGvFymL~~amgLSllvfi~E 847 (1258)
T KOG1053|consen 770 YGIALPKNSPWKRQIDLALLQYLGDGEMEMLETLWLT-GICHNSKNEV-MSSQLDIDNMAGVFYMLAVAMGLSLLVFIWE 847 (1258)
T ss_pred eeeecCCCCcchhhHHHHHHHHhccchHHHHHHHHhh-cccccchhhh-hhcccChhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999996 6777777766 8899999999999999999999999999999
Q ss_pred HHHHHh
Q 003633 743 MVCQYV 748 (806)
Q Consensus 743 ~~~~~~ 748 (806)
.+++.+
T Consensus 848 HlvYw~ 853 (1258)
T KOG1053|consen 848 HLVYWK 853 (1258)
T ss_pred HHHHHH
Confidence 766543
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=5e-70 Score=638.37 Aligned_cols=600 Identities=34% Similarity=0.628 Sum_probs=511.6
Q ss_pred HHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCChhhhhhccceEEEEEeCCCCh
Q 003633 102 VLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQTSLRILQGVVGLRQHTPDSI 181 (806)
Q Consensus 102 ~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~ 181 (806)
.++.+++....+++++++.+..+..++.+|.++||+..+|+|+.++......+.... ....+.++|+++.+.+.|.+.
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 456677778999999999999999999999999999999999999988877766521 345577889999999999999
Q ss_pred hhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHH
Q 003633 182 PKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLL 261 (806)
Q Consensus 182 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~ 261 (806)
..++|..+|+.. ...++.+++++||+++++|.|++........++ .|.+.+.+.++..+.
T Consensus 82 ~~~~~~~~~~~~------~~~~~~~~~~~~D~~~~~a~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~ 141 (656)
T KOG1052|consen 82 LLQNFVTRWQTS------NVELLVYALWAYDAIQALARAVESLLNIGNLSL--------------SCGRNNSWLDALGVF 141 (656)
T ss_pred HHHHHHHHHhhc------cccccchhhHHHHHHHHHHHHHHHhhcCCCCce--------------ecCCCCcccchhHHH
Confidence 999999999875 125778899999999999999999764222222 222223445577777
Q ss_pred HHHHccccC---CceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCccccCcccccCCCCCCCccccccceeee
Q 003633 262 RKLLQTNFT---GLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGFSVLPPETLKGKNVSHSQLDWKLQNITW 338 (806)
Q Consensus 262 ~~l~~~~f~---G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl~~~~~~~~~~~~~~~~~~~~~l~~i~W 338 (806)
+.+...... |.+|.++++.++.+....|+|+|+.+.+.+.||+|++..| .+|.|
T Consensus 142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~n~~~~~~~~ig~W~~~~~-----------------------~~i~~ 198 (656)
T KOG1052|consen 142 NFGKKLLVVNLSGVTGQFQFFRGGLLEYFKYEILNLNGSGERRIGYWYPRGG-----------------------ENISW 198 (656)
T ss_pred HHHHhhhhhccccceeEEEecCCCccccceEEEEEecCcCceeEEEecCCCC-----------------------ceeec
Confidence 777765533 5678888888888999999999999999999999999774 35899
Q ss_pred CCCCccCCCceeecCCCCCeEEeeeccCCccceEEee---cCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCC--CC
Q 003633 339 PGGKTETPRGWVIADNARPLRIGVPRRASFVGFVTEE---HDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGL--SN 413 (806)
Q Consensus 339 pg~~~~~P~~~~~~~~g~~lrv~v~~~~~~~~f~~~~---~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~--~n 413 (806)
||.....|++|.+|.+|++|||+++..+||..+.... .++.++.|||+||++++++.+||+++++.++.+.|. ++
T Consensus 199 ~~~~~~~~~~~~~~~~~~~l~v~~~~~~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~~ 278 (656)
T KOG1052|consen 199 PGKDYFVPKGWFFPTNGKPLRVGVVTEPPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPN 278 (656)
T ss_pred cCCcccCcCCccccCCCceEEEEEeccCCceeeeecccccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCCCCCCCC
Confidence 9999999999999999999999999988877666642 245699999999999999999999888888876654 44
Q ss_pred CCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHH
Q 003633 414 PSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAV 493 (806)
Q Consensus 414 ~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~ 493 (806)
|+|+|++++|.+|++|++ ++++++++|.+++|||.||++.++++++++++.....|.|++||++++|++++++++++++
T Consensus 279 g~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~~~~fl~Pf~~~vW~~i~~~~l~~~~ 357 (656)
T KOG1052|consen 279 GNWDGLVGQLVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSKLWNFLAPFSPEVWLLILASLLLVGL 357 (656)
T ss_pred CChhHHHHHHhcCccccc-cceEEeecccccEEeccceEeccEEEEEEecCCcccceEEecCCcHHHHHHHHHHHHHHHH
Confidence 699999999999999999 9999999999999999999999999999999955449999999999999999999999999
Q ss_pred HhhhhccccCCCCCCCCc------cchhhHHHHHHHhhhccCc-ccccccchhhhHHHHHhhhhhhhccccceeeeeeee
Q 003633 494 VIWILEHRVNDDFRGPPR------RQIATMFLFSFSTLFKTNQ-EATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTV 566 (806)
Q Consensus 494 v~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~l~~~~~-~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~ 566 (806)
++|+++|+.|.++ ++. ..+.+++|+++++++.++. +.|++.++|+++++||++++|++++|||+|+|+||+
T Consensus 358 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~ 435 (656)
T KOG1052|consen 358 LLWILERLSPYEL--PPRQIVTSLFSLLNCLWLTVGSLLQQGSDEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTV 435 (656)
T ss_pred HHHHHhccccccC--CccccceeEeecccchhhhhHHHhccCCCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999988 222 1245678999998888865 589999999999999999999999999999999999
Q ss_pred ccccCCCCChhHhhh-CCCceeEEeCchhHHHhhhh---cccccc-cceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhH
Q 003633 567 QQLSTSVKGIESLIT-NDWPIGYQVGSFAYSYLSDS---LRIQKS-RLISLGSPEDYERALRQGPRNGGVAAIVDELPYV 641 (806)
Q Consensus 567 ~~~~~~i~s~~dL~~-~~~~ig~~~gs~~~~~l~~~---~~~~~~-~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~ 641 (806)
+++.++|++++||++ ++.++|+..+++...++.+. .....+ +.+.+.+.+++.+++.+|.. |+++++.++.++.
T Consensus 436 ~~~~~~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~-~~~~~~~~~~~~~ 514 (656)
T KOG1052|consen 436 PRLRSPIDSLDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLASPEEGVERVRKGPS-GGYAFASDELYLA 514 (656)
T ss_pred cccCCcccCHHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCCCccCCCHHHHHHHHHcCCC-CceEEEeccHHHH
Confidence 999999999999995 78889999999999999766 444445 77889999999999999654 4566666666666
Q ss_pred HHHhhCC-CCeEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccchhHHHHHhhcCCCCCCCcCcCCCCcccccccc
Q 003633 642 QLFLSNQ-TDFGIIGQPFTRSGWGFAFQRDSPLAVGMSTAILKLSENGMLQKLHEKWFCKEGCPEERRQHSEPHQLRLIS 720 (806)
Q Consensus 642 ~~~~~~~-~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~il~l~e~G~~~~i~~kw~~~~~c~~~~~~~~~~~~L~l~~ 720 (806)
+++.+++ |+++++++.+...+++ ++||||||++.++++|+++.|.|.++++++||+....|............|++++
T Consensus 515 ~~~~~~~~c~~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g~l~~~~~kw~~~~~~~~~~~~~~~~~~l~~~~ 593 (656)
T KOG1052|consen 515 YLFLRDEICDLTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQETGILQKLKRKWFSKKPCLPKCSQTEKTKALDLES 593 (656)
T ss_pred HHHhhcCCCceEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhccccHHHHHHHHhccCCCCCCCCCCcccccccchhh
Confidence 6666643 9999999999999999 9999999999999999999999999999999998544322222210367899999
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 003633 721 FWGLYLLCGTITFTAFLVFLLRMVCQYVRYK 751 (806)
Q Consensus 721 ~~g~F~il~~g~~lal~vf~~E~~~~~~~~~ 751 (806)
++|+|+++++|+++|+++|++|++|++++..
T Consensus 594 ~~g~F~i~~~g~~lal~vfi~E~~~~~~~~~ 624 (656)
T KOG1052|consen 594 FWGLFLILLVGYLLALLVFILELLYSRRRTL 624 (656)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999999999999998886
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=2.1e-41 Score=365.36 Aligned_cols=286 Identities=16% Similarity=0.261 Sum_probs=241.3
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
|+++|+.++||+|++++ |..+.. +|++++.|+ +++|++++|++|||++|++||+ ++||...++.|.+++++.
T Consensus 72 v~sic~~~~vP~i~~~~--~~~~~~--~~~i~~~P~---~~~Ai~diI~~~~W~~v~iIYd-~d~g~~~lq~l~~~~~~~ 143 (364)
T cd06390 72 LTSFCGALHVCFITPSF--PVDTSN--QFVLQLRPE---LQDALISVIEHYKWQKFVYIYD-ADRGLSVLQKVLDTAAEK 143 (364)
T ss_pred HHHhhcCCCCCceecCC--CCCCCC--ceEEEeChh---HHHHHHHHHHHcCCcEEEEEEe-CCccHHHHHHHHHhhhcc
Confidence 78899999999999855 444333 468999997 8999999999999999999995 559999999999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
|+||.+...++ .+.++++.+|++++.+++|+||++|+++.+..++.+|.+.+|+..+|+||+|+......+. .
T Consensus 144 ~~~I~~~~~~~--~~~~d~~~~L~~ik~~~~rvIVl~~~~~~~~~~L~~a~~~~~~~~gy~wI~t~l~~~~~~~-----~ 216 (364)
T cd06390 144 NWQVTAVNILT--TTEEGYRKLFQDLDKKKERLIVVDCESERLNAILNQIIKLEKNGIGYHYILANLGFMDIDL-----T 216 (364)
T ss_pred CceeeEEEeec--CChHHHHHHHHhccccCCeEEEEECCHHHHHHHHHHHHHhhccCCceEEEecCCCcccccH-----H
Confidence 99999887766 3466999999999999999999999999999999999999999999999999933222222 3
Q ss_pred hhhhhccceEEEEEeCCCChhhHHHHHHHhhhccC---CCCCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccCCCC
Q 003633 162 TSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQK---GLVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSASHE 237 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~---~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~~~ 237 (806)
...+.++|++|++++.|+++.+++|.++|++.... ..+...++.+++++|||||++|+|++++...+ ..++..
T Consensus 217 ~~~~~~~nitg~r~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~l~yDaV~~~A~A~~~l~~~~~~~~~~~--- 293 (364)
T cd06390 217 KFRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRVDWKRPKYTSALTYDGVRVMAEAFQNLRKQRIDISRRG--- 293 (364)
T ss_pred HHhcCCcCceEEEEecCCCHHHHHHHHHHHhhccccCCCCCcCCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccCC---
Confidence 45668899999999999999999999999876542 22233578899999999999999999986654 332211
Q ss_pred CCCCccccccccc--ccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCc
Q 003633 238 LPDSKATRVQLEQ--LKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGF 311 (806)
Q Consensus 238 l~~~~~~~~~~~~--~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl 311 (806)
+...|.. ..+|+.|..|+++|++++|+|+||+|+||++|+|.+..|+|+|+++.|+++||+|++.+||
T Consensus 294 ------~~~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~i~F~~~G~r~~~~~~I~~~~~~g~~~vG~W~~~~g~ 363 (364)
T cd06390 294 ------NAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDEKL 363 (364)
T ss_pred ------CCCCCCCCCCCCCccHHHHHHHHHhhcccccccceeeCCCCCcccceEEEEEecCCcceEEEEECCCCCc
Confidence 1112322 3468899999999999999999999999999999999999999999999999999999887
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=4.2e-41 Score=362.70 Aligned_cols=288 Identities=17% Similarity=0.303 Sum_probs=231.9
Q ss_pred CHhcccccCCCcEEeccc-----------CCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccc
Q 003633 1 MISEVANGLKVPLVSFAA-----------TDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRN 69 (806)
Q Consensus 1 ~v~~i~~~~~vP~Is~~a-----------t~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~ 69 (806)
.|+++|+.++||+|++++ ++|.++..+||+++|+. ..+.+|++++|++|+|++|++|| |+|||..
T Consensus 77 ~v~sic~~l~VP~is~~~~~~~~~~~~~~~~p~~~~~~~~~~lrp~---~~~~~Ai~dlV~~~~W~~v~~iY-D~d~gl~ 152 (400)
T cd06392 77 ALQSLTDAMHIPHLFVQRNSGGSPRTACHLNPSPEGEEYTLAARPP---VRLNDVMLKLVTELRWQKFIVFY-DSEYDIR 152 (400)
T ss_pred HHHHHhccCcCCcEeecccccccccccccCCCCcCcCceeEEecCc---hHHHHHHHHHHHhCCCcEEEEEE-ECcccHH
Confidence 378999999999999966 56777777888888774 46678999999999999999999 8999999
Q ss_pred hHHHHHHHHHhCCcEEEEEec-------cCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcE
Q 003633 70 GISALSNMLEKNMAKVSYKLP-------LPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYV 142 (806)
Q Consensus 70 ~~~~l~~~l~~~g~~i~~~~~-------~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~ 142 (806)
.++.|.+++.+.+.+|.++.. +++.. .+..+..|.+++.+. |+|||+|+++.+..||++|.++||+..+|+
T Consensus 153 ~lq~L~~~~~~~~~~I~~~~v~~~~~~~~~~~l-~~~~~~~L~~~~~~~-r~iVv~~s~~~~~~il~qA~~lgM~~~~y~ 230 (400)
T cd06392 153 GLQSFLDQASRLGLDVSLQKVDRNISRVFTNLF-TTMKTEELNRYRDTL-RRAILLLSPRGAQTFINEAVETNLASKDSH 230 (400)
T ss_pred HHHHHHHHHhhcCceEEEEEcccCcchhhhhHH-HHHHHhhhhhccccc-eEEEEEcCcHHHHHHHHHHHHhCcccCCeE
Confidence 999999999999999998762 22221 233456677777667 999999999999999999999999999999
Q ss_pred EEEcCcccccccccccCChhhhhhccceE----EEEEeCCCChhhHHHH----HHHhhhccCCCCCC--CCccchhhhhh
Q 003633 143 WLATDWLSATLESFSKMNQTSLRILQGVV----GLRQHTPDSIPKKAFL----SRWSGMQQKGLVSA--GLNTYGLYAYD 212 (806)
Q Consensus 143 wi~t~~~~~~~~~~~~~~~~~~~~~~gv~----~~~~~~~~~~~~~~f~----~~~~~~~~~~~~~~--~~~~~~~~aYD 212 (806)
||+|++.....+. .+.++|.+ +++.+.|.++...+|. .+|++......+.. .++.+++++||
T Consensus 231 wI~t~~~~~~~dl--------~~~~~g~~~niT~~r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~l~~~aalayD 302 (400)
T cd06392 231 WVFVNEEISDTEI--------LELVHSALGRMTVIRQIFPLSKDNNQRCIRNNHRISSLLCDPQEGYLQMLQVSNLYLYD 302 (400)
T ss_pred EEEecCCcccccH--------HHHhcccccceeeEEEecCCcHHHHHHHHHHHHHHHhhhcccccccccccchhHHHHHH
Confidence 9999987765443 34455555 4999988887666554 67765443211111 47889999999
Q ss_pred HHHHHHHHHHHHHhhcCccccCCCCCCCCccccccc--ccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEE
Q 003633 213 TVWAVARSIDKFINEHNITFSASHELPDSKATRVQL--EQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYD 290 (806)
Q Consensus 213 Av~~lA~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~ 290 (806)
|||++|+|++.+++.. +..+. ..++| +...+|+.|..|+++|++++|+|+||+|+||++|+|.++.|+
T Consensus 303 aV~~~A~Al~~ll~~~--------~~~~~--~~l~C~~~~~~~w~~G~~ll~~ik~v~f~GLTG~I~F~~~G~r~~~~ld 372 (400)
T cd06392 303 SVLMLANAFHRKLEDR--------KWHSM--ASLNCIRKSTKPWNGGRSMLETIKKGHITGLTGVMEFKEDGANPHVQFE 372 (400)
T ss_pred HHHHHHHHHHHHhhcc--------ccCCC--CCCccCCCCCCCCCChHHHHHHHHhCCCccCccceeECCCCCCcCCceE
Confidence 9999999999876432 11111 12355 557899999999999999999999999999999999999999
Q ss_pred EEEe-----ecCceEEEEEeeCCCCcc
Q 003633 291 VINI-----DKMEIHRVGYWFDGSGFS 312 (806)
Q Consensus 291 I~~~-----~~~~~~~VG~w~~~~gl~ 312 (806)
|+|+ .+.|+++||+|++.+||.
T Consensus 373 Ii~l~~~~~~g~g~~~iG~W~~~~gl~ 399 (400)
T cd06392 373 ILGTSYSETFGKDVRRLATWDSEKGLN 399 (400)
T ss_pred EEeccccccCCCCceEeEEecCCCCCC
Confidence 9994 477799999999999975
No 7
>cd06387 PBP1_iGluR_AMPA_GluR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=8.3e-39 Score=344.05 Aligned_cols=287 Identities=13% Similarity=0.258 Sum_probs=237.1
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
|..+|+..+||.|.+.-. .+...+|.+++.|+ +.+|++++|++||||+|++|| |+++|...++.|.+.++..
T Consensus 79 v~s~c~~~~iP~i~~~~~----~~~~~~~~l~l~P~---l~~Ai~diI~~~~Wr~~~~iY-d~d~gl~~Lq~L~~~~~~~ 150 (372)
T cd06387 79 LTSFCGALHTSFITPSFP----TDADVQFVIQMRPA---LKGAILSLLAHYKWEKFVYLY-DTERGFSILQAIMEAAVQN 150 (372)
T ss_pred HHHhhccccCCeeeeCCC----CCCCCceEEEEChh---HHHHHHHHHHhcCCCEEEEEe-cCchhHHHHHHHHHhhccC
Confidence 678999999999987332 12334778899998 689999999999999999999 8899999999999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
+..|.++...+.. +.++++.+|++|+.++.|+|||+|+++.+..|+++|.++||+..+|+||+|+......+. .
T Consensus 151 ~~~V~~~~v~~~~-~~~~~~~~l~el~~~~~r~iIld~s~~~~~~il~~a~e~gM~~~~y~~ilt~ld~~~~dl-----~ 224 (372)
T cd06387 151 NWQVTARSVGNIK-DVQEFRRIIEEMDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYHYMLANLGFTDISL-----E 224 (372)
T ss_pred CceEEEEEeccCC-chHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHcCccccceEEEEecCCcccccH-----H
Confidence 9999888655533 456899999999999999999999999999999999999999999999999844433333 2
Q ss_pred hhhhhccceEEEEEeCCCChhhHHHHHHHhhhccC---CCCCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccCCCC
Q 003633 162 TSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQK---GLVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSASHE 237 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~---~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~~~ 237 (806)
+......+++|++++.|+++..++|.++|++.... +.....++.+++++|||||++|+|++++...+ ..+..
T Consensus 225 ~~~~g~~NItg~rl~~~~~~~~~~f~~~w~~~~~~~~~~~~~~~l~~~~al~yDaV~~~A~A~~~l~~~~~~~~~~---- 300 (372)
T cd06387 225 RVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEAKNSPLKYTSALTHDAILVIAEAFRYLRRQRVDVSRR---- 300 (372)
T ss_pred HhccCCcceeEEEEecCCCchHHHHHHHHHhCCcccCCCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCcccC----
Confidence 22233334999999999999999999999876542 22223567899999999999999999986544 22111
Q ss_pred CCCCcccccccc--cccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCc
Q 003633 238 LPDSKATRVQLE--QLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGF 311 (806)
Q Consensus 238 l~~~~~~~~~~~--~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl 311 (806)
+....|. ...+|..|..|+++|++++|+|+||+|+||++|+|.+..|+|+|+.+.|+++||+|++.+||
T Consensus 301 -----~~~~~C~~~~~~~W~~G~~l~~~ik~v~~~GLTG~i~F~~~G~R~~~~ldIinl~~~g~~kIG~W~~~~g~ 371 (372)
T cd06387 301 -----GSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDVYEMKPSGSRKAGYWNEYERF 371 (372)
T ss_pred -----CCCCCcCCCCCCCccchHHHHHHHHhcccCCCccceeeCCCCCcccceEEEEEecCCCceeEEEECCCCCc
Confidence 1112332 24578899999999999999999999999999999999999999999999999999999987
No 8
>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=3.3e-38 Score=344.18 Aligned_cols=291 Identities=16% Similarity=0.275 Sum_probs=232.4
Q ss_pred HhcccccCCCcEEec----ccCC-----CCccc--CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccch
Q 003633 2 ISEVANGLKVPLVSF----AATD-----PTLSA--LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNG 70 (806)
Q Consensus 2 v~~i~~~~~vP~Is~----~at~-----p~Ls~--~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~ 70 (806)
|+++|+.++||+|++ ++|+ |.+++ .+||+++| |+ ..+++|+++++++|+|++|+++| |++||...
T Consensus 78 v~~~~~~~~vP~i~~~~~~~~t~~~~~~~~~~~~~~~y~~~~r--p~-~~~~~ai~~li~~f~W~~v~i~~-d~~~~~~~ 153 (400)
T cd06391 78 LQSLADAMHIPHLFIQRSTAGTPRSSCGLTRSNRNDDYTLSVR--PP-VYLNDVILRVVTEYAWQKFIIFY-DTDYDIRG 153 (400)
T ss_pred HHHHhccCcCCeEEeecccccCccccCCCCCCCCcccceEEec--Ch-HHHHHHHHHHHHHcCCcEEEEEE-eCCccHHH
Confidence 678999999999985 5554 55663 46888888 43 68899999999999999999765 78899999
Q ss_pred HHHHHHHHHhCCcEEEEEeccCCCCCh---hHHHH-HHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEE
Q 003633 71 ISALSNMLEKNMAKVSYKLPLPVQFNQ---HDITV-LLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWL 144 (806)
Q Consensus 71 ~~~l~~~l~~~g~~i~~~~~~~~~~~~---~~~~~-~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi 144 (806)
++.|.+.+++.|+||.+... ....++ ..++. .+.+|+. .+.|+||++|+++.+..+|++|+++||++.+|+||
T Consensus 154 l~~l~~~~~~~~i~I~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~rviVl~~~~~~~~~ll~~a~~~gm~~~~y~wi 232 (400)
T cd06391 154 IQEFLDKVSQQGMDVALQKV-ENNINKMITGLFRTMRIEELNRYRDTLRRAILVMNPATAKSFITEVVETNLVAFDCHWI 232 (400)
T ss_pred HHHHHHHHHHcCCeEEEEec-CcchhhhhHHHHHHHHHHHHHhhcccccEEEEECCcHHHHHHHHHHHHcCCCCCCeEEE
Confidence 99999999999999997542 211110 12332 3445554 56799999999999999999999999999999999
Q ss_pred EcCcccccccccccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCC-----CC-CCCCccchhhhhhHHHHHH
Q 003633 145 ATDWLSATLESFSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKG-----LV-SAGLNTYGLYAYDTVWAVA 218 (806)
Q Consensus 145 ~t~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~-----~~-~~~~~~~~~~aYDAv~~lA 218 (806)
+|++....++.. ....+.+.|+.+++++.|.++...+|..+|..++... .. ...++.+++++|||||++|
T Consensus 233 ~t~~~~~~~dl~----~~~~~~~~~v~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~alayDaV~~~A 308 (400)
T cd06391 233 IINEEISDMDVQ----ELVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSLCDPKDPFAQMMEISNLYIYDTVLLLA 308 (400)
T ss_pred EeCccccccccc----hHHhcccceEEEeccCCchHHHHHHHHHHHhhhccccccCccccccccccchhhHHHHHHHHHH
Confidence 999998888763 3334567788899999998888999999998776310 11 1136789999999999999
Q ss_pred HHHHHHHhhc-CccccCCCCCCCCcccccccc--cccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee
Q 003633 219 RSIDKFINEH-NITFSASHELPDSKATRVQLE--QLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID 295 (806)
Q Consensus 219 ~Al~~~~~~~-~~~~~~~~~l~~~~~~~~~~~--~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~ 295 (806)
+|++++.+.+ ... ....+|. ...+|..|..|+++|++++|+|+||+|+|+++|+|.++.|+|+|+.
T Consensus 309 ~A~~~l~~~~~~~~-----------~~~~~c~~~~~~~w~~G~~ll~~i~~~~f~GlTG~i~f~~~g~r~~~~~dIin~~ 377 (400)
T cd06391 309 NAFHKKLEDRKWHS-----------MASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFNENGGNPNVHFEILGTN 377 (400)
T ss_pred HHHHHHHhhccccC-----------CCCcccccCCCCCCCChHHHHHHHHhcCcccceeceEECCCCCccCCceEEEEee
Confidence 9999976433 111 1111332 3568999999999999999999999999999999999999999996
Q ss_pred -----cCceEEEEEeeCCCCcc
Q 003633 296 -----KMEIHRVGYWFDGSGFS 312 (806)
Q Consensus 296 -----~~~~~~VG~w~~~~gl~ 312 (806)
+.|+++||+|++..||.
T Consensus 378 ~~~~~~~g~rkiG~Ws~~~gl~ 399 (400)
T cd06391 378 YGEDLGRGVRKLGCWNPITGLN 399 (400)
T ss_pred ccccCCCcceEEEEEcCCcCCC
Confidence 88999999999999874
No 9
>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=3e-38 Score=346.79 Aligned_cols=258 Identities=25% Similarity=0.423 Sum_probs=222.3
Q ss_pred HhcccccCCCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++.+++.++||+|++++++|.+++. +||||||+.|+|..|+.++++++++|+|++|++||++++||++.++.+++.+++
T Consensus 101 v~~~~~~~~iP~Is~~a~~~~ls~~~~~~~~~R~~psd~~~~~a~~~~l~~~~w~~vaii~~~~~~g~~~~~~~~~~~~~ 180 (377)
T cd06379 101 VSYTAGFYRIPVVGISTRDSIFSDKNIHLSFLRTVPPYSHQADVWLEMLRSFKWNKVILLVSDDHEGRAAQKRFETLLEE 180 (377)
T ss_pred HHHHhhCCCCcEEecccCCccccCccccccEEEecCCHHHHHHHHHHHHHHcCCeEEEEEEEcCcchhHHHHHHHHHHHh
Confidence 4668889999999999999999875 599999999999999999999999999999999999999999999999999999
Q ss_pred CCc----EEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccc
Q 003633 81 NMA----KVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESF 156 (806)
Q Consensus 81 ~g~----~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~ 156 (806)
.|+ ||+..+.+++ +..|++.+|++||+.++|+||++++.+++..++++|+++||++.+|+||+++.+...
T Consensus 181 ~g~~~~~~v~~~~~~~~--~~~d~~~~l~~ik~~~~~vIvl~~~~~~~~~l~~qa~~~g~~~~~~~wi~t~~~~~~---- 254 (377)
T cd06379 181 REIEFKIKVEKVVEFEP--GEKNVTSLLQEAKELTSRVILLSASEDDAAVIYRNAGMLNMTGEGYVWIVSEQAGAA---- 254 (377)
T ss_pred cCCccceeeeEEEecCC--chhhHHHHHHHHhhcCCeEEEEEcCHHHHHHHHHHHHHcCCCCCCEEEEEecccccc----
Confidence 999 8888777764 357899999999999999999999999999999999999999989999999976321
Q ss_pred ccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCC
Q 003633 157 SKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASH 236 (806)
Q Consensus 157 ~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~ 236 (806)
.+..+|++|+++..+. .+++++|||||++|+|++++++....+
T Consensus 255 -------~~~~~g~~g~~~~~~~-------------------------~~~~~~yDAV~~~A~Al~~~~~~~~~~----- 297 (377)
T cd06379 255 -------RNAPDGVLGLQLINGK-------------------------NESSHIRDAVAVLASAIQELFEKENIT----- 297 (377)
T ss_pred -------ccCCCceEEEEECCCC-------------------------CHHHHHHHHHHHHHHHHHHHHcCCCCC-----
Confidence 1345799999875421 246789999999999999986532111
Q ss_pred CCCCCcccccccccc-cccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCC
Q 003633 237 ELPDSKATRVQLEQL-KVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDG 308 (806)
Q Consensus 237 ~l~~~~~~~~~~~~~-~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~ 308 (806)
.....|.+. .+|..|..|+++|++++|+|+||+|+||++|++..+.|+|+|+++.++++||+|++.
T Consensus 298 ------~~~~~c~~~~~~~~~g~~l~~~l~~v~f~G~tg~i~Fd~~Gd~~~~~~~I~~~~~~~~~~VG~w~~~ 364 (377)
T cd06379 298 ------EPPRECVGNTVIWETGPLFKRALMSSKYPGETGRVEFNDDGDRKFANYDIMNIQNRKLVQVGLYNGD 364 (377)
T ss_pred ------CCCccccCCCCCCcchHHHHHHHHhCCcCCccCceEECCCCCccCccEEEEEecCCCceEeeEEcCc
Confidence 011133322 247779999999999999999999999999998888999999999999999999873
No 10
>cd06365 PBP1_Pheromone_receptor Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptor, the GABAb receptor, the calcium-sensing receptor (CaSR), the T1R taste receptor, and a small group of uncharacterized orphan receptors.
Probab=100.00 E-value=4.9e-38 Score=352.52 Aligned_cols=285 Identities=21% Similarity=0.300 Sum_probs=230.3
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+|||++++|.|++ .+|||||||.|+|..|+.|+++++++|+|++|++|+.|++||+..++.|.+++++
T Consensus 119 va~i~~~~~IP~Is~~sts~~lsd~~~yp~ffRt~psd~~q~~ai~~li~~f~W~~Vaiv~~d~~yg~~~~~~~~~~~~~ 198 (469)
T cd06365 119 IATLLGLYKFPQLTYGPFDPLLSDRVQFPSLYQMAPKDTSLPLGMVSLMLHFSWTWVGLVISDDDRGEQFLSDLREEMQR 198 (469)
T ss_pred HHHHhhhhcccceeeccCCccccchhhCCcceEecCCchhHHHHHHHHHHhcCCeEEEEEEecChhHHHHHHHHHHHHHH
Confidence 688999999999999999999997 4699999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCCh--hHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccccc
Q 003633 81 NMAKVSYKLPLPVQFNQ--HDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSK 158 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~--~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~ 158 (806)
.|+||++.+.++....+ .++...|.+|+++++||||++++.+.+..++.++.+.+. .+++||++++|.......
T Consensus 199 ~gi~I~~~~~i~~~~~~~~~~~~~~l~~i~~~~arvIvl~~~~~~~~~l~~~~~~~~~--~~~~wi~s~~w~~~~~~~-- 274 (469)
T cd06365 199 NGICLAFVEKIPVNMQLYLTRAEKYYNQIMTSSAKVIIIYGDTDSLLEVSFRLWQYLL--IGKVWITTSQWDVTTSPK-- 274 (469)
T ss_pred CCeEEEEEEEecCCchhhHHHHHHHHHHhhcCCCeEEEEEcCcHHHHHHHHHHHHhcc--CceEEEeecccccccccc--
Confidence 99999999989866543 478999999999999999999998888776655554442 479999999876543222
Q ss_pred CChhhhhhccceEEEEEeCCCChhhHHHHHH---------------HhhhccCC--------------CCCC--------
Q 003633 159 MNQTSLRILQGVVGLRQHTPDSIPKKAFLSR---------------WSGMQQKG--------------LVSA-------- 201 (806)
Q Consensus 159 ~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~---------------~~~~~~~~--------------~~~~-------- 201 (806)
....+.++|++|+.++.++.+.+++|.++ |+..|++. ....
T Consensus 275 --~~~~~~~~G~lg~~~~~~~~~~f~~fl~~l~~~~~~~npw~~efwe~~f~c~~~~~~~~~~~~c~~~~~~~~~~~~~~ 352 (469)
T cd06365 275 --DFTLNSFHGTLIFSHHHSEIPGFKDFLQTVNPSKYPEDIFLEKLWWIYFNCSLSKSSCKTLKNCLSNASLEWLPLHYF 352 (469)
T ss_pred --ccccceeeEEEEEEeccCcCcchHHHhhccCcccCCCccHHHhhHhHhcCcccCcCCccccCCCCCCccccccccccc
Confidence 33557899999999999988998888765 55544311 0011
Q ss_pred C--CccchhhhhhHHHHHHHHHHHHHhhc-CccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCcee-eEE
Q 003633 202 G--LNTYGLYAYDTVWAVARSIDKFINEH-NITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSG-QVQ 277 (806)
Q Consensus 202 ~--~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG-~i~ 277 (806)
+ ...++.++||||+++|||||+++.++ ... ...+|.. ... .+.+|++.|++++|+|.+| +|+
T Consensus 353 ~~~~~~~~~~v~dAVya~AhALh~~l~c~~~~~------------~~~~~~~-~~~-~~~~l~~~l~~v~F~~~~g~~v~ 418 (469)
T cd06365 353 DMAMSEESYNVYNAVYAVAHALHEMLLQQVETQ------------SENNGKR-LIF-LPWQLHSFLKNIQFKNPAGDEVN 418 (469)
T ss_pred cchhhhhHHHHHHHHHHHHHHHHHHHHhhccCC------------CcCCCCC-CCc-cHHHHHHHHHhccccCCCCCEEE
Confidence 0 23356789999999999999999875 110 0012221 233 3889999999999999999 599
Q ss_pred EecCCCeecccEEEEEee--cC---ceEEEEEeeC
Q 003633 278 FNQDRNIVSRGYDVINID--KM---EIHRVGYWFD 307 (806)
Q Consensus 278 Fd~~G~~~~~~~~I~~~~--~~---~~~~VG~w~~ 307 (806)
||+|||. ...|+|+|++ ++ .+++||+|++
T Consensus 419 Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~VG~~~~ 452 (469)
T cd06365 419 LNQKRKL-DTEYDILNYWNFPQGLGLKVKVGEFSP 452 (469)
T ss_pred ecCCCCc-CceeeEEEEEECCCCCEEEEEEEEEeC
Confidence 9999994 6789999997 22 3699999976
No 11
>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=6.6e-38 Score=342.52 Aligned_cols=262 Identities=22% Similarity=0.343 Sum_probs=223.6
Q ss_pred HhcccccCCCcEEecccCCCCc-cc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTL-SA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLE 79 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~L-s~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~ 79 (806)
++++++.++||+|+++++++.+ ++ .+||||||+.|+|..|++++++++++|||++|++||++++||++.++.+++.++
T Consensus 82 ~~~v~~~~~iP~Is~~~~~~~~~s~~~~~~~~~R~~p~~~~~~~ai~~ll~~~~w~~vaii~~~~~~g~~~~~~l~~~l~ 161 (362)
T cd06367 82 LDFTSAQTRIPVVGISGRESIFMSDKNIHSLFLQTGPSLEQQADVMLEILEEYDWHQFSVVTSRDPGYRDFLDRVETTLE 161 (362)
T ss_pred hhhhhhhhcCcEEEeeccccccccCCCcccceEeecCcHHHHHHHHHHHHHHcCCeEEEEEEEcCcccHHHHHHHHHHHH
Confidence 6789999999999999999999 76 469999999999999999999999999999999999999999999999999999
Q ss_pred hCCcE--EEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccc
Q 003633 80 KNMAK--VSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFS 157 (806)
Q Consensus 80 ~~g~~--i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~ 157 (806)
+.|+| +.....++... .++++.++.++++.++|+||++|+.+++..++++|.++||+.++|+||+++.+....
T Consensus 162 ~~g~~~~i~~~~~~~~~~-~~~~~~~l~~l~~~~~~vivl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~---- 236 (362)
T cd06367 162 ESFVGWEFQLVLTLDLSD-DDGDARLLRQLKKLESRVILLYCSKEEAERIFEAAASLGLTGPGYVWIVGELALGSG---- 236 (362)
T ss_pred hcccceeeeeeEEeccCC-CcchHHHHHHHHhcCCcEEEEeCCHHHHHHHHHHHHHcCCCCCCcEEEECccccccc----
Confidence 99999 77666666432 237889999999999999999999999999999999999999999999999876421
Q ss_pred cCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccCCC
Q 003633 158 KMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSASH 236 (806)
Q Consensus 158 ~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~~ 236 (806)
....+..+|++|+++..+ ..+++++||||+++|+|++++++++ ....
T Consensus 237 ---~~~~~~~~G~~g~~~~~~-------------------------~~~~~~~~Dav~~~a~Al~~~~~~~~~~~~---- 284 (362)
T cd06367 237 ---LAPEGLPVGLLGVGLDTW-------------------------YSLEARVRDAVAIVARAAESLLRDKGALPE---- 284 (362)
T ss_pred ---CCccCCCCeeEEEEeccc-------------------------ccHHHHHHHHHHHHHHHHHHHHHhcCCCCC----
Confidence 122356789999987642 2357789999999999999987653 2111
Q ss_pred CCCCCccccccccccc--ccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee-cCceEEEEEeeC
Q 003633 237 ELPDSKATRVQLEQLK--VFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID-KMEIHRVGYWFD 307 (806)
Q Consensus 237 ~l~~~~~~~~~~~~~~--~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~-~~~~~~VG~w~~ 307 (806)
+...|.... .+..|..|+++|++++|.|+||+|+||++|++..+.|+|+|++ +.+|++||+|++
T Consensus 285 -------~~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg~v~F~~~G~~~~~~~~I~~l~~~~~~~~VG~W~~ 351 (362)
T cd06367 285 -------PPVNCYDTANKRESSGQYLARFLMNVTFDGETGDVSFNEDGYLSNPKLVIINLRRNRKWERVGSWEN 351 (362)
T ss_pred -------CCCCcCCCCCCCCCchHHHHHHHhcccccCCCCceeECCCcccccceEEEEEecCCCcceEEEEEcC
Confidence 112344432 2667999999999999999999999999999888899999999 889999999975
No 12
>cd06375 PBP1_mGluR_groupII Ligand binding domain of the group II metabotropic glutamate receptor. Ligand binding domain of the group II metabotropic glutamate receptor, a family that contains mGlu2R and mGlu3R, all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes
Probab=100.00 E-value=1.8e-37 Score=346.61 Aligned_cols=285 Identities=20% Similarity=0.369 Sum_probs=235.5
Q ss_pred HhcccccCCCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+||+++++|.|++. +|||||||.|+|..|++|+++++++|||++|++||+|++||++.++.|.+.+++
T Consensus 121 va~~~~~~~IP~Is~~sts~~Ls~~~~~~~ffRt~psd~~qa~ai~~ll~~~~W~~Vaii~~~~~yG~~~~~~~~~~~~~ 200 (458)
T cd06375 121 VANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARL 200 (458)
T ss_pred HHHHhhhccccceeeccCChhhcccccCCCeEEecCCcHHHHHHHHHHHHHCCCeEEEEEEeCchHHHHHHHHHHHHHHH
Confidence 5789999999999999999999984 699999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCC-CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKP-LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~-~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
.|+||++.+.++...+..++..++++|++ .++||||++++.+++..++++|.++|+. ++||++++|.......
T Consensus 201 ~gi~i~~~~~i~~~~~~~d~~~~l~~l~~~~~a~vVvl~~~~~~~~~ll~~a~~~g~~---~~wigs~~~~~~~~~~--- 274 (458)
T cd06375 201 RNICIATSEKVGRSADRKSYDSVIRKLLQKPNARVVVLFTRSEDARELLAAAKRLNAS---FTWVASDGWGAQESIV--- 274 (458)
T ss_pred CCeeEEEEEEecCCCCHHHHHHHHHHHhccCCCEEEEEecChHHHHHHHHHHHHcCCc---EEEEEeccccccchhh---
Confidence 99999999888866667899999999875 6999999999999999999999999975 7999999886432221
Q ss_pred ChhhhhhccceEEEEEeCCCChhhHHHHHH---------------HhhhccCCCC-------------------CCCCcc
Q 003633 160 NQTSLRILQGVVGLRQHTPDSIPKKAFLSR---------------WSGMQQKGLV-------------------SAGLNT 205 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~---------------~~~~~~~~~~-------------------~~~~~~ 205 (806)
....+.++|++|+.+.....+.+++|++. |+..|++... ......
T Consensus 275 -~~~~~~~~G~i~~~~~~~~i~~f~~yl~~l~p~~~~~n~w~~e~w~~~f~c~~~~~~~~~~~C~~~~~~~~~~~~~~~~ 353 (458)
T cd06375 275 -KGSEDVAEGAITIELASHPIPDFDRYFQSLTPETNTRNPWFKDFWEQKFQCSLQNRDCANTTTNDKERLLDKVNYEQES 353 (458)
T ss_pred -hccchhhceEEEEEeccccchhHHHHHHhCCcCcCCCCcHHHHHHHHHcCCCCCCCCccCCCCCchhcccccCcccccc
Confidence 22446789999999998888888877654 6666652110 001234
Q ss_pred chhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHH-HHHHccccC-----Ccee-eEEE
Q 003633 206 YGLYAYDTVWAVARSIDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLL-RKLLQTNFT-----GLSG-QVQF 278 (806)
Q Consensus 206 ~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~-~~l~~~~f~-----G~tG-~i~F 278 (806)
+..++|||||++|||||+++.++ +......|.....++ +.+|+ +.|++++|. |.+| +|.|
T Consensus 354 ~~~~v~~AVyA~AhaLh~~l~~~------------c~~~~~~c~~~~~~~-~~~l~~~~L~~v~F~~~~~~~~~g~~v~F 420 (458)
T cd06375 354 KIMFVVNAVYAMAHALHNMQRDL------------CPNTTKLCDAMKPLD-GKKLYKEYLLNVSFTAPFRPDLADSEVKF 420 (458)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhc------------CCCCCCCCCCCCCCC-HHHHHHHHHHhccccccccCCCCCCeeEE
Confidence 67889999999999999998764 001112355444454 88999 599999999 9998 6999
Q ss_pred ecCCCeecccEEEEEee--cCc----eEEEEEeeC
Q 003633 279 NQDRNIVSRGYDVINID--KME----IHRVGYWFD 307 (806)
Q Consensus 279 d~~G~~~~~~~~I~~~~--~~~----~~~VG~w~~ 307 (806)
|++|| ....|+|+|++ +++ +++||+|++
T Consensus 421 d~nGd-~~~~YdI~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 421 DSQGD-GLGRYNIFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred CCCCC-CCcceEEEEEEEcCCCCcEEEEEEEEEec
Confidence 99999 46789999999 332 689999964
No 13
>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=2.8e-37 Score=348.06 Aligned_cols=291 Identities=19% Similarity=0.344 Sum_probs=234.5
Q ss_pred HhcccccCCCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+|++++++|.|++. +||||||+.|+|..|+.|+++++++|+|++|++||+|++||+..++.|.+.+++
T Consensus 133 va~~~~~~~iP~Is~~ats~~ls~~~~~p~~fRt~p~d~~~~~al~~l~~~~~W~~Vaii~~~~~yg~~~~~~~~~~~~~ 212 (472)
T cd06374 133 VQNLLQLFNIPQIAYSATSIDLSDKTLFKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMEAFKELAAH 212 (472)
T ss_pred HHHHhhhhcccccccccCchhhcccccCCceEEcCCChHHHHHHHHHHHHHCCCcEEEEEEecchHHHHHHHHHHHHHHH
Confidence 6789999999999999999999985 699999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccccc
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSK 158 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~ 158 (806)
.|+||++.+.++...+..+++.+|.+||++ +++||++++....+..++++|+++||. .+++||++++|.+.....
T Consensus 213 ~gi~i~~~~~i~~~~~~~d~~~~l~~lk~~~~da~vvv~~~~~~~~~~~l~~a~~~g~~-~~~~wi~s~~~~~~~~~~-- 289 (472)
T cd06374 213 EGLCIAHSDKIYSNAGEQSFDRLLRKLRSRLPKARVVVCFCEGMTVRGLLMAMRRLGVG-GEFQLIGSDGWADRDDVV-- 289 (472)
T ss_pred CCeeEEEEEEecCCCchHHHHHHHHHHHhcCCCcEEEEEEechHHHHHHHHHHHHhcCC-CceEEEEecccccchHhh--
Confidence 999999988886555678999999999975 556677777777889999999999986 468999999886532222
Q ss_pred CChhhhhhccceEEEEEeCCCChhhHHHHH---------------HHhhhccCCC----CC-------------C----C
Q 003633 159 MNQTSLRILQGVVGLRQHTPDSIPKKAFLS---------------RWSGMQQKGL----VS-------------A----G 202 (806)
Q Consensus 159 ~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~---------------~~~~~~~~~~----~~-------------~----~ 202 (806)
....+.++|++++.++.+..+.+++|.. .|++.|+... .. . .
T Consensus 290 --~~~~~~~~G~l~~~~~~~~~~~F~~~l~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~~~~~~~c~~~~~~~~~~~ 367 (472)
T cd06374 290 --EGYEEEAEGGITIKLQSPEVPSFDDYYLKLRPETNTRNPWFREFWQHRFQCRLPGHPQENPNYIKICTGNESLDEQYV 367 (472)
T ss_pred --hcchhhhheeEEEEecCCCCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCcCCccCcCCccCCCCCCccccccccc
Confidence 2345778999999999888888777543 4665554210 00 0 1
Q ss_pred CccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCcee-eEEEecC
Q 003633 203 LNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSG-QVQFNQD 281 (806)
Q Consensus 203 ~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG-~i~Fd~~ 281 (806)
...++.++|||||++|+|||+++.+.. .+....|...... +|.+|+++|++++|+|++| +|.||++
T Consensus 368 ~~~~~~~vyDAVyaiA~ALh~~~~~~~------------~~~~~~c~~~~~~-~~~~l~~~l~~v~F~g~tG~~v~Fd~~ 434 (472)
T cd06374 368 QDSKMGFVINAIYAMAHGLHNMHQDLC------------PGHVGLCDAMKPI-DGRKLLEYLLKTSFSGVSGEEVYFDEN 434 (472)
T ss_pred ccceeHHHHHHHHHHHHHHHHHHHhhC------------CCCCCCCcCCCCC-CHHHHHHHHHhCcccCCCCCeEEEcCC
Confidence 124667999999999999999876541 0111123332333 4999999999999999999 7999999
Q ss_pred CCeecccEEEEEeec-----CceEEEEEeeCCCCcc
Q 003633 282 RNIVSRGYDVINIDK-----MEIHRVGYWFDGSGFS 312 (806)
Q Consensus 282 G~~~~~~~~I~~~~~-----~~~~~VG~w~~~~gl~ 312 (806)
|++. ..|+|+|++. .++++||+|++ .+|.
T Consensus 435 G~~~-~~ydI~n~~~~~~~~~~~~~VG~w~~-~~l~ 468 (472)
T cd06374 435 GDSP-GRYDIMNLQYTEDLRFDYINVGSWHE-GDLG 468 (472)
T ss_pred CCCC-CceEEEEEEECCCCCEEEEEEEEEeC-Cccc
Confidence 9964 5899999994 35899999974 4564
No 14
>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=4.6e-37 Score=345.78 Aligned_cols=287 Identities=18% Similarity=0.374 Sum_probs=233.5
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+|++++++|.|++ .+||||||+.|+|..|++|+++++++|||++|++||.|++||...++.|.+.+++
T Consensus 119 va~i~~~~~iP~Is~~ats~~ls~~~~~~~ffR~~p~d~~~~~ai~~~i~~~~w~~Vaii~~~~~yg~~~~~~~~~~~~~ 198 (463)
T cd06376 119 VANILRLFQIPQISYASTAPELSDDRRYDFFSRVVPPDSFQAQAMVDIVKALGWNYVSTLASEGNYGESGVEAFTQISRE 198 (463)
T ss_pred HHHHhccccCcccccccCChhhcccccCCceEEccCCHHHHHHHHHHHHHHcCCeEEEEEEeCChHHHHHHHHHHHHHHH
Confidence 578999999999999999999997 4699999999999999999999999999999999999999999999999999998
Q ss_pred C-CcEEEEEeccCCCCChhHHHHHHHhcCC-CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccccc
Q 003633 81 N-MAKVSYKLPLPVQFNQHDITVLLNNSKP-LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSK 158 (806)
Q Consensus 81 ~-g~~i~~~~~~~~~~~~~~~~~~l~~ik~-~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~ 158 (806)
. ++||...+.++...+..|++.+|++||+ .++|+||++++.+++..++++|+++|+++ .|+||+++++.......
T Consensus 199 ~g~~~v~~~~~i~~~~~~~d~~~~l~~ik~~~~~~vIvl~~~~~~~~~ll~~a~~~~~~g-~~~wig~d~~~~~~~~~-- 275 (463)
T cd06376 199 AGGVCIAQSIKIPREPRPGEFDKIIKRLLETPNARAVIIFANEDDIRRVLEAAKRANQVG-HFLWVGSDSWGAKISPI-- 275 (463)
T ss_pred cCCceEEEEEecCCCCCHHHHHHHHHHHhccCCCeEEEEecChHHHHHHHHHHHhcCCcC-ceEEEEecccccccccc--
Confidence 7 5788877767656667899999999986 79999999999999999999999999874 59999999886543332
Q ss_pred CChhhhhhccceEEEEEeCCCChhhHHHHH---------------HHhhhccCCCC----C-------------------
Q 003633 159 MNQTSLRILQGVVGLRQHTPDSIPKKAFLS---------------RWSGMQQKGLV----S------------------- 200 (806)
Q Consensus 159 ~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~---------------~~~~~~~~~~~----~------------------- 200 (806)
....+.++|++++.++.+..+.+++|.. .|+..|++..+ .
T Consensus 276 --~~~~~~~~G~~~~~~~~~~~~~F~~~~~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~~~~~~~C~~~~~~~~~~~ 353 (463)
T cd06376 276 --LQQEDVAEGAITILPKRASIEGFDAYFTSRTLENNRRNVWFAEFWEENFNCKLTISGSKKEDTDRKCTGQERIGRDST 353 (463)
T ss_pred --ccCcceeeeEEEEEeccccchhHHHHHHhCCcccCCCCcHHHHHHHHhCCCcccCCCCccccccCcCcchhhccccCc
Confidence 1234578999999988877777777654 46665542110 0
Q ss_pred CCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCcee-eEEEe
Q 003633 201 AGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSG-QVQFN 279 (806)
Q Consensus 201 ~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG-~i~Fd 279 (806)
.....+++++|||||++|||||+++.++. .+....|.....+ +|.+|+++|++++|+|++| +|+||
T Consensus 354 ~~~~~~~~~v~dAVyaiA~ALh~l~~~~c------------~~~~~~C~~~~~~-~~~~l~~~L~~v~F~g~tg~~v~Fd 420 (463)
T cd06376 354 YEQEGKVQFVIDAVYAMAHALHSMHKDLC------------PGYTGVCPEMEPA-DGKKLLKYIRAVNFNGSAGTPVMFN 420 (463)
T ss_pred ccccchhHHHHHHHHHHHHHHHHHHHhhC------------CCCCCCCccCCCC-CHHHHHHHHHhCCccCCCCCeEEeC
Confidence 01123678999999999999999986541 0111134443333 4999999999999999999 69999
Q ss_pred cCCCeecccEEEEEeec-----CceEEEEEeeC
Q 003633 280 QDRNIVSRGYDVINIDK-----MEIHRVGYWFD 307 (806)
Q Consensus 280 ~~G~~~~~~~~I~~~~~-----~~~~~VG~w~~ 307 (806)
++|++ .+.|+|+|++. .++++||.|++
T Consensus 421 ~~G~~-~~~Ydi~n~q~~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 421 ENGDA-PGRYDIFQYQITNTSSPGYRLIGQWTD 452 (463)
T ss_pred CCCCC-CCceEEEEEEecCCCceeEEEEEEECC
Confidence 99996 45799999982 35899999976
No 15
>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=5.1e-37 Score=337.13 Aligned_cols=268 Identities=25% Similarity=0.332 Sum_probs=223.0
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+|||+||+|.|++ .+||||||++|+|..|++++++++++|||++|++|++|++||+++++.|.+++++
T Consensus 119 va~v~~~~~IP~IS~~ats~~Ls~~~~~~~ffRt~p~D~~qa~ai~~li~~~~w~~Vaii~~~d~yG~~~~~~f~~~~~~ 198 (403)
T cd06361 119 VSRMLNLQLIPQVSYASTAEILSDKIRFPSFLRTVPSDFYQTKAMAHLIKKSGWNWVGIIITDDDYGRSALETFIIQAEA 198 (403)
T ss_pred HHHHhccCCcceEecCcCCcccCCcccCCCeeECCCchHhHHHHHHHHHHHcCCcEEEEEEecCchHHHHHHHHHHHHHH
Confidence 578999999999999999999997 5799999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCCh-----hHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc
Q 003633 81 NMAKVSYKLPLPVQFNQ-----HDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES 155 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~-----~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~ 155 (806)
.|+||+..+.++...++ .+++.++++++++++||||++++.+++..++++|+++|| +++||++++|.+....
T Consensus 199 ~GicIa~~e~~~~~~~~~~~~~~~~~~~~~~ik~~~a~vVvv~~~~~~~~~l~~~a~~~g~---~~~wigs~~w~~~~~~ 275 (403)
T cd06361 199 NGVCIAFKEILPASLSDNTKLNRIIRTTEKIIEENKVNVIVVFARQFHVFLLFNKAIERNI---NKVWIASDNWSTAKKI 275 (403)
T ss_pred CCeEEEEEEEecCccCcchhHHHHHHHHHHHHhcCCCeEEEEEeChHHHHHHHHHHHHhCC---CeEEEEECcccCcccc
Confidence 99999999988765322 456667777899999999999999999999999999998 6899999988764333
Q ss_pred cccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCC
Q 003633 156 FSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSAS 235 (806)
Q Consensus 156 ~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~ 235 (806)
. .....+.+.|++++.++.+..+. |.+.+++.+ ..++|||||++|+||+++..++
T Consensus 276 ~---~~~~~~~~~g~ig~~~~~~~~~~---F~~~~~~~~------------~~~v~~AVyaiA~Al~~~~~~~------- 330 (403)
T cd06361 276 L---TDPNVKKIGKVVGFTFKSGNISS---FHQFLKNLL------------IHSIQLAVFALAHAIRDLCQER------- 330 (403)
T ss_pred c---cCCcccccceEEEEEecCCccch---HHHHHHHhh------------HHHHHHHHHHHHHHHHHhccCC-------
Confidence 2 12233667899999887755555 444455443 3368999999999999964322
Q ss_pred CCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCc----eEEEEEeeCCCC
Q 003633 236 HELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKME----IHRVGYWFDGSG 310 (806)
Q Consensus 236 ~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~----~~~VG~w~~~~g 310 (806)
.|...... ++.+|+++|++++|+|++|++.||++||. ...|+|+|+++++ +++||.|++...
T Consensus 331 -----------~c~~~~~~-~~~~l~~~L~~~~f~g~~~~v~Fd~~gd~-~~~y~I~~~~~~~~~~~~~~vg~~~~~~~ 396 (403)
T cd06361 331 -----------QCQNPNAF-QPWELLGQLKNVTFEDGGNMYHFDANGDL-NLGYDVVLWKEDNGHMTVTIMAEYDPQND 396 (403)
T ss_pred -----------CCCCCCCc-CHHHHHHHHheeEEecCCceEEECCCCCC-CcceEEEEeEecCCcEEEEEEEEEeCCCC
Confidence 23322223 38999999999999999889999999994 6789999998643 699999988663
No 16
>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=7.8e-37 Score=335.83 Aligned_cols=287 Identities=18% Similarity=0.295 Sum_probs=236.9
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
+++++++++||+|++++++|.+++.. +||+|+.|++..++.++++++++|+|++|++||++++ |...++.|.+.+++.
T Consensus 88 v~~i~~~~~iP~Is~~~t~~~lt~~~-~~~~~~~~~~~~~~~a~~~~~~~~~wk~vaily~~~~-g~~~l~~~~~~~~~~ 165 (384)
T cd06393 88 VQSICNALEVPHIQLRWKHHPLDNKD-TFYVNLYPDYASLSHAILDLVQYLKWRSATVVYDDST-GLIRLQELIMAPSRY 165 (384)
T ss_pred HHHHHhccCCCeEeccCCCcccCccc-eeEEEeccCHHHHHHHHHHHHHHcCCcEEEEEEeCch-hHHHHHHHHHhhhcc
Confidence 67899999999999999999998654 5788888999899999999999999999999997654 766677888889999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
|++|+.. .++. ++.|++.+|++||+.++++||++++.+++..+++||+++||+.+.|+|++++......+. .
T Consensus 166 g~~v~~~-~~~~--~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~~~~~~~~~~~~~~~~-----~ 237 (384)
T cd06393 166 NIRLKIR-QLPT--DSDDARPLLKEMKRGREFRIIFDCSHQMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDL-----E 237 (384)
T ss_pred CceEEEE-ECCC--CchHHHHHHHHHhhcCceEEEEECCHHHHHHHHHHHHHhccccCceEEEEccCccccccc-----h
Confidence 9999863 4653 357999999999999999999999999999999999999999999999998864433332 1
Q ss_pred hhhhhccceEEEEEeCCCChhhHHHHHHHhhh-ccCCCC------CCCCccchhhhhhHHHHHHHHHHHHHhhcCccccC
Q 003633 162 TSLRILQGVVGLRQHTPDSIPKKAFLSRWSGM-QQKGLV------SAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSA 234 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~-~~~~~~------~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~ 234 (806)
........+++++...++++..++|+++|+++ ++.... ...+..+++++|||||++|.|+++..+.+
T Consensus 238 ~~~~~~~~it~~~~~~~~~~~~~~f~~~~~~~~~~~~p~~~~~~~~~~~~~~aal~yDav~~~a~A~~~~~~~~------ 311 (384)
T cd06393 238 PYRYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQAAPKPETGLLDGVMMTDAALLYDAVHMVSVCYQRAPQMT------ 311 (384)
T ss_pred hhhcCcceEEEEEecCCCcHHHHHHHHHHHhhhhccccccccccccccccchhHHhhhhHHHHHHHHhhhhhcC------
Confidence 11111223578888888999999999999854 542110 01235789999999999999999743221
Q ss_pred CCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEec-CCCeecccEEEEEeecCceEEEEEeeCCCCcc
Q 003633 235 SHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQ-DRNIVSRGYDVINIDKMEIHRVGYWFDGSGFS 312 (806)
Q Consensus 235 ~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~-~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl~ 312 (806)
...+.|++..+|+.|.+|+++|++++|+|+||+++||+ +|.|.+..++|+|+.++++++||+|++..||+
T Consensus 312 --------~~~~~c~~~~~w~~G~~i~~~l~~~~~~GltG~i~Fd~~~g~r~~~~~~i~~~~~~g~~~vg~W~~~~g~~ 382 (384)
T cd06393 312 --------VNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEKVGVWNPNTGLN 382 (384)
T ss_pred --------CCCCCCCCCCCCcccHHHHHHHhheeecccccceEecCCCCeeeeeEEEEEEecCCcceeeEEEcCCCCcC
Confidence 12345677789999999999999999999999999996 68899999999999999999999999999986
No 17
>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=2.2e-36 Score=328.92 Aligned_cols=289 Identities=16% Similarity=0.253 Sum_probs=233.6
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
++++|+.++||+|+++++. +..++|.+++.|+ ...|+++++++|+|++|++||+ ++||...++.|.+.+++.
T Consensus 73 v~~i~~~~~IP~I~~~~~~----~~~~~f~~~~~p~---~~~ai~d~i~~~~wk~vailYd-sd~gl~~lq~l~~~~~~~ 144 (370)
T cd06389 73 ITSFCGTLHVSFITPSFPT----DGTHPFVIQMRPD---LKGALLSLIEYYQWDKFAYLYD-SDRGLSTLQAVLDSAAEK 144 (370)
T ss_pred HHHhhccCCCCeeeecCCC----CCCCceEEEecch---hhhHHHHHHHhcCCcEEEEEec-CchHHHHHHHHHHhhccC
Confidence 6889999999999986652 3357888899887 5799999999999999999996 679999999999999999
Q ss_pred CcEEEEEec--cCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 82 MAKVSYKLP--LPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 82 g~~i~~~~~--~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
|++|+.... +.......|++++|++||++++|+||++|+++.+..|++||+++||+.++|+||+++......+..
T Consensus 145 g~~V~~~~~~~i~~~~~~~d~~~~L~~ik~~~~~~Iil~~~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l~--- 221 (370)
T cd06389 145 KWQVTAINVGNINNDRKDEAYRSLFQDLENKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLS--- 221 (370)
T ss_pred CceEEEEEeecCCCccchHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHhCccccceEEEEccCCccccchh---
Confidence 988775442 222234569999999999999999999999999999999999999999999999988533332221
Q ss_pred ChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhcc---CCCCCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccCC
Q 003633 160 NQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQ---KGLVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSAS 235 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~---~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~ 235 (806)
.....-.++.|++...++.+..++|.++|++... ++.....+..+++++||||+++|.|++++.+.+ .....
T Consensus 222 --~~~~~~~nitg~~~~~~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~aAl~yDAV~v~a~A~~~l~~~~~~~~~~-- 297 (370)
T cd06389 222 --KIQFGGANVSGFQIVDYDDPLVSKFIQRWSTLEEKEYPGAHTKTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR-- 297 (370)
T ss_pred --hhccCCcceEEEEEecCCCchHHHHHHHHHhcCccccCCCCCcCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccC--
Confidence 1112234678899888889999999999986322 111223577899999999999999999985543 21111
Q ss_pred CCCCCCcccccccc--cccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCcc
Q 003633 236 HELPDSKATRVQLE--QLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGFS 312 (806)
Q Consensus 236 ~~l~~~~~~~~~~~--~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl~ 312 (806)
++...|. ...+|.+|..|+++|++++|+|+||+++||++|+|.+..++|++++++|+++||+|++..||.
T Consensus 298 -------~~~~~C~~~~~~~w~~G~~i~~~l~~~~~~GlTG~i~Fd~~G~r~~~~~~ii~l~~~g~~kvG~W~~~~~~~ 369 (370)
T cd06389 298 -------GNAGDCLANPAVPWGQGVEIERALKQVQVEGLTGNIKFDQNGKRINYTINVMELKSNGPRKIGYWSEVDKMV 369 (370)
T ss_pred -------CCCCCcCCCCCCCCCCcHHHHHHHHhcccCccccceEeCCCCccccceEEEEEecCCcceEEEEEcCCCCcc
Confidence 1122343 245788999999999999999999999999999998889999999999999999999999875
No 18
>cd06362 PBP1_mGluR Ligand binding domain of the metabotropic glutamate receptors (mGluR). Ligand binding domain of the metabotropic glutamate receptors (mGluR), which are members of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses. mGluRs bind to glutamate and function as an excitatory neurotransmitter; they are involved in learning, memory, anxiety, and the perception of pain. Eight subtypes of mGluRs have been cloned so far, and are classified into three groups according to their sequence similarities, transduction mechanisms, and pharmacological profiles. Group I is composed of mGlu1R and mGlu5R that both stimulate PLC hydrolysis. Group II includes mGlu2R and mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R, mGlu6R, mGlu7R, and mGlu8R, which form group III.
Probab=100.00 E-value=1.9e-36 Score=340.94 Aligned_cols=291 Identities=20% Similarity=0.367 Sum_probs=237.0
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+|+++++++.|++ .+||||||+.|+|..|+.++++++++|+|++|++|++|++||++..+.+.+.+++
T Consensus 119 v~~~~~~~~ip~Is~~sts~~ls~~~~~~~~fR~~p~d~~~~~a~~~~l~~~~w~~vaii~~~~~~G~~~~~~~~~~~~~ 198 (452)
T cd06362 119 VANLLRLFKIPQISYASTSPELSDKTRYDYFSRTVPPDSFQAQAMVDIVKAFNWTYVSTVASEGNYGEKGIEAFEKLAAE 198 (452)
T ss_pred HHHHhccccCcccccccCchhhccccccCCEEEecCChHHHHHHHHHHHHHCCCcEEEEEEeCCHHHHHHHHHHHHHHHH
Confidence 578999999999999999999997 4699999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCC-CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKP-LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~-~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
.|+||+..+.++...+..|+++++++|++ .++|+||+.++..++..++++|+++||+ .+++||.++++.......
T Consensus 199 ~gi~i~~~~~~~~~~~~~d~~~~l~~l~~~~~a~viil~~~~~~~~~~~~~a~~~g~~-~~~~~i~~~~~~~~~~~~--- 274 (452)
T cd06362 199 RGICIAGSEKIPSSATEEEFDNIIRKLLSKPNARVVVLFCREDDIRGLLAAAKRLNAE-GHFQWIASDGWGARNSVV--- 274 (452)
T ss_pred CCeeEEEEEEcCCCCCHHHHHHHHHHHhhcCCCeEEEEEcChHHHHHHHHHHHHcCCc-CceEEEEeccccccchhh---
Confidence 99999998888765567899999999987 5799999999999999999999999997 568999999876543221
Q ss_pred ChhhhhhccceEEEEEeCCCChhhHHHH---------------HHHhhhccCC---C-C---------------CCCCcc
Q 003633 160 NQTSLRILQGVVGLRQHTPDSIPKKAFL---------------SRWSGMQQKG---L-V---------------SAGLNT 205 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~~~~~~~f~---------------~~~~~~~~~~---~-~---------------~~~~~~ 205 (806)
....+.++|++++.++....+.+++|+ +.|+..+... . . ....+.
T Consensus 275 -~~~~~~~~g~~~~~~~~~~i~~f~~~l~~l~~~~~~~~~~~~~~w~~~~~c~~~~~~~~~~~~~c~~~~~~~~~~~~~~ 353 (452)
T cd06362 275 -EGLEDVAEGAITIELQSAEVPGFDEYFLSLTPENNSRNPWFREFWEQKFNCKLTGNGSTKDNTCCTERILLLSNYEQES 353 (452)
T ss_pred -cccccccceEEEEEecccccccHHHHhhhCCcCcCCCChHHHHHHHHhcCCCcCCCCccccCCCCcccccccccccccc
Confidence 234567899999888776665555543 2344444311 0 0 012355
Q ss_pred chhhhhhHHHHHHHHHHHHHhhc-CccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCcee-eEEEecCCC
Q 003633 206 YGLYAYDTVWAVARSIDKFINEH-NITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSG-QVQFNQDRN 283 (806)
Q Consensus 206 ~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG-~i~Fd~~G~ 283 (806)
+++++|||||++|+||++++.++ +.. ...|.... +.+|.+|+++|++++|.|++| +|+||++|+
T Consensus 354 ~~~~vyDAV~a~A~AL~~~l~~~~~~~-------------~~~c~~~~-~~~~~~l~~~l~~v~f~g~tg~~v~Fd~~G~ 419 (452)
T cd06362 354 KVQFVIDAVYAMAHALHNMHRDLCPGT-------------TGLCDAMK-PIDGRKLLFYLRNVSFSGLAGGPVRFDANGD 419 (452)
T ss_pred chhHHHHHHHHHHHHHHHHHHhhCCCC-------------CCCCcCcc-CCCHHHHHHHHHhCCcCCCCCceEEECCCCC
Confidence 88999999999999999998764 111 11233322 334999999999999999998 799999999
Q ss_pred eecccEEEEEeec----CceEEEEEeeCCCCcc
Q 003633 284 IVSRGYDVINIDK----MEIHRVGYWFDGSGFS 312 (806)
Q Consensus 284 ~~~~~~~I~~~~~----~~~~~VG~w~~~~gl~ 312 (806)
+ ...|+|+|++. .++++||+|++..||.
T Consensus 420 ~-~~~y~I~~~~~~~~~~~~~~VG~w~~~~~~~ 451 (452)
T cd06362 420 G-PGRYDIFNYQRTNGKYDYVKVGSWKGELSLN 451 (452)
T ss_pred C-CCceEEEEEEEcCCceEEEEEEEEecccccC
Confidence 6 46999999983 3589999999888764
No 19
>cd06388 PBP1_iGluR_AMPA_GluR4 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=3.3e-36 Score=326.65 Aligned_cols=287 Identities=17% Similarity=0.272 Sum_probs=228.1
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
++++|+.++||+|+++++ +...+.|.+++.|+ +..|+++++++|+||+|++|| |+++|.+.++.|.+.+++.
T Consensus 79 v~~i~~~~~IP~I~~~~~----~~~~~~f~i~~~p~---~~~a~~~~i~~~~wk~vaiiY-d~~~~~~~lq~l~~~~~~~ 150 (371)
T cd06388 79 LTSFCSALHISLITPSFP----TEGESQFVLQLRPS---LRGALLSLLDHYEWNRFVFLY-DTDRGYSILQAIMEKAGQN 150 (371)
T ss_pred HHHHhhCCCCCeeecCcc----ccCCCceEEEeChh---hhhHHHHHHHhcCceEEEEEe-cCCccHHHHHHHHHhhHhc
Confidence 689999999999998654 22234444455554 468888899999999999999 5555667899999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
|++|+.....+. ++.|++++|++|+.+++|+||++|+++.+..|++||+++||+.++|+||+++......+. .
T Consensus 151 g~~v~~~~~~~~--~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l-----~ 223 (371)
T cd06388 151 GWQVSAICVENF--NDASYRRLLEDLDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISL-----E 223 (371)
T ss_pred CCeeeeEEeccC--CcHHHHHHHHHhcccccEEEEEECCHHHHHHHHHHHHhcCccccceEEEEccCccccccH-----H
Confidence 999987665543 356999999999999999999999999999999999999999999999999853222221 1
Q ss_pred hhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCC--CCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccCCCCC
Q 003633 162 TSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGL--VSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSASHEL 238 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~--~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~~~l 238 (806)
+....-.++.|++...++++..++|.++|++.+.... ....+..+++++||||+++|.|++++.... ..+.
T Consensus 224 ~~~~g~~nitg~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~aAl~YDaV~l~a~A~~~l~~~~~~~~~------ 297 (371)
T cd06388 224 RFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSESPPKYTSALTYDGVLVMAEAFRNLRRQKIDISR------ 297 (371)
T ss_pred HHhccCCceEEEEeecCCChhHHHHHHHHHhcCccccCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCCccc------
Confidence 1222233388999988888999999999988764211 112577899999999999999999975433 1110
Q ss_pred CCCccccccc--ccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCcc
Q 003633 239 PDSKATRVQL--EQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGFS 312 (806)
Q Consensus 239 ~~~~~~~~~~--~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl~ 312 (806)
.+....| +...+|..|..|+++|++++|+|+||+++||++|+|.+..++|++++++|+++||+|++..||.
T Consensus 298 ---~~~~~~C~~~~~~~w~~G~~i~~~lk~~~~~GlTG~i~Fd~~G~r~~~~l~Ii~l~~~g~~kvG~W~~~~g~~ 370 (371)
T cd06388 298 ---RGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNIQFDHYGRRVNYTMDVFELKSNGPRKIGYWNDMDKLV 370 (371)
T ss_pred ---CCCCCCcCCCCCCCCcccHHHHHHHHhcCcCCCccceeECCCCCcccceEEEEEccCCCceEEEEEcCCCCcc
Confidence 0112234 3356899999999999999999999999999999998889999999999999999999999875
No 20
>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-36 Score=338.42 Aligned_cols=289 Identities=22% Similarity=0.341 Sum_probs=234.3
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+||+++++|.|++ .+|||||||.|+|..|++|+++++++|||++|++|+.|++||+..++.|.+.+++
T Consensus 134 va~~~~~~~IP~IS~~sss~~ls~~~~yp~ffRt~psd~~q~~Ai~~l~~~f~wk~VaiI~~dd~yG~~~~~~~~~~~~~ 213 (510)
T cd06364 134 VANLLGLFYIPQVSYASSSRLLSNKNQFKSFLRTIPNDEHQATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFREEAEE 213 (510)
T ss_pred HHHHhccccccccccccCCcccCCccccCCeeEcCCChHHHHHHHHHHHHHcCCeEEEEEEecCcchHHHHHHHHHHHHH
Confidence 578899999999999999999998 4699999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|+||++.+.++...+..++.+++.+|+++++||||+++...++..++++|+++|+. +.+||++++|....... .
T Consensus 214 ~Gi~I~~~~~i~~~~~~~d~~~~l~klk~~~a~vVvl~~~~~~~~~ll~qa~~~g~~--~~iwI~s~~w~~~~~~~---~ 288 (510)
T cd06364 214 RDICIDFSELISQYSDEEEIQRVVEVIQNSTAKVIVVFSSGPDLEPLIKEIVRRNIT--GKIWLASEAWASSSLIA---M 288 (510)
T ss_pred CCcEEEEEEEeCCCCCHHHHHHHHHHHHhcCCeEEEEEeCcHHHHHHHHHHHHhCCC--CcEEEEEchhhcccccc---c
Confidence 999999988887645678999999999999999999999999999999999999985 57999999776433322 1
Q ss_pred hhhhhhccceEEEEEeCCCChhhHHHHHH---------------HhhhccCC-----CC--------------------C
Q 003633 161 QTSLRILQGVVGLRQHTPDSIPKKAFLSR---------------WSGMQQKG-----LV--------------------S 200 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~~~~~~~~f~~~---------------~~~~~~~~-----~~--------------------~ 200 (806)
....+.+.|++|+.+.....+.+++|+.. |+..|++. .. .
T Consensus 289 ~~~~~~~gg~lg~~~~~~~i~~f~~~l~~l~p~~~~~~~~~~~~we~~f~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 (510)
T cd06364 289 PEYFDVMGGTIGFALKAGQIPGFREFLQKVHPKKSSHNGFAKEFWEETFNCYLEDSPKNALPVDTFLGHEESGDDSENGS 368 (510)
T ss_pred CCccceeeEEEEEEECCCcCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCCCCCcccccccccccccccccccccccc
Confidence 34557889999999887776666655543 55555421 00 0
Q ss_pred --C------------------C--CccchhhhhhHHHHHHHHHHHHHhhc-Cc-cccCCCCCCCCcccccccccccccCc
Q 003633 201 --A------------------G--LNTYGLYAYDTVWAVARSIDKFINEH-NI-TFSASHELPDSKATRVQLEQLKVFDG 256 (806)
Q Consensus 201 --~------------------~--~~~~~~~aYDAv~~lA~Al~~~~~~~-~~-~~~~~~~l~~~~~~~~~~~~~~~~~~ 256 (806)
. + ...++.+.|||||++|||||+++.+. .. ++. ...|.....++
T Consensus 369 ~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~AVyAvAhaLh~~~~c~~~~~~~~-----------~~~c~~~~~~~- 436 (510)
T cd06364 369 TAFRPLCTGDENIASVETPYLDYTHLRISYNVYLAVYSIAHALQDIYTCTPGKGLFT-----------NGSCADIKKVE- 436 (510)
T ss_pred cccCCCCCChhhhcccCCccccccchhhHHHHHHHHHHHHHHHHHHhcCCCCCCCcc-----------CCCCCCCCCCC-
Confidence 0 0 12345679999999999999998764 11 110 01344434444
Q ss_pred hHHHHHHHHccccCCcee-eEEEecCCCeecccEEEEEeec---Cc---eEEEEEeeCC
Q 003633 257 GTFLLRKLLQTNFTGLSG-QVQFNQDRNIVSRGYDVINIDK---ME---IHRVGYWFDG 308 (806)
Q Consensus 257 g~~l~~~l~~~~f~G~tG-~i~Fd~~G~~~~~~~~I~~~~~---~~---~~~VG~w~~~ 308 (806)
+.+|++.|++++|+|.+| +|.||++||. ...|+|+|++. ++ +++||.|++.
T Consensus 437 ~~~l~~~L~~v~F~~~~g~~v~Fd~~Gd~-~~~YdI~n~q~~~~~~~~~~v~VG~~~~~ 494 (510)
T cd06364 437 AWQVLKHLRHLNFTDNMGEQVRFDEGGDL-VGNYSIINWHLSPEDGSVVFKEVGYYNVY 494 (510)
T ss_pred HHHHHHHHHhcEEecCCCCEEEEecCCCC-ccceeEEEeeecCCCCcEEEEEEEEEcCC
Confidence 899999999999999998 6999999994 67899999993 22 5899999864
No 21
>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=7.7e-36 Score=328.71 Aligned_cols=296 Identities=17% Similarity=0.299 Sum_probs=233.3
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
++++++.++||+|+++++.|.++ .++||+||+.|+. ..++++++++++|++|++||++++ |...++.+.+.+++.
T Consensus 78 ~~~~~~~~~iP~i~~~~~~~~l~-~~~~~~fr~~p~~---~~a~~~~~~~~~wk~vaii~~~~~-~~~~~~~~~~~~~~~ 152 (382)
T cd06380 78 LTSYSDALHVPFITPSFPTNDLD-DGNQFVLQMRPSL---IQALVDLIEHYGWRKVVYLYDSDR-GLLRLQQLLDYLREK 152 (382)
T ss_pred HHHHHhcCCCCeEecCCCcccCC-CCCcEEEEeccch---hHHHHHHHHhcCCeEEEEEECCCc-chHHHHHHHHHHhcc
Confidence 57889999999999999999885 4579999998863 458999999999999999997665 667788888999998
Q ss_pred C--cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 82 M--AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 82 g--~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
| ++|.... +....+..|++.+|++||++++|+||++++.+++..+++||+++||+.++|+||++++.....+.
T Consensus 153 g~~i~v~~~~-~~~~~~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~i~~qa~~~gm~~~~y~~i~~~~~~~~~~~---- 227 (382)
T cd06380 153 DNKWQVTARR-VDNVTDEEEFLRLLEDLDRRKEKRIVLDCESERLNKILEQIVDVGKNRKGYHYILANLGFDDIDL---- 227 (382)
T ss_pred CCceEEEEEE-ecCCCcHHHHHHHHHHhhcccceEEEEECCHHHHHHHHHHHHHhhhcccceEEEEccCCcccccH----
Confidence 8 6665432 33222457999999999999999999999999999999999999999999999999865544332
Q ss_pred ChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCC---CCCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccCC
Q 003633 160 NQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKG---LVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSAS 235 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~---~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~ 235 (806)
........++.+++...++.+..++|.++|++.++.. .....++.+++++|||||++|+|++++.+.+ +..+...
T Consensus 228 -~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~aYDav~~~a~Al~~~~~~~~~~~~~~~ 306 (382)
T cd06380 228 -SKFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPGAGTSPIKYTAALAHDAVLVMAEAFRSLRRQRGSGRHRID 306 (382)
T ss_pred -HHhccCceeeEEEeccCCCCHHHHHHHHHHHhcCccccCcCCcCCcchHHHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 1112223456778777777889999999999987521 1122467799999999999999999986543 2111100
Q ss_pred CCCCCCcccccccc--cccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCc
Q 003633 236 HELPDSKATRVQLE--QLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGF 311 (806)
Q Consensus 236 ~~l~~~~~~~~~~~--~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl 311 (806)
.. ....+..|. ...+|.+|.+|+++|++++|+|+||+++||++|++....++|+|++++++++||+|++..||
T Consensus 307 ~~---~~~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG~i~Fd~~G~~~~~~~~i~~~~~~~~~~vg~w~~~~g~ 381 (382)
T cd06380 307 IS---RRGNGGDCLANPAVPWEHGIDIERALKKVQFEGLTGNVQFDEFGQRTNYTLDVVELKTRGLRKVGYWNEDDGL 381 (382)
T ss_pred cc---cCCCCCcCCCCCCCCccchHHHHHHHHhcccCCcccceEECCCCCcccccEEEEEecCCCceEEEEECCCcCc
Confidence 00 001122232 34568889999999999999999999999999999888999999999999999999998886
No 22
>cd06378 PBP1_iGluR_NMDA_NR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=100.00 E-value=5.4e-36 Score=322.73 Aligned_cols=268 Identities=16% Similarity=0.218 Sum_probs=212.4
Q ss_pred CHhcccccCCCcEEecccCCC-Cccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHH
Q 003633 1 MISEVANGLKVPLVSFAATDP-TLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNML 78 (806)
Q Consensus 1 ~v~~i~~~~~vP~Is~~at~p-~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l 78 (806)
+++.++++++||+|+++++++ .+++ .++|||+|+.|+|..|++||++++++|+|++|++||++++.+....+.+++.+
T Consensus 80 ~~s~~~~~~~vP~is~~~~s~~~ls~~~~~p~flr~~Psd~~q~~Ai~~Ii~~f~W~~v~iV~~~~~g~~~~~~~l~~~~ 159 (362)
T cd06378 80 ILDFISAQTFLPILGIHGGSSMIMAAKDSGSTFLQFGPSIEQQAAVMLKIMEEYDWHAFSVVTSRFPGYDDFVSAVRTTV 159 (362)
T ss_pred hhhhhhhceeccEEEecccccccccCCCCCceEEEeCCCHHHHHHHHHHHHHHCCCeEEEEEEEcCCCHHHHHHHHHHHH
Confidence 357788889999999987765 5666 56999999999999999999999999999999999999887777777888777
Q ss_pred HhCCcEEEEEeccCCCCC-hhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccc
Q 003633 79 EKNMAKVSYKLPLPVQFN-QHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFS 157 (806)
Q Consensus 79 ~~~g~~i~~~~~~~~~~~-~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~ 157 (806)
.+.++|+.....++...+ ..++..++.++|.+++|+||++|+.+.+..||++|+++||++.+|+||++++.....+..
T Consensus 160 ~~~~~~~~i~~~~~~~~~~~~~~~~~l~~lk~~~arViVl~~s~~~a~~if~~A~~~gm~g~~yvWI~t~~~~~~~~~~- 238 (362)
T cd06378 160 DNSFVGWELQSVLTLDMSDDDGDARTQRQLKKLESQVILLYCSKEEAEYIFRAARSAGLTGPGYVWIVPSLVLGNTDLG- 238 (362)
T ss_pred hhcccceeEEEEEeeccCCCcchHHHHHHHHhcCCCEEEEECCHHHHHHHHHHHHHcCCcCCCeEEEecccccCCCccc-
Confidence 776666654444443322 234788999999999999999999999999999999999999999999999877663221
Q ss_pred cCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccCCC
Q 003633 158 KMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSASH 236 (806)
Q Consensus 158 ~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~~~ 236 (806)
..+..+|+++++. ++|+.. +.+..||||+++|+|++.+++.+ ..+.
T Consensus 239 -----~~~~~~G~i~v~~------------~~w~~~------------~~a~~~DaV~vva~Al~~l~~~~~~~~~---- 285 (362)
T cd06378 239 -----PSEFPVGLISVSY------------DGWRYS------------LRARVRDGVAIIATGASAMLRQHGFIPE---- 285 (362)
T ss_pred -----cccCCcceEeecc------------cccccc------------HHHHHHHHHHHHHHHHHHHHhccCCCCC----
Confidence 1244578877653 234321 24578999999999999987644 3321
Q ss_pred CCCCCccccccccc-cc-ccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeec-CceEEEEEeeCCCCcc
Q 003633 237 ELPDSKATRVQLEQ-LK-VFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDK-MEIHRVGYWFDGSGFS 312 (806)
Q Consensus 237 ~l~~~~~~~~~~~~-~~-~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~-~~~~~VG~w~~~~gl~ 312 (806)
...+|.. .. +|..|..|+++|++++|+|+ +|+||++|++.++.|+|+|++. .+|++||+|++ .+|.
T Consensus 286 -------~~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~--~i~F~~~G~r~~~~ldIinl~~~~g~~kVG~W~~-~~L~ 354 (362)
T cd06378 286 -------AKGSCYGQAEKRDLPPNTLHRYMMNVTWEGR--DLSFTEDGYLVNPKLVVISLNKERVWEEVGKWEN-GSLR 354 (362)
T ss_pred -------CCCCcCCCCCCCCCchHHHHHHhhcceECCC--ceeECCCCeEccceEEEEEecCCCCceEEEEEcC-CeEE
Confidence 1113322 22 37789999999999999997 9999999999999999999996 59999999995 3344
No 23
>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=9.6e-35 Score=319.12 Aligned_cols=278 Identities=16% Similarity=0.247 Sum_probs=226.4
Q ss_pred HhcccccCCCcEEecccCCCCccc-C-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccch---HHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-L-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNG---ISALSN 76 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~---~~~l~~ 76 (806)
++++++.++||+|++++++|.+++ . +|||+||+.|++..++.++++++++|+|++|++||++++||++. ++.|.+
T Consensus 83 va~ia~~~~iP~Is~~a~~~~~s~~~~~yp~~~R~~p~~~~~~~a~~~ll~~~~W~~vaiiy~~~~~~~~~~~~~~~l~~ 162 (387)
T cd06386 83 VARLASHWNIPMISAGALAAGFSHKKSEYSHLTRVAPSYVKMGETFSALFERFHWRSALLVYEDDKQERNCYFTLEGVHH 162 (387)
T ss_pred HHHHHHhCCCcEEccccCchhhccCcccCCeeEEecCchHHHHHHHHHHHHhCCCeEEEEEEEcCCCCccceehHHHHHH
Confidence 688999999999999999999987 3 49999999999999999999999999999999999999999887 899999
Q ss_pred HHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc-
Q 003633 77 MLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES- 155 (806)
Q Consensus 77 ~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~- 155 (806)
.+++.|++|+..+..+ .++.++..+|+++++.. |+||++++.+.+..++++|+++||+..+|+||..+...+....
T Consensus 163 ~~~~~gi~v~~~~~~~--~~~~d~~~~l~~ik~~~-rvii~~~~~~~~~~ll~~A~~~gm~~~~yv~i~~d~~~~~~~~~ 239 (387)
T cd06386 163 VFQEEGYHMSIYPFDE--TKDLDLDEIIRAIQASE-RVVIMCAGADTIRSIMLAAHRRGLTSGDYIFFNIELFNSSSYGD 239 (387)
T ss_pred HHHhcCceEEEEecCC--CCcccHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCCCCEEEEEEecccccccCC
Confidence 9999999998776554 23568999999999887 9999999999999999999999999999999999866311100
Q ss_pred -----cccCC---hhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccC---CCCCCCCccchhhhhhHHHHHHHHHHHH
Q 003633 156 -----FSKMN---QTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQK---GLVSAGLNTYGLYAYDTVWAVARSIDKF 224 (806)
Q Consensus 156 -----~~~~~---~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~---~~~~~~~~~~~~~aYDAv~~lA~Al~~~ 224 (806)
....+ ....+.++|+.+++++ ++.+++|.+++++++.. ..+...++.|++++|||||++|+|++++
T Consensus 240 ~~w~~~~~~~~~~~~a~~~~~~v~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~~yDav~l~A~Al~~~ 316 (387)
T cd06386 240 GSWKRGDKHDFEAKQAYSSLNTVTLLRTV---KPEFEKFSMEVKSSVEKAGDLNDCDYVNMFVEGFHDAILLYALALHEV 316 (387)
T ss_pred CCCccCCCcCHHHHHHHHhheEEeccCCC---ChHHHHHHHHHHHHHHhCCCCcccccchHHHHHHHHHHHHHHHHHHHH
Confidence 00011 2234556666665554 46788898888855432 1112245689999999999999999997
Q ss_pred HhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee---cCceEE
Q 003633 225 INEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID---KMEIHR 301 (806)
Q Consensus 225 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~---~~~~~~ 301 (806)
++.+ ..+.+|.+|.++|++++|+|+||++.||++|++. ..|.|+.++ .++++.
T Consensus 317 ~~~g-----------------------~~~~~g~~l~~~l~~~~f~G~tG~v~~d~~g~r~-~~~~v~~~~~~~~~~~~~ 372 (387)
T cd06386 317 LKNG-----------------------YSKKDGTKITQRMWNRTFEGIAGQVSIDANGDRY-GDFSVIAMTDVEAGTYEV 372 (387)
T ss_pred hhCC-----------------------CCCCCHHHHHHHHhCCceeeccccEEECCCCCcc-ccEEEEEccCCCCccEEE
Confidence 6543 0123599999999999999999999999999974 599999996 457899
Q ss_pred EEEeeCCC
Q 003633 302 VGYWFDGS 309 (806)
Q Consensus 302 VG~w~~~~ 309 (806)
||+|....
T Consensus 373 ~~~~~~~~ 380 (387)
T cd06386 373 VGNYFGKN 380 (387)
T ss_pred EeEEcccc
Confidence 99997533
No 24
>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=9.2e-35 Score=325.37 Aligned_cols=310 Identities=22% Similarity=0.453 Sum_probs=258.9
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
|+.+..-++||||||+||+|.||+ .+|+||.|++|+|.+|+.||++++++|+|++|..+++++|||+.++++|++..++
T Consensus 141 vanlLrlf~ipQisyaSts~~LSdk~ry~~F~RtVP~D~~Qa~Am~~il~~f~W~yVstv~s~~dYGE~Gieaf~~~a~~ 220 (878)
T KOG1056|consen 141 VANLLRLFLIPQISYASTSPDLSDKTRYDYFLRTVPSDVFQAQAMVDILKKFNWNYVSTVASEGDYGESGIEAFKEEAAE 220 (878)
T ss_pred HHHHHHhhcCceeccccCCcccccchhhhceeeecCChHHHHHHHHHHHHHhCeeEeeehhcCccchhhhHHHHHHhHHh
Confidence 567788899999999999999999 5799999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCC-CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKP-LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~-~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
+|+||...+.++....+..|+.+++++.+ .++|++|+++..++++.++++|..+++.+ .++||++|+|....+..
T Consensus 221 ~~iCIa~s~ki~~~~~~~~~~~~l~kl~~~~~a~vvV~F~~~~~~r~~~~aa~~~n~~g-~~~wiaSd~W~~~~~~~--- 296 (878)
T KOG1056|consen 221 RGICIAFSEKIYQLSIEQEFDCVLRKLLETPNARVVVVFCRGEDARRLLKAARRANLTG-EFLWIASDGWASQNSPT--- 296 (878)
T ss_pred cCceEEehhhcccccchhHHHHHHHHHhhcCCCeEEEEecCcchHHHHHHHHHHhCCCc-ceEEEecchhhccCChh---
Confidence 99999999888877777889999999887 89999999999999999999999999865 59999999998755543
Q ss_pred ChhhhhhccceEEEEEeCCCChhhHHHHHH---------------HhhhccCCCC-----------------------CC
Q 003633 160 NQTSLRILQGVVGLRQHTPDSIPKKAFLSR---------------WSGMQQKGLV-----------------------SA 201 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~---------------~~~~~~~~~~-----------------------~~ 201 (806)
....+..+|++++.+..+.-+.+++|.+. |++.|+.... .+
T Consensus 297 -~~~e~~a~g~i~i~l~~~~v~~F~~y~~s~~p~nn~~n~w~~e~w~~~f~C~l~~~~~~~~~~~~~Ct~~e~~~~~~~~ 375 (878)
T KOG1056|consen 297 -EAPEREAEGAITIKLASPQVPGFDRYFQSLHPENNRRNPWFAEFWEDKFNCSLPNSAFKNENLIRLCTAVERITLDSAY 375 (878)
T ss_pred -hhhhhhhceeEEEEecCCcchhHHHHHHhcCccccccCcccchhhhhcccCCCCcccccchhhhhhcccchhhccccch
Confidence 23345789999999998888887777654 5555541110 00
Q ss_pred CCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecC
Q 003633 202 GLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQD 281 (806)
Q Consensus 202 ~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~ 281 (806)
....-...++|||+++|+||+.+..+- ..+....|......+ |.+|++.+++++|.|..|.+.||++
T Consensus 376 ~q~~k~~~Vi~aVya~A~aLh~m~~~l------------c~~~~~~C~~m~~~d-g~~L~~~l~~vnF~~~~~~v~Fd~~ 442 (878)
T KOG1056|consen 376 EQDSKVQFVIDAVYAMAHALHNMHQDL------------CPGTSGLCSAMKAID-GSLLLKYLLNVNFTGPAGSVRFDEN 442 (878)
T ss_pred hhhcccccHHHHHHHHHHHHHHHHHhh------------cCCccccCcCccccC-HHHHHhhhheeEEecCCCceeecCC
Confidence 111234578999999999999987654 112233577777765 9999999999999999999999999
Q ss_pred CCeecccEEEEEeecC----ceEEEEEeeCCCCccccCcccccCCCCCCCccccccceeeeCCCCccCCCcee
Q 003633 282 RNIVSRGYDVINIDKM----EIHRVGYWFDGSGFSVLPPETLKGKNVSHSQLDWKLQNITWPGGKTETPRGWV 350 (806)
Q Consensus 282 G~~~~~~~~I~~~~~~----~~~~VG~w~~~~gl~~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~P~~~~ 350 (806)
|| ....|+|++++.. .+..||+|++...|. ...+.|.++..+.|++.|
T Consensus 443 gD-~~~~y~I~~~~~~~~~~~y~~vg~w~~~~~l~--------------------i~~~~w~~~~~~v~~S~C 494 (878)
T KOG1056|consen 443 GD-GPGRYDILNYQLTNGSYTYKEVGYWSEGLSLN--------------------IEDLDWTTKPSGVPKSVC 494 (878)
T ss_pred CC-CccceeEEEeeccCCCccceeeeeeccccccc--------------------ceeeeeccCCCCCccccc
Confidence 99 6789999999843 479999999966432 346789999988898887
No 25
>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=1.8e-33 Score=312.08 Aligned_cols=281 Identities=19% Similarity=0.249 Sum_probs=226.7
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEE-EEEEcCC-cccc---hHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVI-AIYVDDD-YGRN---GISALS 75 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~-ii~~d~~-~g~~---~~~~l~ 75 (806)
++++++.++||+||+++++|.+++ .+||||||+.|+|..++.++++++++|+|++++ ++|.|++ +|+. .++.+.
T Consensus 90 va~~a~~~~iP~Is~~a~~~~l~~~~~~~~~~R~~p~~~~~~~a~~~~~~~~~w~~va~ii~~~~~~~~~~~~~~~~~l~ 169 (405)
T cd06385 90 VARFTTHWDVPLVTAGAPALGFGVKDEYATITRTGPTHKKLGEFVLHIHQHFGWRSHAMLIYSDNKVDDRPCYFAMEGLY 169 (405)
T ss_pred HHHHHhccCCcEEccccChhhcCCcccCcceEEecCchHHHHHHHHHHHHhCCCeEEEEEEEecCcccccchHHHHHHHH
Confidence 578999999999999999999998 469999999999999999999999999999998 4565544 3343 468899
Q ss_pred HHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc
Q 003633 76 NMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES 155 (806)
Q Consensus 76 ~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~ 155 (806)
+.+++.|++|+..+..+ .+..+++.+|+++++.. |+||++++...+..++++|.++||+.++|+||+++++......
T Consensus 170 ~~~~~~gi~v~~~~~~~--~~~~d~~~~l~~ik~~~-~iii~~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~~~~~~ 246 (405)
T cd06385 170 MELKKNNITVVDLVFEE--DDLINYTTLLQDIKQKG-RVIYVCCSPDIFRRLMLQFWREGLPSEDYVFFYIDLFGASLQG 246 (405)
T ss_pred HHHHhCCeEEEEeeccC--CchhhHHHHHHHHhhcc-eEEEEeCCHHHHHHHHHHHHHcCCCCCcEEEEEeecchhhccC
Confidence 99999999999876433 23678999999998755 9999999999999999999999999999999999775433221
Q ss_pred ---------cccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhh----ccCCCCCCCCccchhhhhhHHHHHHHHHH
Q 003633 156 ---------FSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGM----QQKGLVSAGLNTYGLYAYDTVWAVARSID 222 (806)
Q Consensus 156 ---------~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~----~~~~~~~~~~~~~~~~aYDAv~~lA~Al~ 222 (806)
....+....+++++++....+.|.++.+++|.++|+++ |+...+...++.+++++|||||++|.||+
T Consensus 247 ~~~~~~w~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aa~~YDav~l~a~Al~ 326 (405)
T cd06385 247 PDPKRPWYRGDADDAAAREAFQSVKILTYKEPQNPEYKEFLSDLKTDAKEMFNFTVEDSLMNIIAGGFYDGVMLYAHALN 326 (405)
T ss_pred CCCCCCCCCCCcccHHHHHhhheeEEEeCCCCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHHHHHHHHHHHHHHHH
Confidence 00011334567899988877788888899999999985 33111111267899999999999999999
Q ss_pred HHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEE---eecCce
Q 003633 223 KFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVIN---IDKMEI 299 (806)
Q Consensus 223 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~---~~~~~~ 299 (806)
++.+.. +.+.+|++|.++|++++|+|++|++.||++|+|. +.|.|++ ++++++
T Consensus 327 ~~~~~~-----------------------~~~~~g~~i~~~l~~~~f~G~tG~v~fd~~G~r~-~~~~~~~~~~~~~g~~ 382 (405)
T cd06385 327 ETMAKG-----------------------GTRPPGTAITQRMWNRTFYGVTGFVKIDDNGDRE-TDFALWDMTDTESGDF 382 (405)
T ss_pred HHHhcC-----------------------CCCCCHHHHHHHhhCceEeeceeEEEEcCCCCEe-ceeEEEEccCCCCCcE
Confidence 975532 1123499999999999999999999999999974 7787774 478899
Q ss_pred EEEEEeeCCC
Q 003633 300 HRVGYWFDGS 309 (806)
Q Consensus 300 ~~VG~w~~~~ 309 (806)
+.||+|...+
T Consensus 383 ~~v~~~~~~~ 392 (405)
T cd06385 383 QVVSVYNGTQ 392 (405)
T ss_pred EEEEEEcccC
Confidence 9999998644
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=1.1e-32 Score=304.82 Aligned_cols=281 Identities=17% Similarity=0.208 Sum_probs=226.4
Q ss_pred HhcccccCCCcEEecccCCCCcccC--CCCceEEecCCcHHHHHHHHHHHHHcCCe-EEEEEEEcCCccc----chHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSAL--QFPYFIRSTQSDSQQMAAMADLIDFYGWK-EVIAIYVDDDYGR----NGISAL 74 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~--~~p~f~Rt~psd~~q~~ai~~ll~~~~W~-~v~ii~~d~~~g~----~~~~~l 74 (806)
++++++.++||+|++++++|.+++. +||||||+.|+|..++.++..++++|+|+ ++++||.++..+. ...+.+
T Consensus 89 v~~i~~~~~iP~Is~~at~~~ls~~~~~y~~~fR~~p~~~~~~~~~~~i~~~~~w~~~vaiiy~~~~~~~~~~~~~~~~~ 168 (399)
T cd06384 89 VARFATHWRLPLITAGAPAFGFSNKTDEYRTTVRTGPSTTKLGEFVNHLHEHFNWTSRAALLYLDLKTDDRPHYFISEGV 168 (399)
T ss_pred HHHHHhhcCCcEEeeccchhhhccccccCCceEEecCcHHHHHHHHHHHHHhCCCcEEEEEEEecCCccCCcceEehHHH
Confidence 6789999999999999999999974 69999999999999999988999999999 6889997543221 135678
Q ss_pred HHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccc
Q 003633 75 SNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLE 154 (806)
Q Consensus 75 ~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~ 154 (806)
.+.+++.|++|+....+. .+..|++++|.++|. ++|||+++++..++..+++||+++||+.++|+||..++....+.
T Consensus 169 ~~~~~~~gi~v~~~~~~~--~~~~d~~~~l~~ik~-~~~vIi~~~~~~~~~~i~~qa~~~g~~~~~y~~i~~d~~~~~~~ 245 (399)
T cd06384 169 FLALQEENANVSAHPYHI--EKNSDIIEIIQFIKQ-NGRIVYICGPLETFLEIMLQAQREGLTPGDYVFFYLDVFGESLR 245 (399)
T ss_pred HHHHHhcCceEEEEEEec--cchhhHHHHHHHHhh-cccEEEEeCCchHHHHHHHHHHHcCCCCCcEEEEEehhcccccc
Confidence 888999999999765544 336799999999997 89999999999999999999999999999999999886543221
Q ss_pred c----------cccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCC-CCCCC---CccchhhhhhHHHHHHHH
Q 003633 155 S----------FSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKG-LVSAG---LNTYGLYAYDTVWAVARS 220 (806)
Q Consensus 155 ~----------~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~-~~~~~---~~~~~~~aYDAv~~lA~A 220 (806)
. ..+..+...+.+++++++.++.|.++.+++|.++|++++... ..... .+.+++++||||+++|.|
T Consensus 246 ~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~p~~~~~~aa~~YDav~l~a~A 325 (399)
T cd06384 246 VKSPRESYKQMNHSSWTVLKEAFKSVFVITYREPENPEYKEFQRELHARAKEDFGVELEPSLMNFIAGCFYDGVMLYAMA 325 (399)
T ss_pred cCCCCccccCCCCcccHHHHHHHhheEEeecCCCCCchHHHHHHHHHHHHhhhcCCCcCcchHhhhhhhhHHHHHHHHHH
Confidence 0 000124455688999999988888888999999998753210 01112 367899999999999999
Q ss_pred HHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEE---EEeecC
Q 003633 221 IDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDV---INIDKM 297 (806)
Q Consensus 221 l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I---~~~~~~ 297 (806)
++++++.+ +.+.+|.+|.++|++++|+|+||++.||++|++ .+.|.+ .+++++
T Consensus 326 l~~~~~~~-----------------------~~~~~g~~i~~~l~~~~f~GvtG~v~fd~~G~r-~~~~~~~~~~~~~~g 381 (399)
T cd06384 326 LNETLAEG-----------------------GSQKDGLNITRKMQDRRFWGVTGLVSIDKNNDR-DIDFDLWAMTDHETG 381 (399)
T ss_pred HHHHHhcC-----------------------CCCCCcHhHHHHHhCceeecceeEEEECCCCCc-ccceEEEEeecCCCC
Confidence 99975432 123358899999999999999999999999996 356666 577899
Q ss_pred ceEEEEEeeCCC
Q 003633 298 EIHRVGYWFDGS 309 (806)
Q Consensus 298 ~~~~VG~w~~~~ 309 (806)
+++.||+|...+
T Consensus 382 ~~~~v~~~~~~~ 393 (399)
T cd06384 382 KYEVVAHYNGIT 393 (399)
T ss_pred eEEEEEEEcCCC
Confidence 999999998754
No 27
>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=1.1e-32 Score=305.82 Aligned_cols=268 Identities=24% Similarity=0.361 Sum_probs=222.7
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++++||+|++++++|.+++ ..|||+||+.|++..++.++++++++|+|++|++|++|++||+...+.+.+.+++
T Consensus 123 v~~i~~~~~vp~is~~~~~~~lt~~~~~~~~fr~~~~~~~~~~al~~~l~~~~~k~vaii~~~~~~g~~~~~~~~~~l~~ 202 (410)
T cd06363 123 VAPLFSFFLIPQISYGASSEVLSNKELYPSFLRTVPSDKDQIEAMVQLLQEFGWNWVAFLGSDDEYGRDGLQLFSELIAN 202 (410)
T ss_pred HHHHhcccccccccccccCccccccccCCCeeEecCCcHHHHHHHHHHHHHCCCcEEEEEEeCChhHHHHHHHHHHHHHH
Confidence 578999999999999999999997 4689999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCC-CChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 81 NMAKVSYKLPLPVQ-FNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 81 ~g~~i~~~~~~~~~-~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
.|++|+..+.++.. .+..|++++|.+|+++++|+||+++..+.+..++++|+++||. +.+||+++++.......
T Consensus 203 ~gi~i~~~~~~~~~~~~~~d~~~~l~~i~~~~~dvIil~~~~~~~~~il~qa~~~g~~--~~~~i~~~~~~~~~~~~--- 277 (410)
T cd06363 203 TGICIAYQGLIPLDTDPETDYQQILKQINQTKVNVIVVFASRQPAEAFFNSVIQQNLT--GKVWIASEAWSLNDELP--- 277 (410)
T ss_pred CCeEEEEEEEecCCCchHHHHHHHHHHHhcCCCeEEEEEcChHHHHHHHHHHHhcCCC--CCEEEEeCccccccccc---
Confidence 99999998888753 2467999999999999999999999999999999999999985 45899988764322211
Q ss_pred ChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 160 NQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
.....+...+++++....+..+..++|.++ +++.+|||||++|+|+++++.++.
T Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~----------------~~~~~YDaV~~~a~Al~~a~~~~~---------- 331 (410)
T cd06363 278 SLPGIRNIGTVLGVAQQTVTIPGFSDFIYS----------------FAFSVYAAVYAVAHALHNVLQCGS---------- 331 (410)
T ss_pred CCccceeeccEEEEEeCCCCCccHHHHHHH----------------HHHHHHHHHHHHHHHHHHHhCCCC----------
Confidence 011223455788888877778888888766 456799999999999999876541
Q ss_pred CCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecC----ceEEEEEeeCC
Q 003633 240 DSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKM----EIHRVGYWFDG 308 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~----~~~~VG~w~~~ 308 (806)
..|...+ ..++++|.++|++++|+|++|+++||++|++ ...+.|++++.. ++++||+|.+.
T Consensus 332 ------~~~~~~~-~~~~~~l~~~L~~~~~~g~~g~i~fd~~G~~-~~~~~i~~~~~~~~~~~~~~vG~~~~~ 396 (410)
T cd06363 332 ------GGCPKRV-PVYPWQLLEELKKVNFTLLGQTVRFDENGDP-NFGYDIVVWWWDNSSGTFEEVGSYSFY 396 (410)
T ss_pred ------CCCCCCC-CCCHHHHHHHHhccEEecCCcEEEeCCCCCC-ccceEEEEEEEcCCceeEEEEEEEECC
Confidence 0122111 2248899999999999999999999999984 567999999533 58999999874
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=1.6e-32 Score=303.66 Aligned_cols=282 Identities=18% Similarity=0.276 Sum_probs=228.1
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcc----cchHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYG----RNGISALSN 76 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g----~~~~~~l~~ 76 (806)
++++++.++||+|++++++|.|++ .+||||||+.|+|..++.++++++++++|++|++||.+++++ ....+.+.+
T Consensus 89 v~~~~~~~~ip~Is~~as~~~lt~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vaii~~~~~~~~~~~~~~~~~~~~ 168 (396)
T cd06373 89 VARFAAHWNVPVLTAGAPAAGFSDKSEYSTLTRTGPSYTKLGEFVLALHEHFNWSRAALLYHDDKNDDRPCYFTLEGVYT 168 (396)
T ss_pred HHHHHhcCCCceECccCCccccccchhcCceeeccccHHHHHHHHHHHHHHcCCeEEEEEEECCCCCcchHHHHHHHHHH
Confidence 578999999999999999999997 569999999999999999999999999999999999988774 556889999
Q ss_pred HHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc-
Q 003633 77 MLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES- 155 (806)
Q Consensus 77 ~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~- 155 (806)
.+++.|++|+... +.......|++++|+++++.. |+||++++..++..++++|+++||+..+|+||..+........
T Consensus 169 ~~~~~g~~v~~~~-~~~~~~~~d~~~~l~~ik~~~-~vii~~~~~~~~~~~~~qa~~~g~~~~~yv~i~~~~~~~~~~~~ 246 (396)
T cd06373 169 VLKEENITVSDFP-FDEDKELDDYKELLRDISKKG-RVVIMCASPDTVREIMLAAHRLGLTSGEYVFFNIDLFGSSLYGG 246 (396)
T ss_pred HHhhcCceeeEEe-ecCCccccCHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCCCcEEEEEEccchhhhccC
Confidence 9999999988543 443211368999999999865 9999999999999999999999999999999997755321100
Q ss_pred -------cccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhh----ccCCCCCCCCccchhhhhhHHHHHHHHHHHH
Q 003633 156 -------FSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGM----QQKGLVSAGLNTYGLYAYDTVWAVARSIDKF 224 (806)
Q Consensus 156 -------~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~----~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~ 224 (806)
.........+..+|++++..+.++++..++|.++|+++ |+...+...++.+++++||||+++|+||+++
T Consensus 247 ~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~Al~~~ 326 (396)
T cd06373 247 GPWWWERGDEDDEKAKEAYQALMTITLREPDNPEYKEFSLEVKERAKKKFNTTSDDSLVNFFAGAFYDAVLLYALALNET 326 (396)
T ss_pred CCCcCCCCCcccHHHHHHHHHheEEecCCCCChHHHHHHHHHHHHhhhcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 00011334456788999888888888899999999875 3211122246779999999999999999997
Q ss_pred HhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEe---ecCceEE
Q 003633 225 INEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINI---DKMEIHR 301 (806)
Q Consensus 225 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~---~~~~~~~ 301 (806)
..++ +...+|.+|.++|++++|+|++|+++||++|++ ...|.|+++ ++++++.
T Consensus 327 ~~~~-----------------------~~~~~~~~i~~~l~~~~f~G~tG~v~fd~~G~~-~~~~~v~~~~~~~~g~~~~ 382 (396)
T cd06373 327 LAEG-----------------------GDPRDGTNITRRMWNRTFEGITGNVSIDENGDR-ESDFSLWDMTDTETGTFEV 382 (396)
T ss_pred Hhcc-----------------------CCCCChHHHHHHhcCCceecccCceEeecCCcc-cceeeeeeccCCCCceEEE
Confidence 5432 011248999999999999999999999999996 467888665 6788999
Q ss_pred EEEeeCCC
Q 003633 302 VGYWFDGS 309 (806)
Q Consensus 302 VG~w~~~~ 309 (806)
||++.+.+
T Consensus 383 ~~~~~~~~ 390 (396)
T cd06373 383 VANYNGSN 390 (396)
T ss_pred Eeeccccc
Confidence 99988754
No 29
>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=3.8e-32 Score=297.80 Aligned_cols=274 Identities=15% Similarity=0.201 Sum_probs=217.8
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++++||+||+++++|.+++ .+||+|+|+.|++ +.++++++++|+|++|++||++++||.+..+.+.+.+++
T Consensus 82 ~a~va~~~~iP~Is~~a~~~~lt~~~~y~~f~r~~~~~---~~~~~~~~~~~~w~~vaii~~~~~~~~~~~~~l~~~l~~ 158 (382)
T cd06371 82 AALLAKEWDKALFSWGCVNYELDDVRSYPTFARTLPSP---SRVLFTVLRYFRWAHVAIVSSPQDIWVETAQKLASALRA 158 (382)
T ss_pred HHHHHHhcCceEEecccCchhhcCcccCCCceecCCCc---HHHHHHHHHHCCCeEEEEEEecccchHHHHHHHHHHHHH
Confidence 678999999999999999999997 5699999999987 467889999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCC-CeEEEEecCc-----chHHHHHHHHHHcCCccCCcEEEEcCccccccc
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLG-PRVYVVHVSP-----DPGLRIFTTAQKLQMMTNNYVWLATDWLSATLE 154 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~-~rvivl~~~~-----~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~ 154 (806)
.|++|+..+.++. +..|++++|++||+.+ +||||++++. .++..+++||+++||+..+|+||.+++.....+
T Consensus 159 ~gi~v~~~~~~~~--~~~d~~~~L~~lk~~~~~~viv~~~~~~~~~~~~~~~i~~qa~~~Gm~~~~y~~i~~d~~~~~~~ 236 (382)
T cd06371 159 HGLPVGLVTSMGP--DEKGAREALKKVRSADRVRVVIMCMHSVLIGGEEQRLLLETALEMGMTDGRYVFIPYDTLLYSLP 236 (382)
T ss_pred CCCcEEEEEEecC--CHHHHHHHHHHHhcCCCcEEEEEEeeccccCcHHHHHHHHHHHHcCCcCCcEEEEEeccccccCC
Confidence 9999998887874 4679999999999987 6999998876 677899999999999999999999986431111
Q ss_pred c----ccc--CChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCC-CCCCCCccchhhhhhHHHHHHHHHHHHHhh
Q 003633 155 S----FSK--MNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKG-LVSAGLNTYGLYAYDTVWAVARSIDKFINE 227 (806)
Q Consensus 155 ~----~~~--~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~-~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~ 227 (806)
. ... .+.+..++++|++++.+..+..+..+.|.+.|+....+. .+....+.|++++|||+|++|+|++++++.
T Consensus 237 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~YDav~~~a~Al~~a~~~ 316 (382)
T cd06371 237 YRNVSYPALRNNSKLRRAYDAVLTITMDSGEQSFYEAFRAAQERGEIPSDLEPEQVSPLFGTIYNSIYLLAHAVENARAA 316 (382)
T ss_pred CCCccccCCCCCHHHHHHhHhhEEEEecCCCCcHHHHHHHHHhcCCCCCCCCccccchhHHHHHHHHHHHHHHHHHHHHh
Confidence 0 000 023344678898888776555444555555543211110 011134567778999999999999997654
Q ss_pred cCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEe
Q 003633 228 HNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYW 305 (806)
Q Consensus 228 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w 305 (806)
+ + . .+|.+|+++|++++|+|++|+++||++|++ .+.|.|+++++.|+|-+=++
T Consensus 317 g---------------~--------~-~d~~~l~~~l~~~~f~GvtG~v~fd~~g~~-~~~~~v~~~~~~~~~~~~~~ 369 (382)
T cd06371 317 G---------------G--------G-VSGANLAQHTRNLEFQGFNQRLRTDSGGGG-QAPYVVLDTDGKGDQLYPTY 369 (382)
T ss_pred C---------------C--------C-ccHHHHHHHHhCccccccceEEEecCCCCc-ccceEEEecCCCCCeeeeeE
Confidence 3 0 0 138999999999999999999999999985 68999999999888765443
No 30
>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=4.1e-32 Score=300.49 Aligned_cols=277 Identities=15% Similarity=0.256 Sum_probs=225.0
Q ss_pred HhcccccCCCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++.+++.++||+|++++++|.|++. +||+|||+.|++..|+.++++++++++|++|++|+++++||++..+.+.+.+++
T Consensus 83 ~a~i~~~~~iP~Is~~a~~~~l~~~~~~~~f~r~~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~g~~~~~~~~~~~~~ 162 (404)
T cd06370 83 EARLAAAWNLPMISYKCDEEPVSDKSKYPTFARTVPPSIQVVKSVIALLKHFNWNKFSVVYENDSKYSSVFETLKEEAEL 162 (404)
T ss_pred HHHHHhhcCCcEEecccCCccccccccCCCeEEcCCCHHHHHHHHHHHHHHCCCcEEEEEEecCcccHHHHHHHHHHHHH
Confidence 4578899999999999999999974 699999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCC-----ChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCc-cCCcEEEEcCccccc--
Q 003633 81 NMAKVSYKLPLPVQF-----NQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMM-TNNYVWLATDWLSAT-- 152 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~-----~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~-~~~~~wi~t~~~~~~-- 152 (806)
.|++|+..+.++... ...++..+|++++.. ++++|++++..++..|+++|+++||+ ..+|+||.++.....
T Consensus 163 ~g~~iv~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~v~~~~~~~~~~~l~qa~~~g~~~~~~y~~i~~~~~~~~~~ 241 (404)
T cd06370 163 RNITISHVEYYADFYPPDPIMDNPFEDIIQRTKET-TRIYVFIGEANELRQFLMSMLDEGLLESGDYMVLGVDIEYYDRD 241 (404)
T ss_pred cCCEEEEEEEECCCCCchhhhHHHHHHHHHhccCC-CEEEEEEcCHHHHHHHHHHHHHcCCCCCCcEEEEEEchhhcccc
Confidence 999999988887542 246899999998865 78888888888899999999999998 678999997631100
Q ss_pred -------------ccccccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCC---------CCCCCCccchhhh
Q 003633 153 -------------LESFSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKG---------LVSAGLNTYGLYA 210 (806)
Q Consensus 153 -------------~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~---------~~~~~~~~~~~~a 210 (806)
............++++|++++.+..+ ++..++|.++|++++... .....++.|++++
T Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aa~~ 320 (404)
T cd06370 242 SQDYYSLHRGFQSREYNRSDDEKALEAMKSVLIIVPTPV-SPDYDSFSIFVRKYNLEPPFNGDLGESELVLEIDIEAAYL 320 (404)
T ss_pred chhhhhhhhhhccccccccccHHHHHHhHheEEEecCCC-CchHHHHHHHHHHhccCCCCcccccccccccccceeeehh
Confidence 01000011345567899988876655 777889999998875421 0122477899999
Q ss_pred hhHHHHHHHHHHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCcee-eEEEecCCCeecccE
Q 003633 211 YDTVWAVARSIDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSG-QVQFNQDRNIVSRGY 289 (806)
Q Consensus 211 YDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG-~i~Fd~~G~~~~~~~ 289 (806)
|||||++|+||+++++++ + ...+|.+|.++|++++|+|+|| +|+||++|++ ...|
T Consensus 321 yDAv~~~a~Al~~~~~~~--------------~---------~~~~g~~i~~~l~~~~f~GvtG~~v~fd~~G~~-~~~y 376 (404)
T cd06370 321 YDAVMLYAKALDETLLEG--------------G---------DIYNGTAIVSHILNRTYRSITGFDMYIDENGDA-EGNY 376 (404)
T ss_pred HHHHHHHHHHHHHHHHhc--------------C---------CCCCHHHHHHHHhCcccccccCceEEEcCCCCc-ccce
Confidence 999999999999976543 0 0124899999999999999999 8999999996 5899
Q ss_pred EEEEeecCceEEEEE
Q 003633 290 DVINIDKMEIHRVGY 304 (806)
Q Consensus 290 ~I~~~~~~~~~~VG~ 304 (806)
.|++++++.|-.-|.
T Consensus 377 ~v~~~~~~~~~~~~~ 391 (404)
T cd06370 377 SVLALQPIPPGDNGS 391 (404)
T ss_pred EEEEeccccccCCCC
Confidence 999999876655443
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=1.5e-31 Score=295.32 Aligned_cols=281 Identities=14% Similarity=0.215 Sum_probs=216.8
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC---Ccc--cchHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD---DYG--RNGISALS 75 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~---~~g--~~~~~~l~ 75 (806)
++++++.++||+|++++++|.|++ ..||+++|+.|++..++.++++++++|||++|++||+++ .|| ....+.+.
T Consensus 84 v~~va~~~~iP~is~~s~s~~ls~~~~~~~~~r~~p~~~~~~~a~~~l~~~~~w~~vaii~~~~~~~~~~~~~~~~~~~~ 163 (391)
T cd06372 84 TGLLASQWNIPMFGFVGQTAKLDNRFLYDTYVKLVPPKQKIGEVLQKSLQHFGWKHIGLFGGSSRDSSWDEVDELWKAVE 163 (391)
T ss_pred HHHHHhccCccEEEeecCCccccccccCCceEEecCchhhHHHHHHHHHHHCCCeEEEEEEeccccchhhhHHHHHHHHH
Confidence 678999999999999999999997 469999999999999999999999999999999998643 344 22344555
Q ss_pred HHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc
Q 003633 76 NMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES 155 (806)
Q Consensus 76 ~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~ 155 (806)
+.++ .++++...+.++.+ ..++...+.+.+.+++|+||++++.+++..++++|+++||+..+|+||++++.....-.
T Consensus 164 ~~~~-~~~~i~~~~~~~~~--~~d~~~~~l~~~~~~~~vii~~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~~~~w~ 240 (391)
T cd06372 164 NQLK-FHFNITATVRYSSS--NPDLLQEKLRYISSVARVIILICSSEDAKAILQAAEKLGLMKGKFVFFLLQQFEDNFWK 240 (391)
T ss_pred HHHh-hCEEEEEEEecCCC--ChHHHHHHHHhhhccceEEEEEcChHHHHHHHHHHHHcCCCCCCEEEEEehhhcCcccc
Confidence 5554 67899888777643 45777666666678999999999999999999999999998878999996432211100
Q ss_pred --ccc-CChhhhhhccceEEEEEeCCC-ChhhHHHHHHHhhhccCCC------CCCCCccchhhhhhHHHHHHHHHHHHH
Q 003633 156 --FSK-MNQTSLRILQGVVGLRQHTPD-SIPKKAFLSRWSGMQQKGL------VSAGLNTYGLYAYDTVWAVARSIDKFI 225 (806)
Q Consensus 156 --~~~-~~~~~~~~~~gv~~~~~~~~~-~~~~~~f~~~~~~~~~~~~------~~~~~~~~~~~aYDAv~~lA~Al~~~~ 225 (806)
... ......+..+|++++.+..+. .+..++|.++|+++++... .....+.|++++|||||++|+|+++++
T Consensus 241 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~f~~~~~~~~~~~p~~~~~~~~~~~~~~a~~~yDav~~~A~Al~~~~ 320 (391)
T cd06372 241 EVLTDDQVQHLPKVYESVFLIAPSSYGGYSGGYEFRKQVYQKLKRPPFQSSLSSEEQVSPYSAYLHDAVLLYALAVKEML 320 (391)
T ss_pred ccCCCcchHHHHHHHhhEEEEecCCCCCCcchhHHHHHHHHHHhcCCccccccccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 000 012244567898888776542 3556788888887764211 112446889999999999999999976
Q ss_pred hhcCccccCCCCCCCCcccccccccccccCchHHHHHHHH---ccccCCceeeEEEecCCCeecccEEEEEeec----Cc
Q 003633 226 NEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLL---QTNFTGLSGQVQFNQDRNIVSRGYDVINIDK----ME 298 (806)
Q Consensus 226 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~---~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~----~~ 298 (806)
+++ ..+.+|.+|.+.|+ +++|+|+||+|.||++|++ .+.|.|+++++ ..
T Consensus 321 ~~g-----------------------~~~~~g~~l~~~l~~~~~~~f~G~tG~v~fd~~G~r-~~~y~i~~~~~~~~~~~ 376 (391)
T cd06372 321 KAG-----------------------KDFRNGRQLVSTLRGANQVELQGITGLVLLDEQGKR-QMDYSVYALQKSGNSSL 376 (391)
T ss_pred hcC-----------------------CCCCCHHHHHHHHhhccCceEeccceeEEECCCCCc-ceeEEEEeccccCCccc
Confidence 543 11234889999999 6899999999999999996 68999999975 24
Q ss_pred eEEEEEeeCCC
Q 003633 299 IHRVGYWFDGS 309 (806)
Q Consensus 299 ~~~VG~w~~~~ 309 (806)
++.||+|...+
T Consensus 377 ~~~vg~~~~~~ 387 (391)
T cd06372 377 FLPFLHYDSHQ 387 (391)
T ss_pred eeeEEEecchh
Confidence 79999998754
No 32
>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=2.3e-31 Score=289.89 Aligned_cols=263 Identities=44% Similarity=0.758 Sum_probs=228.4
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+|++++++|.|++ ..+||+||+.|++..++.++++++++++|++|++|+.|++||+...+.+.+.+++
T Consensus 82 ~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~~~r~~p~~~~~~~a~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~~~ 161 (350)
T cd06366 82 VAEVANEWNVPVLSFAATSPSLSSRLQYPYFFRTTPSDSSQNPAIAALLKKFGWRRVATIYEDDDYGSGGLPDLVDALQE 161 (350)
T ss_pred HHHHhhcCCeeEEeccCCCccccccccCCceEEcccchHhHHHHHHHHHHHCCCcEEEEEEEcCcccchhHHHHHHHHHH
Confidence 568899999999999999999965 4599999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc-cccC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES-FSKM 159 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~-~~~~ 159 (806)
.|++|+....++...+..|+..+|++|++.++|+|++++...++..++++|+++||...+|+||.++++....+. ..+.
T Consensus 162 ~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~dvvi~~~~~~~~~~~~~~a~~~g~~~~~~~~i~~~~~~~~~~~~~~~~ 241 (350)
T cd06366 162 AGIEISYRAAFPPSANDDDITDALKKLKEKDSRVIVVHFSPDLARRVFCEAYKLGMMGKGYVWILTDWLSSNWWSSSDCT 241 (350)
T ss_pred cCCEEEEEeccCCCCChhHHHHHHHHHhcCCCeEEEEECChHHHHHHHHHHHHcCCcCCCEEEEECcchhhhhccCCCCC
Confidence 999999998888654467999999999999999999999999999999999999998888999999876654310 0011
Q ss_pred ChhhhhhccceEEEEEeCCC-ChhhHHHHHHHhhhccCC-CCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCC
Q 003633 160 NQTSLRILQGVVGLRQHTPD-SIPKKAFLSRWSGMQQKG-LVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHE 237 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~-~~~~~~f~~~~~~~~~~~-~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~ 237 (806)
.....+..+|++++.++.++ ++..++|.++|+++++.. .....++.+++++|||+++
T Consensus 242 ~~~~~~~~~gv~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~p~~~a~~~YDav~~--------------------- 300 (350)
T cd06366 242 DEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWRKRFGNENPELTEPSIYALYAYDAVWA--------------------- 300 (350)
T ss_pred hHHHHHhhceEEEEeecccccCccHHHHHHHHHHHhcccCcCcCCCCcccchhhhheee---------------------
Confidence 24456778999999998887 888999999999998621 0012478899999999987
Q ss_pred CCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCccc
Q 003633 238 LPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGFSV 313 (806)
Q Consensus 238 l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl~~ 313 (806)
+++|.|++|+++||++|++....|+++++.+++++.||+|++.+|+++
T Consensus 301 ----------------------------~~~~~G~~G~v~fd~~~~~~~~~~~~~~~~~~~~~~vg~~~~~~~~~~ 348 (350)
T cd06366 301 ----------------------------STNFNGLSGPVQFDGGRRLASPAFEIINIIGKGYRKIGFWSSESGLSV 348 (350)
T ss_pred ----------------------------eceEEeeeeeEEEcCCCccCCcceEEEEecCCceEEEEEEeCCCCccc
Confidence 136899999999999999888999999999999999999999998863
No 33
>PF01094 ANF_receptor: Receptor family ligand binding region The Prosite family is a sub-family of the Pfam family; InterPro: IPR001828 This describes a ligand binding domain and includes extracellular ligand binding domains of a wide range of receptors, as well as the bacterial amino acid binding proteins of known structure [].; PDB: 3SAJ_D 3Q41_B 3QEM_C 3QEK_A 3QEL_C 3MQ4_A 3QLV_G 3OM1_A 3QLU_A 3OM0_A ....
Probab=99.98 E-value=3.4e-31 Score=288.61 Aligned_cols=272 Identities=28% Similarity=0.539 Sum_probs=223.4
Q ss_pred HhcccccCCCcEEecccCCCCccc-C-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-L-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLE 79 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~ 79 (806)
++.+++.++||+|+++++++.|++ . +||+|+|+.|++..+++|+++++++|+|++|++||+++++|.+..+.+.+.++
T Consensus 67 ~~~~~~~~~ip~is~~~~~~~ls~~~~~~~~~~r~~p~~~~~~~a~~~~l~~~~w~~v~vv~~~~~~~~~~~~~~~~~~~ 146 (348)
T PF01094_consen 67 VASLASEWNIPQISPGSTSPSLSDRKTRYPTFFRTVPSDSSQARALVDLLKHFGWTRVSVVYSDDDYGNSLADSFQDLLR 146 (348)
T ss_dssp HHHHHHHTT-EEEESSGGSGGGGSTTTTTTTEEESSB-HHHHHHHHHHHHHHTTSSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred hheeecccccceeeccccccccccchhhccccccccccHHHHHHHHHHhhhcCCCceeeeeccccccccccchhhhhhhc
Confidence 578899999999999999999998 4 59999999999999999999999999999999999999999999999999999
Q ss_pred hCC-cEEEEEeccCCCCChhHHHHHHHhcC--CCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccc
Q 003633 80 KNM-AKVSYKLPLPVQFNQHDITVLLNNSK--PLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESF 156 (806)
Q Consensus 80 ~~g-~~i~~~~~~~~~~~~~~~~~~l~~ik--~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~ 156 (806)
+.+ .++......+. +..++...+.+++ ..++|+||+++....+..++++|.++||...+|+||.++++.......
T Consensus 147 ~~~~~~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~rvvil~~~~~~~~~~l~~a~~~~~~~~~~~~i~~~~~~~~~~~~ 224 (348)
T PF01094_consen 147 ERGGICVAFISVVIS--SDSDAEELLKKLKEIKSGARVVILCSSPEDARQFLEAAYELGMTSGDYVWILTDLDNSSFWQN 224 (348)
T ss_dssp HHTTCEEEEEEEEET--TTSHHHHHHHHHHHHTTTTSEEEEESBHHHHHHHHHHHHHTTTSSTTSEEEEETTTTTTHTST
T ss_pred ccccceecccccccc--cccchhhhhhhhhhccccceeeeeecccccccccccchhhhhccccceeEEeecccccccccc
Confidence 954 55555122322 2234444444444 499999999999999999999999999999999999999876654211
Q ss_pred ccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhcc---CCCCCCCCccchhhhhhHHHHHHHHHHHHHhhc-Cccc
Q 003633 157 SKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQ---KGLVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITF 232 (806)
Q Consensus 157 ~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~---~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~ 232 (806)
.....+...|+++++++.+..+.+++|.++|+.... .......+..+++++||||+++|+|+++++..+ ...
T Consensus 225 ---~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~yDAv~~~a~al~~~~~~~~~~~- 300 (348)
T PF01094_consen 225 ---NEDFREAFQGVLGFTPPPPSSPEFEDFMKKWKESNNQSSTSGSDQEPSPYAAYAYDAVYLLAHALNRALQDGGPVT- 300 (348)
T ss_dssp ---HCHHHCCHTTEEEEEESTTTSHHHHHHHHHHHTTTHTTTTTTTTSSGCHHHHHHHHHHHHHHHHHHHHHHHHSTTT-
T ss_pred ---cccccccccceeeeeeecccccchhhhhcccChhhccCcccccccccceeeeeehhhhHHHHHHHHHHHHhccCCC-
Confidence 245678889999999999999999999999997632 112334678899999999999999999998764 111
Q ss_pred cCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEec-CCCeecccEEEEEee
Q 003633 233 SASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQ-DRNIVSRGYDVINID 295 (806)
Q Consensus 233 ~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~-~G~~~~~~~~I~~~~ 295 (806)
. ....+.+|..|.++|++++|+|++|++.||+ +|++....|+|+|++
T Consensus 301 --------------~--~~~~~~~g~~l~~~l~~~~f~G~tG~v~f~~~~G~~~~~~~~i~~~~ 348 (348)
T PF01094_consen 301 --------------N--GRNPWQNGSQLLKYLRNVSFEGLTGRVSFDSNDGDRTNYDYDILNMQ 348 (348)
T ss_dssp --------------S--SSGTSTTHHHHHHHHHTEEEEETTEEEEEETTTSBEESEEEEEEEE-
T ss_pred --------------C--CccccccHHHHHHHHhheeeeCCCCCEEEeCCCCCcCCCEEEEEECC
Confidence 0 0145667999999999999999999999999 899989999999975
No 34
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=99.97 E-value=1.1e-31 Score=284.38 Aligned_cols=245 Identities=17% Similarity=0.285 Sum_probs=195.3
Q ss_pred HhcccccCCCcEEecccCC-CCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATD-PTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~-p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++|++++||+|+++.+. |.+...+|++ +++.|++..|++|++++|++||||+|++||+|+++ +..|++.++.
T Consensus 82 v~~i~~~~~VP~Is~~~~~~~~~~~~~~~~-i~l~P~~~~~~~Ai~dli~~~~W~~v~~iYe~d~~----l~~L~~~l~~ 156 (333)
T cd06394 82 VSHICGEKEIPHFKVGPEETPKLQYLRFAS-VNLHPSNEDISVAVAGILNSFNYPTASLICAKAEC----LLRLEELLRQ 156 (333)
T ss_pred HHHHhhccCCceEEeccccCcccccccceE-EEecCCHHHHHHHHHHHHHhcCCCEEEEEEeCcHH----HHHHHHHHHh
Confidence 6899999999999987543 5554455555 89999999999999999999999999999999986 5666777765
Q ss_pred CCcEEEEEeccCCC--CChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccccc
Q 003633 81 NMAKVSYKLPLPVQ--FNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSK 158 (806)
Q Consensus 81 ~g~~i~~~~~~~~~--~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~ 158 (806)
.++ ++..++.. .++.|++.+|++|+.+++|+||++|+++.+..|+++|+++||+..+|+||+|+......+..
T Consensus 157 ~~~---~~~~i~~~~~~~~~d~~~~L~~ik~~~~~~iVv~~~~~~a~~il~qa~~lGm~~~~y~~i~T~l~~~~~~L~-- 231 (333)
T cd06394 157 FLI---SKETLSVRMLDDSRDPTPLLKEIRDDKTATIIIDANASMSHTILLKASELGMTSAFYKYILTTMDFPLLRLD-- 231 (333)
T ss_pred hcc---cCCceeeEEccCcccHHHHHHHHHhcCCCEEEEECChHHHHHHHHHHHHcCCCCCceEEEEecCCcccccHH--
Confidence 433 22333322 23568999999999999999999999999999999999999999999999999776644442
Q ss_pred CChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCC--C-CCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCC
Q 003633 159 MNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKG--L-VSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSAS 235 (806)
Q Consensus 159 ~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~--~-~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~ 235 (806)
+.......+.+++...++.+..++|.++|++++... . .......-++.+||||+++
T Consensus 232 ---~~~~~~~niTgF~l~d~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~~al~~D~v~~~------------------ 290 (333)
T cd06394 232 ---SIVDDRSNILGFSMFNQSHAFYQEFIRSLNQSWRENCDHSPYTGPALSSALLFDAVYAV------------------ 290 (333)
T ss_pred ---HhhcCCcceEEEEeecCCcHHHHHHHHHHHHhhhhhcccccCCCcccceeeecceEEEE------------------
Confidence 222224457899999999999999999988866310 0 0011123456667766532
Q ss_pred CCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCcc
Q 003633 236 HELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGFS 312 (806)
Q Consensus 236 ~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl~ 312 (806)
|+||+|+||++|.|.+...+|+++..+|.++||+|++.+||+
T Consensus 291 -----------------------------------glTg~i~f~~~g~R~~~~l~v~~l~~~g~~kig~W~~~~gl~ 332 (333)
T cd06394 291 -----------------------------------GLTGRIEFNSKGQRSNYTLKILQKTRSGFRQIGQWHSNETLS 332 (333)
T ss_pred -----------------------------------eeecceecCCCCcCcccEEEEEEecCCcceEEEEEeCCCCcC
Confidence 899999999999999999999999999999999999999986
No 35
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=99.97 E-value=2.4e-30 Score=286.15 Aligned_cols=284 Identities=18% Similarity=0.350 Sum_probs=238.2
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC-cccchHHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD-YGRNGISALSNMLE 79 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~-~g~~~~~~l~~~l~ 79 (806)
++++++.++||+|++++++|.+++ ..+||+||+.|++..++.+++++++++||+++++++++++ ||....+.+.+.++
T Consensus 84 ~~~~~~~~~ip~Is~~~~~~~~~~~~~~~~~fr~~~~~~~~~~a~~~~l~~~~~~~v~ii~~~~~~~g~~~~~~~~~~~~ 163 (389)
T cd06352 84 VARLAAHWNIPMISWGCVALSLSDKSEYPTLTRTLPPARKLGEAVLALLRWFNWHVAVVVYSDDSENCFFTLEALEAALR 163 (389)
T ss_pred HHHHHhcCCCCEecccccccccCccccCCceeecCCcHHHHHHHHHHHHHHcCceEEEEEEecCCccHHHHHHHHHHHHH
Confidence 578899999999999999999987 4689999999999999999999999999999999998888 99999999999999
Q ss_pred hCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc----
Q 003633 80 KNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES---- 155 (806)
Q Consensus 80 ~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~---- 155 (806)
+.|++|+....++...+..|+..+|+++++.. |+||+++.+.++..+++++.++||...+|+||.++.+......
T Consensus 164 ~~G~~v~~~~~~~~~~~~~d~~~~l~~i~~~~-~vii~~~~~~~~~~~l~q~~~~g~~~~~~~~i~~~~~~~~~~~~~~~ 242 (389)
T cd06352 164 EFNLTVSHVVFMEDNSGAEDLLEILQDIKRRS-RIIIMCGSSEDVRELLLAAHDLGLTSGDYVFILIDLFNYSLPYQNSY 242 (389)
T ss_pred hcCCeEEEEEEecCCccchhHHHHHHHhhhcc-eEEEEECCHHHHHHHHHHHHHcCCCCCcEEEEEEehhccccccCCCC
Confidence 99999999888875422578999999999887 9999999999999999999999998888999998876554211
Q ss_pred ----cccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCC-----CCCCCccchhhhhhHHHHHHHHHHHHHh
Q 003633 156 ----FSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGL-----VSAGLNTYGLYAYDTVWAVARSIDKFIN 226 (806)
Q Consensus 156 ----~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~-----~~~~~~~~~~~aYDAv~~lA~Al~~~~~ 226 (806)
.........+.++|++++.++.+.++..++|.++|+++++... ....++.|++++|||||++|+|++++.+
T Consensus 243 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~Al~~~~~ 322 (389)
T cd06352 243 PWERGDGDDEKAKEAYDAVLTITLRPPDNPEYEEFSEEVKEAAKRPPFNTDAEPEQVSPYAGYLYDAVLLYAHALNETLA 322 (389)
T ss_pred CcccCCcccHHHHHHHHhheEEEecCCCCchHHHHHHHHHHHHhcccCccCCCccccchhhhhHHHHHHHHHHHHHHHHH
Confidence 0011234556789999998888888899999999999885211 1224678999999999999999999765
Q ss_pred hcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeec--CceEEEEE
Q 003633 227 EHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDK--MEIHRVGY 304 (806)
Q Consensus 227 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~--~~~~~VG~ 304 (806)
++ ..+.++.++.+.|++++|.|++|++.||++|++. +.|.|+++++ +.+..++.
T Consensus 323 ~~-----------------------~~~~~~~~v~~~l~~~~f~g~~G~v~fd~~G~~~-~~~~v~~~~~~~~~~~~~~~ 378 (389)
T cd06352 323 EG-----------------------GDYNGGLIITRRMWNRTFSGITGPVTIDENGDRE-GDYSLLDLDSTGGQLEVVYL 378 (389)
T ss_pred hC-----------------------CCCCchHHHHHHhcCcEEEeeeeeEEEcCCCCee-eeEEEEEecCCCceEEEEEe
Confidence 43 0022488899999999999999999999999964 7899999986 56788887
Q ss_pred eeCCCC
Q 003633 305 WFDGSG 310 (806)
Q Consensus 305 w~~~~g 310 (806)
....+|
T Consensus 379 ~~~~~~ 384 (389)
T cd06352 379 YDTSSG 384 (389)
T ss_pred ccccce
Confidence 766553
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=99.97 E-value=1e-29 Score=274.03 Aligned_cols=242 Identities=22% Similarity=0.335 Sum_probs=201.7
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
+++++++++||+|+++++++.++ .++|+||+.|++..|+.++++++++++|++|+++|+|++++.. +.+.+++.
T Consensus 79 v~~~~~~~~vP~Is~~~~~~~~~--~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vavl~~~~~~~~~----l~~~~~~~ 152 (327)
T cd06382 79 VQSICDAKEIPHIQTRWDPEPKS--NRQFTINLYPSNADLSRAYADIVKSFNWKSFTIIYESAEGLLR----LQELLQAF 152 (327)
T ss_pred HHHHHhccCCCceeccCCcCccc--cccceEEeCCCHHHHHHHHHHHHHhcCCcEEEEEecChHHHHH----HHHHHHhh
Confidence 57899999999999999988887 4589999999999999999999999999999999998886543 55555555
Q ss_pred Cc---EEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccccc
Q 003633 82 MA---KVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSK 158 (806)
Q Consensus 82 g~---~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~ 158 (806)
+. .|.. +.+++. . |++++|.+|+++++|+|+++++..++..++++|+++||+...|+|+++++.....+..
T Consensus 153 ~~~g~~v~~-~~~~~~--~-d~~~~l~~i~~~~~d~vv~~~~~~~~~~~~~qa~~~g~~~~~~~~i~~~~~~~~~~l~-- 226 (327)
T cd06382 153 GISGITITV-RQLDDD--L-DYRPLLKEIKNSGDNRIIIDCSADILIELLKQAQQVGMMSEYYHYIITNLDLHTLDLE-- 226 (327)
T ss_pred ccCCCeEEE-EEccCC--c-cHHHHHHHHHhcCceEEEEECCHHHHHHHHHHHHHhCccccceEEEEecCCccccchh--
Confidence 54 4554 445543 3 9999999999999999999999999999999999999999999999988755544332
Q ss_pred CChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCC---CCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCC
Q 003633 159 MNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKG---LVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSAS 235 (806)
Q Consensus 159 ~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~---~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~ 235 (806)
.......++.+++++.++++..++|.++|+++++.. .....++.+++++|||++++
T Consensus 227 ---~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~~a~~yDav~~~------------------ 285 (327)
T cd06382 227 ---DYRYSGVNITGFRLVDPDSPEVKEVIRSLELSWDEGCRILPSTGVTTESALMYDAVYLF------------------ 285 (327)
T ss_pred ---hhccCceeEEEEEEecCCchhHHHHHHHHHhhcccccccCCCCCcchhhhhhhceEEEe------------------
Confidence 122234478888888888899999999999998631 11224778899999987743
Q ss_pred CCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCc
Q 003633 236 HELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGF 311 (806)
Q Consensus 236 ~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl 311 (806)
|+||+|+||++|+|.+..++|+|+++++++.||+|++..||
T Consensus 286 -----------------------------------g~tG~v~f~~~g~r~~~~~~~~~~~~~~~~~vg~w~~~~~~ 326 (327)
T cd06382 286 -----------------------------------GLTGRIEFDSSGQRSNFTLDVIELTESGLRKVGTWNSSEGL 326 (327)
T ss_pred -----------------------------------ecccceeeCCCCCEeeeEEEEEeccccCceEEEEECCCCCc
Confidence 89999999999999999999999999999999999998876
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=99.96 E-value=7.6e-28 Score=259.92 Aligned_cols=260 Identities=14% Similarity=0.212 Sum_probs=191.5
Q ss_pred HhcccccCCCcEEecccC---CCC-----ccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHH
Q 003633 2 ISEVANGLKVPLVSFAAT---DPT-----LSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGIS 72 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at---~p~-----Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~ 72 (806)
++++++.++||+|++++. +|. +.+ ..-+|.|++.|++ .+..|+++++++|||++|+++|++++ |...++
T Consensus 78 v~~i~~~~~IP~Is~~~~~~~~~~~~~~~~~~~~~~~~~f~~rp~~-~~~~ai~~lv~~~~wkkvavly~~d~-g~~~l~ 155 (363)
T cd06381 78 LQSLTDAMHIPHLFIQRGYGGSPRTACGLNPSPRGQQYTLALRPPV-RLNDVMLRLVTEWRWQKFVYFYDNDY-DIRGLQ 155 (363)
T ss_pred HHHHhhCCCCCEEEeecCcCCCcccccccCCCcccceeEEEEeccH-HHHHHHHHHHHhCCCeEEEEEEECCc-hHHHHH
Confidence 678999999999997532 221 111 1223444555664 78999999999999999999998776 556668
Q ss_pred HHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcC-------CCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEE
Q 003633 73 ALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSK-------PLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLA 145 (806)
Q Consensus 73 ~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik-------~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~ 145 (806)
.+.+++++.|+.+.... ...+ ....++.+++.++ ..+.++||++|+++.+..++++|.++||+..+|+||+
T Consensus 156 ~~~~~~~~~g~~v~~~~-~~~~-~~~~~~~l~~~~~~~~l~~~~~~~~~vIl~~~~~~~~~~l~~a~~~gm~~~~~~wi~ 233 (363)
T cd06381 156 EFLDQLSRQGIDVLLQK-VDLN-ISKMATALFTTMRCEELNRYRDTLRRALLLLSPNGAYTFIDASVETNLAIKDSHWFL 233 (363)
T ss_pred HHHHHHHhcCceEEEEe-cccc-cchhhhhhhhHHHHHHHHhhcccceEEEEEcCcHHHHHHHHHHHHcCCCcCceEEEE
Confidence 88889999998776543 2211 1223444444332 3466688999999999999999999999999999998
Q ss_pred cCcccccccccccCChhhhhhccceEEEEEeCCCChhhH----HHHHHHhhhccCCCC-CCCCccchhhhhhHHHHHHHH
Q 003633 146 TDWLSATLESFSKMNQTSLRILQGVVGLRQHTPDSIPKK----AFLSRWSGMQQKGLV-SAGLNTYGLYAYDTVWAVARS 220 (806)
Q Consensus 146 t~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~----~f~~~~~~~~~~~~~-~~~~~~~~~~aYDAv~~lA~A 220 (806)
++.+....... ....+...|++|+++..|.++..+ +|.+.|++...+..+ ...+...++++|||||++
T Consensus 234 ~~~l~~~~~~l----~~~~~~~~nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~yDaV~~~--- 306 (363)
T cd06381 234 INEEISDTEID----ELVRYAHGRMTVIRQTFSKEKTNQRCLRNNHRISSLLCDPKDGYLQMLEISNLYIYDSVLLL--- 306 (363)
T ss_pred eccccccchhh----HHHhhcCccEEEEEEecCCcCchHHHHHHHHHHHHhhcCCCCCCCCChhHHHHHHHHHHHHH---
Confidence 77665532221 345677899999999988777766 455566554432211 124567799999999998
Q ss_pred HHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCc--
Q 003633 221 IDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKME-- 298 (806)
Q Consensus 221 l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~-- 298 (806)
+++|++++|+|+||+|+||++|.|.+..++|+++.-.+
T Consensus 307 ----------------------------------------~~~~~~~~~~GLTG~i~F~~~g~r~~~~l~i~~~~~~~~~ 346 (363)
T cd06381 307 ----------------------------------------LETIKKGPITGLTGKLEFNEGGDNSNVQFEILGTGYSETL 346 (363)
T ss_pred ----------------------------------------HHHHHhcCccCcceeEEeCCCCCccccEEEEEEeccCCcc
Confidence 22355678999999999999999999999999998555
Q ss_pred ---eEEEEEeeCCCCcc
Q 003633 299 ---IHRVGYWFDGSGFS 312 (806)
Q Consensus 299 ---~~~VG~w~~~~gl~ 312 (806)
.+.+|+|++.+||+
T Consensus 347 ~~~~~~~~~w~~~~~~~ 363 (363)
T cd06381 347 GKDGRWLATWNPSKGLN 363 (363)
T ss_pred ccceEEeeeccCCCCCC
Confidence 79999999998863
No 38
>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=99.96 E-value=3e-29 Score=271.30 Aligned_cols=265 Identities=14% Similarity=0.148 Sum_probs=186.9
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHH-HHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGIS-ALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~-~l~~~l~~ 80 (806)
|+++++.++||+|+++.. ..++.+||||+|+.|+|..|++|+++++++|+|++|++||+|++++..... .+.+...+
T Consensus 83 V~si~~~~~IP~Is~s~~--~~~~~~~p~~ir~~Ps~~~~~~Ai~dlI~~f~W~~v~iIYddd~gl~~~l~~~l~~~~~~ 160 (368)
T cd06383 83 IKSVTGALGIPTFSASYG--QEGDLEQPYLIQLMPPADDIVEAIRDIVSYYNITNAAILYDDDFVMDHKYKSLLQNWPTR 160 (368)
T ss_pred HHHHHhccCCCEEEccCC--CcCcccCceEEEEeCChHHHHHHHHHHHHHCCCcEEEEEEEcCchhhHHHHHHHHhHHhc
Confidence 678999999999997543 334457999999999999999999999999999999999976664432333 33333344
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC-cchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS-PDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~-~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
.++++. + ....+++.+|++|+.++.+.||+.+. ++.+..|+++|.++||++.+|+||++++.....+..
T Consensus 161 ~~~~v~-----~--~~~~~~~~~Lk~lk~~~~~rIIi~~s~~~~~~~il~qA~~lgm~~~~y~wilt~ld~~~~dl~--- 230 (368)
T cd06383 161 HVITII-----N--SIIDEVREQIKRLRNLDIKNIFILGSTEEIIRYVLDQALAEGFMGRKYAWFLGNPDLGIYDDL--- 230 (368)
T ss_pred CCEEEE-----e--ccchhHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHHHHHcCCcCCceEEEEcCCCchhhhhh---
Confidence 455543 1 12357889999999998845544454 599999999999999999999999999876655432
Q ss_pred ChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 160 NQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
.....-.++.|+++..+.....+.+.++|.+....+.....+..-++.+||||+++|.|++.+.... ... .
T Consensus 231 --~~~~~~~Nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~Dav~~~~~a~~~l~~~~-~~~------~ 301 (368)
T cd06383 231 --SCQLRNASIFVTRPMMDYQSSVRGALLRTDEPTLRPVFYFEWAFRLFLAYDAVLAVGEWPRRMRKKR-VED------G 301 (368)
T ss_pred --hhccccCcEEEeeccccchhhhccceeeccCCccCchhHHHHHHHHHHHHHHHHHhccccchhheee-ccC------C
Confidence 2233345789999976666555778777733211111111334568899999999999999763221 100 0
Q ss_pred CCcccccccccc---ccc-CchHHHHHHHHccccCCceeeEEEecCCCeecc
Q 003633 240 DSKATRVQLEQL---KVF-DGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSR 287 (806)
Q Consensus 240 ~~~~~~~~~~~~---~~~-~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~ 287 (806)
+.......|... .+| ..|..+.++|++++|+|+||+|+||++|.|.+.
T Consensus 302 ~~~~~~~~~~g~~~~~~w~~~g~~~~~~~k~~~~~gltG~i~f~~~g~R~~~ 353 (368)
T cd06383 302 STGTSVLPGFGISPESPLMTLQSSPFNGSSEIKFEMLAGRVAIDEGSSVSTK 353 (368)
T ss_pred CcCccccCCCCCCcccchhhcccccccCccceeEeeecCeEEEecCceeeee
Confidence 010011122221 234 557799999999999999999999999987543
No 39
>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=99.95 E-value=2.5e-27 Score=255.31 Aligned_cols=243 Identities=20% Similarity=0.331 Sum_probs=199.6
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
+++++++++||+|++++++|.++ .+++|.+ .|++..|+.++++++++++|++|++||+|+++ ...++.+.+.+++.
T Consensus 78 v~~i~~~~~ip~is~~~~~~~~~-~~~~~~~--~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~-~~~l~~~~~~~~~~ 153 (324)
T cd06368 78 VQSICDALEIPHITTSWSPNPKP-RQFTINL--YPSMRDLSDALLDLIKYFGWRKFVYIYDSDEG-LLRLQELLDALSPK 153 (324)
T ss_pred HHHHHhccCCCcEEecCCcCCCC-CcceEEe--cCCHHHHHHHHHHHHHhcCCCEEEEEECCcHh-HHHHHHHHHhhccC
Confidence 57899999999999999999887 3345444 57777999999999999999999999977664 45567777788888
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
|++|+.....+ . .+|++++|.+|+++++|+||++++.+++..++++|+++||+..+|+||+++......+. .
T Consensus 154 g~~v~~~~~~~-~--~~d~~~~l~~i~~~~~d~Vi~~~~~~~~~~i~~qa~~~g~~~~~~~~i~~~~~~~~~~~-----~ 225 (324)
T cd06368 154 GIQVTVRRLDD-D--TDMYRPLLKEIKREKERRIILDCSPERLKEFLEQAVEVGMMSEYYHYILTNLDFHTLDL-----E 225 (324)
T ss_pred CceEEEEEecC-C--chHHHHHHHHHhhccCceEEEECCHHHHHHHHHHHHHhccccCCcEEEEccCCccccch-----h
Confidence 99998765433 2 23899999999999999999999999999999999999999889999998865433222 1
Q ss_pred hhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCC---CCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 162 TSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKG---LVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~---~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
.......++.++....++++..++|.++|+++++.. .....++.+++++||||+++
T Consensus 226 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~aa~~yDav~~~--------------------- 284 (324)
T cd06368 226 LFRYGGVNITGFRLVDPDNPEVQKFIQRWERSDHRICPGSGLKPIKTESALTYDAVLLF--------------------- 284 (324)
T ss_pred hhhcCCceEEEEEEecCCChHHHHHHHHHHhccccccCCCCCCCcchhhHhhhcEEEEe---------------------
Confidence 222334567888888888999999999999998621 11225788999999998743
Q ss_pred CCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeCCCCc
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFDGSGF 311 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~~~gl 311 (806)
||+++||++|+|.+..++|+++..++++.||+|++..||
T Consensus 285 ----------------------------------tg~~~f~~~g~~~~~~~~i~~~~~~~~~~~g~W~~~~~~ 323 (324)
T cd06368 285 ----------------------------------TGRIQFDENGQRSNFTLDILELKEGGLRKVGTWNPEDGL 323 (324)
T ss_pred ----------------------------------eeeeEeCCCCcCcceEEEEEEEcCCCceEEEEECCCCCC
Confidence 889999999999999999999999999999999998875
No 40
>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=99.94 E-value=4.4e-26 Score=248.28 Aligned_cols=229 Identities=35% Similarity=0.585 Sum_probs=194.5
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++++||+|++++++|.|++ ..||||||+.|++..++.+++++++++||++|++++.|++||....+.+.+.+++
T Consensus 107 ~~~~~~~~~vp~is~~~~~~~ls~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~ 186 (348)
T cd06350 107 VAELLGLFKIPQISYGATSPLLSDKLQFPSFFRTVPSDTSQALAIVALLKHFGWTWVGLVYSDDDYGRSGLSDLEEELEK 186 (348)
T ss_pred HHHHHhcCcCceecccCCChhhccccccCCeeEecCCcHHHHHHHHHHHHHCCCeEEEEEEecchhHHHHHHHHHHHHHH
Confidence 577899999999999999999976 4699999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|+||+..+.++...+..|+..++++|+++++|+||++++..++..++++|+++|| ...+ |+.++.+.......
T Consensus 187 ~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vvv~~~~~~~~~~~~~~a~~~g~-~~~~-~i~~~~~~~~~~~~---- 260 (348)
T cd06350 187 NGICIAFVEAIPPSSTEEDIKRILKKLKSSTARVIVVFGDEDDALRLFCEAYKLGM-TGKY-WIISTDWDTSTCLL---- 260 (348)
T ss_pred CCCcEEEEEEccCCCcHHHHHHHHHHHHhCCCcEEEEEeCcHHHHHHHHHHHHhCC-CCeE-EEEEccccCccccc----
Confidence 99999999888865446799999999999999999999999999999999999999 4444 44554443321111
Q ss_pred hhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCC
Q 003633 161 QTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELPD 240 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~ 240 (806)
....+.++|++++..+.|++...++|.+.|++ +++++|||||+
T Consensus 261 ~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~-------------~~~~~YDav~~------------------------ 303 (348)
T cd06350 261 LFTLDAFQGVLGFSGHAPRSGEIPGFKDFLRK-------------YAYNVYDAVYA------------------------ 303 (348)
T ss_pred cCCcceeeeEEEEEEEeecCCcCCChHHHHHH-------------HHHHHHhheeE------------------------
Confidence 23446789999999888876666677777765 67899999885
Q ss_pred CcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeec----CceEEEEEeeCC
Q 003633 241 SKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDK----MEIHRVGYWFDG 308 (806)
Q Consensus 241 ~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~----~~~~~VG~w~~~ 308 (806)
.+.||++||+ ...|.|.+++. .++++||.|.+.
T Consensus 304 ----------------------------------~v~f~~~gd~-~~~~~i~~~~~~~~~~~~~~vg~~~~~ 340 (348)
T cd06350 304 ----------------------------------EVKFDENGDR-LASYDIINWQIFPGGGGFVKVGFWDPQ 340 (348)
T ss_pred ----------------------------------EEEecCCCCc-ccceeEEEEEEcCCcEEEEEEEEEcCC
Confidence 5999999995 56799999976 679999999873
No 41
>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=99.94 E-value=1.3e-25 Score=243.27 Aligned_cols=250 Identities=20% Similarity=0.237 Sum_probs=213.4
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHH-HHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLI-DFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++..+||+|+++++++.+++..||++||+.|++..++.++++++ ++++|++|++++.|++||+...+.+.+.+++
T Consensus 82 ~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~~~~~~ 161 (334)
T cd06342 82 ASPIYADAGIVMISPAATNPKLTERGYKNVFRVVARDDQQGPAAAKYAVETLKAKKVAIIDDKTAYGQGLADEFKKALKA 161 (334)
T ss_pred hHHHHHhCCCeEEecCCCCchhhcCCCceEEeccCCcHHHHHHHHHHHHHhcCCCEEEEEeCCcchhhHHHHHHHHHHHH
Confidence 467888999999999988888877779999999999999999999975 6789999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|++|+....++++ ..|++..+.++++.++++|++.+...++..+++++++.|+. +.|+.++++... ...
T Consensus 162 ~g~~v~~~~~~~~~--~~d~~~~l~~i~~~~~~~vi~~~~~~~~~~~~~~~~~~g~~---~~~~~~~~~~~~-~~~---- 231 (334)
T cd06342 162 AGGKVVAREGTTDG--ATDFSAILTKIKAANPDAVFFGGYYPEAGPLVRQMRQLGLK---APFMGGDGLCDP-EFI---- 231 (334)
T ss_pred cCCEEEEEecCCCC--CccHHHHHHHHHhcCCCEEEEcCcchhHHHHHHHHHHcCCC---CcEEecCccCCH-HHH----
Confidence 99999998888754 56899999999999999999999999999999999999974 467777654321 111
Q ss_pred hhhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 161 QTSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
....+..+|++...++.+ +++..++|.++|+++++. .++.++.++||+++++++|++++ +
T Consensus 232 ~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~yda~~~~~~al~~~---~---------- 293 (334)
T cd06342 232 KIAGDAAEGTYATFPGGPLEKMPAGKAFVARYKAKFGD-----PPGAYAPYAYDAANVLAEAIKKA---G---------- 293 (334)
T ss_pred HHhhHhhCCcEEEecCCCCCCChHHHHHHHHHHHHhCC-----CCchhHHHHHHHHHHHHHHHHHh---C----------
Confidence 233456789988777665 468889999999988852 35778999999999999999984 1
Q ss_pred CCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEe
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINI 294 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~ 294 (806)
..++..++++|++.+|+|++|+++|+++|++.+..|+|+||
T Consensus 294 ---------------~~~~~~v~~~l~~~~~~g~~g~i~f~~~g~~~~~~~~~~~~ 334 (334)
T cd06342 294 ---------------STDPAKVADALRKVDFDGVTGKISFDAKGDLKGAAVTVYQV 334 (334)
T ss_pred ---------------CCCHHHHHHHHHhCCCCCcceeeEECCCCCcccCcEEEEeC
Confidence 11388999999999999999999999999999999999886
No 42
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=99.93 E-value=1e-24 Score=237.93 Aligned_cols=256 Identities=15% Similarity=0.169 Sum_probs=213.6
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHH-HHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLI-DFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++.+||+|++++++|.+++..+||+||+.+.+..++.++++++ +.++|++|++|+.|++||+...+.+.+.+++
T Consensus 108 ~~~~~~~~~ip~i~~~s~~~~l~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~k~va~i~~d~~~g~~~~~~~~~~~~~ 187 (369)
T PRK15404 108 ASDIYEDEGILMITPAATAPELTARGYQLIFRTIGLDSDQGPTAAKYILEKVKPKRIAVLHDKQQYGEGLARSVKDGLKK 187 (369)
T ss_pred hHHHHHHCCCeEEecCCCCHHHhcCCCceEEeCCCCcHHHHHHHHHHHHHhcCCCEEEEEeCCCchhHHHHHHHHHHHHH
Confidence 467889999999999999999998778999999999999999999975 6679999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|.+|+....++.+ ..|+++++.++++.++|+|++.+...+...++++++++|+. ..|+.+++.... ...
T Consensus 188 ~G~~v~~~~~~~~g--~~D~~~~v~~l~~~~~d~v~~~~~~~~~~~~~k~~~~~G~~---~~~i~~~~~~~~-~~~---- 257 (369)
T PRK15404 188 AGANVVFFEGITAG--DKDFSALIAKLKKENVDFVYYGGYHPEMGQILRQAREAGLK---TQFMGPEGVGNK-SLS---- 257 (369)
T ss_pred cCCEEEEEEeeCCC--CCchHHHHHHHHhcCCCEEEECCCchHHHHHHHHHHHCCCC---CeEEecCcCCCH-HHH----
Confidence 99999988888854 56999999999999999999888888889999999999974 357777654321 111
Q ss_pred hhhhhhccceEEEEEeC-CCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 161 QTSLRILQGVVGLRQHT-PDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~-~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
....+..+|+++..++. ..+|..++|.++|+++++ ..++.++..+||++++++.|+++..+
T Consensus 258 ~~~~~~~~Gv~~~~~~~~~~~~~~~~f~~~~~~~~~-----~~~~~~~~~~Y~~~~~l~~Al~~aG~------------- 319 (369)
T PRK15404 258 NIAGPASEGMLVTLPKRYDQDPANKAIVDAFKAKKQ-----DPSGPFVWTTYAAVQSLAAGINRAGS------------- 319 (369)
T ss_pred HhhhhhhcCcEEEccCCCccChhHHHHHHHHHHhcC-----CCCccchHHHHHHHHHHHHHHHhhCC-------------
Confidence 22346678988765432 346778899999998764 23456788999999999999998311
Q ss_pred CCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceE
Q 003633 240 DSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIH 300 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~ 300 (806)
.+++.|.++|++.+|+|++|++.|+++|++....|.|++|++++..
T Consensus 320 ---------------~~~~~l~~al~~~~~~~~~G~~~~~~~g~~~~~~~~i~~~~~~~~~ 365 (369)
T PRK15404 320 ---------------DDPAKVAKYLKANTFDTVIGPLSWDEKGDLKGFEFGVFEWHADGTK 365 (369)
T ss_pred ---------------CCHHHHHHHHHhCCCCcceEeeEECCCCCcccCCEEEEEEEcCCeE
Confidence 1378999999999999999999999999987889999999876543
No 43
>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=99.93 E-value=7.6e-25 Score=238.18 Aligned_cols=250 Identities=17% Similarity=0.199 Sum_probs=205.8
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcC--CeEEEEEEEcCCcccchHHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYG--WKEVIAIYVDDDYGRNGISALSNMLE 79 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~--W~~v~ii~~d~~~g~~~~~~l~~~l~ 79 (806)
+++++++++||+|+++++++.++...+||+||+.|++..++.++++++++++ |+++++++.|++||+...+.+.+.++
T Consensus 87 ~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~~~~~ 166 (345)
T cd06338 87 AAPVAEKYGVPMVAGSGASDSIFAQGFKYVFGTLPPASQYAKSLLEMLVALDPRPKKVAILYADDPFSQDVAEGAREKAE 166 (345)
T ss_pred HHHHHHHhCCcEEecCCCCchHhhcCCceEEEecCchHHHHHHHHHHHHhcCCCCceEEEEecCCcccHHHHHHHHHHHH
Confidence 4678899999999999999988866689999999999999999999999988 99999999999999999999999999
Q ss_pred hCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 80 KNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 80 ~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
+.|++|+....+++. ..|+++++++|++.++|+|++++...+...+++++++.|+... .. ..+.+.... ...
T Consensus 167 ~~g~~v~~~~~~~~~--~~d~~~~v~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~-~~-~~~~~~~~~-~~~--- 238 (345)
T cd06338 167 AAGLEVVYDETYPPG--TADLSPLISKAKAAGPDAVVVAGHFPDAVLLVRQMKELGYNPK-AL-YMTVGPAFP-AFV--- 238 (345)
T ss_pred HcCCEEEEEeccCCC--ccchHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCCC-EE-EEecCCCcH-HHH---
Confidence 999999988777744 4699999999999999999999999999999999999998643 22 222322211 111
Q ss_pred ChhhhhhccceEEEEEeCCC-------ChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccc
Q 003633 160 NQTSLRILQGVVGLRQHTPD-------SIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITF 232 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~-------~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~ 232 (806)
....+..+|+++...+.|. .+..+.|.++|+++|+. .++.++..+||+++++++|+++..+
T Consensus 239 -~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~p~~~~~~~y~a~~~~~~a~~~ag~------ 306 (345)
T cd06338 239 -KALGADAEGVFGPTQWTPALDYKDDLFPSAAEFAAAYKEKYGK-----APDYHAAGAYAAGQVLQEAVERAGS------ 306 (345)
T ss_pred -HHHhhhhCceeecceeccCcccccccCccHHHHHHHHHHHhCC-----CCCcccHHHHHHHHHHHHHHHHhCC------
Confidence 2334556888887766654 36789999999999862 3567888999999999999998411
Q ss_pred cCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEe
Q 003633 233 SASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINI 294 (806)
Q Consensus 233 ~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~ 294 (806)
.+++.+.++|++++|+|++|++.|+++|++.. .+.+++|
T Consensus 307 ----------------------~~~~~v~~al~~~~~~~~~G~~~f~~~~~~~~-~~~~~~~ 345 (345)
T cd06338 307 ----------------------LDPAAVRDALASNDFDTFYGPIKFDETGQNNH-PMTVVQW 345 (345)
T ss_pred ----------------------CCHHHHHHHHHhCCCcccccCeeECCCCCcCC-CceeeeC
Confidence 13789999999999999999999999998644 5556553
No 44
>cd06351 PBP1_iGluR_N_LIVBP_like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors characterized by their response to glutamate agonists: N-methyl-aspartate (NMDA) and non-NMDA receptors
Probab=99.92 E-value=2.7e-24 Score=232.21 Aligned_cols=241 Identities=22% Similarity=0.336 Sum_probs=189.0
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+|+++++++.+++ ..+||++|+.|++..+++++++++++|+|++|++||++++++. .++.+.+....
T Consensus 79 v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~iiy~~~~~~~-~l~~~~~~~~~ 157 (328)
T cd06351 79 VQSICDALEIPHISISGGSEGLSDKEESSTTLQLYPSLEDLADALLDLLEYYNWTKFAIIYDSDEGLS-RLQELLDESGI 157 (328)
T ss_pred HHHHhccCCCCeEEeecCcccccccccccceEEecCCHHHHHHHHHHHHHHcCCcEEEEEEeCchHHH-HHHHHHHhhcc
Confidence 578999999999999999888886 4689999999999999999999999999999999999888543 33444444444
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCC-eEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGP-RVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~-rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
.+..+... .+... .++++..|++++..++ ++|++++..+.+..++++|.++||++.+|+||+++......+.
T Consensus 158 ~~~~v~~~-~~~~~--~~~~~~~l~~l~~~~~~~vil~~~~~~~~~~~l~~a~~~gm~~~~~~~i~~~~~~~~~d~---- 230 (328)
T cd06351 158 KGIQVTVR-RLDLD--DDNYRQLLKELKRSESRRIILDCSSEEEAKEILEQAVELGMMGYGYHWILTNLDLSDIDL---- 230 (328)
T ss_pred cCceEEEE-EecCC--chhHHHHHHHHhhcccceEEEECCcHHHHHHHHHHHHHhccccCCcEEEEecCCccccch----
Confidence 45555544 34433 2379999999999998 6665555558999999999999999999999999977665443
Q ss_pred ChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 160 NQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
........|++|++...+..+...+|..+|..... ......+...++.+||+++++
T Consensus 231 -~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~---------------------- 286 (328)
T cd06351 231 -EPFQYGPANITGFRLVDPDSPDVSQFLQRWLEESP-GVNLRAPIYDAALLYDAVLLL---------------------- 286 (328)
T ss_pred -hhhccCCcceEEEEEeCCCchHHHHHHHhhhhccC-CCCcCccchhhHhhhcEEEEE----------------------
Confidence 23456678999999999999999999999943332 111223344455555553311
Q ss_pred CCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee-cCceEEEEEeeC
Q 003633 240 DSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID-KMEIHRVGYWFD 307 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~-~~~~~~VG~w~~ 307 (806)
||+++||++|+|.+..++|++++ +.++++||.|+.
T Consensus 287 ---------------------------------tg~i~f~~~g~r~~~~l~i~~l~~~~~~~~vg~W~~ 322 (328)
T cd06351 287 ---------------------------------TGTVSFDEDGVRSNFTLDIIELNRSRGWRKVGTWNG 322 (328)
T ss_pred ---------------------------------EeeEEECCCCcccceEEEEEEecCCCCceEEEEecC
Confidence 99999999999999999999999 899999999994
No 45
>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=99.92 E-value=2.9e-24 Score=233.34 Aligned_cols=244 Identities=18% Similarity=0.270 Sum_probs=199.9
Q ss_pred HhcccccCCCcEEecccCCCCccc----CCCCceEEecCCcHHHHHHHHHHHHH-----cCCeEEEEEEEcCCcccchHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA----LQFPYFIRSTQSDSQQMAAMADLIDF-----YGWKEVIAIYVDDDYGRNGIS 72 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~----~~~p~f~Rt~psd~~q~~ai~~ll~~-----~~W~~v~ii~~d~~~g~~~~~ 72 (806)
+++++++++||+|+++++++.++. ..+||+||+.|++..++.++++++.+ ++|++|++++.|++||+...+
T Consensus 83 ~~~~~~~~~vp~i~~~~~~~~~t~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~~~~va~l~~~~~~g~~~~~ 162 (344)
T cd06345 83 LQDVAAENKVPFIVTGAASPEITTADDYETYKYVFRAGPTNSSYAQSVADALKETLVDKHGFKTAAIVAEDAAWGKGIDA 162 (344)
T ss_pred HHHHHHHcCCcEEeccCCCCcccccccccCCceEEecCCCcHHHHHHHHHHHHHhhcccCCCceEEEEecCchhhhHHHH
Confidence 467889999999999999999883 45899999999999999999998876 899999999999999999999
Q ss_pred HHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccc
Q 003633 73 ALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSAT 152 (806)
Q Consensus 73 ~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~ 152 (806)
.+.+.+++.|++|+....++.. ..++++++.+|+..++|+|++.+...++..+++++.+.|+.. .++..+.....
T Consensus 163 ~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~ 237 (344)
T cd06345 163 GIKALLPEAGLEVVSVERFSPD--TTDFTPILQQIKAADPDVIIAGFSGNVGVLFTQQWAEQKVPI---PTIGISVEGNS 237 (344)
T ss_pred HHHHHHHHcCCeEEEEEecCCC--CCchHHHHHHHHhcCCCEEEEeecCchHHHHHHHHHHcCCCC---ceEEecCCcCC
Confidence 9999999999999988877754 568999999999999999999999999999999999999743 23333322111
Q ss_pred ccccccCChhhhhhccceEEEEEeCC----CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhc
Q 003633 153 LESFSKMNQTSLRILQGVVGLRQHTP----DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEH 228 (806)
Q Consensus 153 ~~~~~~~~~~~~~~~~gv~~~~~~~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~ 228 (806)
.... ....+..+|+++...+.| .++..++|.++|+++|+. .++.+++.+||+++++++|+++..+
T Consensus 238 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g~-----~p~~~~~~~yda~~~l~~A~~~ag~-- 306 (344)
T cd06345 238 PAFW----KATNGAGNYVITAESGAPGVEAITDKTVPFTEAYEAKFGG-----PPNYMGASTYDSIYILAEAIERAGS-- 306 (344)
T ss_pred HHHH----HhhchhcceEEeecccccCccCCCHHHHHHHHHHHHHhCC-----CCcccchHHHHHHHHHHHHHHHhcC--
Confidence 1111 223345677766554443 567889999999998862 4788899999999999999998311
Q ss_pred CccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecc
Q 003633 229 NITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSR 287 (806)
Q Consensus 229 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~ 287 (806)
.+++.+.++|++++|+|++|+++||++||+..+
T Consensus 307 --------------------------~~~~~i~~al~~~~~~g~~G~i~f~~~g~~~~~ 339 (344)
T cd06345 307 --------------------------TDGDALVEALEKTDFVGTAGRIQFYGDDSAFAH 339 (344)
T ss_pred --------------------------CCHHHHHHHHHhCCCcCCceeEEECCCCCcCcC
Confidence 137899999999999999999999999996543
No 46
>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=99.92 E-value=4.8e-24 Score=228.07 Aligned_cols=224 Identities=25% Similarity=0.336 Sum_probs=189.6
Q ss_pred hcccccCCCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 3 SEVANGLKVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
++++++.+||+|++++++|.|+.. .++||||+.|++..++.++++++..++|++|++|+.|++||++..+.+.+.+++.
T Consensus 85 ~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~~vail~~~~~~g~~~~~~~~~~~~~~ 164 (312)
T cd06346 85 TSVAVPNGVVMISPSSTSPTLTTLDDNGLFFRTAPSDALQGQALAQLAAERGYKSVATTYINNDYGVGLADAFTKAFEAL 164 (312)
T ss_pred hhhhccCCcEEEecCCCCccceecCCCceEEEecCCcHHHHHHHHHHHHHcCCCeEEEEEccCchhhHHHHHHHHHHHHc
Confidence 678999999999999999999974 4799999999999999999999999999999999999999999999999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
|++|+....++++ ..|+++++++|++.++|+|++.+.+.++..++++++++|+. ..|+.+++.... ... ..
T Consensus 165 G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~---~~~~~~~~~~~~-~~~---~~ 235 (312)
T cd06346 165 GGTVTNVVAHEEG--KSSYSSEVAAAAAGGPDALVVIGYPETGSGILRSAYEQGLF---DKFLLTDGMKSD-SFL---PA 235 (312)
T ss_pred CCEEEEEEeeCCC--CCCHHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCCC---CceEeeccccCh-HHH---Hh
Confidence 9999998888855 67999999999999999999999999999999999999983 347777654332 111 12
Q ss_pred hhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCCC
Q 003633 162 TSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELPDS 241 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~ 241 (806)
...+.++|+++..+..+. +..++|.++|+++|+. .++.+++.+||+++++++|
T Consensus 236 ~~~~~~~g~~~~~~~~~~-~~~~~f~~~~~~~~g~-----~p~~~~~~~Yd~~~~l~~A--------------------- 288 (312)
T cd06346 236 DGGYILAGSYGTSPGAGG-PGLEAFTSAYKAAYGE-----SPSAFADQSYDAAALLALA--------------------- 288 (312)
T ss_pred hhHHHhCCcEEccCCCCc-hhHHHHHHHHHHHhCC-----CCCccchhhHHHHHHHHHH---------------------
Confidence 223567898887665544 7889999999999962 4778899999999998744
Q ss_pred cccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEE
Q 003633 242 KATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYD 290 (806)
Q Consensus 242 ~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~ 290 (806)
|.|++|+++||++|++.. .|+
T Consensus 289 ---------------------------~~g~~g~~~f~~~g~~~~-~~~ 309 (312)
T cd06346 289 ---------------------------YQGASGVVDFDENGDVAG-SYD 309 (312)
T ss_pred ---------------------------hCCCccceeeCCCCCccc-cee
Confidence 678999999999998643 554
No 47
>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=99.92 E-value=2.1e-23 Score=221.13 Aligned_cols=260 Identities=18% Similarity=0.233 Sum_probs=177.6
Q ss_pred HhcccccCCCcEEecccCCCCc-ccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTL-SALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~L-s~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
|..+|+.++||+|+++..++.. +...+.+.+++.|+...++.|++++|++|+|++|++||+.++... ..+.+.+....
T Consensus 98 v~sic~~l~IP~I~~~~~~~~~~~~~~~~l~L~l~P~~~~l~~a~~~ll~~~~W~~f~~iy~~~~gl~-~lq~l~~~~~~ 176 (382)
T cd06377 98 LDFVSAALEIPVVSIVRREFPRGSQNPFHLQMSWASPLSTLLDVLLSVLQRNGWEDVSLVLCRERDPT-GLLLLWTNHAR 176 (382)
T ss_pred HHHHhcCCCCCEEEecCCcccccCCCceeEEEEecCCHHHHHHHHHHHHHHCCCcEEEEEEecCcCHH-HHHHHHHHhcc
Confidence 5679999999999986654333 223333445779999999999999999999999999998776333 33333332222
Q ss_pred CC--cEEEEEeccCCC-CChhHH-HHHHHhcCCCC-CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc
Q 003633 81 NM--AKVSYKLPLPVQ-FNQHDI-TVLLNNSKPLG-PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES 155 (806)
Q Consensus 81 ~g--~~i~~~~~~~~~-~~~~~~-~~~l~~ik~~~-~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~ 155 (806)
.+ ..|..+. .++. .+..++ ++.|++|++.. +++|+++|+.+.+..+++++.+ +|+||+++.. +.
T Consensus 177 ~~~~~~i~v~~-~~~~~~d~~~~~~~~L~~i~~~~~~~~ill~cs~e~~~~il~~~~~------~y~wIv~~~~----~l 245 (382)
T cd06377 177 FHLGSVLNLSR-NDPSTADLLDFLRAQLELLKDPPGPAVVLFGCDVARARRVLELTPP------GPHWILGDPL----PP 245 (382)
T ss_pred cccCceEEEEe-ccCccCChhHHHHHHHHHhhcccCceEEEEECCHHHHHHHHHhhcc------ceEEEEcCCc----Ch
Confidence 22 2233222 3211 134455 99999999999 9999999999999999987654 4999999821 11
Q ss_pred cccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhc-CccccC
Q 003633 156 FSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEH-NITFSA 234 (806)
Q Consensus 156 ~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~-~~~~~~ 234 (806)
.. -.....-.|+++ |.+ . ....-.++.||||+++|.|++.+.... ...+.
T Consensus 246 e~---~~~~g~nigLl~-----------------~~~-~-------~~~~l~ali~DAV~lvA~a~~~l~~~~~~~~l~- 296 (382)
T cd06377 246 EA---LRTEGLPPGLLA-----------------HGE-T-------TQPPLEAYVQDALELVARAVGSATLVQPELALI- 296 (382)
T ss_pred hh---ccCCCCCceEEE-----------------Eee-c-------ccccHHHHHHHHHHHHHHHHHHhhhcccccccC-
Confidence 10 001122233332 211 0 011227799999999999999863111 11111
Q ss_pred CCCCCCCcccccccccc--c-ccCchHHHHHHHHccccCCceeeEEEecCCCe--ecccEEEEEee--cCc---eEEEEE
Q 003633 235 SHELPDSKATRVQLEQL--K-VFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNI--VSRGYDVINID--KME---IHRVGY 304 (806)
Q Consensus 235 ~~~l~~~~~~~~~~~~~--~-~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~--~~~~~~I~~~~--~~~---~~~VG~ 304 (806)
....+|... + +|+.|..|.++|++++|+|+||+|.|+ .|.| .+..++|++++ ..| |++||+
T Consensus 297 --------~~~~~C~~~~~~~~W~~G~~l~~~Lknv~~eGlTG~I~F~-~g~R~~~~~~l~I~~L~~~~~G~~~W~kVG~ 367 (382)
T cd06377 297 --------PATVNCMDLPTKGNESSGQYLARFLANTSFDGRTGPVWVT-GSSQVHSSRHFKVWSLRRDPVGQPTWTTVGS 367 (382)
T ss_pred --------CCCCCcccCCCCCCCCchHHHHHHHHhCcccccceeEEEc-cCeeecccceEEEEEeccccCCCccceEEEE
Confidence 112355433 5 899999999999999999999999995 6888 78899999998 444 599999
Q ss_pred eeCCCCc
Q 003633 305 WFDGSGF 311 (806)
Q Consensus 305 w~~~~gl 311 (806)
|++...+
T Consensus 368 W~~~~~~ 374 (382)
T cd06377 368 WQGGRKI 374 (382)
T ss_pred ecCCCce
Confidence 9997433
No 48
>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=99.91 E-value=4.5e-23 Score=224.03 Aligned_cols=256 Identities=17% Similarity=0.276 Sum_probs=201.1
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHH-HHHHHHHHHc-CCeEEEEEEEcCC-cccchHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQM-AAMADLIDFY-GWKEVIAIYVDDD-YGRNGISALSNML 78 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~-~ai~~ll~~~-~W~~v~ii~~d~~-~g~~~~~~l~~~l 78 (806)
+.+++++.+||+|+++++++.+.. .+||+||+.+++..+. .++..+++++ |||+++++|.+++ ||+...+.+.+.+
T Consensus 83 ~~~~~~~~~ip~i~~~~~~~~~~~-~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~g~~~~~~~~~~~ 161 (344)
T cd06348 83 ADPIAERAGVPVVGPSNTAKGIPE-IGPYVFRVSAPEAVVAPAAIAAALKLNPGIKRVAVFYAQDDAFSVSETEIFQKAL 161 (344)
T ss_pred hhHHHHhCCCCEEeccCCCCCcCC-CCCeEEEccCcHHHHHHHHHHHHHHHhcCCeEEEEEEeCCchHHHHHHHHHHHHH
Confidence 356788999999999888877654 4689999987776554 4555678888 9999999997655 9999999999999
Q ss_pred HhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccccc
Q 003633 79 EKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSK 158 (806)
Q Consensus 79 ~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~ 158 (806)
++.|++|+....++.+ ..|+++++.+|+++++|+|++.+...++..+++++++.|+.. .|+.++++... ...
T Consensus 162 ~~~g~~v~~~~~~~~~--~~d~~~~v~~i~~~~~d~vi~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~-~~~-- 233 (344)
T cd06348 162 RDQGLNLVTVQTFQTG--DTDFQAQITAVLNSKPDLIVISALAADGGNLVRQLRELGYNG---LIVGGNGFNTP-NVF-- 233 (344)
T ss_pred HHcCCEEEEEEeeCCC--CCCHHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCC---ceeccccccCH-HHH--
Confidence 9999999988888754 579999999999999999999999999999999999999853 35655544321 111
Q ss_pred CChhhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCC
Q 003633 159 MNQTSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASH 236 (806)
Q Consensus 159 ~~~~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~ 236 (806)
....+..+|++...++.+ +++..++|.++|+++|+ ..++.++..+|||++++++|++++...++.
T Consensus 234 --~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g-----~~p~~~~~~~yda~~~~~~A~~~a~~~~~~------ 300 (344)
T cd06348 234 --PVCQAACDGVLVAQAYSPENDTPVNRDFVEAYKKKYG-----KAPPQFSAQAFDAVQVVAEALKRLNQKQKL------ 300 (344)
T ss_pred --HhhhHhhcCeEEEeeccCCCCCHHHHHHHHHHHHHHC-----CCccHHHHHHHHHHHHHHHHHHHhcCCCcc------
Confidence 234467789888776654 45678999999998886 246678889999999999999996433200
Q ss_pred CCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEE
Q 003633 237 ELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDV 291 (806)
Q Consensus 237 ~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I 291 (806)
..+. ....+.+|.++|++++|.|++|+|.||++|++....|.|
T Consensus 301 ---------~~~~---~~~~~~~l~~~l~~~~~~g~~G~v~f~~~g~~~~~~~~~ 343 (344)
T cd06348 301 ---------AELP---LPELRTALNAALLSGQYDTPLGEISFTPDGEVLQKAFYV 343 (344)
T ss_pred ---------ccch---hhhHHHHHHHHHhccCCccceeeeEECCCCCcccCceec
Confidence 0000 011267899999999999999999999999987776654
No 49
>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=99.91 E-value=2.7e-24 Score=233.23 Aligned_cols=290 Identities=19% Similarity=0.326 Sum_probs=223.4
Q ss_pred HhcccccCCCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
|+.-+..++.-++||++++|.|+++ .||+|||+.||+..+...+..++++|+|++|+.++++...-....+.+...+.+
T Consensus 128 iaea~~~w~l~~lsy~~ssp~ls~r~rfp~~frt~PS~~~~np~rl~l~~~~~w~rvgt~~q~e~~f~~~~~dl~~~~~~ 207 (865)
T KOG1055|consen 128 IAEAAKMWNLIVLSYGASSPALSNRKRFPTFFRTHPSANAHNPTRIKLLKKFGWKRVATLQQTEEVFSSTLNDLEARLKE 207 (865)
T ss_pred HHhhccccceeeecccCCCccccchhhcchhhhcCCccccCCcceeeechhcCcceeeeeeeehhhhcchHHHHHHhhhc
Confidence 3445566778899999999999985 599999999999999999999999999999999999999888899999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccc-----cc
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATL-----ES 155 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~-----~~ 155 (806)
.+++|+..+.+. .|....+++++..++|+|+...+...|+.++++|++.+|.+..|+|+...|..... +.
T Consensus 208 ~~ieiv~~qsf~-----~dp~~~vk~l~~~D~RiI~g~f~~~~Arkv~C~~Y~~~myg~ky~w~~~g~y~d~w~ev~~~~ 282 (865)
T KOG1055|consen 208 AGIEIVFRQSFS-----SDPADSVKNLKRQDARIIVGLFYETEARKVFCEAYKERLYGRKYVWFLIGWYADNWWEITHPS 282 (865)
T ss_pred cccEEEEeeccc-----cCHHHHHhhccccchhheeccchHhhhhHHHHhhchhhcccceeEEEEEEeeccchhhccCch
Confidence 999999887764 25667789999999999999999999999999999999999999999987655433 22
Q ss_pred cccCChhhhhhccceEEEEEe--CCCC------hhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhh
Q 003633 156 FSKMNQTSLRILQGVVGLRQH--TPDS------IPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINE 227 (806)
Q Consensus 156 ~~~~~~~~~~~~~gv~~~~~~--~~~~------~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~ 227 (806)
..|.-.++.++++|.+++... .++. ..-+.|...+.+..+...+....+..+.++|||+|++|+|++++...
T Consensus 283 ~~ctveem~~A~eg~~s~e~~pl~~~~~~tisg~T~~~~l~~~~~~r~~~~~~~~~~~~~~~ayd~Iwa~ala~n~t~e~ 362 (865)
T KOG1055|consen 283 ENCTVEEMTEAAEGHITTEFVMLSPANITTISGMTAQEFLEELTKYRKRHPEETGGFQEAPLAYDAIWALALALNKTMEG 362 (865)
T ss_pred hhhhHHHHHHHHhhheeeeeeccccccceeeccchhHHHHHHHHhhhccccccccCcccCchHHHHHHHHHHHHHHHHhc
Confidence 223335677889998887532 2211 12345555544433311122345667889999999999999997654
Q ss_pred cCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCceEEEEEeeC
Q 003633 228 HNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEIHRVGYWFD 307 (806)
Q Consensus 228 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~~~VG~w~~ 307 (806)
.. +....+. +..... -.-..+|++++.+++|.|++|.+.|.. |+|. .-..|-|+++|.++++|+|+.
T Consensus 363 l~---~~~~~l~-------~f~y~~-k~i~d~i~eamn~tsF~GvsG~V~F~~-geR~-a~t~ieQ~qdg~y~k~g~Yds 429 (865)
T KOG1055|consen 363 LG---RSHVRLE-------DFNYNN-KTIADQIYEAMNSTSFEGVSGHVVFSN-GERM-ALTLIEQFQDGKYKKIGYYDS 429 (865)
T ss_pred CC---ccceecc-------ccchhh-hHHHHHHHHHhhcccccccccceEecc-hhhH-HHHHHHHHhCCceEeeccccc
Confidence 20 0000011 111100 112678999999999999999999985 9864 567889999999999999988
Q ss_pred CC
Q 003633 308 GS 309 (806)
Q Consensus 308 ~~ 309 (806)
..
T Consensus 430 ~~ 431 (865)
T KOG1055|consen 430 TK 431 (865)
T ss_pred cc
Confidence 65
No 50
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.90 E-value=5e-23 Score=223.59 Aligned_cols=245 Identities=16% Similarity=0.177 Sum_probs=200.5
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc------CCeEEEEEEEcCCcccchHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY------GWKEVIAIYVDDDYGRNGISALS 75 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~------~W~~v~ii~~d~~~g~~~~~~l~ 75 (806)
+++++++.+||+|+++++++.++...+||+||+.|++..++.++++++.++ +|+++++++.|++||....+.+.
T Consensus 86 ~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~fr~~p~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~ 165 (347)
T cd06340 86 ASQVAERYGVPFVVDGAVSDSITERGFKYTFRITPHDGMFTRDMFDFLKDLNEKTGKPLKTVALVHEDTEFGTSVAEAIK 165 (347)
T ss_pred HHHHHHHhCCCEEeccccchHHhhcCCceEEecCCChHHHHHHHHHHHHHhhHhcCCCCceEEEEecCchHhHHHHHHHH
Confidence 467888999999999999999987778999999999999999999999876 46999999999999999999999
Q ss_pred HHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc
Q 003633 76 NMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES 155 (806)
Q Consensus 76 ~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~ 155 (806)
+.+++.|++|+..+.++.. ..|++.++.+|++.++|+|++.++..++..+++++++.|+... .++...++.... ..
T Consensus 166 ~~~~~~G~~vv~~~~~~~~--~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~G~~~~-~~~~~~~~~~~~-~~ 241 (347)
T cd06340 166 KFAKERGFEIVEDISYPAN--ARDLTSEVLKLKAANPDAILPASYTNDAILLVRTMKEQRVEPK-AVYSVGGGAEDP-SF 241 (347)
T ss_pred HHHHHcCCEEEEeeccCCC--CcchHHHHHHHHhcCCCEEEEcccchhHHHHHHHHHHcCCCCc-EEEecCCCcCcH-HH
Confidence 9999999999988888854 5699999999999999999999999999999999999998542 333222222211 11
Q ss_pred cccCChhhhhhccceEEEEEeCCC-ChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccC
Q 003633 156 FSKMNQTSLRILQGVVGLRQHTPD-SIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSA 234 (806)
Q Consensus 156 ~~~~~~~~~~~~~gv~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~ 234 (806)
. ....+..+|++...++.++ .+..++|.++|+++|+. .++.++..+||+++++++|++++.+
T Consensus 242 ~----~~~g~~~~g~~~~~~~~~~~~~~~~~f~~~y~~~~~~-----~~~~~~~~~Y~a~~~l~~A~~~ag~-------- 304 (347)
T cd06340 242 V----KALGKDAEGILTRNEWSDPKDPMAKDLNKRFKARFGV-----DLSGNSARAYTAVLVIADALERAGS-------- 304 (347)
T ss_pred H----HHhhHhhheEEeccccCCCCChHHHHHHHHHHHHhCC-----CCChHHHHHHHHHHHHHHHHHHhcC--------
Confidence 1 2344567899888776664 67889999999999862 4778899999999999999999421
Q ss_pred CCCCCCCcccccccccccccCchHHHH--HHHHccccC---CceeeEEEecCCCeecc
Q 003633 235 SHELPDSKATRVQLEQLKVFDGGTFLL--RKLLQTNFT---GLSGQVQFNQDRNIVSR 287 (806)
Q Consensus 235 ~~~l~~~~~~~~~~~~~~~~~~g~~l~--~~l~~~~f~---G~tG~i~Fd~~G~~~~~ 287 (806)
.+++++. .+|++..+. +..|++.||++|+..++
T Consensus 305 --------------------~~~~~v~~~~~~~~~~~~~~~~~~g~~~f~~~g~~~~~ 342 (347)
T cd06340 305 --------------------ADPEKIRDLAALASTSGEDLIMPYGPIKFDAKGQNTNA 342 (347)
T ss_pred --------------------CCHHHHHHHHHhccCCccccccCCCCeeECCCCCcccc
Confidence 1267787 478777765 56789999999996554
No 51
>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
Probab=99.90 E-value=2.8e-22 Score=217.25 Aligned_cols=247 Identities=15% Similarity=0.245 Sum_probs=206.1
Q ss_pred hcccccCCCcEEecccCCCCcccCC-CCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 3 SEVANGLKVPLVSFAATDPTLSALQ-FPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~~~-~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
.+++++.+||+|+++++++.++... +||+||+.+++..++..+++++...+||+|++++.|+.||+...+.+.+.+++.
T Consensus 82 ~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~ 161 (336)
T cd06360 82 VKVLREPGTPLINPNAGADDLTGRLCAPNFFRTSFSNAQWAAPMGKYAADDGYKKVVTVAWDYAFGYEVVEGFKEAFTEA 161 (336)
T ss_pred HHHHHhcCceEEecCCCCccccccCCCCcEEEEeCchHHHHHHHHHHHHHcCCCeEEEEeccchhhHHHHHHHHHHHHHc
Confidence 4577889999999999999998754 899999999999999999999998999999999999999999999999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
|+++.....++.. ..||++++.++++.++|+|++.....++..+++++.+.|+.. ...|+.++++.... .. .
T Consensus 162 G~~v~~~~~~~~~--~~d~~~~v~~~~~~~pd~v~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~-~~----~ 233 (336)
T cd06360 162 GGKIVKELWVPFG--TSDFASYLAQIPDDVPDAVFVFFAGGDAIKFVKQYDAAGLKA-KIPLIGSGFLTDGT-TL----G 233 (336)
T ss_pred CCEEEEEEecCCC--CcchHHHHHHHHhcCCCEEEEecccccHHHHHHHHHHcCCcc-CCeEEecccccCHH-HH----H
Confidence 9999987777643 669999999999999999999999999999999999999853 34566666543321 11 3
Q ss_pred hhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 162 TSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
...+..+|++...++.+ +++..+.|.++|+++++. .++.++..+||++++++.|+++..+.
T Consensus 234 ~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~~~-----~~~~~~~~~yda~~~~~~A~~~a~~~------------ 296 (336)
T cd06360 234 AAGEAAEGVITALHYADTLDNPANQAFVKAYRAAYPD-----TPSVYAVQGYDAGQALILALEAVGGD------------ 296 (336)
T ss_pred hhHhhhcCceeccccCCCCCCHHHHHHHHHHHHHhCC-----CccHHHHHHHHHHHHHHHHHHHhCCC------------
Confidence 34467789887776654 468899999999999852 57789999999999999999994211
Q ss_pred CCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeeccc
Q 003633 240 DSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRG 288 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~ 288 (806)
..+++.+.++|++++|.|..|+++|+++|++..+.
T Consensus 297 --------------~~~~~~v~~al~~~~~~~~~g~~~f~~~~~~~~~~ 331 (336)
T cd06360 297 --------------LSDGQALIAAMAAAKIDSPRGPFTLDKAHNPIQDN 331 (336)
T ss_pred --------------CCCHHHHHHHHhcCCccCCCcceEECCCCCcccce
Confidence 01277899999999999999999999999876543
No 52
>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=99.90 E-value=1.3e-22 Score=219.16 Aligned_cols=242 Identities=18% Similarity=0.184 Sum_probs=195.0
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcC-CeEEEEEEEcCC-cccchHHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYG-WKEVIAIYVDDD-YGRNGISALSNMLE 79 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~-W~~v~ii~~d~~-~g~~~~~~l~~~l~ 79 (806)
+++++++++||+|+++++++.++ ..+||+||+.|++..+++++++++.+.+ |++|++|+.|++ ||+...+.+.+.++
T Consensus 82 ~~~~~~~~~ip~i~~~a~~~~lt-~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~~~~~g~~~~~~~~~~~~ 160 (332)
T cd06344 82 ALDIYQKAKLVLISPTSTSVKLS-NPGPYFFRTVPSNAVAARALAKYLKKKNKIKKVAIFYNSTSPYSQSLKQEFTSALL 160 (332)
T ss_pred HHHHHhhcCceEEccCcCchhhc-CCCCcEEEeCCCcHHHHHHHHHHHHhhcCCCeEEEEeCCCchHhHHHHHHHHHHHH
Confidence 46789999999999999999888 4579999999999999999999998876 999999998876 99999999999999
Q ss_pred h-CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccccc
Q 003633 80 K-NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSK 158 (806)
Q Consensus 80 ~-~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~ 158 (806)
+ .|.++.....++ ..+.++..++.++++.++++|++.+.......+++++.+.|. ...++.++.+... +..
T Consensus 161 ~~~g~~v~~~~~~~--~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~~---~~~i~~~~~~~~~-~~~-- 232 (332)
T cd06344 161 ERGGGIVVTPCDLS--SPDFNANTAVSQAINNGATVLVLFPDTDTLDKALEVAKANKG---RLTLLGGDSLYTP-DTL-- 232 (332)
T ss_pred HhcCCeeeeeccCC--CCCCCHHHHHHHHHhcCCCEEEEeCChhHHHHHHHHHHhcCC---CceEEecccccCH-HHH--
Confidence 9 599987654443 345578899999999999999999998888888999888763 3345555543321 211
Q ss_pred CChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 159 MNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 159 ~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
....+..+|+++..++.++++..++|.++|+++++. .++.+++.+||+++++++|+++..+.
T Consensus 233 --~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~~~~~a~~~Yda~~~l~~A~~~ag~~----------- 294 (332)
T cd06344 233 --LDGGKDLEGLVLAVPWHPLASPNSPFAKLAQQLWGG-----DVSWRTATAYDATKALIAALSQGPTR----------- 294 (332)
T ss_pred --HhchhhhcCeEEEEecccccccchHHHHHHHHHhcC-----CchHHHHhHHHHHHHHHHHHHhCCCh-----------
Confidence 223456789999888888878889999999999862 46788999999999999999983111
Q ss_pred CCCcccccccccccccCchHHHH-HHHHccccCCceeeEEEecCCCeecc
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLL-RKLLQTNFTGLSGQVQFNQDRNIVSR 287 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~-~~l~~~~f~G~tG~i~Fd~~G~~~~~ 287 (806)
++..+. .++....|.|+.|+++||++||+..+
T Consensus 295 -----------------~~~~~~~~~~~~~~~~g~~g~i~f~~~g~~~~~ 327 (332)
T cd06344 295 -----------------EGVQQVELSLRNFSVQGATGKIKFLPSGDRNGQ 327 (332)
T ss_pred -----------------hhhhhhhhhcccccccCCCceeEeCCCCcccCc
Confidence 134444 56777889999999999999997553
No 53
>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=99.89 E-value=1.2e-21 Score=212.14 Aligned_cols=242 Identities=19% Similarity=0.243 Sum_probs=198.4
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHH-HHcCCeEEEEEEEcC-CcccchHHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLI-DFYGWKEVIAIYVDD-DYGRNGISALSNMLE 79 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W~~v~ii~~d~-~~g~~~~~~l~~~l~ 79 (806)
+++++++.+||+|+++++.+.+++.. +|+||+.|++..++.++++++ ++++|++|++|+.++ +|+....+.+.+.++
T Consensus 83 v~~~~~~~~ip~i~~~~~~~~~~~~~-~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~~~~~~~~~~~~~~~~~~ 161 (334)
T cd06347 83 AGPIAEDAKVPMITPSATNPKVTQGK-DYVFRVCFIDPFQGTVMAKFATENLKAKKAAVLYDNSSDYSKGLAKAFKEAFK 161 (334)
T ss_pred hHHHHHHCCCeEEcCCCCCCCcccCC-CeEEEeeCCcHHHHHHHHHHHHHhcCCcEEEEEEeCCCchhHHHHHHHHHHHH
Confidence 46788999999999999888887643 589999999999999999986 678999999999886 899999999999999
Q ss_pred hCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 80 KNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 80 ~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
+.|++++....++.. ..++++.++++++.++|+|++.+.......+++++++.|+. ..|+.++.+..... .
T Consensus 162 ~~g~~v~~~~~~~~~--~~d~~~~~~~~~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~---~~i~~~~~~~~~~~-~--- 232 (334)
T cd06347 162 KLGGEIVAEETFNAG--DTDFSAQLTKIKAKNPDVIFLPGYYTEVGLIAKQARELGIK---VPILGGDGWDSPKL-E--- 232 (334)
T ss_pred HcCCEEEEEEEecCC--CCcHHHHHHHHHhcCCCEEEEcCchhhHHHHHHHHHHcCCC---CcEEecccccCHHH-H---
Confidence 999999988777744 56899999999999999999999999999999999999973 46777765543211 1
Q ss_pred ChhhhhhccceEEEEEeCCC--ChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCC
Q 003633 160 NQTSLRILQGVVGLRQHTPD--SIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHE 237 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~ 237 (806)
....+..+|++...++.+. ++..+.|.++|+++++ ..++.++..+||++++++.|+++...
T Consensus 233 -~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-----~~~~~~~~~~yda~~~~~~Al~~ag~----------- 295 (334)
T cd06347 233 -EAGGAAAEGVYFTTHFSADDPTPKAKKFVKAYKAKYG-----KEPDAFAALGYDAYYLLADAIERAGS----------- 295 (334)
T ss_pred -HHHHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHC-----CCcchhHHHHHHHHHHHHHHHHHhCC-----------
Confidence 2234567888777766553 5778999999988875 25778889999999999999998310
Q ss_pred CCCCcccccccccccccCchHHHHHHHHcc-ccCCceeeEEEecCCCeecc
Q 003633 238 LPDSKATRVQLEQLKVFDGGTFLLRKLLQT-NFTGLSGQVQFNQDRNIVSR 287 (806)
Q Consensus 238 l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~-~f~G~tG~i~Fd~~G~~~~~ 287 (806)
.+++.+.++|.+. +|+|++|+++|+.+|+....
T Consensus 296 -----------------~~~~~v~~~l~~~~~~~g~~G~v~f~~~g~~~~~ 329 (334)
T cd06347 296 -----------------TDPEAIRDALAKTKDFDGVTGKITIDENGNPVKS 329 (334)
T ss_pred -----------------CCHHHHHHHHHhCCCcccceeeeEECCCCCcCCC
Confidence 1378899998765 69999999999999986543
No 54
>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=99.89 E-value=1.6e-21 Score=211.70 Aligned_cols=259 Identities=17% Similarity=0.116 Sum_probs=202.2
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHH-HcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLID-FYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~-~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+.+++++.++|+|++.++.. ....||+||+.+++..++.++++++. ..++|+|++++.|++||+...+.+.+.+++
T Consensus 83 ~~~~~~~~~~~~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~k~vaii~~d~~~g~~~~~~~~~~~~~ 159 (348)
T cd06355 83 VLPVFERHNGLLFYPVQYEG---LEQSPNVFYTGAAPNQQIIPAVDWLMSNKGGKRFYLVGSDYVYPRTANKILKAQLES 159 (348)
T ss_pred HHHHHhccCCceecCCCccC---CCCCCCEEEeCCChHHhHHHHHHHHHhccCCCeEEEECCcchHHHHHHHHHHHHHHH
Confidence 46788899999998754322 13469999999999999999999865 468999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|++|+....++.+ ..|+++++.++++.++|+|++......+..+++++++.|+......++........+.
T Consensus 160 ~G~~vv~~~~~~~~--~~D~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~------ 231 (348)
T cd06355 160 LGGEVVGEEYLPLG--HTDFQSIINKIKAAKPDVVVSTVNGDSNVAFFKQLKAAGITASKVPVLSFSVAEEELR------ 231 (348)
T ss_pred cCCeEEeeEEecCC--hhhHHHHHHHHHHhCCCEEEEeccCCchHHHHHHHHHcCCCccCCeeEEccccHHHHh------
Confidence 99999998888744 6799999999999999999999999999999999999998654455555432211111
Q ss_pred hhhhhhccceEEEEEeC--CCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 161 QTSLRILQGVVGLRQHT--PDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~--~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
....+.++|+++...+. .++|..++|.++|+++|+. ...++.+++.+||++++++.|++++.+
T Consensus 232 ~~g~~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~g~---~~~~~~~a~~~Y~a~~~~~~Al~~ag~------------ 296 (348)
T cd06355 232 GIGPENLAGHYAAWNYFQSVDTPENKKFVAAFKARYGQ---DRVTNDPMEAAYIGVYLWKQAVEKAGS------------ 296 (348)
T ss_pred hcChHhhcCCEEeccchhhcCCHHHHHHHHHHHHHcCC---CCCCCcHHHHHHHHHHHHHHHHHHhCC------------
Confidence 11224567877655433 3567889999999999862 113455678899999999999998411
Q ss_pred CCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee-cCceEEE
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID-KMEIHRV 302 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~-~~~~~~V 302 (806)
.++++|.++|++++|++..|+++|+++++.....+.|.+++ +++++.|
T Consensus 297 ----------------~~~~~i~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~i~~~~~~g~~~~v 345 (348)
T cd06355 297 ----------------FDVDKVRAALPGQSFDAPEGPVTVDPANHHLWKPVRIGRIQADGQFEIV 345 (348)
T ss_pred ----------------CCHHHHHHHhccCcccCCCcceEeecCCCeeeeeeEEEEEcCCCcEEEE
Confidence 13889999999999999999999998443345567788885 5666554
No 55
>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=99.88 E-value=6.5e-22 Score=214.87 Aligned_cols=245 Identities=16% Similarity=0.151 Sum_probs=197.4
Q ss_pred hcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCC
Q 003633 3 SEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNM 82 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g 82 (806)
++++++.++|+|+++++++.++...+||+||+.|++..++.++++++...+|++|++++.|++||+...+.+.+.+++.|
T Consensus 87 ~~~~~~~~ip~i~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~~~l~~~G 166 (347)
T cd06336 87 QQITERNKVLLLTAYSSDLSIDTAGNPLTFRVPPIYNVYGVPFLAYAKKPGGKKVALLGPNDAYGQPWVAAYKAAWEAAG 166 (347)
T ss_pred hhhhhhcCceEEeccCCcccccccCCceEEEecCCchhHHHHHHHHHhhcCCceEEEEccCCchhHHHHHHHHHHHHHcC
Confidence 46888999999999999999986567999999999999999999998889999999999999999999999999999999
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc-hHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD-PGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~-~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
++|+....++.. ..|++.++.+|++.++|+|++.+... ++..++++++++|+... ++...+.... ... ..
T Consensus 167 ~~vv~~~~~~~~--~~D~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~-~~~---~~ 237 (347)
T cd06336 167 GKVVSEEPYDPG--TTDFSPIVTKLLAEKPDVIFLGGPSPAPAALVIKQARELGFKGG---FLSCTGDKYD-ELL---VA 237 (347)
T ss_pred CEEeeecccCCC--CcchHHHHHHHHhcCCCEEEEcCCCchHHHHHHHHHHHcCCCcc---EEeccCCCch-HHH---HH
Confidence 999988888754 67999999999999999999999998 99999999999998642 2222221111 101 02
Q ss_pred hhhhhccceEEEEEeCC----CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCC
Q 003633 162 TSLRILQGVVGLRQHTP----DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHE 237 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~ 237 (806)
...+.++|++...++.+ ++|..++|.++|+++|+. .++.++..+||+++++++|+++....
T Consensus 238 ~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~p~~~~~~~y~~~~~~~~Al~~ag~~---------- 302 (347)
T cd06336 238 TGADFMEGVYFQFPDVDDPALAFPRAKAFVEEYKKRYGE-----PPNSEAAVSYDAVYILKAAMEAAGSV---------- 302 (347)
T ss_pred hcHHhhCceEEEeecccccccCCHHHHHHHHHHHHHHCC-----CCcHHHHHHHHHHHHHHHHHHhcCCC----------
Confidence 23456789988777654 477889999999999862 37788999999999999999984211
Q ss_pred CCCCcccccccccccccCchHHHHHHHH--------ccccCCceeeEEEecCCCeecccE
Q 003633 238 LPDSKATRVQLEQLKVFDGGTFLLRKLL--------QTNFTGLSGQVQFNQDRNIVSRGY 289 (806)
Q Consensus 238 l~~~~~~~~~~~~~~~~~~g~~l~~~l~--------~~~f~G~tG~i~Fd~~G~~~~~~~ 289 (806)
++..+.+++. ...|.+..|.+.||++||+..|.+
T Consensus 303 ------------------~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 344 (347)
T cd06336 303 ------------------DDTAAVAALAAMLGVGKPAFGYARWWGKELFGVNGALVGPWP 344 (347)
T ss_pred ------------------CcHHHHHHHhhccCCCcCccccccccccccccCCCccccCcc
Confidence 1334444433 256889999999999999766544
No 56
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=99.88 E-value=2.1e-21 Score=211.42 Aligned_cols=257 Identities=24% Similarity=0.201 Sum_probs=203.5
Q ss_pred HhcccccCCCcEEecccCCCCcccCCC-CceEEecCCcHHHHHHHHHHHH-HcCCeEEEEEEEcCCcccchHHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQF-PYFIRSTQSDSQQMAAMADLID-FYGWKEVIAIYVDDDYGRNGISALSNMLE 79 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~-p~f~Rt~psd~~q~~ai~~ll~-~~~W~~v~ii~~d~~~g~~~~~~l~~~l~ 79 (806)
+++++++.++|+|++++|+|.++..++ +++||++|+|..|+.++++++. ..+.|+|++|+.|+.||++..+.+++.++
T Consensus 94 ~~~v~~~~~i~~i~p~st~~~~~~~~~~~~vfr~~~~~~~q~~~~~~~l~~~~~~k~v~ii~~~~~yg~~~~~~~~~~l~ 173 (366)
T COG0683 94 ASPVAEEAGVPLISPSATAPQLTGRGLKPNVFRTGPTDNQQAAAAADYLVKKGGKKRVAIIGDDYAYGEGLADAFKAALK 173 (366)
T ss_pred chhhHhhcCceEEeecCCCCcccccccccceEEecCChHHHHHHHHHHHHHhcCCcEEEEEeCCCCcchhHHHHHHHHHH
Confidence 567899999999999999999887665 4599999999999999999864 66777999999999999999999999999
Q ss_pred hCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 80 KNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 80 ~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
+.|.++...+.+.+.. .++..++.++++.++|+|++.+..+++..+++++++.|+... ..++.+........
T Consensus 174 ~~G~~~~~~~~~~~~~--~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~~~~~G~~~~-~~~~~~~~~~~~~~----- 245 (366)
T COG0683 174 ALGGEVVVEEVYAPGD--TDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQAREQGLKAK-LIGGDGAGTAEFEE----- 245 (366)
T ss_pred hCCCeEEEEEeeCCCC--CChHHHHHHHHhcCCCEEEECCCCccchHHHHHHHHcCCCCc-cccccccCchhhhh-----
Confidence 9999866667777553 359999999999999999999999999999999999997643 23333222211111
Q ss_pred Chhhhhhccc-e-EEEEEeCC-CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCC
Q 003633 160 NQTSLRILQG-V-VGLRQHTP-DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASH 236 (806)
Q Consensus 160 ~~~~~~~~~g-v-~~~~~~~~-~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~ 236 (806)
......++ + +......+ ++|..+.|+++|+++++ ....++.++..+||++++++.|++++.. .
T Consensus 246 --~~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~~g---~~~~~~~~~~~~y~a~~~~~~ai~~a~~-~-------- 311 (366)
T COG0683 246 --IAGAGGAGAGLLATAYSTPDDSPANKKFVEAYKAKYG---DPAAPSYFAAAAYDAVKLLAKAIEKAGK-S-------- 311 (366)
T ss_pred --hcccCccccEEEEecccccccCcchHHHHHHHHHHhC---CCCCcccchHHHHHHHHHHHHHHHHHhc-C--------
Confidence 11122222 2 33333333 45677789999999996 3345677899999999999999999531 0
Q ss_pred CCCCCcccccccccccccCchHHHHHHHHccc-cCCceeeEEEecCCCeecccEEEEEeecCc
Q 003633 237 ELPDSKATRVQLEQLKVFDGGTFLLRKLLQTN-FTGLSGQVQFNQDRNIVSRGYDVINIDKME 298 (806)
Q Consensus 237 ~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~-f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~ 298 (806)
. +++++.++|+... +.+.+|++.||++|++....+.|.+++.++
T Consensus 312 -----------------~-d~~~v~~al~~~~~~~~~~G~v~~~~~~~~~~~~~~i~~~~~~~ 356 (366)
T COG0683 312 -----------------S-DREAVAEALKGGKFFDTAGGPVTFDEKGDRGSKPVYVGQVQKGG 356 (366)
T ss_pred -----------------C-CHHHHHHHHhhCCCCccCCcceeECCCCCcCCCceEEEEEEecC
Confidence 1 2788999999887 799999999999999999999999998543
No 57
>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=99.88 E-value=8.1e-22 Score=213.18 Aligned_cols=244 Identities=16% Similarity=0.141 Sum_probs=199.2
Q ss_pred HhcccccCCCcEEecccCCCCcccCC-CCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQ-FPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~-~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++.+||+|+++++++.++..+ +||+||+.+++..|+.++++++...++++|++++.|++||+...+.+.+.+++
T Consensus 82 ~~~~~~~~~vp~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~~~~g~~~~~~~~~~~~~ 161 (334)
T cd06327 82 VQEVAREKKKIYIVTGAGSDDLTGKDCSPYTFHWAYDTYMLANGTAPALVKAGGKKWFFLTADYAFGHSLERDARKVVKA 161 (334)
T ss_pred HHHHHHHhCceEEecCCCccccccCCCCCceEEccCChHHHHHHHHHHHHHhcCCeEEEEecchHHhHHHHHHHHHHHHh
Confidence 45778899999999999999998754 89999999999999999999887777999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|++|+....++.. ..|+++++.++++.++|+|++.+....+..+++++++.|+.. +..++....... ...
T Consensus 162 ~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~--~~~---- 232 (334)
T cd06327 162 NGGKVVGSVRHPLG--TSDFSSYLLQAQASGADVLVLANAGADTVNAIKQAAEFGLTK-GQKLAGLLLFLT--DVH---- 232 (334)
T ss_pred cCCEEcCcccCCCC--CccHHHHHHHHHhCCCCEEEEeccchhHHHHHHHHHHhCCcc-CCcEEEecccHH--HHH----
Confidence 99999988888754 569999999999999999999999999999999999999862 333333221111 110
Q ss_pred hhhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 161 QTSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
....+..+|++...++.+ +++..++|.++|+++++. .++.++..+||+++++++|++++.+.
T Consensus 233 ~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~-----~p~~~~~~~Y~~~~~~~~A~~~ag~~----------- 296 (334)
T cd06327 233 SLGLDAAQGLYLTTAWYWDLPNDETRAFVKRFQAKYGK-----MPSMVQAGAYSAVLHYLKAVEAAGTD----------- 296 (334)
T ss_pred hhchhhhcCeEEeeeccccCCCHHHHHHHHHHHHHHCc-----CCCcHHHHHHHHHHHHHHHHHHHCCC-----------
Confidence 223356789888777654 367889999999999862 46778889999999999999994221
Q ss_pred CCCcccccccccccccCchHHHHHHHHccc-cCCceeeEEEec-CCCeecc
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQTN-FTGLSGQVQFNQ-DRNIVSR 287 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~-f~G~tG~i~Fd~-~G~~~~~ 287 (806)
++.++.++|++++ ++++.|++.|+. +|+...+
T Consensus 297 -----------------~~~~v~~al~~~~~~~~~~g~~~~~~~~~~~~~~ 330 (334)
T cd06327 297 -----------------DADKVVAKMKETPIYDLFAGNGYIRACDHQMVHD 330 (334)
T ss_pred -----------------ChHHHHHhccccceeccCCCCceeeccccchhcc
Confidence 2677999999975 688999999986 6764433
No 58
>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=99.88 E-value=1.4e-21 Score=212.03 Aligned_cols=234 Identities=16% Similarity=0.142 Sum_probs=195.2
Q ss_pred hcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcC-CeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 3 SEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYG-WKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~-W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++.++||+|+++++++.++. ..+||+||+.|++..++.++++++...+ ||+|++++.|+.||+...+.+.+.+++
T Consensus 90 ~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~k~v~i~~~~~~~g~~~~~~~~~~~~~ 169 (342)
T cd06329 90 NQRNPGKEVLYLNYASVAPALTGEKCSFWHFRTDANTDMKMEALASYIKKQPDGKKVYLINQDYSWGQDVAAAFKAMLAA 169 (342)
T ss_pred hhhhccCCeEEEecCCCCchhhhccCcceEEEecCChHHHHHHHHHHHHhcccCceEEEEeCChHHHHHHHHHHHHHHHh
Confidence 46678899999999999999987 4579999999999999999999998876 999999999999999999999999999
Q ss_pred --CCcEEEEEeccCCCCCh-hHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccc
Q 003633 81 --NMAKVSYKLPLPVQFNQ-HDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFS 157 (806)
Q Consensus 81 --~g~~i~~~~~~~~~~~~-~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~ 157 (806)
.|++|+....++.. . .|+++++.++++.++|+|++...+.++..+++++++.|+.. .++...+.... ..
T Consensus 170 ~~~G~~vv~~~~~~~~--~~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~--~~- 241 (342)
T cd06329 170 KRPDIQIVGEDLHPLG--KVKDFSPYVAKIKASGADTVITGNWGNDLLLLVKQAADAGLKL---PFYTPYLDQPG--NP- 241 (342)
T ss_pred hcCCcEEeceeccCCC--CCCchHHHHHHHHHcCCCEEEEcccCchHHHHHHHHHHcCCCc---eEEeccccchh--HH-
Confidence 99999988777744 4 69999999999999999999998889999999999999843 35554433222 11
Q ss_pred cCChhhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCC
Q 003633 158 KMNQTSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSAS 235 (806)
Q Consensus 158 ~~~~~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~ 235 (806)
....+..+|++....+.+ +++..++|.++|+++++ ..++.++..+||++++++.|+++..+
T Consensus 242 ---~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-----~~~~~~~~~~y~~~~~~~~a~~~ag~--------- 304 (342)
T cd06329 242 ---AALGEAGLGLVVAVAYWHPNDTPANRAFVEAFKAKYG-----RVPDYYEGQAYNGIQMLADAIEKAGS--------- 304 (342)
T ss_pred ---HhhcccccceEEeeeccCCCCCHHHHHHHHHHHHHhC-----CCCCchHHHHHHHHHHHHHHHHHhCC---------
Confidence 334456788887766544 46788999999999885 25677889999999999999998311
Q ss_pred CCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEec
Q 003633 236 HELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQ 280 (806)
Q Consensus 236 ~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~ 280 (806)
.+++.+.++|++++|+|..|+++|+.
T Consensus 305 -------------------~~~~~v~~al~~~~~~~~~g~~~~~~ 330 (342)
T cd06329 305 -------------------TDPEAVAKALEGMEVDTPVGPVTMRA 330 (342)
T ss_pred -------------------CCHHHHHHHHhCCccccCCCCeEEcc
Confidence 13789999999999999999999985
No 59
>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=99.88 E-value=4.2e-21 Score=210.18 Aligned_cols=260 Identities=14% Similarity=0.195 Sum_probs=207.9
Q ss_pred HhcccccCCCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHH-HHHcCCeEEEEEEEcCCcccchHHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADL-IDFYGWKEVIAIYVDDDYGRNGISALSNMLE 79 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~l-l~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~ 79 (806)
+++++++.+||+|+++++++.+++. .+||+||+.|++..++.+++++ ++++||++|++|+.|++||+...+.+.+.++
T Consensus 90 ~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~ii~~~~~~g~~~~~~~~~~~~ 169 (362)
T cd06343 90 VQKYLNEKKVPQLFPASGASKWNDPKPFPWTFGWQPSYQDEARIYAKYLVEEKPNAKIAVLYQNDDFGKDYLKGLKDGLG 169 (362)
T ss_pred hHHHHHhcCCceEecccccHhhhCCCCCCceEecCCChHHHHHHHHHHHHHhCCCceEEEEEeccHHHHHHHHHHHHHHH
Confidence 4577889999999998888888875 6999999999999999999996 5678999999999999999999999999999
Q ss_pred hCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 80 KNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 80 ~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
+.|++++....++.. ..|+++++.++++.++|+|++.+...++..+++++++.|+.. .++.+++........
T Consensus 170 ~~G~~vv~~~~~~~~--~~d~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~~~~~--- 241 (362)
T cd06343 170 DAGLEIVAETSYEVT--EPDFDSQVAKLKAAGADVVVLATTPKFAAQAIRKAAELGWKP---TFLLSSVSASVASVL--- 241 (362)
T ss_pred HcCCeEEEEeeecCC--CccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHHcCCCc---eEEEEecccccHHHH---
Confidence 999999988888754 569999999999999999999999999999999999999753 356665543322101
Q ss_pred ChhhhhhccceEEEEEeC-------CCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccc
Q 003633 160 NQTSLRILQGVVGLRQHT-------PDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITF 232 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~-------~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~ 232 (806)
.....+..+|+++...+. .+++..++|.+.|+++++. ...++.++..+||++.++++|++++..
T Consensus 242 ~~~~~~~~~g~~~~~~~~~~~~p~~~~~~~~~~f~~~~~~~~~~---~~~~~~~~~~~y~a~~~~~~a~~~ag~------ 312 (362)
T cd06343 242 KPAGLEAAEGVIAAAYLKDPTDPAWADDPGVKEFIAFYKKYFPE---GDPPDTYAVYGYAAAETLVKVLKQAGD------ 312 (362)
T ss_pred HHhhhHhhCceEEEEEecCCCccccccCHHHHHHHHHHHHhcCC---CCCCchhhhHHHHHHHHHHHHHHHhCC------
Confidence 122335678887765442 2467788999999988852 124778899999999999999998410
Q ss_pred cCCCCCCCCcccccccccccccCchHHHHHHHHcccc---CCc-eeeEEEecCCCeecccEEEEEeecCce
Q 003633 233 SASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNF---TGL-SGQVQFNQDRNIVSRGYDVINIDKMEI 299 (806)
Q Consensus 233 ~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f---~G~-tG~i~Fd~~G~~~~~~~~I~~~~~~~~ 299 (806)
..+++.+.++|.++++ .+. .|++.|+.+..+....+.|.++++++|
T Consensus 313 ---------------------~~~~~~v~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~~ 362 (362)
T cd06343 313 ---------------------DLTRENIMKQAESLKDVLPDLLPGIRINTSPDDHLPIEQMQLMRFEGGRW 362 (362)
T ss_pred ---------------------CCCHHHHHHHHHhCCCCCccccCccceecCccccccceeEEEEEEecCcC
Confidence 0127899999999987 333 358999865545566788888887764
No 60
>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=99.88 E-value=4.8e-21 Score=207.78 Aligned_cols=252 Identities=15% Similarity=0.200 Sum_probs=200.3
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHH-HHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLI-DFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++.+||+|+++++++.+++. .+|+||+.|++..++.++++++ +.++|++|++++.|++||+...+.+.+.+++
T Consensus 83 ~~~~~~~~~vp~i~~~~~~~~~~~~-~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~~~ 161 (340)
T cd06349 83 ASPIYQRAGLVQLSPTNSHPDFTKG-GDFIFRNSTSQAIEAPLLADYAVKDLGFKKVAILSVNTDWGRTSADIFVKAAEK 161 (340)
T ss_pred hHHHHHhCCCeEEecCCCCCccccC-CCeEEEccCCcHHHHHHHHHHHHHHcCCcEEEEEecCChHhHHHHHHHHHHHHH
Confidence 4678889999999999888888754 5999999999999999999985 7789999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|++|+....+++. ..|+++.+.+++++++|+|++.+...+...+++++++.|+.. .++.++..... ...
T Consensus 162 ~g~~v~~~~~~~~~--~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~-~~~---- 231 (340)
T cd06349 162 LGGQVVAHEEYVPG--EKDFRPTITRLRDANPDAIILISYYNDGAPIARQARAVGLDI---PVVASSSVYSP-KFI---- 231 (340)
T ss_pred cCCEEEEEEEeCCC--CCcHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCCCC---cEEccCCcCCH-HHH----
Confidence 99999988777754 568999999999999999999999999999999999999753 34544433211 111
Q ss_pred hhhhhhccceEEEEEeCCC--ChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 161 QTSLRILQGVVGLRQHTPD--SIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
....+..+|++...++.|+ ++..++|.++|+++|+. .++.++..+||++++++.|+++....
T Consensus 232 ~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~p~~~~~~~y~~~~~~~~a~~~ag~~----------- 295 (340)
T cd06349 232 ELGGDAVEGVYTPTAFFPGDPRPEVQSFVSAYEAKYGA-----QPDAFAAQAYDAVGILAAAVRRAGTD----------- 295 (340)
T ss_pred HHhHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHCC-----CcchhhhhHHHHHHHHHHHHHHhCCC-----------
Confidence 2233567898887776664 56789999999888852 46788999999999999999983110
Q ss_pred CCCcccccccccccccCchHHHHHH-HHccccCCceeeEEEecC-CCeecccEEEEEeecCc
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRK-LLQTNFTGLSGQVQFNQD-RNIVSRGYDVINIDKME 298 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~-l~~~~f~G~tG~i~Fd~~-G~~~~~~~~I~~~~~~~ 298 (806)
....+... +.+..+.|++|+++|+++ |+. ...+.++.+++++
T Consensus 296 -----------------~~~~~~~~~~~~~~~~~~~g~i~~~~~~~~~-~~~~~~~~~~~g~ 339 (340)
T cd06349 296 -----------------RRAARDGFAKAEDVYSGVTGSTKFDPNTRRV-IKRFVPLVVRNGK 339 (340)
T ss_pred -----------------CHHHHHHHHHhccCcccceEeEEECCCCCCc-cCceEEEEEeCCc
Confidence 12222222 245568899999999986 654 4588888887765
No 61
>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=99.88 E-value=2.7e-21 Score=208.93 Aligned_cols=248 Identities=15% Similarity=0.217 Sum_probs=196.7
Q ss_pred HhcccccCCCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++.+||+|+++++.+.++.. .+||+||+.|++..++.++++++...||++|++++.|++||+...+.+.+.++
T Consensus 81 ~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~g~~~vail~~~~~~g~~~~~~~~~~~~- 159 (333)
T cd06359 81 VVPPVLESGTFYISTNAGPSQLAGKQCSPYFFSTSWQNDQVHEAMGKYAQDKGYKRVFLIAPNYQAGKDALAGFKRTFK- 159 (333)
T ss_pred HHHHHHHcCCeEEecCCCccccccccCCCcEEEeeCChHhhHHHHHHHHHHhCCCeEEEEecCchhhHHHHHHHHHHhC-
Confidence 3567889999999997777777654 48999999999999999999999889999999999999999999998888774
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.++.....++ ....|++.++.++++.++|+|++......+..++++++++|+.. ...++.+++.... +..
T Consensus 160 --~~v~~~~~~~--~~~~d~~~~i~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~-~~~~~~~~~~~~~-~~~---- 229 (333)
T cd06359 160 --GEVVGEVYTK--LGQLDFSAELAQIRAAKPDAVFVFLPGGMGVNFVKQYRQAGLKK-DIPLYSPGFSDEE-DTL---- 229 (333)
T ss_pred --ceeeeeecCC--CCCcchHHHHHHHHhCCCCEEEEEccCccHHHHHHHHHHcCccc-CCeeeccCcccCH-HHH----
Confidence 3555555455 34569999999999999999999888888999999999999853 3445555443321 111
Q ss_pred hhhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 161 QTSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
....+..+|+++..++.+ +++..++|.++|+++++ ..++.++..+||++++++.|++++...
T Consensus 230 ~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-----~~~~~~~~~~yda~~~~~~A~~~ag~~----------- 293 (333)
T cd06359 230 PAVGDAALGLYNTAQWAPDLDNPANKKFVADFEKKYG-----RLPTLYAAQAYDAAQLLDSAVRKVGGN----------- 293 (333)
T ss_pred HhcchhhcCeeeccccCCCCCCHHHHHHHHHHHHHhC-----CCCcHHHHHHHHHHHHHHHHHHHhcCC-----------
Confidence 233456789888777766 46888999999999885 257788999999999999999984110
Q ss_pred CCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEE
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVI 292 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~ 292 (806)
..+++.+.++|++++|+|++|+++|+.+|+.. ....|+
T Consensus 294 ---------------~~~~~~v~~al~~~~~~~~~G~~~~~~~~~~~-~~~~~~ 331 (333)
T cd06359 294 ---------------LSDKDALRAALRAADFKSVRGAFRFGTNHFPI-QDFYLR 331 (333)
T ss_pred ---------------CCCHHHHHHHHhcCccccCccceEECCCCCcc-eeEEEE
Confidence 01378999999999999999999999888743 334444
No 62
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.88 E-value=3.2e-21 Score=203.47 Aligned_cols=224 Identities=20% Similarity=0.299 Sum_probs=187.8
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHH----hCCC-CcceEEEEcCCCCCCCCHHHHHHHHHcCccc
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALK----LVPY-DVPYKFELFGDGLSNPSYDGLVKMVANDVFD 429 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~----~l~~-~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D 429 (806)
.+.|+||+.. .|+||.+.+. ++.+.||++|+++++++ ++|. .+++++++. +|..++..|..|++|
T Consensus 39 ~g~L~Vg~~~--~~pP~~f~~~-~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~-------~~~~~i~~L~~G~~D 108 (302)
T PRK10797 39 NGVIVVGHRE--SSVPFSYYDN-QQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPI-------TSQNRIPLLQNGTFD 108 (302)
T ss_pred CCeEEEEEcC--CCCCcceECC-CCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEEc-------ChHhHHHHHHCCCcc
Confidence 4679999875 7888988764 57899999998777665 6664 366888884 688899999999999
Q ss_pred EEEeeEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCC
Q 003633 430 AAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGP 509 (806)
Q Consensus 430 ~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~ 509 (806)
++++.+++|++|.+.++||.||+.++..+++++..
T Consensus 109 i~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~--------------------------------------------- 143 (302)
T PRK10797 109 FECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG--------------------------------------------- 143 (302)
T ss_pred EEecCCccCcchhhcceecccEeeccEEEEEECCC---------------------------------------------
Confidence 99999999999999999999999999999997654
Q ss_pred CccchhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEE
Q 003633 510 PRRQIATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQ 589 (806)
Q Consensus 510 ~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~ 589 (806)
.|++++|| .|++||+.
T Consensus 144 --------------------------------------------------------------~i~sl~dL--~Gk~V~v~ 159 (302)
T PRK10797 144 --------------------------------------------------------------DIKDFADL--KGKAVVVT 159 (302)
T ss_pred --------------------------------------------------------------CCCChHHc--CCCEEEEe
Confidence 57899999 78999999
Q ss_pred eCchhHHHhhhhcc--cccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhC--CC-CeEEeCCccccCCce
Q 003633 590 VGSFAYSYLSDSLR--IQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSN--QT-DFGIIGQPFTRSGWG 664 (806)
Q Consensus 590 ~gs~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~--~~-~l~~~~~~~~~~~~~ 664 (806)
.|+....++.+... ....+++.+.+.++.+++|.. |++||++.+...+.+.+.+ .. .+.++++.+...+++
T Consensus 160 ~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~----GrvDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~ 235 (302)
T PRK10797 160 SGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLES----GRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYG 235 (302)
T ss_pred CCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHc----CCceEEEccHHHHHHHHHcCCCCcceEECCccCCcCcee
Confidence 99998887753211 123577888999999999999 9999999998776654433 22 478888887788899
Q ss_pred eeecCCCC-chHHHHHHHHhhhccchhHHHHHhhcCCC
Q 003633 665 FAFQRDSP-LAVGMSTAILKLSENGMLQKLHEKWFCKE 701 (806)
Q Consensus 665 ~~~~k~sp-l~~~~n~~il~l~e~G~~~~i~~kw~~~~ 701 (806)
++++|+++ +++.+|.+|.++.++|.+++|.+||+...
T Consensus 236 ~a~~k~~~~L~~~in~~L~~l~~~G~l~~i~~kw~~~~ 273 (302)
T PRK10797 236 CMLRKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFKNP 273 (302)
T ss_pred EEEeCCCHHHHHHHHHHHHHHHhCchHHHHHHHHcCCC
Confidence 99999988 99999999999999999999999999843
No 63
>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=99.87 E-value=1.8e-21 Score=211.77 Aligned_cols=242 Identities=17% Similarity=0.118 Sum_probs=193.8
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCCcccchHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDDYGRNGISALSNML 78 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~~g~~~~~~l~~~l 78 (806)
+++++++.+||+|++.++++.+++ ..+||+||+.|++..+..+++++++.+ +|++|++++.|++||....+.+.+.+
T Consensus 83 ~~~~~~~~~ip~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~~~~ 162 (346)
T cd06330 83 VAPVAEELKVFFIATDPGTPRLTEEPDNPYVFRTRNSTIMDAVAGALYAAKLDKKAKTWATINPDYAYGQDAWADFKAAL 162 (346)
T ss_pred HHHHHHHcCCeEEEcCCCCcccccCCCCCceEEecCChHHHHHHHHHHHHHhCcCccEEEEECCchHHHHHHHHHHHHHH
Confidence 567889999999999999888887 468999999999999999999998877 49999999999999999999999999
Q ss_pred HhCC--cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccc
Q 003633 79 EKNM--AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESF 156 (806)
Q Consensus 79 ~~~g--~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~ 156 (806)
++.| ++++....++ ...+|++.++.+|++.++|+|++++...+...+++++++.|+.. +..|+.+.+....+.
T Consensus 163 ~~~g~~~~~v~~~~~~--~~~~d~~~~v~~i~~~~~d~ii~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~~-- 237 (346)
T cd06330 163 KRLRPDVEVVSEQWPK--LGAPDYGSEITALLAAKPDAIFSSLWGGDLVTFVRQANARGLFD-GTTVVLTLTGAPELA-- 237 (346)
T ss_pred HHhCCCCeecccccCC--CCCcccHHHHHHHHhcCCCEEEEecccccHHHHHHHHHhcCccc-CceEEeeccchhhhh--
Confidence 9985 5555444333 34679999999999999999999999999999999999999865 678888775443211
Q ss_pred ccCChhhhhhccceEEEEE--eC--CCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccc
Q 003633 157 SKMNQTSLRILQGVVGLRQ--HT--PDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITF 232 (806)
Q Consensus 157 ~~~~~~~~~~~~gv~~~~~--~~--~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~ 232 (806)
....+..+|++.... +. ++++..++|.++|+++++ ..++.++..+||++++++.|++++....
T Consensus 238 ----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~g-----~~p~~~~~~~y~a~~~l~~a~~~a~~~~---- 304 (346)
T cd06330 238 ----PLGDEMPEGVIIGGRGPYFIPPDTPENKAFVDAYQEKYG-----DYPTYGAYGAYQAVMALAAAVEKAGATD---- 304 (346)
T ss_pred ----hhhcccCCceEEeccccCCCCCCChHHHHHHHHHHHHHC-----CCCChHHHHHHHHHHHHHHHHHHhcCCC----
Confidence 222355677765432 21 157889999999999885 2456788899999999999999853221
Q ss_pred cCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecC
Q 003633 233 SASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQD 281 (806)
Q Consensus 233 ~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~ 281 (806)
.... .+.+.++|++++|.|+.|++.|+++
T Consensus 305 -------------------~~~~-~~~v~~al~~~~~~~~~G~~~f~~~ 333 (346)
T cd06330 305 -------------------GGAP-PEQIAAALEGLSFETPGGPITMRAA 333 (346)
T ss_pred -------------------CCCc-HHHHHHHHcCCCccCCCCceeeecC
Confidence 0001 2579999999999999999999873
No 64
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.87 E-value=9e-21 Score=195.51 Aligned_cols=220 Identities=24% Similarity=0.454 Sum_probs=188.2
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
+.++|+||+.. +|+||.+.+ ++.+.|+++|+++++++++|.+ +++++ .+|.+++.++.+|++|++++
T Consensus 23 ~~~~l~v~~~~--~~~P~~~~~--~g~~~G~~vdl~~~ia~~lg~~--~~~~~-------~~~~~~~~~l~~G~vDi~~~ 89 (247)
T PRK09495 23 ADKKLVVATDT--AFVPFEFKQ--GDKYVGFDIDLWAAIAKELKLD--YTLKP-------MDFSGIIPALQTKNVDLALA 89 (247)
T ss_pred cCCeEEEEeCC--CCCCeeecC--CCceEEEeHHHHHHHHHHhCCc--eEEEe-------CCHHHHHHHHhCCCcCEEEe
Confidence 34689999764 688888754 5789999999999999999976 66665 26999999999999999988
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
+++.+++|.+.++||.||+.+++.++++...
T Consensus 90 ~~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~------------------------------------------------- 120 (247)
T PRK09495 90 GITITDERKKAIDFSDGYYKSGLLVMVKANN------------------------------------------------- 120 (247)
T ss_pred cCccCHHHHhhccccchheecceEEEEECCC-------------------------------------------------
Confidence 8899999999999999999999999987654
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCch
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSF 593 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~ 593 (806)
.++++++|| .+++||+..|+.
T Consensus 121 ---------------------------------------------------------~~~~~~~dL--~g~~I~v~~g~~ 141 (247)
T PRK09495 121 ---------------------------------------------------------NDIKSVKDL--DGKVVAVKSGTG 141 (247)
T ss_pred ---------------------------------------------------------CCCCChHHh--CCCEEEEecCch
Confidence 357899999 688999999998
Q ss_pred hHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCC--CeEEeCCccccCCceeeecCCC
Q 003633 594 AYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQT--DFGIIGQPFTRSGWGFAFQRDS 671 (806)
Q Consensus 594 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~--~l~~~~~~~~~~~~~~~~~k~s 671 (806)
...++.+. .+...++.+++..+.+++|.+ |++|+++.+...+.+++++.. ++..++.......++++++|++
T Consensus 142 ~~~~l~~~--~~~~~i~~~~~~~~~~~~L~~----grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~ 215 (247)
T PRK09495 142 SVDYAKAN--IKTKDLRQFPNIDNAYLELGT----GRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGS 215 (247)
T ss_pred HHHHHHhc--CCCCceEEcCCHHHHHHHHHc----CceeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcH
Confidence 88887543 244567788889999999999 999999999988888777642 4777777667778999999999
Q ss_pred CchHHHHHHHHhhhccchhHHHHHhhcCC
Q 003633 672 PLAVGMSTAILKLSENGMLQKLHEKWFCK 700 (806)
Q Consensus 672 pl~~~~n~~il~l~e~G~~~~i~~kw~~~ 700 (806)
.+++.+|++|.++.++|.+++|.+||+..
T Consensus 216 ~l~~~~n~al~~~~~~g~~~~i~~k~~~~ 244 (247)
T PRK09495 216 ELREKVNGALKTLKENGTYAEIYKKWFGT 244 (247)
T ss_pred HHHHHHHHHHHHHHHCCcHHHHHHHHcCC
Confidence 99999999999999999999999999964
No 65
>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=99.87 E-value=6.1e-21 Score=206.23 Aligned_cols=242 Identities=17% Similarity=0.136 Sum_probs=194.2
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
+++++++.+||+|++++++.. ...||+||+.|++..++.++++++...+|++|++|+.|++||+...+.+.+.+++.
T Consensus 83 ~~~~~~~~~vp~i~~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~~~~~~~ 159 (333)
T cd06331 83 VLPVVERGRGLLFYPTQYEGG---ECSPNVFYTGATPNQQLLPLIPYLMEKYGKRFYLIGSDYVWPRESNRIARALLEEL 159 (333)
T ss_pred HHHHHHhcCceEEeCCCCCCC---cCCCCeEEccCChHHhHHHHHHHHHHhcCCeEEEECCCchhHHHHHHHHHHHHHHc
Confidence 567889999999997654322 23589999999999999999998766569999999999999999999999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
|.+|+....+++. ..|+++++.++++.++|+|++++...++..+++++.+.|+..... ++.+...... ... .
T Consensus 160 G~~vv~~~~~~~~--~~d~~~~v~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~-~~~~~~~~~~-~~~----~ 231 (333)
T cd06331 160 GGEVVGEEYLPLG--TSDFGSVIEKIKAAGPDVVLSTLVGDSNVAFYRQFAAAGLDADRI-PILSLTLDEN-ELA----A 231 (333)
T ss_pred CCEEEEEEEecCC--cccHHHHHHHHHHcCCCEEEEecCCCChHHHHHHHHHcCCCcCCC-eeEEcccchh-hhh----c
Confidence 9999988888854 679999999999999999999999999999999999999864343 3443322221 111 2
Q ss_pred hhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 162 TSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
......+|+++..++.+ +.+..+.|.++|+++++. ...++.+++.+|||+++++.|+++..+
T Consensus 232 ~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~---~~~~~~~~~~~yda~~~~~~A~~~ag~------------- 295 (333)
T cd06331 232 IGAEAAEGHYSAASYFQSLDTPENKAFVARYRARYGD---DAVINSPAEAAYEAVYLWAAAVEKAGS------------- 295 (333)
T ss_pred cChhhhCCcEeechhhhhcCChhHHHHHHHHHHHcCC---CcCCCchhHHHHHHHHHHHHHHHHcCC-------------
Confidence 22345788888776654 467789999999988852 114678899999999999999998311
Q ss_pred CCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCee
Q 003633 240 DSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIV 285 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~ 285 (806)
.++++|.++|++++|+|++|+++|++++++.
T Consensus 296 ---------------~~~~~l~~al~~~~~~~~~G~i~f~~~~~~~ 326 (333)
T cd06331 296 ---------------TDPEAVRAALEGVSFDAPQGPVRIDPDNHHT 326 (333)
T ss_pred ---------------CCHHHHHHHhhcCcccCCCCceEecCCCCcc
Confidence 1388999999999999999999999877643
No 66
>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=99.86 E-value=1.6e-20 Score=203.23 Aligned_cols=243 Identities=16% Similarity=0.236 Sum_probs=196.5
Q ss_pred hcccccCCCcEEecccCCCCcccCC-CCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 3 SEVANGLKVPLVSFAATDPTLSALQ-FPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~~~-~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
.+.+++.++|+|+++++.+.+++.. +|++||+.|++..++..+++++...||+++++++.+++||+...+.+.+.++
T Consensus 82 ~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~g~~~v~il~~~~~~~~~~~~~~~~~~~-- 159 (333)
T cd06332 82 VPSLTESGTFLISPNAGPSDLAGKLCSPNFFRTSWQNDQVHEAMGKYAADKGYKKVVIIAPDYAAGKDAVAGFKRTFK-- 159 (333)
T ss_pred HHHHhhcCCeEEecCCCCccccccCCCCcEEEeeCChHHhHHHHHHHHHHhCCceEEEEecCcchhHHHHHHHHHhhc--
Confidence 4677888999999998888888754 7999999999999999999999999999999999999999999999999887
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
..+.....++. ...|+..+++++++.++|+|++......+..++++++++|+.. ...++.++.+.... .. .
T Consensus 160 -~~~~~~~~~~~--~~~d~~~~i~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~-~~----~ 230 (333)
T cd06332 160 -GEVVEEVYTPL--GQLDFSAELAQIRAAKPDAVFVFLPGGMAVNFVKQYDQAGLKK-KIPLYGPGFLTDQD-TL----P 230 (333)
T ss_pred -EEEeeEEecCC--CCcchHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCccc-CCceeccCCCCCHH-HH----H
Confidence 35555555553 3457999999999999999999888889999999999999843 45566665544321 11 2
Q ss_pred hhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 162 TSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
...+.++|+++..++.+ +++..++|.++|+++++. .++.++..+||++++++.|++++...
T Consensus 231 ~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~yda~~~~~~a~~~ag~~------------ 293 (333)
T cd06332 231 AQGDAAVGVLTALHWAPDLDNPANKRFVAAYKAAYGR-----VPSVYAAQGYDAAQLLDAALRAVGGD------------ 293 (333)
T ss_pred hhchhhcCeeeeeccCCCCCCHHHHHHHHHHHHHhCC-----CCcHHHHHHHHHHHHHHHHHHHhcCC------------
Confidence 34466788888777766 357889999999999862 46778999999999999999994110
Q ss_pred CCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecc
Q 003633 240 DSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSR 287 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~ 287 (806)
..++..+.++|++++|+|++|+++|+++|+...+
T Consensus 294 --------------~~~~~~v~~al~~~~~~~~~g~i~f~~~~~~~~~ 327 (333)
T cd06332 294 --------------LSDKDALRAALRAADFDSPRGPFKFNPNHNPIQD 327 (333)
T ss_pred --------------CCCHHHHHHHHhcCceecCccceeECCCCCcccc
Confidence 1126789999999999999999999999985443
No 67
>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=99.86 E-value=3.6e-20 Score=201.73 Aligned_cols=261 Identities=13% Similarity=0.113 Sum_probs=196.8
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHH-HcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLID-FYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~-~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++.++|+|....... ....||+||+.|++..++.++++++. ..+ +++++|+.|++||+...+.+.+.+++
T Consensus 84 ~~~~~~~~~~~~i~~~~~~~---~~~~~~~Fr~~~~~~~~~~~~~~~~~~~~g-~~va~l~~d~~~g~~~~~~~~~~~~~ 159 (374)
T TIGR03669 84 IRPIIDRNEQLYFYTNQYEG---GVCDEYTFAVGATARQQLGTVVPYMVEEYG-KKIYTIAADYNFGQLSADWVRVIAKE 159 (374)
T ss_pred HHHHHHhcCceEEcCccccc---ccCCCCEEEcCCChHHHHHHHHHHHHHcCC-CeEEEEcCCcHHHHHHHHHHHHHHHH
Confidence 46788899999996432111 12358999999999999999999875 456 67999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|++|+....++.+ ..||++++.+|++.+||+|++.....+...+++|++++|+..+ ++............
T Consensus 160 ~G~~vv~~~~~~~g--~~Df~~~l~~i~~~~pD~V~~~~~g~~~~~~~kq~~~~G~~~~---~~~~~~~~~~~~~~---- 230 (374)
T TIGR03669 160 NGAEVVGEEFIPLS--VSQFSSTIQNIQKADPDFVMSMLVGANHASFYEQAASANLNLP---MGTSTAMAQGYEHK---- 230 (374)
T ss_pred cCCeEEeEEecCCC--cchHHHHHHHHHHcCCCEEEEcCcCCcHHHHHHHHHHcCCCCc---ccchhhhhhhhhhh----
Confidence 99999988888754 6799999999999999999999988899999999999998532 22222111111110
Q ss_pred hhhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 161 QTSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
....+..+|+++...+.+ +++..++|.++|+++|+. ...++.+++.+|||++++++|++++.+
T Consensus 231 ~~~~~~~~g~~~~~~~~~~~~~~~~~~F~~~y~~~~g~---~p~~~~~a~~~Yda~~~l~~Ai~~AGs------------ 295 (374)
T TIGR03669 231 RFEPPALKDVYAGVNYMEEIDTPENEAFVERFYAKFPD---APYINQEAENNYFSVYMYKQAVEEAGT------------ 295 (374)
T ss_pred hcCchhhCCcEEeeeccccCCCHHHHHHHHHHHHHcCC---CCCCChHHHHHHHHHHHHHHHHHHhCC------------
Confidence 111234677776665554 467889999999999852 112456788899999999999999421
Q ss_pred CCCcccccccccccccCchHHHHHHHHc-cccCCceeeEEEecCCCeecccEEEEEeecC-ceEEEEEee
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQ-TNFTGLSGQVQFNQDRNIVSRGYDVINIDKM-EIHRVGYWF 306 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~-~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~-~~~~VG~w~ 306 (806)
.+++++.++|++ .+|.|++|+++||++++.....+.|.+++.+ +...+..|.
T Consensus 296 ----------------~d~~av~~aL~~~~~~~~~~G~i~fd~~~~~~~~~~~v~~~~~~~~~~~~~~~~ 349 (374)
T TIGR03669 296 ----------------TDQDAVRDVLESGVEMDAPEGKVCIDGATHHMSHTMRLARADADHNITFVKEQE 349 (374)
T ss_pred ----------------CCHHHHHHHHHcCCeEECCCccEEEcCCCCeeeeeeEEEEEcCCCCEEEEEecC
Confidence 138899999997 6799999999999776555556677777643 355555554
No 68
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.85 E-value=3.4e-20 Score=191.73 Aligned_cols=218 Identities=16% Similarity=0.277 Sum_probs=181.3
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhC-CCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEE
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLV-PYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAV 432 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l-~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~ 432 (806)
..++||||+.. +++||.+.+.+++++.||++|+++++++++ |..+++++.+. +|.....+|.+|++|+++
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 45789999975 788998865446899999999999999994 86666777764 567778999999999999
Q ss_pred eeEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCcc
Q 003633 433 GDIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRR 512 (806)
Q Consensus 433 ~~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~ 512 (806)
+.+++|++|.+.++||.||+.++..++++...
T Consensus 107 ~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~------------------------------------------------ 138 (259)
T PRK11917 107 ATFTITPERKRIYNFSEPYYQDAIGLLVLKEK------------------------------------------------ 138 (259)
T ss_pred ecccCChhhhheeeeccCceeeceEEEEECCC------------------------------------------------
Confidence 99999999999999999999999999998765
Q ss_pred chhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCc
Q 003633 513 QIATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGS 592 (806)
Q Consensus 513 ~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs 592 (806)
++++++|| .|++||+..|+
T Consensus 139 -----------------------------------------------------------~~~s~~dL--~g~~V~v~~gs 157 (259)
T PRK11917 139 -----------------------------------------------------------NYKSLADM--KGANIGVAQAA 157 (259)
T ss_pred -----------------------------------------------------------CCCCHHHh--CCCeEEEecCC
Confidence 57899999 79999999999
Q ss_pred hhHHHhhhhccc--ccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeCCccccCCceeeecCC
Q 003633 593 FAYSYLSDSLRI--QKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIGQPFTRSGWGFAFQRD 670 (806)
Q Consensus 593 ~~~~~l~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k~ 670 (806)
.....+.+.... ...+++.+++..+.+++|.. |++||++.+...+..+..+ +..++++.+...+++++++|+
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 877665432211 12355678889999999999 9999999998877665554 345667777778899999999
Q ss_pred CC-chHHHHHHHHhhhccchhHHHHHhh
Q 003633 671 SP-LAVGMSTAILKLSENGMLQKLHEKW 697 (806)
Q Consensus 671 sp-l~~~~n~~il~l~e~G~~~~i~~kw 697 (806)
++ ++..+|++|.++.. .+++|.+||
T Consensus 232 ~~~l~~~ln~~l~~~~~--~~~~i~~kw 257 (259)
T PRK11917 232 DPAFAKYVDDFVKEHKN--EIDALAKKW 257 (259)
T ss_pred CHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 98 99999999999864 899999999
No 69
>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=99.85 E-value=1e-19 Score=198.50 Aligned_cols=262 Identities=16% Similarity=0.129 Sum_probs=201.4
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
+++++++.++|++++++... . ...|++|++.+++..++.++++++..-+-+++++|+.|++||+...+.+.+.+++.
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~-~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~d~~~g~~~~~~~~~~~~~~ 159 (360)
T cd06357 83 VLPVVERHDALLWYPTLYEG-F--EYSPNVIYTGAAPNQNSVPLADYLLRHYGKRVFLVGSNYIYPYESNRIMRDLLEQR 159 (360)
T ss_pred HHHHHHhcCceEEeCCCccC-C--cccCCEEEeCCCcHHHHHHHHHHHHhcCCcEEEEECCCCcchHHHHHHHHHHHHHc
Confidence 46788899999998765322 1 12367888888888888899998765555899999999999999999999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
|++|+....++.+.+..||++++.++++.++|+|++......+..++++++++|+.... ..+.+...... ... .
T Consensus 160 G~~vv~~~~~~~~~~~~d~s~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~~~-~~~~~~~~~~~-~~~----~ 233 (360)
T cd06357 160 GGEVLGERYLPLGASDEDFARIVEEIREAQPDFIFSTLVGQSSYAFYRAYAAAGFDPAR-MPIASLTTSEA-EVA----A 233 (360)
T ss_pred CCEEEEEEEecCCCchhhHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHHHHcCCCccC-ceeEEeeccHH-HHh----h
Confidence 99998765566554578999999999999999999999999999999999999986432 33333322211 111 2
Q ss_pred hhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 162 TSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
...+..+|+++..++.+ ++|..++|.++|+++|+. ...++.+++.+||+++++++|++++.+
T Consensus 234 ~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~g~---~~~~~~~~~~~yda~~~l~~Al~~ag~------------- 297 (360)
T cd06357 234 MGAEAAAGHITAAPYFSSIDTPANRAFVARYRARFGE---DAPVSACAEAAYFQVHLFARALQRAGS------------- 297 (360)
T ss_pred cchHhhCCcEEecccccccCChhHHHHHHHHHHHcCC---CCCCCcHHHHHHHHHHHHHHHHHHcCC-------------
Confidence 23466789888766543 568889999999999862 113567889999999999999998311
Q ss_pred CCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEe-ecCceEEEE
Q 003633 240 DSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINI-DKMEIHRVG 303 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~-~~~~~~~VG 303 (806)
.+++.|.++|++++|+|+.|.+.||..++.......+.++ ++|++..+.
T Consensus 298 ---------------~~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~~~~~~~~G~~~~~~ 347 (360)
T cd06357 298 ---------------DDPEDVLAALLGFSFDAPQGPVRIDPDNNHTYLWPRIARVNADGQFDIVR 347 (360)
T ss_pred ---------------CCHHHHHHHhccCcccCCCcceEEeCCCCeeeeeeEEEEEcCCCCEEEEE
Confidence 1278899999999999999999999766544455666677 566666654
No 70
>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=99.85 E-value=7.7e-20 Score=199.34 Aligned_cols=252 Identities=14% Similarity=0.125 Sum_probs=191.4
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHH-cCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDF-YGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~-~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+.+++++.++|++++..... ....||+||+.+++..++.++++++.. .|.|+|++++.|++||+...+.+++.+++
T Consensus 84 ~~~~~~~~~~~~i~~~~~~~---~~~~~~~F~~~~~~~~~~~~~~~~~~~~~g~k~v~~l~~d~~~g~~~~~~~~~~~~~ 160 (359)
T TIGR03407 84 VLPVFEENNGLLFYPVQYEG---EECSPNIFYTGAAPNQQIIPAVDYLLSKKGAKRFFLLGSDYVFPRTANKIIKAYLKS 160 (359)
T ss_pred HHHHHhccCCceEeCCcccC---cccCCCEEEcCCChHHHHHHHHHHHHhccCCceEEEecCccHHHHHHHHHHHHHHHH
Confidence 35677888999997643221 234689999999999999999998655 69999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|++|+....++. +..|+++++++|++.++|+|++......+..++++++++|+......++.+......+.
T Consensus 161 ~G~~vv~~~~~~~--~~~D~s~~v~~l~~~~pDav~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~------ 232 (359)
T TIGR03407 161 LGGTVVGEDYTPL--GHTDFQTIINKIKAFKPDVVFNTLNGDSNVAFFKQLKNAGITAKDVPVVSFSVAEEEIR------ 232 (359)
T ss_pred cCCEEEeeEEecC--ChHhHHHHHHHHHHhCCCEEEEeccCCCHHHHHHHHHHcCCCccCCcEEEeecCHHHHh------
Confidence 9999998887874 46799999999999999999988888888899999999998643333444332111111
Q ss_pred hhhhhhccceEEEEEe--CCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 161 QTSLRILQGVVGLRQH--TPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~--~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
....+.++|+++...+ ..+++..++|.++|+++|+. ...++.+++.+|||+++++.|++++.+
T Consensus 233 ~~g~~~~~G~~~~~~~~~~~~~~~~~~f~~~~~~~~~~---~~~~~~~~~~~y~a~~~~~~A~~~ag~------------ 297 (359)
T TIGR03407 233 GIGPENLVGHLAAWNYFQSVDTPANKKFVKAFKAKYGD---DRVTNDPMEAAYLGVYLWKAAVEKAGS------------ 297 (359)
T ss_pred hcChHhhCCeEEeccchhcCCCHHHHHHHHHHHHHcCC---CCCCCcHHHHHHHHHHHHHHHHHHhCC------------
Confidence 1123457887754333 23567889999999998852 122344567899999999999999411
Q ss_pred CCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID 295 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~ 295 (806)
. +++++.++|++++|+++.|+++|+++++.....+.+.+++
T Consensus 298 ---------------~-~~~~i~~al~~~~~~~~~G~i~f~~~~~~~~~~~~~~~~~ 338 (359)
T TIGR03407 298 ---------------F-DVDAVRDAAIGIEFDAPEGKVKVDGKNHHLTKTVRIGEIR 338 (359)
T ss_pred ---------------C-CHHHHHHHhcCCcccCCCccEEEeCCCCeeeeeeEEEEEc
Confidence 1 3889999999999999999999997333244455566664
No 71
>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=1.4e-20 Score=190.99 Aligned_cols=221 Identities=25% Similarity=0.403 Sum_probs=183.8
Q ss_pred eEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEE
Q 003633 358 LRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAI 437 (806)
Q Consensus 358 lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~i 437 (806)
||||+.. .++||.+.+. ++...|+++|+++++++++|++ +++++. +|.+++.+|.+|++|+++++++.
T Consensus 1 l~V~~~~--~~~P~~~~~~-~~~~~G~~~dl~~~i~~~~g~~--~~~~~~-------~~~~~~~~l~~g~~D~~~~~~~~ 68 (225)
T PF00497_consen 1 LRVGVDE--DYPPFSYIDE-DGEPSGIDVDLLRAIAKRLGIK--IEFVPM-------PWSRLLEMLENGKADIIIGGLSI 68 (225)
T ss_dssp EEEEEES--EBTTTBEEET-TSEEESHHHHHHHHHHHHHTCE--EEEEEE-------EGGGHHHHHHTTSSSEEESSEB-
T ss_pred CEEEEcC--CCCCeEEECC-CCCEEEEhHHHHHHHHhhcccc--cceeec-------ccccccccccccccccccccccc
Confidence 6899854 6788988875 7899999999999999999987 555542 59999999999999999999999
Q ss_pred ecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchhhH
Q 003633 438 VTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIATM 517 (806)
Q Consensus 438 t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~ 517 (806)
+.+|.+.++||.||+....++++++.....
T Consensus 69 ~~~r~~~~~~s~p~~~~~~~~~~~~~~~~~-------------------------------------------------- 98 (225)
T PF00497_consen 69 TPERAKKFDFSDPYYSSPYVLVVRKGDAPP-------------------------------------------------- 98 (225)
T ss_dssp BHHHHTTEEEESESEEEEEEEEEETTSTCS--------------------------------------------------
T ss_pred cccccccccccccccchhheeeeccccccc--------------------------------------------------
Confidence 999999999999999999999998753100
Q ss_pred HHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCchhHHH
Q 003633 518 FLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSFAYSY 597 (806)
Q Consensus 518 ~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~~~~~ 597 (806)
...+++++|| .+.+||+..|+....+
T Consensus 99 ----------------------------------------------------~~~~~~~~dl--~~~~i~~~~g~~~~~~ 124 (225)
T PF00497_consen 99 ----------------------------------------------------IKTIKSLDDL--KGKRIGVVRGSSYADY 124 (225)
T ss_dssp ----------------------------------------------------TSSHSSGGGG--TTSEEEEETTSHHHHH
T ss_pred ----------------------------------------------------cccccchhhh--cCcccccccchhHHHH
Confidence 1367788899 6789999999988888
Q ss_pred hhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCC--eEEeCCccccCCceeeecCCCC-ch
Q 003633 598 LSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTD--FGIIGQPFTRSGWGFAFQRDSP-LA 674 (806)
Q Consensus 598 l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~--l~~~~~~~~~~~~~~~~~k~sp-l~ 674 (806)
+.+... ...+++.+.+.++++++|.+ |++|+++.+...+.+++++... ...........++++++.++.+ |+
T Consensus 125 l~~~~~-~~~~~~~~~~~~~~~~~l~~----g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 199 (225)
T PF00497_consen 125 LKQQYP-SNINIVEVDSPEEALEALLS----GRIDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKNPELL 199 (225)
T ss_dssp HHHHTH-HTSEEEEESSHHHHHHHHHT----TSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTTHHHH
T ss_pred hhhhcc-chhhhcccccHHHHHHHHhc----CCeeeeeccchhhhhhhhhcccccccccccccccceeEEeecccccHHH
Confidence 765331 14567788999999999999 9999999999999998888643 3332455666677788877666 99
Q ss_pred HHHHHHHHhhhccchhHHHHHhhcC
Q 003633 675 VGMSTAILKLSENGMLQKLHEKWFC 699 (806)
Q Consensus 675 ~~~n~~il~l~e~G~~~~i~~kw~~ 699 (806)
+.||++|.++.++|.+++|.+||++
T Consensus 200 ~~~n~~i~~l~~~G~~~~i~~ky~g 224 (225)
T PF00497_consen 200 EIFNKAIRELKQSGEIQKILKKYLG 224 (225)
T ss_dssp HHHHHHHHHHHHTTHHHHHHHHHHS
T ss_pred HHHHHHHHHHHhCcHHHHHHHHHcC
Confidence 9999999999999999999999986
No 72
>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=99.84 E-value=5.6e-20 Score=198.42 Aligned_cols=239 Identities=16% Similarity=0.118 Sum_probs=188.1
Q ss_pred HhcccccCCCcEEecccCCCCcccCC-CCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQ-FPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~-~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++.++|+|++++++|.++... .+|+||+.+++..++.++++.+... +|+|++|+.|++||++..+.+.+.+++
T Consensus 84 ~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~-~~~v~~i~~~~~~g~~~~~~~~~~~~~ 162 (333)
T cd06328 84 VLPVAEENKKILIVEPAAADSITGKNWNRYTFRTGRNSSQDAIAAAAALGKP-GKKIATLAQDYAFGRDGVAAFKAALEK 162 (333)
T ss_pred HHHHHHHhCCcEEecCCCCchhhccCCCCcEEEecCChHHHHHHHHHHHHhc-CCeEEEEecCccccHHHHHHHHHHHHh
Confidence 45678899999999999999998754 6999999999999999988887655 899999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc-hHHHHHHHHHHcCCccCCcEEEEcCcccccccccccC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD-PGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKM 159 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~-~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~ 159 (806)
.|++|+....++++ ..|+++++.+|++.++|+|++..... ....+++++.+.|+... .............
T Consensus 163 ~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~~~---- 233 (333)
T cd06328 163 LGAAIVTEEYAPTD--TTDFTPYAQRLLDALKKVLFVIWAGAGGPWPKLQQMGVLGYGIE---ITLAGDILANLTM---- 233 (333)
T ss_pred CCCEEeeeeeCCCC--CcchHHHHHHHHhcCCCEEEEEecCchhHHHHHHHhhhhcCCCe---EEecccccCcccc----
Confidence 99999998888854 67999999999999999998876555 56777888877765421 2222222111110
Q ss_pred ChhhhhhccceEEEEEeC-CCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 160 NQTSLRILQGVVGLRQHT-PDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~-~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
.......+|++....+. +.+|..+.|.++|+++|+ ..++.+++.+||++.+++.|++++.+
T Consensus 234 -~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g-----~~p~~~~~~~y~a~~~l~~Ai~~ag~------------ 295 (333)
T cd06328 234 -YKAGPGMSGASYYYHYFLPKNPVNDWLVEEHKARFG-----SPPDLFTAGGMSAAIAVVEALEETGD------------ 295 (333)
T ss_pred -ccccccccceeeeecCCCCCCHHHHHHHHHHHHHhC-----CCcchhhHHHHHHHHHHHHHHHHhCC------------
Confidence 12233456766655544 677888999999999985 24778899999999999999998421
Q ss_pred CCCcccccccccccccCchHHHHHHHHccccCCceeeEEEec-CCCe
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQ-DRNI 284 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~-~G~~ 284 (806)
.+++++.++|++..|+++.|+++|+. +++.
T Consensus 296 ----------------~~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~ 326 (333)
T cd06328 296 ----------------TDTEALIAAMEGMSFETPKGTMTFRKEDHQA 326 (333)
T ss_pred ----------------CCHHHHHHHHhCCeeecCCCceEECcccchh
Confidence 13789999999999999999999984 4443
No 73
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.84 E-value=1.1e-19 Score=188.85 Aligned_cols=223 Identities=19% Similarity=0.338 Sum_probs=180.1
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
..++|+|++.. .|+||.+.++ ++.+.|+++||++++++.+|.+ +++++ .+|..++.++..|++|++++
T Consensus 24 ~~~~l~v~~~~--~~pPf~~~~~-~g~~~G~~vdl~~~ia~~lg~~--~~~~~-------~~~~~~~~~l~~g~~Di~~~ 91 (260)
T PRK15010 24 LPETVRIGTDT--TYAPFSSKDA-KGDFVGFDIDLGNEMCKRMQVK--CTWVA-------SDFDALIPSLKAKKIDAIIS 91 (260)
T ss_pred cCCeEEEEecC--CcCCceeECC-CCCEEeeeHHHHHHHHHHhCCc--eEEEe-------CCHHHHHHHHHCCCCCEEEe
Confidence 45789999863 5889998764 6889999999999999999977 56655 26999999999999999998
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
.+..+++|.+.++||.||+.+..++++++..
T Consensus 92 ~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~------------------------------------------------- 122 (260)
T PRK15010 92 SLSITDKRQQEIAFSDKLYAADSRLIAAKGS------------------------------------------------- 122 (260)
T ss_pred cCcCCHHHHhhcccccceEeccEEEEEECCC-------------------------------------------------
Confidence 8999999999999999999999999988765
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCch
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSF 593 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~ 593 (806)
+...+++|| .|++||+..|+.
T Consensus 123 ---------------------------------------------------------~~~~~~~dl--~g~~Igv~~gs~ 143 (260)
T PRK15010 123 ---------------------------------------------------------PIQPTLDSL--KGKHVGVLQGST 143 (260)
T ss_pred ---------------------------------------------------------CCCCChhHc--CCCEEEEecCch
Confidence 122368899 788999999998
Q ss_pred hHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHH-HhhCC--CCeEEeCCcc-----ccCCcee
Q 003633 594 AYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQL-FLSNQ--TDFGIIGQPF-----TRSGWGF 665 (806)
Q Consensus 594 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~-~~~~~--~~l~~~~~~~-----~~~~~~~ 665 (806)
...++.+.+.....+++.+++.++.+++|.+ |++|+++.+...+.+ +..+. .++...+..+ ...++++
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~----griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 219 (260)
T PRK15010 144 QEAYANETWRSKGVDVVAYANQDLVYSDLAA----GRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGV 219 (260)
T ss_pred HHHHHHHhcccCCceEEecCCHHHHHHHHHc----CCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEE
Confidence 8777754332233456778888999999999 999999999877754 33432 2355554322 2234678
Q ss_pred eecCCCC-chHHHHHHHHhhhccchhHHHHHhhcCC
Q 003633 666 AFQRDSP-LAVGMSTAILKLSENGMLQKLHEKWFCK 700 (806)
Q Consensus 666 ~~~k~sp-l~~~~n~~il~l~e~G~~~~i~~kw~~~ 700 (806)
+++++.+ |+..+|++|.++.++|.+++|.+||++.
T Consensus 220 a~~~~~~~L~~~ln~~l~~l~~~G~~~~i~~ky~~~ 255 (260)
T PRK15010 220 GLRKDDAELTAAFNKALGELRQDGTYDKMAKKYFDF 255 (260)
T ss_pred EEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcCC
Confidence 9999887 9999999999999999999999999974
No 74
>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=99.84 E-value=3.3e-20 Score=197.03 Aligned_cols=148 Identities=39% Similarity=0.623 Sum_probs=137.3
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++.++||+|+++++++.+++ .++||++|+.|++..++.+++++++++||++|+++|+|+++|....+.+.+.+++
T Consensus 87 v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~~v~~~~~~~~~~~~~~~~~~~~ 166 (298)
T cd06269 87 VASLLGALHIPQISYSATSPLLSDKEQFPSFLRTVPSDSSQAQAIVDLLKHFGWTWVGLVYSDDDYGRRLLELLEEELEK 166 (298)
T ss_pred HHHHhccCCCcEEecccCchhhcChhhCCCeEecCCCcHHHHHHHHHHHHHCCCeEEEEEEecchhhHHHHHHHHHHHHH
Confidence 578999999999999999999987 4699999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccc
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSAT 152 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~ 152 (806)
.|+|+.....++.. ..++...+++++..++||||+++.++.+..++++|.++||+ .+++||+++.+...
T Consensus 167 ~~~~v~~~~~~~~~--~~~~~~~l~~l~~~~~~viv~~~~~~~~~~~l~~a~~~g~~-~~~~~i~~~~~~~~ 235 (298)
T cd06269 167 NGICVAFVESIPDG--SEDIRRLLKELKSSTARVIVVFSSEEDALRLLEEAVELGMM-TGYHWIITDLWLTS 235 (298)
T ss_pred CCeeEEEEEEcCCC--HHHHHHHHHHHHhcCCcEEEEEechHHHHHHHHHHHHcCCC-CCeEEEEEChhhcc
Confidence 99999998888743 47899999999999999999999999999999999999999 89999999976543
No 75
>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=99.84 E-value=4.7e-20 Score=200.42 Aligned_cols=254 Identities=24% Similarity=0.346 Sum_probs=202.8
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHH-HHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLI-DFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++..++|+|+++++++ ...+||+||+.|++..++.++++.+ +++|.++|++|+.|++||+...+.+.+.+++
T Consensus 85 ~~~~~~~~~ip~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~iv~~~~~~g~~~~~~~~~~~~~ 161 (343)
T PF13458_consen 85 VAPIAEEAGIPYISPSASSP---SPDSPNVFRLSPSDSQQAAALAEYLAKKLGAKKVAIVYPDDPYGRSLAEAFRKALEA 161 (343)
T ss_dssp HHHHHHHHT-EEEESSGGGG---TTTHTTEEESS--HHHHHHHHHHHHHHTTTTSEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhcCcEEEEeeccCC---CCCCCcEEEEeccccHHHHHHHHHHHHHcCCcEEEEEecCchhhhHHHHHHHHHHhh
Confidence 45678889999999664443 3557999999999999999999975 5689999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|++|+....++++ ..|++.++.++++.++|+|++.+.+.+...+++++.+.|+....+....+......+.
T Consensus 162 ~G~~vv~~~~~~~~--~~d~~~~~~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~------ 233 (343)
T PF13458_consen 162 AGGKVVGEIRYPPG--DTDFSALVQQLKSAGPDVVVLAGDPADAAAFLRQLRQLGLKPPRIPLFGTSLDDASLQ------ 233 (343)
T ss_dssp TTCEEEEEEEE-TT--SSHHHHHHHHHHHTTTSEEEEESTHHHHHHHHHHHHHTTGCSCTEEEEEGGGSSHHHH------
T ss_pred cCceeccceecccc--cccchHHHHHHhhcCCCEEEEeccchhHHHHHHHHHhhccccccceeeccccCcHHHH------
Confidence 99999877778744 5799999999999999999999999999999999999997543233333332222211
Q ss_pred hhhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 161 QTSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
....+.++|+++..++.| +++..++|.++|++.++. ...++.++..+||++.+++.|++++.+
T Consensus 234 ~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~---~~~~~~~~~~~yda~~~~~~al~~~g~------------ 298 (343)
T PF13458_consen 234 QLGGDALEGVYIVSPWFPDPDSPAVKQFQERYRAAYGE---EPPPSLYAAQGYDAARLLAQALERAGS------------ 298 (343)
T ss_dssp HHHGGGGTTEEEEESGGGTGGSHHHHHHHHHHHHHHSS---TGGTCHHHHHHHHHHHHHHHHHHHHTS------------
T ss_pred HhhhhhccCceeecccCCCCCCHHHHHHHHHHHHHcCC---CCCCchhHHHHHHHHHHHHHHHHHhCC------------
Confidence 223356889998888766 467889999999999962 114788999999999999999999411
Q ss_pred CCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee-cC
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID-KM 297 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~-~~ 297 (806)
.+++.+.++|+++.|+|+.|++.|+..+......+.|++++ +|
T Consensus 299 ----------------~~~~~v~~al~~~~~~g~~g~~~~~~~~~~~~~~~~i~~v~~~G 342 (343)
T PF13458_consen 299 ----------------LDREAVREALESLKYDGLFGPISFDPPDHQANKPVYIVQVKSDG 342 (343)
T ss_dssp ----------------HHHHHHHHHHHTSEEEETTEEEEEETTTSBEEEEEEEEEEETTT
T ss_pred ----------------CCHHHHHHHHHhCCCcccccceEEeCCCCccccCeEEEEEecCC
Confidence 13899999999999999999999986555577889999998 54
No 76
>PRK11260 cystine transporter subunit; Provisional
Probab=99.84 E-value=1.1e-19 Score=189.45 Aligned_cols=222 Identities=21% Similarity=0.396 Sum_probs=189.6
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
..++||||+.. .++||.+.+. ++.+.|+.+|+++.+++++|.+ +++++. +|.+++.+|.+|++|++++
T Consensus 39 ~~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~--~e~~~~-------~~~~~~~~l~~G~~D~~~~ 106 (266)
T PRK11260 39 ERGTLLVGLEG--TYPPFSFQGE-DGKLTGFEVEFAEALAKHLGVK--ASLKPT-------KWDGMLASLDSKRIDVVIN 106 (266)
T ss_pred cCCeEEEEeCC--CcCCceEECC-CCCEEEehHHHHHHHHHHHCCe--EEEEeC-------CHHHHHHHHhcCCCCEEEe
Confidence 45789999864 6888887653 6789999999999999999977 666652 6999999999999999998
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
+++.+.+|...+.||.||+..+..+++++...
T Consensus 107 ~~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~~------------------------------------------------ 138 (266)
T PRK11260 107 QVTISDERKKKYDFSTPYTVSGIQALVKKGNE------------------------------------------------ 138 (266)
T ss_pred ccccCHHHHhccccCCceeecceEEEEEcCCc------------------------------------------------
Confidence 88999999999999999999999999876541
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCch
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSF 593 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~ 593 (806)
..+++++|| ++++||+..|+.
T Consensus 139 ---------------------------------------------------------~~~~~~~dL--~g~~Igv~~G~~ 159 (266)
T PRK11260 139 ---------------------------------------------------------GTIKTAADL--KGKKVGVGLGTN 159 (266)
T ss_pred ---------------------------------------------------------CCCCCHHHc--CCCEEEEecCCc
Confidence 257889999 788999999998
Q ss_pred hHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCC-eEEeCCccccCCceeeecCCCC
Q 003633 594 AYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTD-FGIIGQPFTRSGWGFAFQRDSP 672 (806)
Q Consensus 594 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~-l~~~~~~~~~~~~~~~~~k~sp 672 (806)
...++.+. .+...+..+++..+.+++|.+ |++|+++.+...+.+++.+... +.+....+...++++++++++|
T Consensus 160 ~~~~l~~~--~~~~~i~~~~~~~~~l~~L~~----GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 233 (266)
T PRK11260 160 YEQWLRQN--VQGVDVRTYDDDPTKYQDLRV----GRIDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNP 233 (266)
T ss_pred HHHHHHHh--CCCCceEecCCHHHHHHHHHc----CCCCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCH
Confidence 88887543 345677889999999999999 9999999999888887777544 5555666777889999999988
Q ss_pred -chHHHHHHHHhhhccchhHHHHHhhcCC
Q 003633 673 -LAVGMSTAILKLSENGMLQKLHEKWFCK 700 (806)
Q Consensus 673 -l~~~~n~~il~l~e~G~~~~i~~kw~~~ 700 (806)
+++.+|++|.++.++|.+++|.+||+..
T Consensus 234 ~l~~~ln~~l~~~~~~g~~~~i~~k~~~~ 262 (266)
T PRK11260 234 DLLKAVNQAIAEMQKDGTLKALSEKWFGA 262 (266)
T ss_pred HHHHHHHHHHHHHHhCCcHHHHHHHhcCC
Confidence 9999999999999999999999999873
No 77
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.83 E-value=1.8e-19 Score=186.40 Aligned_cols=218 Identities=24% Similarity=0.456 Sum_probs=183.6
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
++|||++.. .++||.+.++ +++++|+++|+++++++.+|.+ +++++. +|..++.++.+|++|++++++
T Consensus 24 ~~l~v~~~~--~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~--~~~~~~-------~~~~~~~~l~~G~~D~~~~~~ 91 (250)
T TIGR01096 24 GSVRIGTET--GYPPFESKDA-NGKLVGFDVDLAKALCKRMKAK--CKFVEQ-------NFDGLIPSLKAKKVDAIMATM 91 (250)
T ss_pred CeEEEEECC--CCCCceEECC-CCCEEeehHHHHHHHHHHhCCe--EEEEeC-------CHHHHHHHHhCCCcCEEEecC
Confidence 689999853 7888988764 6899999999999999999976 666662 699999999999999998888
Q ss_pred EEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchh
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIA 515 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 515 (806)
+.+.+|.+.+.||.|++..+..++++...
T Consensus 92 ~~~~~r~~~~~~s~p~~~~~~~~~~~~~~--------------------------------------------------- 120 (250)
T TIGR01096 92 SITPKRQKQIDFSDPYYATGQGFVVKKGS--------------------------------------------------- 120 (250)
T ss_pred ccCHHHhhccccccchhcCCeEEEEECCC---------------------------------------------------
Confidence 88999999999999999999999997765
Q ss_pred hHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCchhH
Q 003633 516 TMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSFAY 595 (806)
Q Consensus 516 ~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~~~ 595 (806)
+.+.+++|| .+.+||+..|+...
T Consensus 121 -------------------------------------------------------~~~~~~~dl--~g~~i~~~~g~~~~ 143 (250)
T TIGR01096 121 -------------------------------------------------------DLAKTLEDL--DGKTVGVQSGTTHE 143 (250)
T ss_pred -------------------------------------------------------CcCCChHHc--CCCEEEEecCchHH
Confidence 234678899 68899999999888
Q ss_pred HHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCC---CeEEeCCcccc-----CCceeee
Q 003633 596 SYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQT---DFGIIGQPFTR-----SGWGFAF 667 (806)
Q Consensus 596 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~---~l~~~~~~~~~-----~~~~~~~ 667 (806)
.++.+.+.. ..++..+.+.++++++|.+ |++|+++.+...+.+.+++.. ++.+++..+.. ..+++++
T Consensus 144 ~~l~~~~~~-~~~~~~~~s~~~~~~~L~~----g~vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 218 (250)
T TIGR01096 144 QYLKDYFKP-GVDIVEYDSYDNANMDLKA----GRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGL 218 (250)
T ss_pred HHHHHhccC-CcEEEEcCCHHHHHHHHHc----CCCCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEE
Confidence 887554321 4567778899999999999 999999999999988877643 37766654432 2478999
Q ss_pred cCCCC-chHHHHHHHHhhhccchhHHHHHhhc
Q 003633 668 QRDSP-LAVGMSTAILKLSENGMLQKLHEKWF 698 (806)
Q Consensus 668 ~k~sp-l~~~~n~~il~l~e~G~~~~i~~kw~ 698 (806)
+++++ |+..+|++|.++.++|.+++|.+||+
T Consensus 219 ~~~~~~l~~~ln~~l~~l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 219 RKGDTELKAAFNKALAAIRADGTYQKISKKWF 250 (250)
T ss_pred eCCCHHHHHHHHHHHHHHHHCCcHHHHHHhhC
Confidence 99988 99999999999999999999999995
No 78
>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=99.83 E-value=1.3e-19 Score=197.37 Aligned_cols=253 Identities=12% Similarity=0.048 Sum_probs=189.9
Q ss_pred HhcccccCCCcEEecccCCCCc-------ccCCCCceEEecCCcHHHHHHHHHHHHHcC-CeEEEEEEEcCCcccchHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTL-------SALQFPYFIRSTQSDSQQMAAMADLIDFYG-WKEVIAIYVDDDYGRNGISA 73 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~L-------s~~~~p~f~Rt~psd~~q~~ai~~ll~~~~-W~~v~ii~~d~~~g~~~~~~ 73 (806)
+++++++.+||+|+..++.+.+ ....+||+||+.+++..++.+++++++..+ +++|++++.|++||+...+.
T Consensus 85 ~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~k~v~ii~~~~~~g~~~~~~ 164 (357)
T cd06337 85 VSDQCEANGVPCISTMAPWQAWFFGRGGNPATGFKWTYHFFWGAEDVVATYVGMWKQLETNKKVGILYPNDPDGNAFADP 164 (357)
T ss_pred HHHHHHHhCCCeEEeccchhhhhccCCCCcccCCceeEEecCCHHHHHHHHHHHHHhCCCCceEEEEeecCchhHHHHHh
Confidence 4578899999999975543221 123479999999999888999999888887 99999999999999987666
Q ss_pred HH---HHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc-Ccc
Q 003633 74 LS---NMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT-DWL 149 (806)
Q Consensus 74 l~---~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t-~~~ 149 (806)
+. +.+++.|++|+..+.++++ ..|+++++++|+++++|+|++.+.+.++..++++++++|...+ ++.. .+.
T Consensus 165 ~~~~~~~~~~~G~~vv~~~~~~~~--~~D~~~~v~~ik~a~pD~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~ 239 (357)
T cd06337 165 VIGLPAALADAGYKLVDPGRFEPG--TDDFSSQINAFKREGVDIVTGFAIPPDFATFWRQAAQAGFKPK---IVTIAKAL 239 (357)
T ss_pred hhcccHHHHhCCcEEecccccCCC--CCcHHHHHHHHHhcCCCEEEeCCCccHHHHHHHHHHHCCCCCC---eEEEeccc
Confidence 54 5777899999988888865 5699999999999999999999999999999999999997543 3332 222
Q ss_pred cccccccccCChhhhhhccceEEEEEeCCC--------ChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHH
Q 003633 150 SATLESFSKMNQTSLRILQGVVGLRQHTPD--------SIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSI 221 (806)
Q Consensus 150 ~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~--------~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al 221 (806)
.. .... ....+..+|++....+.|. ++..++|.++|+++++. .+...+.++||++++++.|+
T Consensus 240 ~~-~~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~g~-----~~~~~~~~~~~~~~~l~~Ai 309 (357)
T cd06337 240 LF-PEDV----EALGDRGDGMSTEVWWSPSHPFRSSLTGQSAAELADAYEAATGR-----QWTQPLGYAHALFEVGVKAL 309 (357)
T ss_pred cC-HHHH----HHhhhhhcCccccceeccCCCcccccCCccHHHHHHHHHHHhCC-----CccCcchHHHHHHHHHHHHH
Confidence 11 1111 1223345777665444443 23478999999998862 34456678999999999999
Q ss_pred HHHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEeecCce
Q 003633 222 DKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINIDKMEI 299 (806)
Q Consensus 222 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~~~~~ 299 (806)
+++.+ ..++++|.++|++++++++.|++.|+++ ......|+.+.+++|
T Consensus 310 ~~Ags---------------------------~~d~~~v~~aL~~~~~~~~~G~~~f~~~---~~~~~~~~~~~~~~~ 357 (357)
T cd06337 310 VRADD---------------------------PDDPAAVADAIATLKLDTVVGPVDFGNS---PIKNVAKTPLVGGQW 357 (357)
T ss_pred HHcCC---------------------------CCCHHHHHHHHHcCCcccceeeeecCCC---CCccccccccccCCC
Confidence 98311 1137899999999999999999999854 234566777776654
No 79
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.83 E-value=2.5e-19 Score=184.45 Aligned_cols=217 Identities=19% Similarity=0.386 Sum_probs=179.9
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
.++||||+.. .++||.+.+. ++.+.|+++|+++++++.+|.+ ++++. .+|..++.++.+|++|++++.
T Consensus 20 ~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~--~~~~~-------~~~~~~~~~l~~g~~D~~~~~ 87 (243)
T PRK15007 20 AETIRFATEA--SYPPFESIDA-NNQIVGFDVDLAQALCKEIDAT--CTFSN-------QAFDSLIPSLKFRRVEAVMAG 87 (243)
T ss_pred CCcEEEEeCC--CCCCceeeCC-CCCEEeeeHHHHHHHHHHhCCc--EEEEe-------CCHHHHhHHHhCCCcCEEEEc
Confidence 4689999863 6788988763 6889999999999999999977 55554 269999999999999999888
Q ss_pred EEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccch
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQI 514 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 514 (806)
++.+++|...++||.||+..+.+++.+..
T Consensus 88 ~~~~~~r~~~~~fs~p~~~~~~~~v~~~~--------------------------------------------------- 116 (243)
T PRK15007 88 MDITPEREKQVLFTTPYYDNSALFVGQQG--------------------------------------------------- 116 (243)
T ss_pred CccCHHHhcccceecCccccceEEEEeCC---------------------------------------------------
Confidence 88999999999999999998877765422
Q ss_pred hhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCchh
Q 003633 515 ATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSFA 594 (806)
Q Consensus 515 ~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~~ 594 (806)
.+++++|| .+.+||+..|+..
T Consensus 117 ---------------------------------------------------------~~~~~~dL--~g~~Igv~~g~~~ 137 (243)
T PRK15007 117 ---------------------------------------------------------KYTSVDQL--KGKKVGVQNGTTH 137 (243)
T ss_pred ---------------------------------------------------------CCCCHHHh--CCCeEEEecCcHH
Confidence 35688999 7889999999988
Q ss_pred HHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeCCc-----cccCCceeeecC
Q 003633 595 YSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIGQP-----FTRSGWGFAFQR 669 (806)
Q Consensus 595 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~~~~~~k 669 (806)
.+++.+. .+...++.+++.++.+++|.+ |++|+++.+...+.+++++..++..++.. ....++++++++
T Consensus 138 ~~~l~~~--~~~~~~~~~~~~~~~~~~L~~----grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 211 (243)
T PRK15007 138 QKFIMDK--HPEITTVPYDSYQNAKLDLQN----GRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQ 211 (243)
T ss_pred HHHHHHh--CCCCeEEEcCCHHHHHHHHHc----CCCCEEEeCHHHHHHHHhcCCCceeecCcccccccCCcceEEEEeC
Confidence 8887543 244567778899999999999 99999999998888887776655554432 223457899998
Q ss_pred CCC-chHHHHHHHHhhhccchhHHHHHhhcC
Q 003633 670 DSP-LAVGMSTAILKLSENGMLQKLHEKWFC 699 (806)
Q Consensus 670 ~sp-l~~~~n~~il~l~e~G~~~~i~~kw~~ 699 (806)
+++ |++.||++|.++.++|.+++|.+||+.
T Consensus 212 ~~~~l~~~ln~~l~~l~~~g~~~~i~~~w~~ 242 (243)
T PRK15007 212 GNTELQQKLNTALEKVKKDGTYETIYNKWFQ 242 (243)
T ss_pred CCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 876 999999999999999999999999985
No 80
>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=99.83 E-value=2.9e-19 Score=193.68 Aligned_cols=248 Identities=16% Similarity=0.121 Sum_probs=194.3
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcC-----CeEEEEEEEcCCcccchHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYG-----WKEVIAIYVDDDYGRNGISALS 75 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~-----W~~v~ii~~d~~~g~~~~~~l~ 75 (806)
+++++++++||+|+++++++.+++ ..+||+||+.|++..++.++++++...+ .++|++|+.|++||+...+.+.
T Consensus 82 ~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~~Fr~~~~~~~~~~~l~~~~~~~~~~~~~~~kvaiv~~~~~~g~~~~~~~~ 161 (351)
T cd06334 82 LIPKIAADKIPLMSGSYGATLADDGAVFPYNFPVGPTYSDQARALVQYIAEQEGGKLKGKKIALVYHDSPFGKEPIEALK 161 (351)
T ss_pred hhHHHhhcCCcEEecccchhhccCCCCCCeeeeCCCCHHHHHHHHHHHHHHhcccCCCCCeEEEEeCCCccchhhHHHHH
Confidence 467889999999999888777774 5689999999999999999999987655 7999999999999999999999
Q ss_pred HHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccc
Q 003633 76 NMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLES 155 (806)
Q Consensus 76 ~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~ 155 (806)
+.+++.|++|+....++.+ ..|+++++.++++.++|+|++.+...++..++++++++|+. -.|+.+++... ...
T Consensus 162 ~~~~~~G~~vv~~~~~~~~--~~D~~~~v~~i~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~---~~~~~~~~~~~-~~~ 235 (351)
T cd06334 162 ALAEKLGFEVVLEPVPPPG--PNDQKAQWLQIRRSGPDYVILWGWGVMNPVAIKEAKRVGLD---DKFIGNWWSGD-EED 235 (351)
T ss_pred HHHHHcCCeeeeeccCCCC--cccHHHHHHHHHHcCCCEEEEecccchHHHHHHHHHHcCCC---ceEEEeeccCc-HHH
Confidence 9999999999988888754 56999999999999999999999999999999999999983 23555543322 111
Q ss_pred cccCChhhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCC-CCCCccchhhhhhHHHHHHHHHHHHHhhcCccc
Q 003633 156 FSKMNQTSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLV-SAGLNTYGLYAYDTVWAVARSIDKFINEHNITF 232 (806)
Q Consensus 156 ~~~~~~~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~-~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~ 232 (806)
. ....+..+|+++..++.+ ++|..++|.+.|+++++.... +..++.+++.+|||+++++.||+++.+...
T Consensus 236 ~----~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~~~~~~~~~~~~~~~~~gy~a~~~l~~Al~~ag~~~~--- 308 (351)
T cd06334 236 V----KPAGDAAKGYKGVTPFAGGADDPVGKEIVKEVYDKGKGSGNDKEIGSVYYNRGVVNAMIMVEAIRRAQEKGG--- 308 (351)
T ss_pred H----HHhhhhhcCcEEeecccCCCCchHHHHHHHHHHHccCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHhcC---
Confidence 1 334466789887776654 678899999999998852110 123467889999999999999999866540
Q ss_pred cCCCCCCCCcccccccccccccCc------hHHHHHHHHccccCCceeeEEEec
Q 003633 233 SASHELPDSKATRVQLEQLKVFDG------GTFLLRKLLQTNFTGLSGQVQFNQ 280 (806)
Q Consensus 233 ~~~~~l~~~~~~~~~~~~~~~~~~------g~~l~~~l~~~~f~G~tG~i~Fd~ 280 (806)
...... -+..++.+.+....|+.|++.|..
T Consensus 309 ------------------~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 344 (351)
T cd06334 309 ------------------ETTIAGEEQLENLKLDAARLEELGAEGLGPPVSVSC 344 (351)
T ss_pred ------------------CCCCcHHHHHHhhhhhhhhhhhcCcccccCCceecc
Confidence 001110 123345666677889999999974
No 81
>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=99.83 E-value=2.4e-19 Score=194.81 Aligned_cols=241 Identities=19% Similarity=0.182 Sum_probs=186.6
Q ss_pred HhcccccCCCcEEecccCCCCccc--CCCCceEEecCCcHHHHHHHHHHH-HHcCCeEEEEEEEcCCcccchHHHHHHHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA--LQFPYFIRSTQSDSQQMAAMADLI-DFYGWKEVIAIYVDDDYGRNGISALSNML 78 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~--~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W~~v~ii~~d~~~g~~~~~~l~~~l 78 (806)
+.+++++.+||+|++.++++.++. ..++|+||+.+++..++.++++++ ++.+|++|+++|.|++||+...+.+.+.+
T Consensus 83 ~~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~~Fr~~~~~~~~~~~~a~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~ 162 (347)
T cd06335 83 NLEFIQQNKIPLIGPWAAGTPITRNGAPPNYIFRVSADDSIQAPFLVDEAVKRGGFKKVALLLDNTGWGRSNRKDLTAAL 162 (347)
T ss_pred hhHHHHhcCCcEEecCCCCcccccCCCCCCCEEEeccChHHHHHHHHHHHHHhcCCCeEEEEeccCchhhhHHHHHHHHH
Confidence 457889999999999888888875 347999999999999999999986 56679999999999999999999999999
Q ss_pred HhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccccc
Q 003633 79 EKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSK 158 (806)
Q Consensus 79 ~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~ 158 (806)
++.|++++....+++. ..|+++.+.+|++.++++|++.+...+...+++++++.|+.. .++..+.....+..
T Consensus 163 ~~~G~~v~~~~~~~~~--~~d~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~----~~~~~~~~~~~~~~-- 234 (347)
T cd06335 163 AARGLKPVAVEWFNWG--DKDMTAQLLRAKAAGADAIIIVGNGPEGAQIANGMAKLGWKV----PIISHWGLSGGNFI-- 234 (347)
T ss_pred HHcCCeeEEEeeecCC--CccHHHHHHHHHhCCCCEEEEEecChHHHHHHHHHHHcCCCC----cEecccCCcCchhh--
Confidence 9999999988888754 569999999999999999999999999999999999999742 23332222111111
Q ss_pred CChhhhhhccceEEEEEeC---CCChhhHHHHHHHhhhccCCCC-CCCCccchhhhhhHHHHHHHHHHHHHhhcCccccC
Q 003633 159 MNQTSLRILQGVVGLRQHT---PDSIPKKAFLSRWSGMQQKGLV-SAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSA 234 (806)
Q Consensus 159 ~~~~~~~~~~gv~~~~~~~---~~~~~~~~f~~~~~~~~~~~~~-~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~ 234 (806)
....+..+|++....+. ++++..++|.++|+++++.... ...++.+++++||+++++++|+++...
T Consensus 235 --~~~g~~~~g~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYd~~~~l~~A~~~ag~-------- 304 (347)
T cd06335 235 --EGAGPAANDALMIQTFIFEPPSNPKAKAFLAAYHKKYPEKKPADIPAPVGAAHAYDAVHLLAAAIKQAGS-------- 304 (347)
T ss_pred --hccchhhcCcEEEEeeccccCCCHHHHHHHHHHHHHhCCCcccccCcchhHHHHHHHHHHHHHHHHHhcC--------
Confidence 12334567877665433 3568889999999999862110 113456678899999999999998411
Q ss_pred CCCCCCCcccccccccccccCchHHHHHHHHcc--ccCCceee--EEEec
Q 003633 235 SHELPDSKATRVQLEQLKVFDGGTFLLRKLLQT--NFTGLSGQ--VQFNQ 280 (806)
Q Consensus 235 ~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~--~f~G~tG~--i~Fd~ 280 (806)
. .++.+.++|.++ .+.|+.|. +.|++
T Consensus 305 -------------------~-~~~~v~~al~~~~~~~~G~~~~~~~~~~~ 334 (347)
T cd06335 305 -------------------T-DGRAIKRALENLKKPVEGLVKTYDKPFSK 334 (347)
T ss_pred -------------------C-CHHHHHHHHHhccCCceeeecccCCCCCh
Confidence 1 146788888875 46787774 45653
No 82
>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=99.83 E-value=3.2e-19 Score=192.81 Aligned_cols=238 Identities=15% Similarity=0.156 Sum_probs=187.4
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHH-HHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLI-DFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+.++++ .+||+|++++.+.. ...||+||+.+++..++.++++.+ +..+|++|++++.|++||+...+.+.+.+++
T Consensus 83 ~~~~~~-~~vp~i~~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~i~~~~~~~g~~~~~~~~~~~~~ 158 (333)
T cd06358 83 VAPVVA-GRVPYVYTSLYEGG---ECNPGVFLTGETPEQQLAPAIPWLAEEKGARRWYLIGNDYVWPRGSLAAAKRYIAE 158 (333)
T ss_pred HHHHHh-cCceEEeCCCcCCC---CCCCCEEEcCCCcHHHHHHHHHHHHHhcCCCeEEEEeccchhhHHHHHHHHHHHHH
Confidence 346677 99999997554332 236899999999999988788764 6689999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcC-cccccccccccC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD-WLSATLESFSKM 159 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~-~~~~~~~~~~~~ 159 (806)
.|++|+....+++. ..|+++.+.++++.++|+|++.........+++++++.|+..+ ++..+ .+.... .
T Consensus 159 ~G~~v~~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~~~~-~---- 228 (333)
T cd06358 159 LGGEVVGEEYVPLG--TTDFTSVLERIAASGADAVLSTLVGQDAVAFNRQFAAAGLRDR---ILRLSPLMDENM-L---- 228 (333)
T ss_pred cCCEEeeeeeecCC--hHHHHHHHHHHHHcCCCEEEEeCCCCchHHHHHHHHHcCCCcc---CceeecccCHHH-H----
Confidence 99999988888844 7799999999999999999999998888999999999998653 33222 111111 1
Q ss_pred ChhhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCC
Q 003633 160 NQTSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHE 237 (806)
Q Consensus 160 ~~~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~ 237 (806)
.....+.++|++....+.+ ..+..++|.++|+++|+. ....++.++.++||++++++.|+++. +
T Consensus 229 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~--~~~~~~~~~~~~yda~~~~~~A~~~a---g--------- 294 (333)
T cd06358 229 LASGAEAAEGLYSSSGYFASLQTPANAAFLARYRARFGD--DAPPLNSLSESCYEAVHALAAAAERA---G--------- 294 (333)
T ss_pred HhcChHhhCCcEEeccchhhcCCHHHHHHHHHHHHHcCC--CCCCCChHHHHHHHHHHHHHHHHHHh---C---------
Confidence 0112345788877665543 568899999999999862 11246778899999999999999983 1
Q ss_pred CCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCC
Q 003633 238 LPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRN 283 (806)
Q Consensus 238 l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~ 283 (806)
. .++.+|.++|++++|+|++|+++|++++.
T Consensus 295 ---------------~-~~~~~v~~al~~~~~~~~~G~~~~~~~~~ 324 (333)
T cd06358 295 ---------------S-LDPEALIAALEDVSYDGPRGTVTMRGRHA 324 (333)
T ss_pred ---------------C-CCHHHHHHHhccCeeeCCCcceEEccccc
Confidence 0 12789999999999999999999998754
No 83
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.82 E-value=4e-19 Score=184.52 Aligned_cols=223 Identities=18% Similarity=0.308 Sum_probs=177.7
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
...+|+|++.. .++||.+.++ ++++.|+++|+++++++++|.+ +++++. +|++++.++.+|++|++++
T Consensus 24 ~~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~vdi~~~ia~~lg~~--i~~~~~-------pw~~~~~~l~~g~~D~~~~ 91 (259)
T PRK15437 24 IPQNIRIGTDP--TYAPFESKNS-QGELVGFDIDLAKELCKRINTQ--CTFVEN-------PLDALIPSLKAKKIDAIMS 91 (259)
T ss_pred cCCeEEEEeCC--CCCCcceeCC-CCCEEeeeHHHHHHHHHHcCCc--eEEEeC-------CHHHHHHHHHCCCCCEEEe
Confidence 34789999853 5788888654 6789999999999999999977 555542 6999999999999999999
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
+++.|++|.+.++||.||...+..+++++..
T Consensus 92 ~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~------------------------------------------------- 122 (259)
T PRK15437 92 SLSITEKRQQEIAFTDKLYAADSRLVVAKNS------------------------------------------------- 122 (259)
T ss_pred cCCCCHHHhhhccccchhhcCceEEEEECCC-------------------------------------------------
Confidence 9999999999999999999999999987765
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCch
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSF 593 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~ 593 (806)
+...+++|| .+.+||+..|+.
T Consensus 123 ---------------------------------------------------------~~~~~~~dl--~g~~Igv~~g~~ 143 (259)
T PRK15437 123 ---------------------------------------------------------DIQPTVESL--KGKRVGVLQGTT 143 (259)
T ss_pred ---------------------------------------------------------CCCCChHHh--CCCEEEEecCcH
Confidence 122378899 788999999998
Q ss_pred hHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHH-HhhCC--CCeEEeCC-----ccccCCcee
Q 003633 594 AYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQL-FLSNQ--TDFGIIGQ-----PFTRSGWGF 665 (806)
Q Consensus 594 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~-~~~~~--~~l~~~~~-----~~~~~~~~~ 665 (806)
.+.++.+.......+++.+++.++.+++|.. |++|+++.+...+.+ ++.+. .++.+.+. .+....+++
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~----grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i 219 (259)
T PRK15437 144 QETFGNEHWAPKGIEIVSYQGQDNIYSDLTA----GRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGM 219 (259)
T ss_pred HHHHHHhhccccCceEEecCCHHHHHHHHHc----CCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEE
Confidence 8777754322223567788888999999999 999999998876653 33332 23443322 222334678
Q ss_pred eecCCCC-chHHHHHHHHhhhccchhHHHHHhhcCC
Q 003633 666 AFQRDSP-LAVGMSTAILKLSENGMLQKLHEKWFCK 700 (806)
Q Consensus 666 ~~~k~sp-l~~~~n~~il~l~e~G~~~~i~~kw~~~ 700 (806)
+++++.+ |++.+|.+|.++..+|.+++|.+||++.
T Consensus 220 a~~~~~~~l~~~~n~~l~~~~~~G~~~~i~~k~~~~ 255 (259)
T PRK15437 220 GLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDF 255 (259)
T ss_pred EEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHHhcCC
Confidence 8888776 9999999999999999999999999974
No 84
>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=99.81 E-value=1.3e-18 Score=187.96 Aligned_cols=240 Identities=13% Similarity=0.124 Sum_probs=184.3
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
+.+++++.++|+|+.++....+ ..||+||+.+++..++.++++++...+-++|++|+.|++||....+.+.+.+++.
T Consensus 83 ~~~~~~~~~vp~i~~~~~~~~~---~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~vail~~d~~~g~~~~~~~~~~~~~~ 159 (334)
T cd06356 83 IRPIMDRTKQLYFYTTQYEGGV---CDRNTFCTGATPAQQFSTLVPYMMEKYGKKVYTIAADYNFGQISAEWVRKIVEEN 159 (334)
T ss_pred HHHHHHhcCceEEeCCCccCCc---ccCCEEEeCCCcHHHHHHHHHHHHHccCCeEEEECCCchhhHHHHHHHHHHHHHc
Confidence 4678899999999864433222 2489999999999999999998766444889999999999999999999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCCh
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQ 161 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~ 161 (806)
|++++....++++ ..|+++++++|++.++|+|++.....+...+++++++.|+ . ....+.+.+........ .
T Consensus 160 G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~-~-~~~~~~~~~~~~~~~~~----~ 231 (334)
T cd06356 160 GGEVVGEEFIPLD--VSDFGSTIQKIQAAKPDFVMSILVGANHLSFYRQWAAAGL-G-NIPMASSTLGAQGYEHK----R 231 (334)
T ss_pred CCEEEeeeecCCC--chhHHHHHHHHHhcCCCEEEEeccCCcHHHHHHHHHHcCC-c-cCceeeeecccchhHHh----c
Confidence 9999988888854 6799999999999999999999988899999999999998 2 11222221111111010 1
Q ss_pred hhhhhccceEEEEEeCC--CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 162 TSLRILQGVVGLRQHTP--DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 162 ~~~~~~~gv~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
.....++|+++...+.+ +.|..++|.++|+++|+. ...++.+++.+||++++++.|++++.+
T Consensus 232 ~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~---~p~~~~~~~~~y~a~~~~~~A~~~ag~------------- 295 (334)
T cd06356 232 LKPPALKDMYATANYIEELDTPANKAFVERFRAKFPD---APYINEEAENNYEAIYLYKEAVEKAGT------------- 295 (334)
T ss_pred cCchhcCCeEEecchhhhcCCHHHHHHHHHHHHHcCC---CCCCCchhHHHHHHHHHHHHHHHHHCC-------------
Confidence 12245678877665544 357789999999999852 112367889999999999999998421
Q ss_pred CCcccccccccccccCchHHHHHHHHc-cccCCceeeEEEecCCC
Q 003633 240 DSKATRVQLEQLKVFDGGTFLLRKLLQ-TNFTGLSGQVQFNQDRN 283 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~l~~~l~~-~~f~G~tG~i~Fd~~G~ 283 (806)
.+++.|.++|++ ..|+|+.|+++|+.++.
T Consensus 296 ---------------~~~~~v~~aL~~~~~~~~~~g~~~~~~~~h 325 (334)
T cd06356 296 ---------------TDRDAVIEALESGLVCDGPEGKVCIDGKTH 325 (334)
T ss_pred ---------------CCHHHHHHHHHhCCceeCCCceEEEecCCC
Confidence 127899999997 57899999999996443
No 85
>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=99.81 E-value=7.2e-19 Score=184.16 Aligned_cols=223 Identities=17% Similarity=0.209 Sum_probs=179.3
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
..++|+|++. +++||.+.+. ++.+.|+++||++++++.+|... +++.. .+|+.++..+.+|++|++++
T Consensus 31 ~~~~l~v~~~---~~pP~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~-~~~~~-------~~w~~~~~~l~~G~~Di~~~ 98 (275)
T TIGR02995 31 EQGFARIAIA---NEPPFTYVGA-DGKVSGAAPDVARAIFKRLGIAD-VNASI-------TEYGALIPGLQAGRFDAIAA 98 (275)
T ss_pred hCCcEEEEcc---CCCCceeECC-CCceecchHHHHHHHHHHhCCCc-eeecc-------CCHHHHHHHHHCCCcCEEee
Confidence 4578999986 5678887653 67899999999999999999751 22332 26999999999999999988
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
+++++++|...++||.||+.+...+++++...
T Consensus 99 ~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~------------------------------------------------ 130 (275)
T TIGR02995 99 GLFIKPERCKQVAFTQPILCDAEALLVKKGNP------------------------------------------------ 130 (275)
T ss_pred cccCCHHHHhccccccceeecceeEEEECCCC------------------------------------------------
Confidence 89999999999999999999999999887651
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhh-CCCceeEEeCc
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLIT-NDWPIGYQVGS 592 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~-~~~~ig~~~gs 592 (806)
..+++++||.. .+.+||+..|+
T Consensus 131 ---------------------------------------------------------~~i~~~~dl~~~~g~~Igv~~g~ 153 (275)
T TIGR02995 131 ---------------------------------------------------------KGLKSYKDIAKNPDAKIAAPGGG 153 (275)
T ss_pred ---------------------------------------------------------CCCCCHHHhccCCCceEEEeCCc
Confidence 24678888843 26789999999
Q ss_pred hhHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCC--CeEEeCCc---cccCCceeee
Q 003633 593 FAYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQT--DFGIIGQP---FTRSGWGFAF 667 (806)
Q Consensus 593 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~--~l~~~~~~---~~~~~~~~~~ 667 (806)
....++.+ .+.+..+++.+++.++.+++|.+ |++|+++.+...+.+++++.. ++..+... .....+++++
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 98888754 34444567788999999999999 999999999998888877532 34433321 1112347888
Q ss_pred cCCCC-chHHHHHHHHhhhccchhHHHHHhhc
Q 003633 668 QRDSP-LAVGMSTAILKLSENGMLQKLHEKWF 698 (806)
Q Consensus 668 ~k~sp-l~~~~n~~il~l~e~G~~~~i~~kw~ 698 (806)
+++++ |++.||++|.++.++|.+++|.+||-
T Consensus 229 ~~~~~~l~~~~n~~l~~~~~sG~~~~i~~ky~ 260 (275)
T TIGR02995 229 RPEDKELRDAFNVELAKLKESGEFAKIIAPYG 260 (275)
T ss_pred CCCCHHHHHHHHHHHHHHHhChHHHHHHHHhC
Confidence 88777 99999999999999999999999993
No 86
>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=99.79 E-value=5.3e-18 Score=174.98 Aligned_cols=258 Identities=14% Similarity=0.194 Sum_probs=194.1
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHH------HHcCCeEEEEEEEcCCcccc---hHH
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLI------DFYGWKEVIAIYVDDDYGRN---GIS 72 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll------~~~~W~~v~ii~~d~~~g~~---~~~ 72 (806)
|+.+...+++|+||-++-. |+-...+.+-|+.|+..-.+..+.++- .+++|+.+- ||.+++--++ .+.
T Consensus 97 ~~~~~~~~~~P~ISaGsfg--lscd~k~~LTR~~pparK~~~~~~~f~~~~~~~~~~~W~~ay-vyk~~~~~edCf~~i~ 173 (380)
T cd06369 97 MVDDEFNLSLPIISAGSFG--LSCDYKENLTRLLPPARKISDFFVDFWKEKNFPKKPKWETAY-VYKKQENTEDCFWYIN 173 (380)
T ss_pred hhhhhhcCCCceEeccccc--cCCCchhhhhhcCchHHHHHHHHHHHHhcccccCCCCCceeE-EEcCCCCccceeeEhH
Confidence 4556678999999966633 444445689999999999999999998 589998655 9987753332 266
Q ss_pred HHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccc
Q 003633 73 ALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSAT 152 (806)
Q Consensus 73 ~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~ 152 (806)
++....+..+..+..++.. .+.+++..+|+.++ ..+||||+++.+++.+.|+.+ ++...+|++|..|.....
T Consensus 174 al~a~~~~f~~~~~~~~~l---~~~~~~~~il~~~~-~~sRIiImCG~p~~ir~lm~~----~~~~gDYVf~~IDlF~~s 245 (380)
T cd06369 174 ALEAGVAYFSSALKFKELL---RTEEELQKLLTDKN-RKSNVIIMCGTPEDIVNLKGD----RAVAEDIVIILIDLFNDV 245 (380)
T ss_pred hhhhhhhhhhhcccceeee---cCchhHHHHHHHhc-cCccEEEEeCCHHHHHHHHhc----CccCCCEEEEEEecccch
Confidence 6666666666566555443 23478999998876 678999999999999999886 444569999999866543
Q ss_pred ccccccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCCc-cchhhhhhHHHHHHHHHHHHHhhcCcc
Q 003633 153 LESFSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGLN-TYGLYAYDTVWAVARSIDKFINEHNIT 231 (806)
Q Consensus 153 ~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~-~~~~~aYDAv~~lA~Al~~~~~~~~~~ 231 (806)
... +....++++.|+.+++..|+.+.++++ ..+. ..+. .|++..||||.++|+||++++..+.
T Consensus 246 y~~----d~~a~~amqsVLvIT~~~p~~~~~~~~-----~~fn-----~~l~~~~aa~fyDaVLLYa~AL~EtL~~G~-- 309 (380)
T cd06369 246 YYE----NTTSPPYMRNVLVLTLPPRNSTNNSSF-----TTDN-----SLLKDDYVAAYHDGVLLFGHVLKKFLESQE-- 309 (380)
T ss_pred hcc----CcchHHHHhceEEEecCCCCCcccccC-----CCCC-----cchHHHHHHHHHHHHHHHHHHHHHHHHhCC--
Confidence 321 234567899999999888766544331 1111 1222 8999999999999999999987750
Q ss_pred ccCCCCCCCCcccccccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee--cCceEEEEEeeCCC
Q 003633 232 FSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID--KMEIHRVGYWFDGS 309 (806)
Q Consensus 232 ~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~--~~~~~~VG~w~~~~ 309 (806)
. .. +.++.+.+++.+|.|++|.+.+|+|||| ...|.++-+. .++++.||.++...
T Consensus 310 --------------------~-~~-~~~I~~~m~NrTF~GitG~V~IDeNGDR-d~dfsLl~ms~~tg~y~vV~~y~t~~ 366 (380)
T cd06369 310 --------------------G-VQ-TFSFINEFRNISFEGAGGPYTLDEYGDR-DVNFTLLYTSTDTSKYKVLFEFDTST 366 (380)
T ss_pred --------------------C-CC-cHHHHHHHhCcceecCCCceEeCCCCCc-cCceEEEEeeCCCCCeEEEEEEECCC
Confidence 0 12 4789999999999999999999999996 6889998774 57899999998855
No 87
>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=99.79 E-value=1.4e-18 Score=187.58 Aligned_cols=231 Identities=14% Similarity=0.097 Sum_probs=176.5
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN 81 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~ 81 (806)
+++++++.+||+|+++++.+ +.. .|++||+.+++..++.++++++...|+|+|++++.+++||++..+.+.+.+++.
T Consensus 75 ~~~~~~~~~ip~i~~~~~~~-~~~--~~~~f~~~~~~~~~~~~~~~~~~~~g~k~vaii~~~~~~g~~~~~~f~~~~~~~ 151 (336)
T cd06339 75 LAAAAAELGVPVLALNNDES-VAA--GPNLFYFGLSPEDEARRAAEYARSQGKRRPLVLAPDGAYGQRVADAFRQAWQQL 151 (336)
T ss_pred HHhhhccCCCCEEEccCCcc-ccC--CCCEEEecCChHHHHHHHHHHHHhcCccceEEEecCChHHHHHHHHHHHHHHHc
Confidence 34778899999999865544 332 589999999999999999999887899999999999999999999999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCC---------------------CCeEEEEecCcc-hHHHHHHHHHHcCCccC
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPL---------------------GPRVYVVHVSPD-PGLRIFTTAQKLQMMTN 139 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~---------------------~~rvivl~~~~~-~~~~i~~~a~~~gm~~~ 139 (806)
|++|+..+.++. +..|++.++++|++. ++|+|++.+.+. .+..+.+++...+....
T Consensus 152 G~~vv~~~~~~~--~~~d~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~~ 229 (336)
T cd06339 152 GGTVVAIESYDP--SPTDLSDAIRRLLGVDDSEQRIAQLKSLESEPRRRQDIDAIDAVALPDGEARLIKPQLLFYYGVPG 229 (336)
T ss_pred CCceeeeEecCC--CHHHHHHHHHHHhccccchhhhhhhhhcccCccccCCCCcEEEEecChhhhhhhcchhhhhccCcC
Confidence 999998888874 477999999999998 999999988886 66667777766553112
Q ss_pred CcEEEEcCcccccccccccCChhhhhhccceEEEEEeCCCChhhHHHHHHHhhhccCCCCCCCC-ccchhhhhhHHHHHH
Q 003633 140 NYVWLATDWLSATLESFSKMNQTSLRILQGVVGLRQHTPDSIPKKAFLSRWSGMQQKGLVSAGL-NTYGLYAYDTVWAVA 218 (806)
Q Consensus 140 ~~~wi~t~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~-~~~~~~aYDAv~~lA 218 (806)
+-.++.++++.+.. .. ....+..+|++...+.. ....+|.++|+++|+. .+ +.|++.+|||+.+++
T Consensus 230 ~~~~~g~~~~~~~~-~~----~~~g~~~~g~~~~~~~~---~~~~~f~~~y~~~~~~-----~p~~~~~a~~YDa~~l~~ 296 (336)
T cd06339 230 DVPLYGTSRWYSGT-PA----PLRDPDLNGAWFADPPW---LLDANFELRYRAAYGW-----PPLSRLAALGYDAYALAA 296 (336)
T ss_pred CCCEEEeccccCCC-CC----cccCcccCCcEEeCCCc---ccCcchhhhHHHHhcC-----CCCchHHHHHHhHHHHHH
Confidence 34577777665431 11 22335577876544311 1233799999998862 45 789999999999998
Q ss_pred HHHHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHHHc-cccCCceeeEEEecCCCe
Q 003633 219 RSIDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKLLQ-TNFTGLSGQVQFNQDRNI 284 (806)
Q Consensus 219 ~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l~~-~~f~G~tG~i~Fd~~G~~ 284 (806)
.++++. + .+ . ++.+ ..|+|++|+++|+++|+.
T Consensus 297 ~~~~~~---~-------------------------~~-~-----al~~~~~~~g~~G~~~f~~~g~~ 329 (336)
T cd06339 297 ALAQLG---Q-------------------------GD-A-----ALTPGAGFSGVTGVLRLDPDGVI 329 (336)
T ss_pred HHHHcc---c-------------------------cc-c-----ccCCCCccccCcceEEECCCCeE
Confidence 877762 0 00 1 3333 469999999999999974
No 88
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.78 E-value=2.7e-18 Score=192.94 Aligned_cols=222 Identities=14% Similarity=0.174 Sum_probs=177.3
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
..++||||+... |+.+.+. ++...||++||++++++.+|.+ ++++.. .+|++++.+|.+|++|++++
T Consensus 41 ~~g~LrVg~~~~----P~~~~~~-~~~~~G~~~DLl~~ia~~LGv~--~e~v~~------~~~~~ll~aL~~G~iDi~~~ 107 (482)
T PRK10859 41 ERGELRVGTINS----PLTYYIG-NDGPTGFEYELAKRFADYLGVK--LEIKVR------DNISQLFDALDKGKADLAAA 107 (482)
T ss_pred hCCEEEEEEecC----CCeeEec-CCCcccHHHHHHHHHHHHhCCc--EEEEec------CCHHHHHHHHhCCCCCEEec
Confidence 467899999742 3333332 2334999999999999999977 555532 37999999999999999988
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
++++|++|.+.++||.||+....+++++...
T Consensus 108 ~lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~------------------------------------------------- 138 (482)
T PRK10859 108 GLTYTPERLKQFRFGPPYYSVSQQLVYRKGQ------------------------------------------------- 138 (482)
T ss_pred cCcCChhhhccCcccCCceeeeEEEEEeCCC-------------------------------------------------
Confidence 8999999999999999999999999987655
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCch
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSF 593 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~ 593 (806)
+.+++++|| .|++||+..|+.
T Consensus 139 ---------------------------------------------------------~~i~~l~dL--~Gk~I~V~~gS~ 159 (482)
T PRK10859 139 ---------------------------------------------------------PRPRSLGDL--KGGTLTVAAGSS 159 (482)
T ss_pred ---------------------------------------------------------CCCCCHHHh--CCCeEEEECCCc
Confidence 367899999 789999999998
Q ss_pred hHHHhhhhc-cccccc--ceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeCCccccCCceeeecC-
Q 003633 594 AYSYLSDSL-RIQKSR--LISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIGQPFTRSGWGFAFQR- 669 (806)
Q Consensus 594 ~~~~l~~~~-~~~~~~--~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k- 669 (806)
....+.+.. ..+... ...+.+.++++++|.+ |++|+++.+...+.+......++.+........+++++++|
T Consensus 160 ~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~----G~iDa~v~d~~~~~~~~~~~p~l~v~~~l~~~~~~~~av~k~ 235 (482)
T PRK10859 160 HVETLQELKKKYPELSWEESDDKDSEELLEQVAE----GKIDYTIADSVEISLNQRYHPELAVAFDLTDEQPVAWALPPS 235 (482)
T ss_pred HHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHC----CCCCEEEECcHHHHHHHHhCCCceeeeecCCCceeEEEEeCC
Confidence 887764311 112222 2345789999999999 99999999988776655555566665544455678999999
Q ss_pred CCC-chHHHHHHHHhhhccchhHHHHHhhcCC
Q 003633 670 DSP-LAVGMSTAILKLSENGMLQKLHEKWFCK 700 (806)
Q Consensus 670 ~sp-l~~~~n~~il~l~e~G~~~~i~~kw~~~ 700 (806)
+++ |+..+|++|.++.++|.+++|.+||++.
T Consensus 236 ~~~~L~~~ln~~L~~i~~~G~l~~L~~kyfg~ 267 (482)
T PRK10859 236 GDDSLYAALLDFFNQIKEDGTLARLEEKYFGH 267 (482)
T ss_pred CCHHHHHHHHHHHHHhhcCCHHHHHHHHHhhh
Confidence 456 9999999999999999999999999974
No 89
>PF00060 Lig_chan: Ligand-gated ion channel; InterPro: IPR001320 The ability of synapses to modify their synaptic strength in response to activity is a fundamental property of the nervous system and may be an essential component of learning and memory. There are three classes of ionotropic glutamate receptor, namely NMDA (N-methyl-D-aspartate), AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole-4-propionic acid) and kainate receptors. They are believed to play critical roles in synaptic plasticity. At many synapses in the brain, transient activation of NMDA receptors leads to a persistent modification in the strength of synaptic transmission mediated by AMPA receptors and kainate receptors can act as the induction trigger for long-term changes in synaptic transmission [].; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 3FAT_A 3KFM_A 3KEI_A 3EN3_A 3EPE_B 3FAS_A 2F34_A 3C34_B 3S2V_A 3GBB_B ....
Probab=99.74 E-value=2e-19 Score=169.73 Aligned_cols=107 Identities=24% Similarity=0.538 Sum_probs=82.4
Q ss_pred chhhHHHHHHHHHHHHHHhhhhccccCCCCCC-------CCccchhhHHHHHHHhhhccCc-ccccccchhhhHHHHHhh
Q 003633 477 TVEMWCVTAASFVMIAVVIWILEHRVNDDFRG-------PPRRQIATMFLFSFSTLFKTNQ-EATVSSLGRFVMVVWLFL 548 (806)
Q Consensus 477 ~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~~-~~~~s~~~R~v~~~w~~~ 548 (806)
++++|++++++++++++++|++++..+.+++. .....+.+++|+++++++.|+. ..|++.++|++.++|+++
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 2234589999999999986654 589999999999999999
Q ss_pred hhhhhccccceeeeeeeeccccCCCCChhHhhhCC
Q 003633 549 LMVITSSYTASLSSILTVQQLSTSVKGIESLITND 583 (806)
Q Consensus 549 ~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~ 583 (806)
++++.++|||+|+|+||.++.+++|+|++||.+++
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 99999999999999999999999999999998766
No 90
>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=99.73 E-value=5e-17 Score=174.48 Aligned_cols=233 Identities=15% Similarity=0.133 Sum_probs=168.4
Q ss_pred HhcccccCCCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+++++++.++|+|+++++++.++.. .+||+||+.|++..+++++++++..-+.|+|++|+.|++||....+.+.+.+++
T Consensus 75 v~~~a~~~~vp~i~~~a~~~~lt~~~c~~~~Fr~~~~~~~~~~ala~~~~~~g~kkvaii~~~~~~g~~~~~~~~~~~~~ 154 (347)
T TIGR03863 75 LADAAKAKGALLFNAGAPDDALRGADCRANLLHTLPSRAMLADALAQYLAAKRWRRILLIQGPLPADALYADAFRRSAKR 154 (347)
T ss_pred HHHHHHhCCcEEEeCCCCChHHhCCCCCCCEEEecCChHhHHHHHHHHHHHcCCCEEEEEeCCCcccHHHHHHHHHHHHH
Confidence 5678999999999999999999974 479999999999999999999987779999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCC--hhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccccccccccc
Q 003633 81 NMAKVSYKLPLPVQFN--QHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSK 158 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~--~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~ 158 (806)
.|++|+..+.++...+ ..++.......+.+++|+|++.....+....+.... +. ....
T Consensus 155 ~G~~vv~~~~~~~~~~~~~~d~s~~~~~~~~s~pDvv~~~~~~~~~~~~~~~~~--~~---~~~~--------------- 214 (347)
T TIGR03863 155 FGAKIVAERPFTFSGDPRRTDQSEVPLFTQGADYDVVVVADEAGEFARYLPYAT--WL---PRPV--------------- 214 (347)
T ss_pred CCCEEEEeEEeccCCchhhhhcccCceeecCCCCCEEEEecchhhHhhhccccc--cc---cccc---------------
Confidence 9999998888875422 234543233344589999998755432211100000 00 0000
Q ss_pred CChhhhhhccceEEEEE-eCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCC
Q 003633 159 MNQTSLRILQGVVGLRQ-HTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHE 237 (806)
Q Consensus 159 ~~~~~~~~~~gv~~~~~-~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~ 237 (806)
....|+..... +..+.+..++|.++|+++|+. .|+.+++.+||+|++++.|++++.+
T Consensus 215 ------~g~~G~~~~~~~~~~~~~~~~~f~~~f~~~~g~-----~p~~~~a~aY~av~~~a~Ai~~AGs----------- 272 (347)
T TIGR03863 215 ------AGSAGLVPTAWHRAWERWGATQLQSRFEKLAGR-----PMTELDYAAWLAVRAVGEAVTRTRS----------- 272 (347)
T ss_pred ------ccccCccccccCCcccchhHHHHHHHHHHHhCC-----CCChHHHHHHHHHHHHHHHHHHhcC-----------
Confidence 11122221111 122346678999999999862 4667788899999999999999522
Q ss_pred CCCCcccccccccccccCchHHHHHHHHcccc--CCcee-eEEEec-CCCeecccEEEEEe
Q 003633 238 LPDSKATRVQLEQLKVFDGGTFLLRKLLQTNF--TGLSG-QVQFNQ-DRNIVSRGYDVINI 294 (806)
Q Consensus 238 l~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f--~G~tG-~i~Fd~-~G~~~~~~~~I~~~ 294 (806)
.+++++.++|+++++ .+..| ++.|.+ +|+... ...+.+.
T Consensus 273 -----------------~d~~aV~~aL~~~~~~~~~~~g~~~~~R~~Dhq~~~-~~~~~~~ 315 (347)
T TIGR03863 273 -----------------ADPATLRDYLLSDEFELAGFKGRPLSFRPWDGQLRQ-PVLLVHP 315 (347)
T ss_pred -----------------CCHHHHHHHHcCCCceecccCCCcceeeCCCccccc-ceEeccc
Confidence 138999999999887 47887 699985 777543 3444433
No 91
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.73 E-value=1.9e-16 Score=200.05 Aligned_cols=217 Identities=16% Similarity=0.165 Sum_probs=179.1
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
.++|+||+.. .|+||.+.+. +|++.||++|++++|++++|.+ +++++. .+|..+..+|.+|++|++.+
T Consensus 301 ~~~l~v~~~~--~~pP~~~~d~-~g~~~G~~~Dll~~i~~~~g~~--~~~v~~------~~~~~~~~~l~~g~~D~i~~- 368 (1197)
T PRK09959 301 HPDLKVLENP--YSPPYSMTDE-NGSVRGVMGDILNIITLQTGLN--FSPITV------SHNIHAGTQLNPGGWDIIPG- 368 (1197)
T ss_pred CCceEEEcCC--CCCCeeEECC-CCcEeeehHHHHHHHHHHHCCe--EEEEec------CCHHHHHHHHHCCCceEeec-
Confidence 4689998764 7899999874 6899999999999999999966 777765 36888899999999998765
Q ss_pred EEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccch
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQI 514 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 514 (806)
+..|++|.+.++||.||+.+..++++++..
T Consensus 369 ~~~t~~r~~~~~fs~py~~~~~~~v~~~~~-------------------------------------------------- 398 (1197)
T PRK09959 369 AIYSEDRENNVLFAEAFITTPYVFVMQKAP-------------------------------------------------- 398 (1197)
T ss_pred ccCCccccccceeccccccCCEEEEEecCC--------------------------------------------------
Confidence 567999999999999999999999986543
Q ss_pred hhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCchh
Q 003633 515 ATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSFA 594 (806)
Q Consensus 515 ~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~~ 594 (806)
..+ .++. .|++||+..|+..
T Consensus 399 --------------------------------------------------------~~~---~~~~-~g~~vav~~g~~~ 418 (1197)
T PRK09959 399 --------------------------------------------------------DSE---QTLK-KGMKVAIPYYYEL 418 (1197)
T ss_pred --------------------------------------------------------CCc---cccc-cCCEEEEeCCcch
Confidence 111 2222 5889999999988
Q ss_pred HHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCC--C-eEEeCCccccCCceeeecCCC
Q 003633 595 YSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQT--D-FGIIGQPFTRSGWGFAFQRDS 671 (806)
Q Consensus 595 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~--~-l~~~~~~~~~~~~~~~~~k~s 671 (806)
..++.+.+ +..+++.+++.++++++|.+ |++||++.+...+.|+++++. + +......+....++|+++|+.
T Consensus 419 ~~~~~~~~--p~~~~~~~~~~~~~l~av~~----G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~ 492 (1197)
T PRK09959 419 HSQLKEMY--PEVEWIKVDNASAAFHKVKE----GELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGE 492 (1197)
T ss_pred HHHHHHHC--CCcEEEEcCCHHHHHHHHHc----CCCCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCC
Confidence 88876543 55788999999999999999 999999999999999888742 2 333444455667899999999
Q ss_pred C-chHHHHHHHHhhhccchhHHHHHhhcCC
Q 003633 672 P-LAVGMSTAILKLSENGMLQKLHEKWFCK 700 (806)
Q Consensus 672 p-l~~~~n~~il~l~e~G~~~~i~~kw~~~ 700 (806)
| |...+|++|..+.++ .+++|.+||+..
T Consensus 493 ~~L~~~lnk~l~~i~~~-~~~~i~~kW~~~ 521 (1197)
T PRK09959 493 PELKDIINKALNAIPPS-EVLRLTEKWIKM 521 (1197)
T ss_pred HHHHHHHHHHHHhCCHH-HHHHHHhhcccC
Confidence 8 999999999999998 888999999863
No 92
>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=99.72 E-value=2.7e-16 Score=170.36 Aligned_cols=237 Identities=13% Similarity=0.103 Sum_probs=183.0
Q ss_pred hcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCC
Q 003633 3 SEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNM 82 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g 82 (806)
.+++.+.+||+|+++++++.++....|++||+.+++..++.++++++...||++|++++.|+.+|+...+.+.+.+++.|
T Consensus 85 ~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~v~~l~~~~~~~~~~~~~~~~~~~~~G 164 (336)
T cd06326 85 LPLLEEAGVPLVGPFTGASSLRDPPDRNVFNVRASYADEIAAIVRHLVTLGLKRIAVFYQDDAFGKDGLAGVEKALAARG 164 (336)
T ss_pred HHHHHHcCCeEEEecCCcHHhcCCCCCceEEeCCChHHHHHHHHHHHHHhCCceEEEEEecCcchHHHHHHHHHHHHHcC
Confidence 35677889999998777776765457899999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCChh
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQT 162 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~~ 162 (806)
+++.....++.. ..|+..++.++++.++|+|++......+..++++++++|+.. .. +...+.... ... ..
T Consensus 165 ~~~~~~~~~~~~--~~d~~~~~~~l~~~~~dav~~~~~~~~a~~~i~~~~~~G~~~-~~--~~~~~~~~~-~~~----~~ 234 (336)
T cd06326 165 LKPVATASYERN--TADVAAAVAQLAAARPQAVIMVGAYKAAAAFIRALRKAGGGA-QF--YNLSFVGAD-ALA----RL 234 (336)
T ss_pred CCeEEEEeecCC--cccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHhcCCCC-cE--EEEeccCHH-HHH----HH
Confidence 998776667643 468999999999989999999998888999999999999743 22 222222211 111 23
Q ss_pred hhhhccceEEEE--E--eCCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCC
Q 003633 163 SLRILQGVVGLR--Q--HTPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHEL 238 (806)
Q Consensus 163 ~~~~~~gv~~~~--~--~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l 238 (806)
.....+|++... + ...++|..++|.+.|++++.. ..++.++..+||++++++.|+++...
T Consensus 235 ~g~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~----~~~~~~~~~~y~~~~~~~~a~~~~g~------------ 298 (336)
T cd06326 235 LGEYARGVIVTQVVPNPWSRTLPIVREYQAAMKAYGPG----APPSYVSLEGYIAAKVLVEALRRAGP------------ 298 (336)
T ss_pred hhhhhcceEEEEEecCccccCCHHHHHHHHHHHhhCCC----CCCCeeeehhHHHHHHHHHHHHHcCC------------
Confidence 345567876432 2 122467789999999988741 25677888999999999999998311
Q ss_pred CCCcccccccccccccCchHHHHHHHHcccc-CCceeeEEEec
Q 003633 239 PDSKATRVQLEQLKVFDGGTFLLRKLLQTNF-TGLSGQVQFNQ 280 (806)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f-~G~tG~i~Fd~ 280 (806)
-.+++.+.++|++++. .+..|.+.|++
T Consensus 299 ---------------~~~~~~v~~al~~~~~~~~~g~~~~~~~ 326 (336)
T cd06326 299 ---------------DPTRESLLAALEAMGKFDLGGFRLDFSP 326 (336)
T ss_pred ---------------CCCHHHHHHHHHhcCCCCCCCeEEecCc
Confidence 0137899999999875 45545899964
No 93
>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=99.71 E-value=1.3e-16 Score=163.99 Aligned_cols=208 Identities=16% Similarity=0.226 Sum_probs=157.0
Q ss_pred CeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHH---HHHHcCcccEEEe
Q 003633 357 PLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLV---KMVANDVFDAAVG 433 (806)
Q Consensus 357 ~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~---~~l~~g~~D~~~~ 433 (806)
+||||+.. .|+||.+.+ + .||++||+++|++++|.+ +++++. +|++++ ..|.+|++|++++
T Consensus 1 ~l~vg~~~--~~pPf~~~~---~--~Gfdvdl~~~ia~~lg~~--~~~~~~-------~~~~~~~~~~~L~~g~~Dii~~ 64 (246)
T TIGR03870 1 TLRVCAAT--KEAPYSTKD---G--SGFENKIAAALAAAMGRK--VVFVWL-------AKPAIYLVRDGLDKKLCDVVLG 64 (246)
T ss_pred CeEEEeCC--CCCCCccCC---C--CcchHHHHHHHHHHhCCC--eEEEEe-------ccchhhHHHHHHhcCCccEEEe
Confidence 47899865 789999863 2 699999999999999977 666663 577766 6999999999984
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
++++++| ++||.||+.++.++++++.+.
T Consensus 65 -~~~t~~r---~~fS~PY~~~~~~~v~~k~~~------------------------------------------------ 92 (246)
T TIGR03870 65 -LDTGDPR---VLTTKPYYRSSYVFLTRKDRN------------------------------------------------ 92 (246)
T ss_pred -CCCChHH---HhcccCcEEeeeEEEEeCCCC------------------------------------------------
Confidence 8777776 689999999999999987751
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhH--hhhCCC-ceeEEe
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIES--LITNDW-PIGYQV 590 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~d--L~~~~~-~ig~~~ 590 (806)
..+++++| | .|+ +||+..
T Consensus 93 ---------------------------------------------------------~~~~~~~d~~L--~g~~~vgv~~ 113 (246)
T TIGR03870 93 ---------------------------------------------------------LDIKSWNDPRL--KKVSKIGVIF 113 (246)
T ss_pred ---------------------------------------------------------CCCCCccchhh--ccCceEEEec
Confidence 24677765 6 687 999999
Q ss_pred CchhHHHhhhhcccc-----cccceeCC---------CHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCC-CCeE--E
Q 003633 591 GSFAYSYLSDSLRIQ-----KSRLISLG---------SPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQ-TDFG--I 653 (806)
Q Consensus 591 gs~~~~~l~~~~~~~-----~~~~~~~~---------~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~-~~l~--~ 653 (806)
|+..+.++.+..... ...++.+. +.++.+++|.. |++||++.+.+.+.+++.++ .++. .
T Consensus 114 gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~----GrvDa~i~~~~~~~~~~~~~~~~~~~~~ 189 (246)
T TIGR03870 114 GSPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVAT----GKADLAVAFAPEVARYVKASPEPLRMTV 189 (246)
T ss_pred CChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHc----CCCCEEEeeHHhHHHHHHhCCCCceEEe
Confidence 999998885421110 11122221 35788999999 99999999887777776653 2333 3
Q ss_pred eCCccc---------cCCceeeecCCCC-chHHHHHHHHhhhccchhHHHHHhh
Q 003633 654 IGQPFT---------RSGWGFAFQRDSP-LAVGMSTAILKLSENGMLQKLHEKW 697 (806)
Q Consensus 654 ~~~~~~---------~~~~~~~~~k~sp-l~~~~n~~il~l~e~G~~~~i~~kw 697 (806)
+++... ..+++++++|+++ |++.+|++|.+|. |.+++|..+|
T Consensus 190 ~~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l~--~~~~~i~~~y 241 (246)
T TIGR03870 190 IPDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKAK--PRIDAILKEE 241 (246)
T ss_pred ccccccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHhH--HHHHHHHHHc
Confidence 333211 1135899999998 9999999999999 4899999998
No 94
>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=99.70 E-value=2.1e-16 Score=164.85 Aligned_cols=226 Identities=15% Similarity=0.157 Sum_probs=163.8
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhC-CCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLV-PYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l-~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
.++|++++. +|+||.+.+ +++...|+..++++++++.+ ++. +++.. .+|++++.++ .|+.|+++.
T Consensus 17 ~~~l~~~~~---~~pPf~~~~-~~~~~~G~~~~i~~~i~~~~~~~~--~~~~~-------~pw~r~l~~l-~~~~d~~~~ 82 (268)
T TIGR02285 17 KEAITWIVN---DFPPFFIFS-GPSKGRGVFDVILQEIRRALPQYE--HRFVR-------VSFARSLKEL-QGKGGVCTV 82 (268)
T ss_pred cceeEEEec---ccCCeeEeC-CCCCCCChHHHHHHHHHHHcCCCc--eeEEE-------CCHHHHHHHH-hcCCCeEEe
Confidence 478998876 678888765 35788999999999999998 766 55544 2699999999 788888877
Q ss_pred eEEEecCccceeEecccccc-cceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCcc
Q 003633 434 DIAIVTNRTKIVDFSQPYIS-TGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRR 512 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~-~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~ 512 (806)
++++|++|.+.++||.||+. ...++++++..... .
T Consensus 83 ~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~-~------------------------------------------- 118 (268)
T TIGR02285 83 NLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAG-V------------------------------------------- 118 (268)
T ss_pred eccCCcchhhceeecCCccccCCceEEEccchhhh-c-------------------------------------------
Confidence 79999999999999999975 57888887654100 0
Q ss_pred chhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccC---CCCChhHhhhCCCceeEE
Q 003633 513 QIATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLST---SVKGIESLITNDWPIGYQ 589 (806)
Q Consensus 513 ~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~---~i~s~~dL~~~~~~ig~~ 589 (806)
..+.. .+.++.|| ++.++|+.
T Consensus 119 ------------------------------------------------------~~~~d~~~~~~~l~~l--~g~~vgv~ 142 (268)
T TIGR02285 119 ------------------------------------------------------RDEQDGDVDLKKLLAS--KKKRLGVI 142 (268)
T ss_pred ------------------------------------------------------cccCCCCccHHHHhcC--CCeEEEEe
Confidence 00000 11222334 57789999
Q ss_pred eCchhH----HHhhhhccc-ccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCC----CCeEEeCCcc--
Q 003633 590 VGSFAY----SYLSDSLRI-QKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQ----TDFGIIGQPF-- 658 (806)
Q Consensus 590 ~gs~~~----~~l~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~----~~l~~~~~~~-- 658 (806)
.|+... +++++ .+. ...++..+.+.++.+++|.. |++|+++.+...+.+++++. ..+.......
T Consensus 143 ~g~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~L~~----GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (268)
T TIGR02285 143 ASRSYGQQIDDILSD-SGYQHNTRIIGNAAMGNLFKMLEK----GRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMP 217 (268)
T ss_pred cceeccHHHHHHHHh-CCcccceeeeccchHHHHHHHHHc----CCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCc
Confidence 877553 33322 221 11235556677789999999 99999999999999887742 1344443221
Q ss_pred ccCCceeeecCCC---CchHHHHHHHHhhhccchhHHHHHhhcC
Q 003633 659 TRSGWGFAFQRDS---PLAVGMSTAILKLSENGMLQKLHEKWFC 699 (806)
Q Consensus 659 ~~~~~~~~~~k~s---pl~~~~n~~il~l~e~G~~~~i~~kw~~ 699 (806)
...+++++++|++ .+++.||++|.+|.++|.+++|.+||++
T Consensus 218 ~~~~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~i~~k~~~ 261 (268)
T TIGR02285 218 AHISVWVACPKTEWGRKVIADIDQALSELNVDPKYYKYFDRWLS 261 (268)
T ss_pred cceEEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhCC
Confidence 2235789999974 3999999999999999999999999996
No 95
>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=99.69 E-value=3.3e-16 Score=166.20 Aligned_cols=202 Identities=29% Similarity=0.394 Sum_probs=163.8
Q ss_pred HhcccccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
++++++..+||+|++.++++.+++ ..+|++||+.|++..++.++++++++++|++|++++.++++|....+.+.+.+++
T Consensus 83 ~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~v~iv~~~~~~~~~~~~~~~~~~~~ 162 (299)
T cd04509 83 VAPVAEALKIPLISPGATAPGLTDKKGYPYLFRTGPSDEQQAEALADYIKEYNWKKVAILYDDDSYGRGLLEAFKAAFKK 162 (299)
T ss_pred HHHHHhhCCceEEeccCCCcccccccCCCCEEEecCCcHHHHHHHHHHHHHcCCcEEEEEecCchHHHHHHHHHHHHHHH
Confidence 456788899999999888887765 4589999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|+++.....++.. .+++...++++++.++|+|++++....+..+++++++.|+. .++.||..+.+......
T Consensus 163 ~g~~i~~~~~~~~~--~~~~~~~~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~g~~-~~~~~i~~~~~~~~~~~----- 234 (299)
T cd04509 163 KGGTVVGEEYYPLG--TTDFTSLLQKLKAAKPDVIVLCGSGEDAATILKQAAEAGLT-GGYPILGITLGLSDVLL----- 234 (299)
T ss_pred cCCEEEEEecCCCC--CccHHHHHHHHHhcCCCEEEEcccchHHHHHHHHHHHcCCC-CCCcEEecccccCHHHH-----
Confidence 99999876666643 35788999999888899999999889999999999999998 78999999876543321
Q ss_pred hhhhhhccceEEEEEeCCCCh--hhHHHH---HHHhhhccCCCCCCCCccchhhhhhHHHH
Q 003633 161 QTSLRILQGVVGLRQHTPDSI--PKKAFL---SRWSGMQQKGLVSAGLNTYGLYAYDTVWA 216 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~~~~--~~~~f~---~~~~~~~~~~~~~~~~~~~~~~aYDAv~~ 216 (806)
....+.++|+++..++.+..+ ..+.|. ..++..++ ..++.+++++|||+++
T Consensus 235 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~yda~~~ 290 (299)
T cd04509 235 EAGGEAAEGVLTGTPYFPGDPPPESFFFVRAAAREKKKYE-----DQPDYFAALAYDAVLL 290 (299)
T ss_pred HHhHHhhcCcEEeeccCCCCCChHHHHHHhHHHHHHHHhC-----CCCChhhhhhcceeee
Confidence 234567889998887765433 233332 23333332 3678899999999998
No 96
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.69 E-value=9.3e-16 Score=161.04 Aligned_cols=226 Identities=23% Similarity=0.370 Sum_probs=182.7
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
....++|++... ..+||.+.+.+.+++.||++|+++++++.++.....++++ .+|++++..|..|++|++++
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 456788888742 4458888875336999999999999999988653345554 37999999999999999999
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
.+++|.+|.+.++||.||+..+..++++..+.
T Consensus 104 ~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~------------------------------------------------ 135 (275)
T COG0834 104 GMTITPERKKKVDFSDPYYYSGQVLLVKKDSD------------------------------------------------ 135 (275)
T ss_pred ccccCHHHhccccccccccccCeEEEEECCCC------------------------------------------------
Confidence 99999999999999999999999999987761
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCch
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSF 593 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~ 593 (806)
..+.+++|| .++++|++.|+.
T Consensus 136 ---------------------------------------------------------~~~~~~~DL--~gk~v~v~~gt~ 156 (275)
T COG0834 136 ---------------------------------------------------------IGIKSLEDL--KGKKVGVQLGTT 156 (275)
T ss_pred ---------------------------------------------------------cCcCCHHHh--CCCEEEEEcCcc
Confidence 137799999 789999999998
Q ss_pred --hHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHH--hhCCCC-eEEeCCcccc-CCceeee
Q 003633 594 --AYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLF--LSNQTD-FGIIGQPFTR-SGWGFAF 667 (806)
Q Consensus 594 --~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~--~~~~~~-l~~~~~~~~~-~~~~~~~ 667 (806)
....... ......++.+++..+.+.+|.. |++||++.+.+.+.+. ..+..+ .......... .++++++
T Consensus 157 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~al~~----Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (275)
T COG0834 157 DEAEEKAKK--PGPNAKIVAYDSNAEALLALKN----GRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIAL 230 (275)
T ss_pred hhHHHHHhh--ccCCceEEeeCCHHHHHHHHHc----CCccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEe
Confidence 4443322 2234678889999999999999 9999999999988883 433333 3333333333 6899999
Q ss_pred cCC--CCchHHHHHHHHhhhccchhHHHHHhhcCC
Q 003633 668 QRD--SPLAVGMSTAILKLSENGMLQKLHEKWFCK 700 (806)
Q Consensus 668 ~k~--spl~~~~n~~il~l~e~G~~~~i~~kw~~~ 700 (806)
+|+ ..+++.+|.+|.++.++|.+++|.+||+..
T Consensus 231 ~~~~~~~l~~~in~~l~~l~~~G~~~~i~~kw~~~ 265 (275)
T COG0834 231 RKGDDPELLEAVNKALKELKADGTLQKISDKWFGP 265 (275)
T ss_pred ccCCcHHHHHHHHHHHHHHHhCccHHHHHHHhcCc
Confidence 999 469999999999999999999999999973
No 97
>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=99.68 E-value=2.8e-15 Score=150.50 Aligned_cols=214 Identities=25% Similarity=0.468 Sum_probs=178.2
Q ss_pred eEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEE
Q 003633 358 LRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAI 437 (806)
Q Consensus 358 lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~i 437 (806)
|+|++.. .++||.+.+ +++...|++.++++.+.+++|.+ +++++. .|.+++.+|.+|++|+++.....
T Consensus 1 l~i~~~~--~~~p~~~~~-~~g~~~G~~~~~~~~~~~~~g~~--~~~~~~-------~~~~~~~~l~~g~~D~~~~~~~~ 68 (218)
T cd00134 1 LTVGTAG--TYPPFSFRD-ANGELTGFDVDLAKAIAKELGVK--VKFVEV-------DWDGLITALKSGKVDLIAAGMTI 68 (218)
T ss_pred CEEecCC--CCCCeeEEC-CCCCEEeeeHHHHHHHHHHhCCe--EEEEeC-------CHHHHHHHHhcCCcCEEeecCcC
Confidence 5778765 677888875 47899999999999999999965 667663 48999999999999999987777
Q ss_pred ecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchhhH
Q 003633 438 VTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIATM 517 (806)
Q Consensus 438 t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~ 517 (806)
+.+|...+.|+.|+.....+++++...
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------------------------- 95 (218)
T cd00134 69 TPERAKQVDFSDPYYKSGQVILVKKGS----------------------------------------------------- 95 (218)
T ss_pred CHHHHhhccCcccceeccEEEEEECCC-----------------------------------------------------
Confidence 888888899999999999999998766
Q ss_pred HHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCchhHHH
Q 003633 518 FLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSFAYSY 597 (806)
Q Consensus 518 ~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~~~~~ 597 (806)
++.+++|| .|+++++..|+....+
T Consensus 96 ------------------------------------------------------~~~~~~dl--~g~~i~~~~~~~~~~~ 119 (218)
T cd00134 96 ------------------------------------------------------PIKSVKDL--KGKKVAVQKGSTAEKY 119 (218)
T ss_pred ------------------------------------------------------CCCChHHh--CCCEEEEEcCchHHHH
Confidence 45589999 7889999988877777
Q ss_pred hhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCC-CCeEEeCCc--cccCCceeeecCCCC-c
Q 003633 598 LSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQ-TDFGIIGQP--FTRSGWGFAFQRDSP-L 673 (806)
Q Consensus 598 l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~-~~l~~~~~~--~~~~~~~~~~~k~sp-l 673 (806)
+.+... ...+..+.+.++.+++|.+ |++|+++.+.....+...+. +++.++... .....++++..++++ +
T Consensus 120 ~~~~~~--~~~~~~~~~~~~~~~~l~~----g~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l 193 (218)
T cd00134 120 LKKALP--EAKVVSYDDNAEALAALEN----GRADAVIVDEIALAALLKKHPPELKIVGPSIDLEPLGFGVAVGKDNKEL 193 (218)
T ss_pred HHHhCC--cccEEEeCCHHHHHHHHHc----CCccEEEeccHHHHHHHHhcCCCcEEeccccCCCccceEEEEcCCCHHH
Confidence 754332 3467778889999999999 99999999999888877665 667776653 444556777777775 9
Q ss_pred hHHHHHHHHhhhccchhHHHHHhhc
Q 003633 674 AVGMSTAILKLSENGMLQKLHEKWF 698 (806)
Q Consensus 674 ~~~~n~~il~l~e~G~~~~i~~kw~ 698 (806)
...++++|.++.++|.++.|.+||+
T Consensus 194 ~~~~~~~l~~~~~~g~~~~i~~~~~ 218 (218)
T cd00134 194 LDAVNKALKELRADGELKKISKKWF 218 (218)
T ss_pred HHHHHHHHHHHHhCccHHHHHHhhC
Confidence 9999999999999999999999996
No 98
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.67 E-value=3e-15 Score=150.17 Aligned_cols=215 Identities=25% Similarity=0.494 Sum_probs=180.5
Q ss_pred CeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEE
Q 003633 357 PLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIA 436 (806)
Q Consensus 357 ~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~ 436 (806)
+|+||+. +.++||...+. ++...|+++|+++.+.+.+|.+ +++.+. +|..++.++.+|++|++++...
T Consensus 1 ~l~v~~~--~~~~p~~~~~~-~g~~~G~~~~~~~~~~~~~g~~--~~~~~~-------~~~~~~~~l~~g~~D~~~~~~~ 68 (219)
T smart00062 1 TLRVGTN--GDYPPFSFADE-DGELTGFDVDLAKAIAKELGLK--VEFVEV-------SFDNLLTALKSGKIDVVAAGMT 68 (219)
T ss_pred CEEEEec--CCCCCcEEECC-CCCcccchHHHHHHHHHHhCCe--EEEEec-------cHHHHHHHHHCCcccEEecccc
Confidence 4789986 47888888763 6789999999999999999966 666663 5899999999999999998776
Q ss_pred EecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchhh
Q 003633 437 IVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIAT 516 (806)
Q Consensus 437 it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 516 (806)
.+.+|...+.++.|+...+.+++++...
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------------------------------- 96 (219)
T smart00062 69 ITPERAKQVDFSDPYYKSGQVILVRKDS---------------------------------------------------- 96 (219)
T ss_pred CCHHHHhheeeccceeeceeEEEEecCC----------------------------------------------------
Confidence 6778888899999999999999887655
Q ss_pred HHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCchhHH
Q 003633 517 MFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSFAYS 596 (806)
Q Consensus 517 ~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~~~~ 596 (806)
++++++|| .|+++++..|+....
T Consensus 97 -------------------------------------------------------~~~~~~dL--~g~~i~~~~g~~~~~ 119 (219)
T smart00062 97 -------------------------------------------------------PIKSLEDL--KGKKVAVVAGTTGEE 119 (219)
T ss_pred -------------------------------------------------------CCCChHHh--CCCEEEEecCccHHH
Confidence 57899999 688999999888777
Q ss_pred HhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCC--CCeEEeCCcccc-CCceeeecCCCC-
Q 003633 597 YLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQ--TDFGIIGQPFTR-SGWGFAFQRDSP- 672 (806)
Q Consensus 597 ~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~--~~l~~~~~~~~~-~~~~~~~~k~sp- 672 (806)
++... .....+..+.+..+.+.+|.. |++|+++...+.+.+...+. +++.++...... ..++++++++++
T Consensus 120 ~~~~~--~~~~~~~~~~~~~~~~~~l~~----g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 (219)
T smart00062 120 LLKKL--YPEAKIVSYDSQAEALAALKA----GRADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAVRKGDPE 193 (219)
T ss_pred HHHHh--CCCceEEEcCCHHHHHHHhhc----CcccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEEECCCHH
Confidence 77443 233466778888999999999 99999999999888877764 567777665555 788999999997
Q ss_pred chHHHHHHHHhhhccchhHHHHHhhc
Q 003633 673 LAVGMSTAILKLSENGMLQKLHEKWF 698 (806)
Q Consensus 673 l~~~~n~~il~l~e~G~~~~i~~kw~ 698 (806)
+.+.++++|.++.++|.+++|.++|+
T Consensus 194 ~~~~~~~~l~~~~~~~~~~~i~~~~~ 219 (219)
T smart00062 194 LLDKINKALKELKADGTLKKIYEKWF 219 (219)
T ss_pred HHHHHHHHHHHHHhCchHHHHHhccC
Confidence 99999999999999999999999995
No 99
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.67 E-value=1e-15 Score=193.46 Aligned_cols=221 Identities=13% Similarity=0.135 Sum_probs=184.4
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
+.++||||+.. +++|+.+..+.+|++.||.+|+++.+++.+|.+ +++++. .+|++++.++.+|++|++.+
T Consensus 54 ~~~~l~vgv~~--~~~p~~~~~~~~g~~~G~~~D~l~~ia~~lG~~--~e~v~~------~~~~~~l~~l~~g~iDl~~~ 123 (1197)
T PRK09959 54 SKKNLVIAVHK--SQTATLLHTDSQQRVRGINADYLNLLKRALNIK--LTLREY------ADHQKAMDALEEGEVDIVLS 123 (1197)
T ss_pred hCCeEEEEecC--CCCCCceeecCCCccceecHHHHHHHHHhcCCc--eEEEeC------CCHHHHHHHHHcCCCcEecC
Confidence 45789999875 555544443347899999999999999999966 888874 38999999999999999998
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
.++.+++|.+.++||.||+.+..+++++...
T Consensus 124 ~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~------------------------------------------------- 154 (1197)
T PRK09959 124 HLVASPPLNDDIAATKPLIITFPALVTTLHD------------------------------------------------- 154 (1197)
T ss_pred ccccccccccchhcCCCccCCCceEEEeCCC-------------------------------------------------
Confidence 8999999999999999999999999997754
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCch
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSF 593 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~ 593 (806)
.+++++++ .++++++..|+.
T Consensus 155 ----------------------------------------------------------~~~~~~~l--~~~~i~~~~g~~ 174 (1197)
T PRK09959 155 ----------------------------------------------------------SMRPLTSS--KPVNIARVANYP 174 (1197)
T ss_pred ----------------------------------------------------------CCCCcccc--cCeEEEEeCCCC
Confidence 45677788 678899999998
Q ss_pred hHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCC--CeEEeCCc-cccCCceeeecCC
Q 003633 594 AYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQT--DFGIIGQP-FTRSGWGFAFQRD 670 (806)
Q Consensus 594 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~--~l~~~~~~-~~~~~~~~~~~k~ 670 (806)
..+++++. ++..+++.+++..+++++|.. |++||++++...+.++++++. ++.+++.. ......+++++|+
T Consensus 175 ~~~~~~~~--~p~~~i~~~~s~~~al~av~~----G~~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 248 (1197)
T PRK09959 175 PDEVIHQS--FPKATIISFTNLYQALASVSA----GQNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKE 248 (1197)
T ss_pred CHHHHHHh--CCCCEEEeCCCHHHHHHHHHc----CCCCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCC
Confidence 88888654 466789999999999999999 999999999999999888742 35554322 2234466889999
Q ss_pred CC-chHHHHHHHHhhhccchhHHHHHhhcCC
Q 003633 671 SP-LAVGMSTAILKLSENGMLQKLHEKWFCK 700 (806)
Q Consensus 671 sp-l~~~~n~~il~l~e~G~~~~i~~kw~~~ 700 (806)
.| |...+|++|..+.+.|.. +|.+||+..
T Consensus 249 ~~~L~~~lnkal~~i~~~~~~-~i~~kW~~~ 278 (1197)
T PRK09959 249 SVILNEVLNRFVDALTNEVRY-EVSQNWLDT 278 (1197)
T ss_pred cHHHHHHHHHHHHhCCHHHHH-HHHHhccCC
Confidence 99 999999999999999988 999999964
No 100
>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=99.64 E-value=6.3e-15 Score=159.96 Aligned_cols=230 Identities=11% Similarity=0.061 Sum_probs=176.8
Q ss_pred cccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC-cccchHHHHHHHHHhCC
Q 003633 4 EVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD-YGRNGISALSNMLEKNM 82 (806)
Q Consensus 4 ~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~g 82 (806)
+++++.++|+|+.+++++.++. .|++||+.+++..++.++++++...+.+++++++.+++ ||+...+.+.+.+++.|
T Consensus 84 ~~~~~~~ip~v~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~i~~~~~~~g~~~~~~~~~~~~~~G 161 (341)
T cd06341 84 PYLAGAGIPVIGGAGTSAWELT--SPNSFPFSGGTPASLTTWGDFAKDQGGTRAVALVTALSAAVSAAAALLARSLAAAG 161 (341)
T ss_pred HHHhhcCCceecCCCCCchhhc--CCCeEEecCCCcchhHHHHHHHHHcCCcEEEEEEeCCcHHHHHHHHHHHHHHHHcC
Confidence 5678899999999888777664 57889999999999999999998889999999987766 99999999999999999
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCChh
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQT 162 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~~ 162 (806)
+++.....++.. ..|++..+.++++.++|+|++......+..++++++++|+..+. +........ ... ..
T Consensus 162 ~~v~~~~~~~~~--~~d~~~~~~~i~~~~pdaV~~~~~~~~a~~~~~~~~~~G~~~~~---~~~~~~~~~-~~~----~~ 231 (341)
T cd06341 162 VSVAGIVVITAT--APDPTPQAQQAAAAGADAIITVLDAAVCASVLKAVRAAGLTPKV---VLSGTCYDP-ALL----AA 231 (341)
T ss_pred CccccccccCCC--CCCHHHHHHHHHhcCCCEEEEecChHHHHHHHHHHHHcCCCCCE---EEecCCCCH-HHH----Hh
Confidence 998876666643 56899999999999999999998888999999999999986532 222221111 111 33
Q ss_pred hhhhccceEEEEEeCC---CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCC
Q 003633 163 SLRILQGVVGLRQHTP---DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELP 239 (806)
Q Consensus 163 ~~~~~~gv~~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~ 239 (806)
..+..+|++....+.| ++|..+.|.+.+++... . ....++.++..+||+++++++|++++..
T Consensus 232 ~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~~~-~-~~~~~~~~~~~~yda~~~~~~a~~~ag~------------- 296 (341)
T cd06341 232 PGPALAGVYIAVFYRPFESGTPAVALYLAAMARYAP-Q-LDPPEQGFALIGYIAADLFLRGLSGAGG------------- 296 (341)
T ss_pred cCcccCceEEEeeeccccCCCHHHHHHHHHHHHhCC-C-CCCCcchHHHHHHHHHHHHHHHHHhcCC-------------
Confidence 4467899888877665 46777888776554321 1 1125788999999999999999999411
Q ss_pred CCcccccccccccccCchHH-HHHHHHccccCCcee
Q 003633 240 DSKATRVQLEQLKVFDGGTF-LLRKLLQTNFTGLSG 274 (806)
Q Consensus 240 ~~~~~~~~~~~~~~~~~g~~-l~~~l~~~~f~G~tG 274 (806)
-.+++. ++++|++++.....|
T Consensus 297 --------------~~~~~~~v~~al~~~~~~~~~g 318 (341)
T cd06341 297 --------------CPTRASQFLRALRAVTDYDAGG 318 (341)
T ss_pred --------------CCChHHHHHHHhhcCCCCCCCC
Confidence 012566 999999987655444
No 101
>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=99.64 E-value=6.3e-15 Score=157.80 Aligned_cols=201 Identities=17% Similarity=0.207 Sum_probs=157.7
Q ss_pred hcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCC
Q 003633 3 SEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNM 82 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g 82 (806)
.+++.+.+||+|+++++++.++ ...+|+||+.+++..++.++++++...||++|++++.++++|+...+.+.+.+++.|
T Consensus 83 ~~~~~~~~vP~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~vail~~~~~~~~~~~~~~~~~~~~~G 161 (312)
T cd06333 83 APVAEEAKTPMISLAPAAAIVE-PKRKWVFKTPQNDRLMAEAILADMKKRGVKTVAFIGFSDAYGESGLKELKALAPKYG 161 (312)
T ss_pred HHHHHhcCCCEEEccCCccccC-CCCCcEEEcCCCcHHHHHHHHHHHHHcCCCEEEEEecCcHHHHHHHHHHHHHHHHcC
Confidence 4567788999999887665444 446899999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCChh
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQT 162 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~~ 162 (806)
+++.....++.. ..++...+.++++.++|+|++......+..+++++++.|+..+ ++.++.... .+.. ..
T Consensus 162 ~~v~~~~~~~~~--~~d~~~~~~~l~~~~pdaIi~~~~~~~~~~~~~~l~~~g~~~p---~~~~~~~~~-~~~~----~~ 231 (312)
T cd06333 162 IEVVADERYGRT--DTSVTAQLLKIRAARPDAVLIWGSGTPAALPAKNLRERGYKGP---IYQTHGVAS-PDFL----RL 231 (312)
T ss_pred CEEEEEEeeCCC--CcCHHHHHHHHHhCCCCEEEEecCCcHHHHHHHHHHHcCCCCC---EEeecCcCc-HHHH----HH
Confidence 999877677643 4578889999988899999999888888889999999997532 334443332 1111 33
Q ss_pred hhhhccceEEEEE------eCC----CChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHH
Q 003633 163 SLRILQGVVGLRQ------HTP----DSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVA 218 (806)
Q Consensus 163 ~~~~~~gv~~~~~------~~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA 218 (806)
..+..+|++.... ..| .++..++|.++|+++|+. ..++.+++++|||+++++
T Consensus 232 ~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~f~~~~~~~~g~----~~~~~~~~~~Yda~~~~~ 293 (312)
T cd06333 232 AGKAAEGAILPAGPVLVADQLPDSDPQKKVALDFVKAYEAKYGA----GSVSTFGGHAYDALLLLA 293 (312)
T ss_pred hhHhhcCcEeecccceeeeeCCCCCcchHHHHHHHHHHHHHhCC----CCCCchhHHHHHHHHHHH
Confidence 4456788765432 223 245789999999999862 137789999999999999
No 102
>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=99.64 E-value=7.4e-15 Score=149.96 Aligned_cols=211 Identities=13% Similarity=0.155 Sum_probs=157.8
Q ss_pred CeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEE
Q 003633 357 PLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIA 436 (806)
Q Consensus 357 ~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~ 436 (806)
.|||++.. .|+||.+. ...||++||++++++++|.++++++.++ .+..++..+.+|++|++++
T Consensus 1 ~l~v~~~~--~~~P~~~~-----~~~G~~~el~~~i~~~~g~~i~~~~~~~-------~~~~~~~~l~~g~~Di~~~--- 63 (232)
T TIGR03871 1 ALRVCADP--NNLPFSNE-----KGEGFENKIAQLLADDLGLPLEYTWFPQ-------RRGFVRNTLNAGRCDVVIG--- 63 (232)
T ss_pred CeEEEeCC--CCCCccCC-----CCCchHHHHHHHHHHHcCCceEEEecCc-------chhhHHHHHhcCCccEEEe---
Confidence 37888764 78888763 2369999999999999998855555442 2444567899999999876
Q ss_pred EecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchhh
Q 003633 437 IVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIAT 516 (806)
Q Consensus 437 it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 516 (806)
+.+|.+.++||.||+..+.+++++....
T Consensus 64 -~~~r~~~~~fs~py~~~~~~lv~~~~~~--------------------------------------------------- 91 (232)
T TIGR03871 64 -VPAGYEMVLTTRPYYRSTYVFVTRKDSL--------------------------------------------------- 91 (232)
T ss_pred -ccCccccccccCCcEeeeEEEEEeCCCc---------------------------------------------------
Confidence 4678888999999999999999987741
Q ss_pred HHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCchhHH
Q 003633 517 MFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSFAYS 596 (806)
Q Consensus 517 ~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~~~~ 596 (806)
..+++++|+...+.+||+..|+...+
T Consensus 92 ------------------------------------------------------~~~~~~~d~~l~g~~V~v~~g~~~~~ 117 (232)
T TIGR03871 92 ------------------------------------------------------LDVKSLDDPRLKKLRIGVFAGTPPAH 117 (232)
T ss_pred ------------------------------------------------------ccccchhhhhhcCCeEEEEcCChHHH
Confidence 25778888222688999999999888
Q ss_pred Hhhhhcccccccce---------eCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCC-CCeEEeCCc------ccc
Q 003633 597 YLSDSLRIQKSRLI---------SLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQ-TDFGIIGQP------FTR 660 (806)
Q Consensus 597 ~l~~~~~~~~~~~~---------~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~-~~l~~~~~~------~~~ 660 (806)
++.+. +.. ..+. ...+..+.+.+|.. |++||++.+...+.+++++. .++.+.... ...
T Consensus 118 ~l~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~----G~~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (232)
T TIGR03871 118 WLARH-GLV-ENVVGYSLFGDYRPESPPGRMVEDLAA----GEIDVAIVWGPIAGYFAKQAGPPLVVVPLLPEDGGIPFD 191 (232)
T ss_pred HHHhc-Ccc-cccccccccccccccCCHHHHHHHHHc----CCcCEEEeccHHHHHHHHhCCCCceeeccccCCCCCCcc
Confidence 88542 211 1221 13367899999999 99999999988888777653 234443321 123
Q ss_pred CCceeeecCCCC-chHHHHHHHHhhhccchhHHHHHhhc
Q 003633 661 SGWGFAFQRDSP-LAVGMSTAILKLSENGMLQKLHEKWF 698 (806)
Q Consensus 661 ~~~~~~~~k~sp-l~~~~n~~il~l~e~G~~~~i~~kw~ 698 (806)
.+++++++++++ |+..||++|.++. |.+++|.+||-
T Consensus 192 ~~~~~~~~~~~~~l~~~~n~~l~~~~--~~~~~i~~kyg 228 (232)
T TIGR03871 192 YRIAMGVRKGDKAWKDELNAVLDRRQ--AEIDAILREYG 228 (232)
T ss_pred ceEEEEEecCCHHHHHHHHHHHHHHH--HHHHHHHHHcC
Confidence 357888999877 9999999999985 47999999993
No 103
>cd06268 PBP1_ABC_transporter_LIVBP_like Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC
Probab=99.60 E-value=2.8e-14 Score=151.30 Aligned_cols=202 Identities=28% Similarity=0.339 Sum_probs=163.9
Q ss_pred HhcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcC-CeEEEEEEEcCCcccchHHHHHHHHHh
Q 003633 2 ISEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYG-WKEVIAIYVDDDYGRNGISALSNMLEK 80 (806)
Q Consensus 2 v~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~-W~~v~ii~~d~~~g~~~~~~l~~~l~~ 80 (806)
+.+++.+.+||+|++.++++.+++..+|++|++.|++..++.++++++...+ |++|++++.++++|....+.+.+++++
T Consensus 82 ~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~~~~~~~~~~~~~~~ 161 (298)
T cd06268 82 AAPVAEEAGVPLISPGATSPALTGKGNPYVFRTAPSDAQQAAALADYLAEKGKVKKVAIIYDDYAYGRGLAAAFREALKK 161 (298)
T ss_pred hHHHHHhCCCcEEccCCCCcccccCCCceEEEcccCcHHHHHHHHHHHHHhcCCCEEEEEEcCCchhHHHHHHHHHHHHH
Confidence 4567888999999998888777654579999999999999999999998888 999999999999999999999999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMN 160 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~ 160 (806)
.|+++.....++.. ..++...+.++++.++++|++.+.+..+..+++++++.|+ +..|+..+........
T Consensus 162 ~g~~i~~~~~~~~~--~~~~~~~~~~l~~~~~~~vi~~~~~~~~~~~~~~~~~~g~---~~~~~~~~~~~~~~~~----- 231 (298)
T cd06268 162 LGGEVVAEETYPPG--ATDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQAREAGL---KVPIVGGDGAAAPALL----- 231 (298)
T ss_pred cCCEEEEEeccCCC--CccHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCC---CCcEEecCccCCHHHH-----
Confidence 99999877666643 4578899999999999999999988999999999999987 4567877765443221
Q ss_pred hhhhhhccceEEEEEeCCCC--hhhHHHH-HHHhhhccCCCCCCCCccchhhhhhHHHHHH
Q 003633 161 QTSLRILQGVVGLRQHTPDS--IPKKAFL-SRWSGMQQKGLVSAGLNTYGLYAYDTVWAVA 218 (806)
Q Consensus 161 ~~~~~~~~gv~~~~~~~~~~--~~~~~f~-~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA 218 (806)
....+..+|+++..++.+.. +....|. ++|++.++ ..++.++..+||++++++
T Consensus 232 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~y~~~~~~~ 287 (298)
T cd06268 232 ELAGDAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAKYG-----RPPDSYAAAAYDAVRLLA 287 (298)
T ss_pred HhhhHhhCCcEEeccCCCCCCChhhhHHHHHHHHHHhC-----CCcccchHHHHHHHHHHc
Confidence 22345678988887766533 3344554 67777664 367889999999999998
No 104
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=99.52 E-value=7e-13 Score=137.96 Aligned_cols=228 Identities=17% Similarity=0.164 Sum_probs=160.8
Q ss_pred CCceEEecCCcHHHHHHHHHH-HHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHh
Q 003633 28 FPYFIRSTQSDSQQMAAMADL-IDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNN 106 (806)
Q Consensus 28 ~p~f~Rt~psd~~q~~ai~~l-l~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ 106 (806)
.|++|=|.....+|...++++ +++||-+++.+|-+|.-|++.....+++.+++.|++|....-+|.+ .+|+..++.+
T Consensus 107 S~nviYtGa~PNQ~~~pl~~~~~~~~G~~r~~lvGSdYv~pre~Nri~r~~l~~~GgevvgE~Y~plg--~td~~~ii~~ 184 (363)
T PF13433_consen 107 SPNVIYTGAAPNQQLLPLIDYLLENFGAKRFYLVGSDYVYPRESNRIIRDLLEARGGEVVGERYLPLG--ATDFDPIIAE 184 (363)
T ss_dssp -TTEEE-S--GGGTHHHHHHHHHHHS--SEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE-S---HHHHHHHHHH
T ss_pred CCceEEcCCCchhhHHHHHHHHHhccCCceEEEecCCccchHHHHHHHHHHHHHcCCEEEEEEEecCC--chhHHHHHHH
Confidence 578888888888888989987 6889999999999999999999999999999999999988888854 6899999999
Q ss_pred cCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCChhhhhhccceEEEEEeCC--CChhhH
Q 003633 107 SKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQTSLRILQGVVGLRQHTP--DSIPKK 184 (806)
Q Consensus 107 ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~--~~~~~~ 184 (806)
|++.+||+|+-....+....|+++.++.|+... -.-|++-..... +. .....+...|.++..++.. ++|..+
T Consensus 185 I~~~~Pd~V~stlvG~s~~aF~r~~~~aG~~~~-~~Pi~S~~~~E~-E~----~~~g~~~~~Gh~~~~~YFqsidtp~N~ 258 (363)
T PF13433_consen 185 IKAAKPDFVFSTLVGDSNVAFYRAYAAAGLDPE-RIPIASLSTSEA-EL----AAMGAEAAAGHYTSAPYFQSIDTPENQ 258 (363)
T ss_dssp HHHHT-SEEEEE--TTCHHHHHHHHHHHH-SSS----EEESS--HH-HH----TTS-HHHHTT-EEEES--TT-SSHHHH
T ss_pred HHhhCCCEEEEeCcCCcHHHHHHHHHHcCCCcc-cCeEEEEecCHH-HH----hhcChhhcCCcEEeehhhhhCCcHHHH
Confidence 999999999999999999999999999998643 344554433221 11 1223467889999887654 789999
Q ss_pred HHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCCCcccccccccccccCchHHHHHHH
Q 003633 185 AFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELPDSKATRVQLEQLKVFDGGTFLLRKL 264 (806)
Q Consensus 185 ~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~l~~~l 264 (806)
+|+++|+++|+. +...+...--+|-+|+++|+|++++.+ .+.++++++|
T Consensus 259 ~Fv~~~~~~~g~---~~v~s~~~eaaY~~v~l~a~Av~~ags----------------------------~d~~~vr~al 307 (363)
T PF13433_consen 259 AFVARFRARYGD---DRVTSDPMEAAYFQVHLWAQAVEKAGS----------------------------DDPEAVREAL 307 (363)
T ss_dssp HHHHHHHTTS-T---T----HHHHHHHHHHHHHHHHHHHHTS------------------------------HHHHHHHH
T ss_pred HHHHHHHHHhCC---CCCCCcHHHHHHHHHHHHHHHHHHhCC----------------------------CCHHHHHHHh
Confidence 999999999972 224555666799999999999999522 1388999999
Q ss_pred HccccCCceeeEEEecCCCeecccEEEEEe
Q 003633 265 LQTNFTGLSGQVQFNQDRNIVSRGYDVINI 294 (806)
Q Consensus 265 ~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~ 294 (806)
....|+...|.+++|+..+-....-.|-++
T Consensus 308 ~g~~~~aP~G~v~id~~n~H~~l~~rIg~~ 337 (363)
T PF13433_consen 308 AGQSFDAPQGRVRIDPDNHHTWLPPRIGRV 337 (363)
T ss_dssp TT--EEETTEEEEE-TTTSBEEB--EEEEE
T ss_pred cCCeecCCCcceEEcCCCCeecccceEEEE
Confidence 999999999999999744323333334444
No 105
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.41 E-value=1.1e-12 Score=121.38 Aligned_cols=123 Identities=33% Similarity=0.470 Sum_probs=107.0
Q ss_pred CCCChhHhhhC-CCceeEEeCchhHHHhhhhcccc------c---ccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhH
Q 003633 572 SVKGIESLITN-DWPIGYQVGSFAYSYLSDSLRIQ------K---SRLISLGSPEDYERALRQGPRNGGVAAIVDELPYV 641 (806)
Q Consensus 572 ~i~s~~dL~~~-~~~ig~~~gs~~~~~l~~~~~~~------~---~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~ 641 (806)
||++++||..+ +.+||++.|+..+.++.+..... . ..++.+++..+++.+|.. |+ ||++.+.+.+
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 57899999533 36899999999999986543210 0 256778899999999999 89 9999999999
Q ss_pred HHHhhCCCCeEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccchhHHHHHhhcC
Q 003633 642 QLFLSNQTDFGIIGQPFTRSGWGFAFQRDSPLAVGMSTAILKLSENGMLQKLHEKWFC 699 (806)
Q Consensus 642 ~~~~~~~~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~il~l~e~G~~~~i~~kw~~ 699 (806)
.++.++.|++.++++.+...++|++++|+++|++.+|.+|.++.++|.++++.+||++
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=99.30 E-value=2.1e-11 Score=123.00 Aligned_cols=223 Identities=16% Similarity=0.139 Sum_probs=178.9
Q ss_pred CCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 354 NARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 354 ~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
..+.|||++.++| ..+.. +++...|+++++.+++++.||.+ .++.+.. +.+.++.+|.+|++|++++
T Consensus 21 ~rGvLrV~tinsp----~sy~~-~~~~p~G~eYelak~Fa~yLgV~--Lki~~~~------n~dqLf~aL~ng~~DL~Aa 87 (473)
T COG4623 21 ARGVLRVSTINSP----LSYFE-DKGGPTGLEYELAKAFADYLGVK--LKIIPAD------NIDQLFDALDNGNADLAAA 87 (473)
T ss_pred hcCeEEEEeecCc----cceec-cCCCccchhHHHHHHHHHHhCCe--EEEEecC------CHHHHHHHHhCCCcceecc
Confidence 4578999998753 33333 24566799999999999999955 7777653 5799999999999999999
Q ss_pred eEEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccc
Q 003633 434 DIAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQ 513 (806)
Q Consensus 434 ~~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 513 (806)
++....+|.+.+...+.|+...+.++.++..
T Consensus 88 gl~~~~~~l~~~~~gP~y~svs~qlVyRkG~------------------------------------------------- 118 (473)
T COG4623 88 GLLYNSERLKNFQPGPTYYSVSQQLVYRKGQ------------------------------------------------- 118 (473)
T ss_pred cccCChhHhcccCCCCceecccHHHHhhcCC-------------------------------------------------
Confidence 9999999999999999999999998888776
Q ss_pred hhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCch
Q 003633 514 IATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSF 593 (806)
Q Consensus 514 ~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~ 593 (806)
...+++++| .+..|-+..|+.
T Consensus 119 ---------------------------------------------------------~Rp~~l~~L--~g~~i~v~~gs~ 139 (473)
T COG4623 119 ---------------------------------------------------------YRPRSLGQL--KGRQITVAKGSA 139 (473)
T ss_pred ---------------------------------------------------------CCCCCHHHc--cCceeeccCCcH
Confidence 356789999 677788889987
Q ss_pred hHHHhhhhcc-ccccccee---CCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeCCccccCCceeeecC
Q 003633 594 AYSYLSDSLR-IQKSRLIS---LGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIGQPFTRSGWGFAFQR 669 (806)
Q Consensus 594 ~~~~l~~~~~-~~~~~~~~---~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k 669 (806)
..+.++.... .-+..+.. -...+|.++.+.. |.++..+.+...+..+.+-++++.+.-+.....++++.+|+
T Consensus 140 ~~~~l~~lk~~kyP~l~~k~d~~~~~~dLle~v~~----Gkldytiads~~is~~q~i~P~laVafd~tde~~v~Wy~~~ 215 (473)
T COG4623 140 HVEDLKLLKETKYPELIWKVDDKLGVEDLLEMVAE----GKLDYTIADSVEISLFQRVHPELAVAFDLTDEQPVAWYLPR 215 (473)
T ss_pred HHHHHHHHHHhhcchhhhhhcccccHHHHHHHHhc----CCcceeeeccHHHHHHHHhCccceeeeecccccCceeeccC
Confidence 6665532111 11112222 2367899999999 99999999999999888888887777666667899999999
Q ss_pred CCC--chHHHHHHHHhhhccchhHHHHHhhcCCC
Q 003633 670 DSP--LAVGMSTAILKLSENGMLQKLHEKWFCKE 701 (806)
Q Consensus 670 ~sp--l~~~~n~~il~l~e~G~~~~i~~kw~~~~ 701 (806)
+.- |...+...+..+.|.|.++++++||++..
T Consensus 216 ~dd~tL~a~ll~F~~~~~e~g~larleeky~gH~ 249 (473)
T COG4623 216 DDDSTLSAALLDFLNEAKEDGLLARLEEKYLGHG 249 (473)
T ss_pred CchHHHHHHHHHHHHHhhcchHHHHHHHHHhccc
Confidence 654 99999999999999999999999999754
No 107
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=98.93 E-value=9.7e-09 Score=106.33 Aligned_cols=198 Identities=16% Similarity=0.130 Sum_probs=141.0
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
++|+||+.. .+.|+ .+.+...++.+.+.+++|.+ ++++.. .+|+.++..+.+|++|+++.+.
T Consensus 32 ~~l~vg~~~--~~~~~--------~~~~~~~~l~~~l~~~~g~~--v~~~~~------~~~~~~~~~l~~g~~Di~~~~~ 93 (254)
T TIGR01098 32 KELNFGILP--GENAS--------NLTRRWEPLADYLEKKLGIK--VQLFVA------TDYSAVIEAMRFGRVDIAWFGP 93 (254)
T ss_pred CceEEEECC--CCCHH--------HHHHHHHHHHHHHHHHhCCc--EEEEeC------CCHHHHHHHHHcCCccEEEECc
Confidence 579999864 33332 23345678999999999977 555543 3799999999999999998655
Q ss_pred EEec---CccceeEeccccccc------ceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCC
Q 003633 436 AIVT---NRTKIVDFSQPYIST------GLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDF 506 (806)
Q Consensus 436 ~it~---~r~~~vdft~p~~~~------~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~ 506 (806)
.... +|....+|+.|+... ...+++++..
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~------------------------------------------ 131 (254)
T TIGR01098 94 SSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADS------------------------------------------ 131 (254)
T ss_pred HHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCC------------------------------------------
Confidence 4332 466667888876543 2456665443
Q ss_pred CCCCccchhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCce
Q 003633 507 RGPPRRQIATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPI 586 (806)
Q Consensus 507 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~i 586 (806)
+|++++|| .|++|
T Consensus 132 -----------------------------------------------------------------~i~~~~dL--~gk~I 144 (254)
T TIGR01098 132 -----------------------------------------------------------------PIKSLKDL--KGKTF 144 (254)
T ss_pred -----------------------------------------------------------------CCCChHHh--cCCEE
Confidence 68899999 68899
Q ss_pred eEEe-Cchh-----HHHhhhhccccc----ccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCC----CeE
Q 003633 587 GYQV-GSFA-----YSYLSDSLRIQK----SRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQT----DFG 652 (806)
Q Consensus 587 g~~~-gs~~-----~~~l~~~~~~~~----~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~----~l~ 652 (806)
++.. ++.. ..++.+..+... ..+....+..+.+++|.. |++||.+.+.+.+..+..+.. ++.
T Consensus 145 ~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~----G~~Da~~~~~~~~~~~~~~~~~~~~~~~ 220 (254)
T TIGR01098 145 AFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVAN----GKVDAATNNSSAIGRLKKRGPSDMKKVR 220 (254)
T ss_pred EeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHc----CCCCeEEecHHHHHHHHHhCccchhheE
Confidence 9874 3322 233434333221 345555667889999999 999999999988877666542 478
Q ss_pred EeCCccccCCceeeecCC-CC-chHHHHHHHHhh
Q 003633 653 IIGQPFTRSGWGFAFQRD-SP-LAVGMSTAILKL 684 (806)
Q Consensus 653 ~~~~~~~~~~~~~~~~k~-sp-l~~~~n~~il~l 684 (806)
++.+.....+++++++|+ .+ +++.+|++|+.+
T Consensus 221 ~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 221 VIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred EEEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 887766667789999999 55 999999999864
No 108
>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=98.88 E-value=2.8e-08 Score=102.87 Aligned_cols=145 Identities=25% Similarity=0.351 Sum_probs=116.4
Q ss_pred hcccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC-CcccchHHHHHHHHHhC
Q 003633 3 SEVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD-DYGRNGISALSNMLEKN 81 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~-~~g~~~~~~l~~~l~~~ 81 (806)
...+...++|+|++.++.+... .+++++++.+++..+++++++++.+++|+++++++.+. .++....+.+.+.+++.
T Consensus 75 ~~~~~~~~ip~v~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~ 152 (269)
T cd01391 75 VELAAAAGIPVVSLDATAPDLT--GYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKA 152 (269)
T ss_pred HHHHHHcCCcEEEecCCCCccC--CCceEEEEcCCcHHHHHHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHHhc
Confidence 4566788999999988776655 57899999999999999999999999999999999877 67788889999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCC-CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccc
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPL-GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSA 151 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~-~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~ 151 (806)
|.++......+.. .+.++......++.. ++++|++++. ..+..+++++.+.|+..+++.|+..+....
T Consensus 153 ~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~i~~~~~-~~a~~~~~~~~~~g~~~~~~~ii~~~~~~~ 221 (269)
T cd01391 153 GIEVVAIEYGDLD-TEKGFQALLQLLKAAPKPDAIFACND-EMAAGALKAAREAGLTPGDISIIGFDGSPA 221 (269)
T ss_pred CcEEEeccccCCC-ccccHHHHHHHHhcCCCCCEEEEcCc-hHHHHHHHHHHHcCCCCCCCEEEecccccc
Confidence 9777644433322 225677777777766 7888888777 888999999999998755677777775543
No 109
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.84 E-value=1.6e-08 Score=105.88 Aligned_cols=164 Identities=20% Similarity=0.266 Sum_probs=131.9
Q ss_pred CHHHHHHHHHcCcccEEEeeEEEecCccceeEeccc--ccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHH
Q 003633 415 SYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQP--YISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIA 492 (806)
Q Consensus 415 s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p--~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~ 492 (806)
+|.+++..|.+|++|+++++.+++.+|.+.++|+.| |....+++++|...
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 689999999999999999998889999888999988 77778888887665
Q ss_pred HHhhhhccccCCCCCCCCccchhhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCC
Q 003633 493 VVIWILEHRVNDDFRGPPRRQIATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTS 572 (806)
Q Consensus 493 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~ 572 (806)
+
T Consensus 104 -------------------------------------------------------------------------------~ 104 (287)
T PRK00489 104 -------------------------------------------------------------------------------D 104 (287)
T ss_pred -------------------------------------------------------------------------------C
Confidence 6
Q ss_pred CCChhHhhhCCCceeEEeCchhHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeE
Q 003633 573 VKGIESLITNDWPIGYQVGSFAYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFG 652 (806)
Q Consensus 573 i~s~~dL~~~~~~ig~~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~ 652 (806)
|++++|| .|+++++..+.....++.+ .+. ..+++.+.+..|. ++.. |..||+++.......+..+ ++.
T Consensus 105 i~sl~DL--~Gk~ia~~~~~~~~~~l~~-~gi-~~~iv~~~gs~ea--a~~~----G~aDaivd~~~~~~~l~~~--~L~ 172 (287)
T PRK00489 105 WQGVEDL--AGKRIATSYPNLTRRYLAE-KGI-DAEVVELSGAVEV--APRL----GLADAIVDVVSTGTTLRAN--GLK 172 (287)
T ss_pred CCChHHh--CCCEEEEcCcHHHHHHHHH-cCC-ceEEEECCCchhh--hhcC----CcccEEEeeHHHHHHHHHC--CCE
Confidence 8889999 7889999888888888854 333 2455666655553 5555 8999999888777766654 566
Q ss_pred EeCCccccCCceeeecC--CCC-chHHHHHHHHhhhccchhHHHHHhhcCC
Q 003633 653 IIGQPFTRSGWGFAFQR--DSP-LAVGMSTAILKLSENGMLQKLHEKWFCK 700 (806)
Q Consensus 653 ~~~~~~~~~~~~~~~~k--~sp-l~~~~n~~il~l~e~G~~~~i~~kw~~~ 700 (806)
++ +.+.....+++.+| .+| ..+.++..+.++ .|.+..+.+||+..
T Consensus 173 ~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g~l~a~~~k~~~~ 220 (287)
T PRK00489 173 IV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QGVLRARESKYLMM 220 (287)
T ss_pred EE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HHHHHhhceEEEEE
Confidence 66 46566778999999 677 888999999999 59999999999973
No 110
>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=98.71 E-value=9.1e-09 Score=79.09 Aligned_cols=47 Identities=30% Similarity=0.637 Sum_probs=37.0
Q ss_pred CCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCC-----CCCCHHHHHHHHHc
Q 003633 377 DSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGL-----SNPSYDGLVKMVAN 425 (806)
Q Consensus 377 ~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~-----~n~s~~~l~~~l~~ 425 (806)
++.+++|||+||+++|++.+||+ |++....+++ +|++|+|++++|.+
T Consensus 14 g~~~~eGyciDll~~la~~l~F~--y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 14 GNDRYEGYCIDLLEELAEELNFT--YEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp GGGGEESHHHHHHHHHHHHHT-E--EEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred CCccEEEEHHHHHHHHHHHcCCe--EEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 46699999999999999999999 6655544433 67899999999874
No 111
>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=98.15 E-value=2.6e-05 Score=82.27 Aligned_cols=116 Identities=18% Similarity=0.186 Sum_probs=76.2
Q ss_pred CCCChhHhhhCCCceeEEe-CchhHH-----Hhhhhcccccc---cceeCC-CHhHHHHHHhcCCCCCCeEEEEeCchhH
Q 003633 572 SVKGIESLITNDWPIGYQV-GSFAYS-----YLSDSLRIQKS---RLISLG-SPEDYERALRQGPRNGGVAAIVDELPYV 641 (806)
Q Consensus 572 ~i~s~~dL~~~~~~ig~~~-gs~~~~-----~l~~~~~~~~~---~~~~~~-~~~~~~~~l~~~~~~g~~~a~i~~~~~~ 641 (806)
+|++++|| .|++|++.. ++.... .+.+..+.... +.+.+. +..+.+.+|.. |++||.+.+...+
T Consensus 126 ~i~sl~DL--~Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~----G~vDa~~~~~~~~ 199 (288)
T TIGR03431 126 PIKSLEDL--KGKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVAN----GTVDAATTNDENL 199 (288)
T ss_pred CCCcHHHh--CCCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHc----CCCCeEeccHHHH
Confidence 78999999 688899863 443221 22122232211 233444 57889999999 9999999988877
Q ss_pred HHHhhCC-----CCeEEeCCccccCCceeeecCCC-C-chHHHHHHHHhhhccchhHHH
Q 003633 642 QLFLSNQ-----TDFGIIGQPFTRSGWGFAFQRDS-P-LAVGMSTAILKLSENGMLQKL 693 (806)
Q Consensus 642 ~~~~~~~-----~~l~~~~~~~~~~~~~~~~~k~s-p-l~~~~n~~il~l~e~G~~~~i 693 (806)
..+..+. .++.++...-.....+++++++- + +.+.++++|.++.+++..+++
T Consensus 200 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~~~ 258 (288)
T TIGR03431 200 DRMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDKACFE 258 (288)
T ss_pred HHHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcHHHHH
Confidence 7666532 12444432212234678889984 3 999999999999999666543
No 112
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=97.86 E-value=0.00043 Score=78.66 Aligned_cols=228 Identities=15% Similarity=0.189 Sum_probs=117.9
Q ss_pred CCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEe
Q 003633 10 KVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKL 89 (806)
Q Consensus 10 ~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~ 89 (806)
.||++.....+.. ....--|.|-..| ...++.+|+.+..-|+++..||+.++++|+...++|.+.+++.|..+.-..
T Consensus 304 ~vp~LaLN~~~~~-~~~~~l~~f~Lsp--EdEA~q~A~~a~~~g~~~alvl~p~~~~g~R~~~aF~~~W~~~gg~~~~~~ 380 (536)
T PF04348_consen 304 PVPVLALNQPDNS-QAPPNLYQFGLSP--EDEARQAAQKAFQDGYRRALVLAPQNAWGQRMAEAFNQQWQALGGQVAEVS 380 (536)
T ss_dssp T-EEEES---TT-----TTEEE----H--HHHHHHHHHHHHHTT--S-EEEEESSHHHHHHHHHHHHHHHHHHSS--EEE
T ss_pred CCceeeccCCCcc-cCccceEEEeCCc--HHHHHHHHHHHHhcCCCCEEEEcCCChHHHHHHHHHHHHHHHcCCCceeeE
Confidence 7899988666544 2111125555555 556899999999999999999999999999999999999999888876555
Q ss_pred ccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCcccccccccccCChhhhhhccc
Q 003633 90 PLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLSATLESFSKMNQTSLRILQG 169 (806)
Q Consensus 90 ~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~~~~~~~~~~~~~~~~~~~g 169 (806)
.+. ...++...++.-...+.|.|++.+.+.+++.|--...-. ...+-.-+.|+-..+... +......++|
T Consensus 381 ~~~---~~~~~~~~i~~r~r~d~D~ifl~a~~~~ar~ikP~l~~~--~a~~lPvyatS~~~~g~~-----~~~~~~dL~g 450 (536)
T PF04348_consen 381 YYG---SPADLQAAIQPRRRQDIDAIFLVANPEQARLIKPQLDFH--FAGDLPVYATSRSYSGSP-----NPSQDRDLNG 450 (536)
T ss_dssp EES---STTHHHHHHHHS--TT--EEEE---HHHHHHHHHHHTT---T-TT-EEEE-GGG--HHT------HHHHHHTTT
T ss_pred ecC---CHHHHHHHHhhcCCCCCCEEEEeCCHHHHHHHhhhcccc--cCCCCCEEEeccccCCCC-----CcchhhhhcC
Confidence 554 245888888866667899999999999888876654321 112223344433221111 2334566889
Q ss_pred eEEEEE-e--CCCChhhHHHHHHHhhhccCCCCCCCCccchhhhhhHHHHHHHHHHHHHhhcCccccCCCCCCCCccccc
Q 003633 170 VVGLRQ-H--TPDSIPKKAFLSRWSGMQQKGLVSAGLNTYGLYAYDTVWAVARSIDKFINEHNITFSASHELPDSKATRV 246 (806)
Q Consensus 170 v~~~~~-~--~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aYDAv~~lA~Al~~~~~~~~~~~~~~~~l~~~~~~~~ 246 (806)
+..... + .+..+..+.+...|.+... ...-.-+..|||..++.+ +..
T Consensus 451 v~f~d~Pwll~~~~~~~~~~~~~~~~~~~------~~~RL~AlG~DA~~L~~~-l~~----------------------- 500 (536)
T PF04348_consen 451 VRFSDMPWLLDPNSPLRQQLAALWPNASN------SLQRLYALGIDAYRLAPR-LPQ----------------------- 500 (536)
T ss_dssp -EEEE-GGGG---SHHHHHHH-HHTTT-H------HHHHHHHHHHHHHHHHHT-HHH-----------------------
T ss_pred CEEeccccccCCCchHHHHHHhhccCCcc------HHHHHHHHHHHHHHHHHH-HHH-----------------------
Confidence 877653 2 2334444444444433211 111122345666443321 111
Q ss_pred ccccccccCchHHHHHHHHccccCCceeeEEEecCCCeecccEEEEEee
Q 003633 247 QLEQLKVFDGGTFLLRKLLQTNFTGLSGQVQFNQDRNIVSRGYDVINID 295 (806)
Q Consensus 247 ~~~~~~~~~~g~~l~~~l~~~~f~G~tG~i~Fd~~G~~~~~~~~I~~~~ 295 (806)
+.......+.|+||.+++|++|. +.-...-.++.
T Consensus 501 --------------l~~~~~~~~~G~TG~L~~~~~g~-i~R~l~wa~f~ 534 (536)
T PF04348_consen 501 --------------LRQFPGYRLDGLTGQLSLDEDGR-IERQLSWAQFR 534 (536)
T ss_dssp --------------HHHSTT--EEETTEEEEE-TT-B-EEEE-EEEEEE
T ss_pred --------------HhhCCCCcccCCceeEEECCCCe-EEEeecceeec
Confidence 22233456899999999999885 44444444443
No 113
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.28 E-value=0.0025 Score=68.09 Aligned_cols=70 Identities=23% Similarity=0.285 Sum_probs=48.8
Q ss_pred CCCChhHhhhCCCceeEEeCchhHHHhhh---hcccccccc-eeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhC
Q 003633 572 SVKGIESLITNDWPIGYQVGSFAYSYLSD---SLRIQKSRL-ISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSN 647 (806)
Q Consensus 572 ~i~s~~dL~~~~~~ig~~~gs~~~~~l~~---~~~~~~~~~-~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~ 647 (806)
+|++++|| .|++|++..|+....++.+ +.+.+...+ ..+.+..+...+|.. |++||++...++......+
T Consensus 120 ~i~s~~dL--~Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~----G~vDa~~~~ep~~~~~~~~ 193 (314)
T PRK11553 120 PIKTVADL--KGHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQ----GNVDAWAIWDPYYSAALLQ 193 (314)
T ss_pred CCCCHHHh--CCCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHc----CCCCEEEEcCcHHHHHHhc
Confidence 68899999 6888999888766655433 223322222 234466678899999 9999999888877665554
No 114
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=97.17 E-value=0.002 Score=66.08 Aligned_cols=121 Identities=14% Similarity=0.193 Sum_probs=76.6
Q ss_pred CCCCChhHhhhCCCceeEEeCchhH-----HHhh-hhccccc---ccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhH
Q 003633 571 TSVKGIESLITNDWPIGYQVGSFAY-----SYLS-DSLRIQK---SRLISLGSPEDYERALRQGPRNGGVAAIVDELPYV 641 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs~~~-----~~l~-~~~~~~~---~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~ 641 (806)
.+|++++|| .|+++++...+... .+.. ++.++.. ...+...+.+..+.+|.+ |.+||.+......
T Consensus 95 s~i~~l~dL--~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~----G~~Da~~~~~~~~ 168 (243)
T PF12974_consen 95 SPITSLADL--KGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLN----GKADAAAIPSDAF 168 (243)
T ss_dssp SS--SHHHH--GGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHT----TSSSEEEEEHHHH
T ss_pred CCCCChhhc--CCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHc----CCccEEEEechhH
Confidence 479999999 79999997644322 2222 2334332 133345677889999999 9999999888777
Q ss_pred HHHhhCC----CCeEEeCCccccCCceeeecCCCC--chHHHHHHHHhhhccchhHHHHHhh
Q 003633 642 QLFLSNQ----TDFGIIGQPFTRSGWGFAFQRDSP--LAVGMSTAILKLSENGMLQKLHEKW 697 (806)
Q Consensus 642 ~~~~~~~----~~l~~~~~~~~~~~~~~~~~k~sp--l~~~~n~~il~l~e~G~~~~i~~kw 697 (806)
+.+.... .++.++...-......++..++-| .++.+-.+++.+..+-.-.++.+.+
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 7666542 347777654444556777777766 8999999999999865555555554
No 115
>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=97.10 E-value=0.0047 Score=63.68 Aligned_cols=135 Identities=8% Similarity=0.050 Sum_probs=94.2
Q ss_pred cccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhC
Q 003633 4 EVANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKN 81 (806)
Q Consensus 4 ~i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~ 81 (806)
+.+...++|+|.+....+. .+++++...++...+..+++.+...|-++|+++..+++ ++....+.+.+.+++.
T Consensus 73 ~~l~~~~ip~v~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~ 147 (264)
T cd01537 73 KLARKAGIPVVLVDRDIPD-----GDRVPSVGSDNEQAGYLAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALKEA 147 (264)
T ss_pred HHhhhcCCCEEEeccCCCC-----CcccceEecCcHHHHHHHHHHHHHhcCCcEEEEECCCCCCcHHHHHHHHHHHHHHc
Confidence 4556789999998776543 25667788888889999999988889999999987655 5667789999999988
Q ss_pred C-cEEEEEeccCCCCChhHHHHHHHhcCCCC--CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 82 M-AKVSYKLPLPVQFNQHDITVLLNNSKPLG--PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 82 g-~~i~~~~~~~~~~~~~~~~~~l~~ik~~~--~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
| ..+.... ....+.++....+.++.+.+ +++++.. +...+..+++++.+.|+..++.+-|++
T Consensus 148 ~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~~~~~~g~~i~~~i~i~~ 212 (264)
T cd01537 148 GPIEIVLVQ--EGDWDAEKGYQAAEELLTAHPDPTAIFAA-NDDMALGALRALREAGLRVPDDISVIG 212 (264)
T ss_pred CCcChhhhc--cCCCCHHHHHHHHHHHHhcCCCCCEEEEc-CcHHHHHHHHHHHHhCCCCCCCeEEEe
Confidence 7 4433221 22234556667777776666 4444433 445677788999999975434444443
No 116
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=96.99 E-value=0.01 Score=61.34 Aligned_cols=134 Identities=7% Similarity=0.053 Sum_probs=88.8
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC--cccchHHHHHHHHHh
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD--YGRNGISALSNMLEK 80 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~--~g~~~~~~l~~~l~~ 80 (806)
.+...++|+|......+. .+.+..+.+++...+..+++.+... |-+++++++.+++ ++....+.+.+.+++
T Consensus 75 ~l~~~~ip~V~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~ 149 (267)
T cd01536 75 KANAAGIPVVTVDSDIDG-----GNRLAYVGTDNYEAGRLAGEYLAKLLGGKGKVAIIEGPPGSSNAQERVKGFRDALKE 149 (267)
T ss_pred HHHHCCCcEEEecCCCCc-----cceeEEEecCHHHHHHHHHHHHHHHhCCCceEEEEEcccccchHHHHHHHHHHHHHh
Confidence 345678999998665432 1334556677777788888887666 8999999986553 677788999999999
Q ss_pred C-CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeE-EEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 81 N-MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRV-YVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 81 ~-g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rv-ivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
. |.++.... ....+..+..+.+.++.+..+++ .+++++...+..+++++++.|+. ++...+..
T Consensus 150 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~d~~a~~~~~~l~~~g~~-~~i~ivg~ 214 (267)
T cd01536 150 YPDIEIVAVQ--DGNWDREKALQAMEDLLQANPDIDAIFAANDSMALGAVAALKAAGRK-GDVKIVGV 214 (267)
T ss_pred CCCcEEEEEe--cCCCcHHHHHHHHHHHHHhCCCccEEEEecCCchHHHHHHHHhcCCC-CCceEEec
Confidence 8 46654332 22233445666777765555443 34444557778899999999975 34333333
No 117
>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=96.81 E-value=0.0095 Score=61.38 Aligned_cols=135 Identities=11% Similarity=0.040 Sum_probs=89.6
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCC
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNM 82 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g 82 (806)
.+...+||+|.+....+. +.+....+++...+..+++.+...|.+++++++.+.. ++....+.+.+.+++.+
T Consensus 73 ~~~~~~ipvv~~~~~~~~------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~ 146 (264)
T cd06267 73 ELAALGIPVVLVDRPLDG------LGVDSVGIDNRAGAYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAG 146 (264)
T ss_pred HHHHcCCCEEEecccccC------CCCCEEeeccHHHHHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHHcC
Confidence 356789999998665432 3445566777777888888877779999999986544 66777888999999888
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCCC--CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPLG--PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~~--~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
..+.....+....+.++....+.++.+.. +++|+ +.+...+..+++++++.|+..++.+.|++
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~~~~a~~~~~al~~~g~~~~~~i~i~~ 211 (264)
T cd06267 147 IPLDEELIVEGDFSEESGYEAARELLASGERPTAIF-AANDLMAIGALRALRELGLRVPEDVSVVG 211 (264)
T ss_pred CCCCcceEEecccchhhHHHHHHHHHhcCCCCcEEE-EcCcHHHHHHHHHHHHhCCCCCCceEEEe
Confidence 54322222222233455666677666555 55555 34556677888889998875434444444
No 118
>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=96.50 E-value=0.031 Score=59.28 Aligned_cols=70 Identities=16% Similarity=0.175 Sum_probs=48.5
Q ss_pred CCCCChhHhhhCCCceeEEeCchhHHHhhh---hccccccc--ceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHh
Q 003633 571 TSVKGIESLITNDWPIGYQVGSFAYSYLSD---SLRIQKSR--LISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFL 645 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs~~~~~l~~---~~~~~~~~--~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~ 645 (806)
..|++++|| .|++||+..++....++.. ..++.... ++.. ...+...+|.. |++||++...++.....
T Consensus 90 s~I~s~~DL--kGK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~----G~vDa~~~~~p~~~~~~ 162 (300)
T TIGR01729 90 SGIEKPEDL--KGKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQR----GDIDAAYVWPPALSELL 162 (300)
T ss_pred CCCCChhHc--CCCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHc----CCcCEEEEecHHHHHHH
Confidence 379999999 7999999887755543322 23333222 2323 46688999999 99999999888876555
Q ss_pred hC
Q 003633 646 SN 647 (806)
Q Consensus 646 ~~ 647 (806)
..
T Consensus 163 ~~ 164 (300)
T TIGR01729 163 KS 164 (300)
T ss_pred hc
Confidence 44
No 119
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=96.10 E-value=0.012 Score=60.66 Aligned_cols=74 Identities=20% Similarity=0.236 Sum_probs=49.6
Q ss_pred CCCCChhHhhh-----CCCceeEE-eCchhHHHhh---hhccccc---ccceeCCCHhHHHHHHhcCCCCCCeEEEEeCc
Q 003633 571 TSVKGIESLIT-----NDWPIGYQ-VGSFAYSYLS---DSLRIQK---SRLISLGSPEDYERALRQGPRNGGVAAIVDEL 638 (806)
Q Consensus 571 ~~i~s~~dL~~-----~~~~ig~~-~gs~~~~~l~---~~~~~~~---~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~ 638 (806)
+.+++++||.+ .|++|++. .|+.....+. ++.+++. -+++.++. .+...+|.. |++|+++...
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 47899999955 57789984 5554433332 3444444 35555555 899999999 9999999999
Q ss_pred hhHHHHhhCCC
Q 003633 639 PYVQLFLSNQT 649 (806)
Q Consensus 639 ~~~~~~~~~~~ 649 (806)
|+......+.-
T Consensus 179 P~~~~~~~~g~ 189 (252)
T PF13379_consen 179 PFASQAEAKGI 189 (252)
T ss_dssp THHHHHHHTTS
T ss_pred CHHHHHHhccC
Confidence 99888776653
No 120
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=95.92 E-value=0.091 Score=54.26 Aligned_cols=131 Identities=11% Similarity=0.136 Sum_probs=83.3
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEc---CCcccchHHHHHHHHHhC
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVD---DDYGRNGISALSNMLEKN 81 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d---~~~g~~~~~~l~~~l~~~ 81 (806)
.+.+.++|+|......+ ..++++ ..++...+..+++.+...|.++++++..+ ++++....+.+.+.+++.
T Consensus 74 ~~~~~~ipvV~~~~~~~----~~~~~v---~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~ 146 (266)
T cd06282 74 LLDAERVPYVLAYNDPQ----PGRPSV---SVDNRAAARDVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAMRAA 146 (266)
T ss_pred HHhhCCCCEEEEeccCC----CCCCEE---eeCcHHHHHHHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHHHHc
Confidence 45677899988743321 223443 45667778888888877899999999742 346667789999999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHh-cCCC-CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEE
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNN-SKPL-GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLA 145 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~-ik~~-~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~ 145 (806)
|+.+......+ .+..+....+.+ +++. .+++|+. ++...+..+++++++.|+..++.+-++
T Consensus 147 ~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~~p~di~v~ 209 (266)
T cd06282 147 GLAPLPPVEIP--FNTAALPSALLALLTAHPAPTAIFC-SNDLLALAVIRALRRLGLRVPDDLSVV 209 (266)
T ss_pred CCCCCccccCC--CcHHHHHHHHHHHhcCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 87643222122 222233334444 3332 4565554 566778889999999997544444333
No 121
>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=95.85 E-value=0.04 Score=58.71 Aligned_cols=68 Identities=18% Similarity=0.168 Sum_probs=49.9
Q ss_pred CCChhHhhhCCCceeEEeCchhHHHhhh---hccccc--ccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhC
Q 003633 573 VKGIESLITNDWPIGYQVGSFAYSYLSD---SLRIQK--SRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSN 647 (806)
Q Consensus 573 i~s~~dL~~~~~~ig~~~gs~~~~~l~~---~~~~~~--~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~ 647 (806)
|++++|| .|++||+..|+....++.+ +.+++. -+++.. ++.+...++.+ |.+||.+...|+......+
T Consensus 98 i~svaDL--KGKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~-~~~d~~aAl~~----G~VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 98 GKSLADL--KGQKVNLVELSVSHYLLARALESVGLSEKDVKVVNT-SDADIVAAFIT----KDVTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred CCCHHHc--CCCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeC-ChHHHHHHHhc----CCCcEEEEcCchHHHHHhC
Confidence 8999999 7999999999876655543 223332 334444 45678899999 9999999988887655544
No 122
>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=95.81 E-value=0.083 Score=54.90 Aligned_cols=124 Identities=13% Similarity=0.079 Sum_probs=82.9
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEc--CCcccchHHHHHHHHHh
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVD--DDYGRNGISALSNMLEK 80 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d--~~~g~~~~~~l~~~l~~ 80 (806)
.+...++|+|.+....+ . +.+.+..+++...+..+++.+... |-++++++..+ ...+....+.+.+++++
T Consensus 80 ~~~~~~iPvv~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~g~~~a~~~ 153 (272)
T cd06300 80 EACEAGIPVVSFDGTVT---T---PCAYNVNEDQAEFGKQGAEWLVKELGGKGNVLVVRGLAGHPVDEDRYAGAKEVLKE 153 (272)
T ss_pred HHHHCCCeEEEEecCCC---C---CceeEecCCHHHHHHHHHHHHHHHcCCCceEEEEECCCCCcchHHHHHHHHHHHHH
Confidence 34567999999754321 1 345667888888888888887655 88999999743 23455667889999998
Q ss_pred CC-cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEE-ecCcchHHHHHHHHHHcCCc
Q 003633 81 NM-AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVV-HVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 81 ~g-~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl-~~~~~~~~~i~~~a~~~gm~ 137 (806)
.+ +.+... .....+.++....+.++.+..+++-.+ +.+.. +..+++++++.|+.
T Consensus 154 ~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~d~-A~g~~~al~~~g~~ 209 (272)
T cd06300 154 YPGIKIVGE--VYGDWDQAVAQKAVADFLASNPDVDGIWTQGGD-AVGAVQAFEQAGRD 209 (272)
T ss_pred CCCcEEEee--cCCCCCHHHHHHHHHHHHHhCCCcCEEEecCCC-cHHHHHHHHHcCCC
Confidence 87 776532 222233445566677765555443333 33344 88999999999973
No 123
>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=95.75 E-value=0.089 Score=54.47 Aligned_cols=134 Identities=13% Similarity=0.121 Sum_probs=83.8
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEc---CCcccchHHHHHHHHHhC
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVD---DDYGRNGISALSNMLEKN 81 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d---~~~g~~~~~~l~~~l~~~ 81 (806)
.+.+.++|+|......+ ....+| ...++...+..+++.+...|.++|++|... +.++......|.+++++.
T Consensus 73 ~l~~~~iPvv~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~ 146 (268)
T cd06273 73 LLARRGVPYVATWNYSP---DSPYPC---VGFDNREAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALAEA 146 (268)
T ss_pred HHHhCCCCEEEEcCCCC---CCCCCE---EEeChHHHHHHHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHHHHHHc
Confidence 34567899998754322 123344 345677778888888776799999999743 234667788999999998
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEE
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLA 145 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~ 145 (806)
++.+.....+....+.++....+.++.+ ..+++|+. ++...+..+++++++.|+..++.+-+.
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~~~~a~~~~~~l~~~g~~~p~~i~vi 211 (268)
T cd06273 147 GLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVIC-GNDVLALGALYEARRLGLSVPEDLSIV 211 (268)
T ss_pred CCCCCHHHeeeCCCcHHHHHHHHHHHHcCCCCCCEEEE-cChHHHHHHHHHHHHcCCCCCCceEEE
Confidence 8654322122212222333344555433 34666654 566778889999999997644444333
No 124
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=95.50 E-value=0.25 Score=53.81 Aligned_cols=175 Identities=10% Similarity=0.042 Sum_probs=97.6
Q ss_pred CCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEE
Q 003633 9 LKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYK 88 (806)
Q Consensus 9 ~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~ 88 (806)
..+|++....++-.=...+ -..|-..|.|. ++..|+-+-.-|-|...++...+++|+..+++|.+..++.|...+..
T Consensus 341 ~~i~vLALN~~~n~r~~~~-~cyfaLSPEDE--a~~AA~~l~~qG~R~plvlvPr~~lG~Rv~~AF~~~Wq~~gg~~v~~ 417 (604)
T COG3107 341 QPIPVLALNQPENSRNPAQ-LCYFALSPEDE--ARDAANHLWDQGKRNPLVLVPRNDLGDRVANAFNQEWQKLGGGTVLQ 417 (604)
T ss_pred CCCceeeecCCccccCccc-ceeeecChhHH--HHHHHHHHHHccccCceEEecchHHHHHHHHHHHHHHHHhcCCchhH
Confidence 4566665543332111122 23355666655 68888999999999999999999999999999999999988854444
Q ss_pred eccCCC----------------CChhHHHHHH----HhcCCCC-CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 89 LPLPVQ----------------FNQHDITVLL----NNSKPLG-PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 89 ~~~~~~----------------~~~~~~~~~l----~~ik~~~-~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
+.|-.. ....+....+ .-+.... .|.|++...++++..|--...-.+... .-.-++++
T Consensus 418 ~~fg~~~~l~~~i~~~a~ir~~~~p~~~~~~~g~~~~p~~~~d~iDaVyivAtp~el~~IKP~ia~~~~~~-~~p~yaSS 496 (604)
T COG3107 418 QKFGSTSELRQGINDGAGIRLTGLPADLTTTNGLQTPPLDDQDTIDAVYIVATPSELALIKPMIAMANGSD-SPPLYASS 496 (604)
T ss_pred hhcCcHHHHHhhcccccceeecCCccchhcccCCCCCCcccccccceEEEEecchhHhHHhhHHHhhcCCC-Ccceeeec
Confidence 333210 0001111000 1222333 788888888887776654333222111 11233333
Q ss_pred cccccccccccCChhhhhhccceEEE-EE--eCCCChhhHHHHHHHhh
Q 003633 148 WLSATLESFSKMNQTSLRILQGVVGL-RQ--HTPDSIPKKAFLSRWSG 192 (806)
Q Consensus 148 ~~~~~~~~~~~~~~~~~~~~~gv~~~-~~--~~~~~~~~~~f~~~~~~ 192 (806)
-.... .. .++....++|+..- .| ..+..|.++....+|..
T Consensus 497 r~~~g--T~---~P~~~~~m~GiqysdiP~l~~~~~p~~qq~a~~~p~ 539 (604)
T COG3107 497 RSSQG--TN---GPDFRLEMEGIQYSDIPWLAQPNPPLMQQAAAAWPN 539 (604)
T ss_pred ccccc--CC---CccHHHhccCccccCCchhcCCCchHHHHHHHhcCC
Confidence 22211 00 13344557776432 12 23566777777777765
No 125
>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=95.14 E-value=0.2 Score=52.23 Aligned_cols=125 Identities=16% Similarity=0.088 Sum_probs=83.1
Q ss_pred cccCCCcEEecccCCCCcc----cCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC-cccchHHHHHHHH
Q 003633 6 ANGLKVPLVSFAATDPTLS----ALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD-YGRNGISALSNML 78 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls----~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~-~g~~~~~~l~~~l 78 (806)
+...++|+|.++.+++... ....+....+..++...+..+++++... |.+++++++.+.+ ++....+.+.+.+
T Consensus 77 ~~~~~iPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~r~~g~~~~~ 156 (281)
T cd06325 77 NATKDIPIVFTAVTDPVGAGLVKSLEKPGGNVTGVSDLVPVETQLELLKKLLPDAKTVGVLYNPSEANSVVQVKELKKAA 156 (281)
T ss_pred HcCCCCCEEEEecCCccccccccccccCCCceeCeecccchHHHHHHHHHHCCCCcEEEEEeCCCCccHHHHHHHHHHHH
Confidence 3467899998875544221 1111222223445666678888887765 9999999986543 6777789999999
Q ss_pred HhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCC
Q 003633 79 EKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQM 136 (806)
Q Consensus 79 ~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm 136 (806)
++.|+++.... . .+.+++...++++.+. +++|++ .+...+..+++++.+.|+
T Consensus 157 ~~~g~~~~~~~-~---~~~~~~~~~~~~~~~~-~dai~~-~~d~~a~~~~~~~~~~~~ 208 (281)
T cd06325 157 AKLGIEVVEAT-V---SSSNDVQQAAQSLAGK-VDAIYV-PTDNTVASAMEAVVKVAN 208 (281)
T ss_pred HhCCCEEEEEe-c---CCHHHHHHHHHHhccc-CCEEEE-cCchhHHhHHHHHHHHHH
Confidence 99999876532 1 2345677777777643 576665 445577788888888775
No 126
>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=94.94 E-value=0.45 Score=49.43 Aligned_cols=125 Identities=10% Similarity=0.032 Sum_probs=77.5
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC--cccchHHHHHHHHHh
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD--YGRNGISALSNMLEK 80 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~--~g~~~~~~l~~~l~~ 80 (806)
.+.+.++|+|.+....+ ....++ +..++...++.+++.+... |.++++++....+ ......+.+.+++++
T Consensus 77 ~~~~~~iPvV~~~~~~~---~~~~~~---V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~ 150 (275)
T cd06320 77 RAKKKGIPVVNVNDKLI---PNATAF---VGTDNKANGVRGAEWIIDKLAEGGKVAIIEGKAGAFAAEQRTEGFTEAIKK 150 (275)
T ss_pred HHHHCCCeEEEECCCCC---CccceE---EecCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHHHhh
Confidence 34567999998754321 111222 3556666688888877655 8999999975333 234456889999999
Q ss_pred C-CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEE-EecCcchHHHHHHHHHHcCCc
Q 003633 81 N-MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYV-VHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 81 ~-g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rviv-l~~~~~~~~~i~~~a~~~gm~ 137 (806)
. |+++.... ....+..+....+.++.+..+++-. ++.+...+..+++++++.|+.
T Consensus 151 ~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~~~~~al~~~g~~ 207 (275)
T cd06320 151 ASGIEVVASQ--PADWDREKAYDVATTILQRNPDLKAIYCNNDTMALGVVEAVKNAGKQ 207 (275)
T ss_pred CCCcEEEEec--CCCccHHHHHHHHHHHHHhCCCccEEEECCchhHHHHHHHHHhcCCC
Confidence 8 88875432 1122333444556665444444433 344556667788989998874
No 127
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=94.89 E-value=1.1 Score=43.53 Aligned_cols=73 Identities=11% Similarity=0.131 Sum_probs=48.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++...+++.|.+|++|++++.......-...+.+ .+..+..++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~ 83 (202)
T cd08468 13 AVMPRLMARLEELAP-SVRLNLVH-------AEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEE-RDWWEDTYVVIASR 83 (202)
T ss_pred HHhHHHHHHHHhhCC-CCEEEEEE-------CChHhHHHHHHCCCccEEEecccccccCCCCEEE-EEEecCcEEEEEeC
Confidence 456678888888775 34566665 3678999999999999998643221000123333 46777788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 84 ~h 85 (202)
T cd08468 84 DH 85 (202)
T ss_pred CC
Confidence 55
No 128
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=94.82 E-value=0.91 Score=43.20 Aligned_cols=70 Identities=17% Similarity=0.225 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+..++++.+.+..+ .+++++.. .....++..|.+|++|++++.... ....++ ..++....++++++.
T Consensus 13 ~~l~~~i~~~~~~~p-~i~i~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~ 80 (197)
T cd05466 13 YLLPPLLAAFRQRYP-GVELSLVE-------GGSSELLEALLEGELDLAIVALPV---DDPGLE-SEPLFEEPLVLVVPP 80 (197)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEE-------CChHHHHHHHHcCCceEEEEcCCC---CCCcce-EeeeeccceEEEecC
Confidence 455677777777665 35566665 246789999999999999875433 222333 346667788888776
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (197)
T cd05466 81 DH 82 (197)
T ss_pred CC
Confidence 55
No 129
>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=94.78 E-value=0.13 Score=51.49 Aligned_cols=62 Identities=23% Similarity=0.264 Sum_probs=40.0
Q ss_pred CCCCChhHhhhCCCceeEEeCchhHHHhh---hhcccccccceeCC-CHhHHHHHHhcCCCCCCeEEEEeCc
Q 003633 571 TSVKGIESLITNDWPIGYQVGSFAYSYLS---DSLRIQKSRLISLG-SPEDYERALRQGPRNGGVAAIVDEL 638 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs~~~~~l~---~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~g~~~a~i~~~ 638 (806)
+.|++++|| .|++||+..++.....+. +..+++.+.+.... +..+...+|.+ |++||.+...
T Consensus 83 s~i~~~~DL--kGK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~----g~vDa~~~~~ 148 (216)
T PF09084_consen 83 SGIKSPADL--KGKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLS----GQVDAAILWY 148 (216)
T ss_dssp TS-SSGGGG--TTSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHT----TSSSEEEEEE
T ss_pred CCCCCHHHh--CCCEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhc----CCCCEEEEcc
Confidence 369999999 799999998765444332 33444444443322 35667779999 8999988333
No 130
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=94.70 E-value=0.51 Score=49.30 Aligned_cols=110 Identities=16% Similarity=0.157 Sum_probs=75.4
Q ss_pred CCCCChhHhhhCCCceeEEeCchhHHHh------hhhccccc---ccceeCCC-HhHHHHHHhcCCCCCCeEEEEeCchh
Q 003633 571 TSVKGIESLITNDWPIGYQVGSFAYSYL------SDSLRIQK---SRLISLGS-PEDYERALRQGPRNGGVAAIVDELPY 640 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs~~~~~l------~~~~~~~~---~~~~~~~~-~~~~~~~l~~~~~~g~~~a~i~~~~~ 640 (806)
++|++++|| .|+++++..-+....|+ .++.+.+. -.-+.+.. -+..+.+|.+ |.+|+.......
T Consensus 134 s~i~sl~dl--kgk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~a~~aV~n----G~vDva~~~~~~ 207 (299)
T COG3221 134 SPIKSLEDL--KGKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDAAVLAVAN----GQVDVAAVNSSA 207 (299)
T ss_pred CCcchHHHh--cCCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHHHHHHHHc----CCceEEeccHHH
Confidence 689999999 79999998644333333 22222221 11223333 6788899999 999988887766
Q ss_pred HHHHhhCC-----CCeEEeCCccccCCceeeecCCCC--chHHHHHHHHhhhc
Q 003633 641 VQLFLSNQ-----TDFGIIGQPFTRSGWGFAFQRDSP--LAVGMSTAILKLSE 686 (806)
Q Consensus 641 ~~~~~~~~-----~~l~~~~~~~~~~~~~~~~~k~sp--l~~~~n~~il~l~e 686 (806)
...+.... .++.++...-......++++++-| +++.+..+++.+.+
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 247777665555566788888876 99999999999986
No 131
>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=94.67 E-value=0.35 Score=51.83 Aligned_cols=130 Identities=13% Similarity=0.058 Sum_probs=80.5
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC--C-cccchHHHHHHHHHhCC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD--D-YGRNGISALSNMLEKNM 82 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~--~-~g~~~~~~l~~~l~~~g 82 (806)
+...++|+|......+ ...+++ ...++..-+..+++.+...|.++++++..+. . .+....+.+.+++++.|
T Consensus 134 l~~~~iPvV~~~~~~~---~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~~R~~Gf~~~l~~~g 207 (329)
T TIGR01481 134 FSRSPVPVVLAGTVDK---ENELPS---VNIDYKQATKEAVGELIAKGHKSIAFVGGPLSDSINGEDRLEGYKEALNKAG 207 (329)
T ss_pred HHhcCCCEEEEecCCC---CCCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEecCcccccchHHHHHHHHHHHHHcC
Confidence 4456899987654321 122333 3455555567777877778999999996432 2 34667888999999998
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcE
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYV 142 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~ 142 (806)
+.+.-........+.++-...+.++.+..+++|+ +.+...+..+++++++.|+..++-+
T Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~~ll~~~p~ai~-~~~d~~A~g~~~al~~~g~~vP~dv 266 (329)
T TIGR01481 208 IQFGEDLVCEGKYSYDAGYKAFAELKGSLPTAVF-VASDEMAAGILNAAMDAGIKVPEDL 266 (329)
T ss_pred CCCCcceEEecCCChHHHHHHHHHHhCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCCce
Confidence 7643111111112222333445555555677655 4566788899999999998654433
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=94.63 E-value=0.33 Score=50.09 Aligned_cols=135 Identities=13% Similarity=0.118 Sum_probs=82.9
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC---cccchHHHHHHHHHhCC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD---YGRNGISALSNMLEKNM 82 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~---~g~~~~~~l~~~l~~~g 82 (806)
+...++|+|.+....+ ....++ ..+++...+..+++.+...|-++++++..+.. .+....+.+.+.+++.|
T Consensus 74 l~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~gf~~~~~~~~ 147 (268)
T cd06298 74 FKRSPTPVVLAGSVDE---DNELPS---VNIDYKKAAFEATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEALSEAN 147 (268)
T ss_pred HhcCCCCEEEEccccC---CCCCCE---EEECcHHHHHHHHHHHHHcCCceEEEEeCCcccccchhHHHHHHHHHHHHcC
Confidence 3456899998854322 122333 45566666778888877779999999985433 56677889999999988
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCCC-CeEEEEecCcchHHHHHHHHHHcCCccCCc-EEEEcC
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPLG-PRVYVVHVSPDPGLRIFTTAQKLQMMTNNY-VWLATD 147 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~~-~rvivl~~~~~~~~~i~~~a~~~gm~~~~~-~wi~t~ 147 (806)
+.+..........+.......+.++.+.. +++|+. ++...+..+++++++.|+..++. ..+.-|
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~vp~di~vvg~d 213 (268)
T cd06298 148 IEFDESLIFEGDYTYESGYELAEELLEDGKPTAAFV-TDDELAIGILNAAQDAGLKVPEDFEIIGFN 213 (268)
T ss_pred CCCCHHHeEeCCCChhHHHHHHHHHhcCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCccceEEEeec
Confidence 65421111111112222334445554443 566664 55566788999999999864433 344444
No 133
>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=94.52 E-value=0.55 Score=48.41 Aligned_cols=123 Identities=12% Similarity=0.073 Sum_probs=74.2
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEc--CCcccchHHHHHHHHHhC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVD--DDYGRNGISALSNMLEKN 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d--~~~g~~~~~~l~~~l~~~ 81 (806)
+...++|+|......+ ..+.+-.+..++...+..+++.+... |-+++++++.+ ..++....+.+.++++++
T Consensus 76 l~~~~ipvv~~~~~~~-----~~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~l~~~ 150 (268)
T cd06323 76 ANEAGIPVFTIDREAN-----GGEVVSQIASDNVAGGKMAAEYLVKLLGGKGKVVELQGIPGASAARERGKGFHEVVDKY 150 (268)
T ss_pred HHHCCCcEEEEccCCC-----CCceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHHHHhC
Confidence 3466899999855432 11122234444455567788877666 78999999863 335666678899999984
Q ss_pred -CcEEEEEeccCCCCChhHHHHHHHhcCCCC--CeEEEEecCcchHHHHHHHHHHcCC
Q 003633 82 -MAKVSYKLPLPVQFNQHDITVLLNNSKPLG--PRVYVVHVSPDPGLRIFTTAQKLQM 136 (806)
Q Consensus 82 -g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~--~rvivl~~~~~~~~~i~~~a~~~gm 136 (806)
|+++...... ..+.++....+.++.+.. +++ +++.+...+..+++++++.|+
T Consensus 151 ~~~~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~ 205 (268)
T cd06323 151 PGLKVVASQPA--DFDRAKGLNVMENILQAHPDIKG-VFAQNDEMALGAIEALKAAGK 205 (268)
T ss_pred CCcEEEecccC--CCCHHHHHHHHHHHHHHCCCcCE-EEEcCCchHHHHHHHHHHcCC
Confidence 7775432111 122233333444443333 344 445555666778999999997
No 134
>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=94.42 E-value=0.79 Score=44.48 Aligned_cols=70 Identities=14% Similarity=0.086 Sum_probs=47.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++.+.+..+|.+|++|+++..... ....+. +.|.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~v~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~ 80 (201)
T cd08459 13 YFLPRLLAALREVAP-GVRIETVR-------LPVDELEEALESGEIDLAIGYLPD---LGAGFF-QQRLFRERYVCLVRK 80 (201)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe-------cCccCHHHHhhCCCceEEEEcCCC---Ccccce-EEEeecCceEEEEcC
Confidence 445677888887765 34566654 345788999999999999863321 122233 467788888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (201)
T cd08459 81 DH 82 (201)
T ss_pred CC
Confidence 54
No 135
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=94.40 E-value=0.38 Score=50.29 Aligned_cols=71 Identities=17% Similarity=0.194 Sum_probs=48.2
Q ss_pred CCCCChhHhhhCCCceeEEeCchhHHHhhh---hcccccccc-eeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhh
Q 003633 571 TSVKGIESLITNDWPIGYQVGSFAYSYLSD---SLRIQKSRL-ISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLS 646 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs~~~~~l~~---~~~~~~~~~-~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~ 646 (806)
.+|++++|| .|++|++..++.....+.. ..+.+...+ ....+..+...++.+ |++|+++...++......
T Consensus 91 ~~i~s~~dL--~Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~----g~vda~~~~~p~~~~~~~ 164 (288)
T TIGR01728 91 SPIRTVADL--KGKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAA----GQVDAWAIWEPWGSALVE 164 (288)
T ss_pred CCCCCHHHc--CCCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHC----CCCCEEEeccchHhHHhh
Confidence 378999999 6888998877654443322 223333222 223456788899999 899999998888766555
Q ss_pred C
Q 003633 647 N 647 (806)
Q Consensus 647 ~ 647 (806)
+
T Consensus 165 ~ 165 (288)
T TIGR01728 165 E 165 (288)
T ss_pred c
Confidence 4
No 136
>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=94.40 E-value=0.62 Score=48.36 Aligned_cols=127 Identities=9% Similarity=0.051 Sum_probs=74.9
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc------CCeEEEEEEEc--CCcccchHHHHHH
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY------GWKEVIAIYVD--DDYGRNGISALSN 76 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~------~W~~v~ii~~d--~~~g~~~~~~l~~ 76 (806)
.+.+.++|+|.+.... .. ..++..+.+++..-+..+++++... |-++++++..+ ...+....+.+.+
T Consensus 75 ~~~~~~ipvV~~~~~~---~~--~~~~~~v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~ 149 (277)
T cd06319 75 LAAQAKIPVVIADIGA---EG--GDYVSYIKSDNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTKGFKE 149 (277)
T ss_pred HHHHCCCCEEEEecCC---CC--CceEEEEeeccHHHHHHHHHHHHHHHHhhCCCCCcEEEEeccCCCccHHHHHHHHHH
Confidence 4556789999864321 11 1122334445554466677765443 67899999743 2346667889999
Q ss_pred HHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeE-EEEecCcchHHHHHHHHHHcCCc
Q 003633 77 MLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRV-YVVHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 77 ~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rv-ivl~~~~~~~~~i~~~a~~~gm~ 137 (806)
.+++.|+.+.... ...+.+.++....+.++.+..++. .|++.+...+..+++++++.|+.
T Consensus 150 ~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~al~~~g~~ 210 (277)
T cd06319 150 AMKEAGCDLAGIR-QQKDFSYQETFDYTNDLLTANPDIRAIWLQGSDRYQGALDAIATAGKT 210 (277)
T ss_pred HHHhcCCceEeec-cCCCCCHHHHHHHHHHHHHhCCCCCEEEECCCccchHHHHHHHHcCCC
Confidence 9999988654221 111223233334455554444443 34445566677899999999975
No 137
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=94.33 E-value=0.4 Score=49.55 Aligned_cols=129 Identities=13% Similarity=0.103 Sum_probs=77.1
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcc--cchHHHHHHHHHhCC
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYG--RNGISALSNMLEKNM 82 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g--~~~~~~l~~~l~~~g 82 (806)
.+...++|+|.+....+. ..+++ ...++...+..+++.+...|.++++++..+..+. ......+.+++++.|
T Consensus 75 ~~~~~~ipvv~i~~~~~~---~~~~~---V~~d~~~~g~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~ 148 (270)
T cd01545 75 LLDEAGVPYVRIAPGTPD---PDSPC---VRIDDRAAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAG 148 (270)
T ss_pred HHHhcCCCEEEEecCCCC---CCCCe---EEeccHHHHHHHHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHHHHcC
Confidence 345678999987654332 22333 2345555567778887778999999998655443 334677889998888
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCC
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNN 140 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~ 140 (806)
+.+..........+.++-...+.++.+ .++++|+ +++...+..+++++++.|...++
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~d~~a~~~~~~~~~~g~~~p~ 207 (270)
T cd01545 149 LPLDPELVAQGDFTFESGLEAAEALLALPDRPTAIF-ASNDDMAAGVLAVAHRRGLRVPD 207 (270)
T ss_pred CCCChhhEEeCCCChhhHHHHHHHHHhCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCC
Confidence 765210001111111222233444432 3456655 45667888999999999975433
No 138
>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=94.23 E-value=0.62 Score=48.28 Aligned_cols=128 Identities=12% Similarity=0.058 Sum_probs=73.8
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCc-HHHHHHHHHHHHHc--CCeEEEEEEEcCCc--ccchHHHHHHHHHh
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSD-SQQMAAMADLIDFY--GWKEVIAIYVDDDY--GRNGISALSNMLEK 80 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd-~~q~~ai~~ll~~~--~W~~v~ii~~d~~~--g~~~~~~l~~~l~~ 80 (806)
+...++|+|.+....+ ..+.++.+..+..| ...+..+++.+... |-++|+++..+.++ +....+.+.+.+++
T Consensus 77 ~~~~~iPvV~~~~~~~---~~~~~~v~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~ 153 (275)
T cd06317 77 AKQAGIPVVITNSNIS---EKGFEFIKSFTGPDDISQGERSAEAMCKALGGKGQIVVIAGQPGNGTAIERQKGFEDELAE 153 (275)
T ss_pred HHHCCCcEEEeCCCCC---CCccchhhhhccccHHHHHHHHHHHHHHHcCCCceEEEEecCCCCchHHHHHHHHHHHHHh
Confidence 4567899998754322 22345544433444 45566666665443 77899999864444 34446888999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcC-C--CCCeEEEEecCcchHHHHHHHHHHcCCc
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSK-P--LGPRVYVVHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik-~--~~~rvivl~~~~~~~~~i~~~a~~~gm~ 137 (806)
.|..+..........+.++....+.++. + .++++|+ +++...+..+++++++.|+.
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~ 212 (275)
T cd06317 154 VCPGVEVLDTQPADWDREKAQVAMEALITKFGDDIDGVY-AGDDNMARGALNAAKEAGLA 212 (275)
T ss_pred hCCCCEEEeccCCCCCHHHHHHHHHHHHHhCCCCccEEE-ECCCcHHHHHHHHHHhcCCc
Confidence 8643332222221122222222333332 2 3456666 45566788899999999975
No 139
>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=94.11 E-value=2.6 Score=40.46 Aligned_cols=70 Identities=23% Similarity=0.281 Sum_probs=47.4
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++..+++.++.+|++|+++.... .....+. ..++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~ 80 (198)
T cd08421 13 EFLPEDLASFLAAHP-DVRIDLEE-------RLSADIVRAVAEGRADLGIVAGN---VDAAGLE-TRPYRTDRLVVVVPR 80 (198)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------cCcHHHHHHHhcCCceEEEEecC---CCCCCcE-EEEeecCcEEEEeCC
Confidence 344578888887765 34566654 35688999999999999986322 2223333 457778888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (198)
T cd08421 81 DH 82 (198)
T ss_pred CC
Confidence 54
No 140
>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=94.11 E-value=0.41 Score=49.76 Aligned_cols=134 Identities=10% Similarity=0.061 Sum_probs=80.2
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~ 83 (806)
+...++|+|.+....+. ..+++ ..+++...+..+++.+...|.++++++..+.. .+....+.+.+.+++.|+
T Consensus 83 ~~~~~ipvV~~~~~~~~---~~~~~---V~~d~~~~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~ 156 (275)
T cd06295 83 LAETGLPFVVWGRPLPG---QPYCY---VGSDNVGGGRLATEHLLARGRRRIAFLGGPQDMPEGEERLEGYREALAEAGL 156 (275)
T ss_pred HHhCCCCEEEECCccCC---CCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHcCC
Confidence 34678999987553332 22333 55667777888888887889999999975433 244557889999998875
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.+..........+.+.-...+.++.+. .+++|+.. +...+..+++.+++.|+..++-+.|++
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~~~~a~g~~~~l~~~g~~ip~~i~ii~ 220 (275)
T cd06295 157 PLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFAA-SDLMALGALRALREAGRRVPEDVAVVG 220 (275)
T ss_pred CCChhhEEeccCCHHHHHHHHHHHHhCCCCCCEEEEC-CcHHHHHHHHHHHHhCCCCccceEEEe
Confidence 432211112112222223344444333 35554444 456677888999999975444444443
No 141
>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=94.03 E-value=0.51 Score=48.65 Aligned_cols=134 Identities=10% Similarity=0.090 Sum_probs=80.6
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~ 83 (806)
+.+.++|+|.+....+ ...+++ ..+++...+..+++.+...|-++++++..... .+....+.+.+.+++.|.
T Consensus 78 ~~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~ 151 (268)
T cd06271 78 LLERGFPFVTHGRTEL---GDPHPW---VDFDNEAAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGL 151 (268)
T ss_pred HHhcCCCEEEECCcCC---CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHHHHHHHhCC
Confidence 3457899998754322 123444 34566666777888877779999999974332 344567889999999887
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.+.....+....+.......+.++.+. .+++|+. .+...+..+++++++.|+..++.+-|++
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~vp~~i~iig 215 (268)
T cd06271 152 PLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIVC-SSELMALGVLAALAEAGLRPGRDVSVVG 215 (268)
T ss_pred CCCCceEEeCCCChHHHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHhCCCCCcceeEEE
Confidence 542111111112222333444444322 3555554 4556777899999999986554444443
No 142
>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=93.94 E-value=3 Score=39.76 Aligned_cols=70 Identities=17% Similarity=0.156 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++..++...+.+|++|+++... ......+ -..+.....++++++.
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 455788888888776 34566664 3567899999999999998532 2222222 2456667778888766
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (193)
T cd08442 81 GH 82 (193)
T ss_pred CC
Confidence 54
No 143
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=93.89 E-value=2.1 Score=45.28 Aligned_cols=83 Identities=12% Similarity=0.161 Sum_probs=55.2
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
+.++|++.... ..++-..++..+.+..+ .+++.+.. .+-+.++++|.+|++|+++...
T Consensus 91 g~l~i~~~~~~--------------~~~~~~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 148 (305)
T PRK11151 91 GPLHIGLIPTV--------------GPYLLPHIIPMLHQTFP-KLEMYLHE-------AQTHQLLAQLDSGKLDCAILAL 148 (305)
T ss_pred ceEEEEecchh--------------HHHHHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEec
Confidence 57888886311 12444567777777655 35566664 2568999999999999998643
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
... ...+ .+.|+....+++++++..
T Consensus 149 ~~~---~~~l-~~~~l~~~~~~~~~~~~h 173 (305)
T PRK11151 149 VKE---SEAF-IEVPLFDEPMLLAVYEDH 173 (305)
T ss_pred CCC---CCCe-EEEEeccCcEEEEecCCC
Confidence 222 1122 457888889999987665
No 144
>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=93.89 E-value=0.4 Score=49.55 Aligned_cols=134 Identities=11% Similarity=0.034 Sum_probs=82.0
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~ 84 (806)
...++|+|......+. ..++ .+.+++...+..+++.+...|-++++++..+.. ......+.+.+.+++.|+.
T Consensus 75 ~~~~ipvv~~~~~~~~---~~~~---~v~~d~~~~~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (269)
T cd06288 75 ELLSVPTVLLNCYDAD---GALP---SVVPDEEQGGYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGIP 148 (269)
T ss_pred HhcCCCEEEEecccCC---CCCC---eEEEccHHHHHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCCC
Confidence 3457898887543221 1233 356677777888888877779999999985433 2345678899999998865
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
+..........+..+....+.++.+. ++++| ++++...+..+++++++.|+..++-+.+++-
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~~l~~~g~~vp~di~v~g~ 212 (269)
T cd06288 149 FDPDLVVHGDWSADDGYEAAAALLDLDDRPTAI-FCGNDRMAMGAYQALLERGLRIPQDVSVVGF 212 (269)
T ss_pred CCHHHeEeCCCChHHHHHHHHHHHhCCCCCCEE-EEeCcHHHHHHHHHHHHcCCCCcccceEEee
Confidence 32111111112222333444554433 35665 4566677888999999999865555555553
No 145
>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=93.88 E-value=0.23 Score=53.04 Aligned_cols=61 Identities=11% Similarity=0.079 Sum_probs=39.7
Q ss_pred CCCCChhHhhhCCCceeEEeC-chhHHH---hhhhccccccc--ceeCCCHhHHHHHHhcCCCCCCeEEEEeC
Q 003633 571 TSVKGIESLITNDWPIGYQVG-SFAYSY---LSDSLRIQKSR--LISLGSPEDYERALRQGPRNGGVAAIVDE 637 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~g-s~~~~~---l~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~g~~~a~i~~ 637 (806)
.++++++|| .++++++... +..... +.+..+..... .+.+.+..+...+|.. |++|+++..
T Consensus 131 ~~i~sl~dL--~gk~v~~~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~----G~vDa~~~~ 197 (320)
T TIGR02122 131 SGIKTVADL--KGKRVAVGAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKD----GKIDAAFYT 197 (320)
T ss_pred CCCCcHHHc--CCCEEecCCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHC----CCccEEEEe
Confidence 368899999 4777777543 322221 11333433222 3566778899999999 999999987
No 146
>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=93.66 E-value=0.98 Score=46.77 Aligned_cols=132 Identities=12% Similarity=0.112 Sum_probs=82.8
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHH-cCCeEEEEEEEcC--CcccchHHHHHHHHHhCC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDF-YGWKEVIAIYVDD--DYGRNGISALSNMLEKNM 82 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~-~~W~~v~ii~~d~--~~g~~~~~~l~~~l~~~g 82 (806)
+...++|+|......+... ..+.+..+..++...+..+++.+.. -|-++++++..+. ..+....+.+.+++++.+
T Consensus 78 ~~~~~ipvV~~~~~~~~~~--~~~~~~~V~~d~~~~g~~~~~~l~~~~g~~~i~~i~g~~~~~~~~~r~~g~~~~~~~~~ 155 (271)
T cd06312 78 AVAAGIPVISFNAGDPKYK--ELGALAYVGQDEYAAGEAAGERLAELKGGKNVLCVIHEPGNVTLEDRCAGFADGLGGAG 155 (271)
T ss_pred HHHCCCeEEEeCCCCCccc--cccceEEeccChHHHHHHHHHHHHHhcCCCeEEEEecCCCCccHHHHHHHHHHHHHhcC
Confidence 3556899999854332211 1234455677888888899998877 8999999997533 335566888999999888
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEE
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLA 145 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~ 145 (806)
+.+.. +....+..+....++++.+. ++++ |++.+...+..+++.+++.|+. +.+.|+
T Consensus 156 ~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~~a-I~~~~d~~a~g~~~al~~~g~~--~di~vv 214 (271)
T cd06312 156 ITEEV---IETGADPTEVASRIAAYLRANPDVDA-VLTLGAPSAAPAAKALKQAGLK--GKVKLG 214 (271)
T ss_pred ceeeE---eecCCCHHHHHHHHHHHHHhCCCccE-EEEeCCccchHHHHHHHhcCCC--CCeEEE
Confidence 75432 11122223334444444323 3454 4444556788889999999975 334444
No 147
>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=93.64 E-value=1.9 Score=42.05 Aligned_cols=196 Identities=20% Similarity=0.210 Sum_probs=120.1
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
++||||+... + ...+-.+++..+.+..+- +++++.. ++...+++.|.+|++|+++...
T Consensus 6 ~~l~Ig~~~~--~------------~~~~l~~~l~~~~~~~P~-i~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 63 (209)
T PF03466_consen 6 GTLRIGASPS--F------------ASSLLPPLLAEFRERHPN-IRIEIRE-------GDSDELIEALRSGELDLAITFG 63 (209)
T ss_dssp EEEEEEEEHH--H------------HHHTHHHHHHHHHHHSTT-EEEEEEE-------ESHHHHHHHHHTTSSSEEEESS
T ss_pred eEEEEEEEhH--H------------HHHHHHHHHHHHHHHCCC-cEEEEEe-------ccchhhhHHHhcccccEEEEEe
Confidence 5688887631 1 124456788888887763 5566665 3678999999999999998744
Q ss_pred EEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchh
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIA 515 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 515 (806)
.. ....+. ..|+....++++++...+...
T Consensus 64 ~~---~~~~~~-~~~l~~~~~~~~~~~~~pl~~----------------------------------------------- 92 (209)
T PF03466_consen 64 PP---PPPGLE-SEPLGEEPLVLVVSPDHPLAQ----------------------------------------------- 92 (209)
T ss_dssp SS---SSTTEE-EEEEEEEEEEEEEETTSGGGT-----------------------------------------------
T ss_pred ec---cccccc-cccccceeeeeeeeccccccc-----------------------------------------------
Confidence 33 222233 457778888999887652110
Q ss_pred hHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEe-Cchh
Q 003633 516 TMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQV-GSFA 594 (806)
Q Consensus 516 ~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~-gs~~ 594 (806)
..++ +++|| .+.++.... +...
T Consensus 93 ------------------------------------------------------~~~i-~~~dL--~~~~~i~~~~~~~~ 115 (209)
T PF03466_consen 93 ------------------------------------------------------KKPI-TLEDL--ADYPLILLSPGSPY 115 (209)
T ss_dssp ------------------------------------------------------TSSS-SGGGG--TTSEEEEESTTTSH
T ss_pred ------------------------------------------------------cccc-hhhhh--hhcccccccccccc
Confidence 0234 88999 455554433 4434
Q ss_pred HHHhhh---hcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeCC-ccccCCceeeecCC
Q 003633 595 YSYLSD---SLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIGQ-PFTRSGWGFAFQRD 670 (806)
Q Consensus 595 ~~~l~~---~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~~~~k~ 670 (806)
...+.+ ..+.........++.+.....+.. |..-+++-+.....+..........+.+ .+. ..+.++.+++
T Consensus 116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~----g~gi~~~p~~~~~~~~~~~~l~~~~~~~~~~~-~~~~l~~~~~ 190 (209)
T PF03466_consen 116 RDQLDRWLREHGFSPNIVIEVDSFESILSLVAS----GDGIAILPDSLAQDELESGELVFLPLPDPPLP-RPIYLVWRKD 190 (209)
T ss_dssp HHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHT----TSEBEEEEHHHHHHHHHCTTEEEEEESSSTEE-EEEEEEEETT
T ss_pred ccccccccccccccccccccccchhhhcccccc----ccceeecCcccccccccCCCEEEEECCCCCCc-eEEEEEEECC
Confidence 443332 234444445667889999999998 6655665544333333222223334444 444 7788899998
Q ss_pred CCchHHHHHHHHhhhc
Q 003633 671 SPLAVGMSTAILKLSE 686 (806)
Q Consensus 671 spl~~~~n~~il~l~e 686 (806)
.+....+...+..+.+
T Consensus 191 ~~~~~~~~~~~~~l~~ 206 (209)
T PF03466_consen 191 RPLSPAIQWFIDLLRE 206 (209)
T ss_dssp GTTHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHH
Confidence 8777766666655543
No 148
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=93.54 E-value=3.8 Score=39.39 Aligned_cols=72 Identities=18% Similarity=0.207 Sum_probs=47.2
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. .+...+..+|.+|++|++++..... .....+. +.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~~-~~~l~~~~~~~v~~~ 82 (201)
T cd08418 13 TLMPAVINRFKEQFP-DVQISIYE-------GQLSSLLPELRDGRLDFAIGTLPDE-MYLKELI-SEPLFESDFVVVARK 82 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CcHHHHHHHHHcCCCcEEEEecCCC-CCCccee-EEeecCCceEEEeCC
Confidence 455677788887765 45566664 3578999999999999998632111 1112233 356667788888765
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 83 ~~ 84 (201)
T cd08418 83 DH 84 (201)
T ss_pred CC
Confidence 54
No 149
>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=93.50 E-value=0.83 Score=47.27 Aligned_cols=126 Identities=13% Similarity=0.000 Sum_probs=75.0
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHH--cCCeEEEEEEEcC-CcccchHHHHHHHHHhCC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDF--YGWKEVIAIYVDD-DYGRNGISALSNMLEKNM 82 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~--~~W~~v~ii~~d~-~~g~~~~~~l~~~l~~~g 82 (806)
+...++|+|.+....+. +.+..+..++...++.+++.+.. -|.++++++...+ .........+.+.+++.+
T Consensus 76 ~~~~~ipvV~~~~~~~~------~~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~R~~g~~~~~~~~~ 149 (273)
T cd06305 76 ALDAGIPVVAFDVDSDN------PKVNNTTQDDYSLARLSLDQLVKDLGGKGNVGYVNVAGFPPLDRRYDVWQAVLKAYP 149 (273)
T ss_pred HHHcCCCEEEecCCCCC------CccceeeechHHHHHHHHHHHHHHhCCCCCEEEEEccCCchHHHHHHHHHHHHHHCC
Confidence 45678999987543221 22233556677777878887654 5899999997531 123344567888888877
Q ss_pred -cEEEEEeccCCCCChhHHHHHHHhcCCCCCeE---EEEecCcchHHHHHHHHHHcCCc
Q 003633 83 -AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRV---YVVHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 83 -~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rv---ivl~~~~~~~~~i~~~a~~~gm~ 137 (806)
+.+..........+.++....+.++....+++ .|++.+...+..++.++++.|..
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~~d~~a~g~~~~l~~~g~~ 208 (273)
T cd06305 150 GIKEVAELGDVSNNTAQDAAAQVEAVLKKYPKGGIDAIWAAWDEFAKGAKQALDEAGRT 208 (273)
T ss_pred CcEEecccccccccchhHHHHHHHHHHHHCCCcccCeEEEcChhhhHHHHHHHHHcCCC
Confidence 55443211111122233344555554344443 34444566778888999999975
No 150
>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=93.47 E-value=4.3 Score=38.66 Aligned_cols=70 Identities=14% Similarity=0.226 Sum_probs=47.4
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. .+..++.+.+.+|++|+++..... ....+. +.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~ 80 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRD-------VSAEQVIEAVRSGEVDFGIGSEPE---ADPDLE-FEPLLRDPFVLVCPK 80 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEe-------CChHHHHHHHHcCCccEEEEeCCC---CCCCee-EEEeecccEEEEecC
Confidence 556688888887765 44566654 356889999999999999863222 222232 356777788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (197)
T cd08440 81 DH 82 (197)
T ss_pred CC
Confidence 54
No 151
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=93.35 E-value=2.4 Score=43.42 Aligned_cols=121 Identities=14% Similarity=0.084 Sum_probs=68.0
Q ss_pred CCCCChhHhhhCCCceeEEeCchhHHH-h--hhhccc--------------------ccccceeCCCHhHHHHHHhcCCC
Q 003633 571 TSVKGIESLITNDWPIGYQVGSFAYSY-L--SDSLRI--------------------QKSRLISLGSPEDYERALRQGPR 627 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs~~~~~-l--~~~~~~--------------------~~~~~~~~~~~~~~~~~l~~~~~ 627 (806)
..+++++||. .|.+|++..+...... | .++.++ ..-+++++ ...+...++.+
T Consensus 106 ~~~~sl~dlk-~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel-~~~~~~~al~~--- 180 (258)
T TIGR00363 106 KKIKNVNELQ-DGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITEL-ETSQLPRALDD--- 180 (258)
T ss_pred cCCCCHHHcC-CCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEc-CHHHHHHHhhc---
Confidence 5899999994 4889999876543322 1 122222 11233333 34566788888
Q ss_pred CCCeEEEEeCchhHHHHhhCCC-CeEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccchhHHHHHhh
Q 003633 628 NGGVAAIVDELPYVQLFLSNQT-DFGIIGQPFTRSGWGFAFQRDSPLAVGMSTAILKLSENGMLQKLHEKW 697 (806)
Q Consensus 628 ~g~~~a~i~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~il~l~e~G~~~~i~~kw 697 (806)
|.+||.+...+++.....+.. +-......-..+-..++++.+.-=.+.+.+.+..++....-+.|.++|
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 899999998887765422211 111111111122234556655335566666666676666666666664
No 152
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=93.17 E-value=3.5 Score=43.86 Aligned_cols=208 Identities=17% Similarity=0.115 Sum_probs=118.4
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
.++|+||+... ....+-.+++..+.++.+ .+.+.+.. ++.+.++..|.+|++|+++..
T Consensus 92 ~g~l~Ig~~~~--------------~~~~~l~~~l~~~~~~~p-~i~l~~~~-------~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 92 QGNLTIATTHT--------------QARYALPAAIKEFKKRYP-KVRLSILQ-------GSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred CCeEEEEechH--------------HHHHHhHHHHHHHHHHCC-CceEEEEe-------CChHHHHHHHHCCCcCEEEee
Confidence 46799998631 112445677777777654 34566654 357899999999999999863
Q ss_pred EEEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccch
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQI 514 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 514 (806)
-.... ...+ -+.|+....++++++...+..
T Consensus 150 ~~~~~--~~~l-~~~~l~~~~~~~v~~~~~pl~----------------------------------------------- 179 (313)
T PRK12684 150 EAIAD--YKEL-VSLPCYQWNHCVVVPPDHPLL----------------------------------------------- 179 (313)
T ss_pred cCCCC--CCCc-eEEEeccceEEEEeCCCCccc-----------------------------------------------
Confidence 21111 1122 246777788888887655211
Q ss_pred hhHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCchh
Q 003633 515 ATMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSFA 594 (806)
Q Consensus 515 ~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~~ 594 (806)
....-+++||.+.. -|.+..++..
T Consensus 180 -------------------------------------------------------~~~~i~~~dL~~~~-~i~~~~~~~~ 203 (313)
T PRK12684 180 -------------------------------------------------------ERKPLTLEDLAQYP-LITYDFAFAG 203 (313)
T ss_pred -------------------------------------------------------cCCCcCHHHHhcCC-cEecCCCCcH
Confidence 01224678885322 2555455533
Q ss_pred HHHhhh---hcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeC--CccccCCceeeecC
Q 003633 595 YSYLSD---SLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIG--QPFTRSGWGFAFQR 669 (806)
Q Consensus 595 ~~~l~~---~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~k 669 (806)
...+.+ ..+.........++.+...+++.. |..-+++.+. ...... ..++..+. .......+.++.+|
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~----g~Gv~~lp~~-~~~~~~--~~~l~~~~i~~~~~~~~~~l~~~~ 276 (313)
T PRK12684 204 RSKINKAFALRGLKPDIVLEAIDADVIKTYVEL----GLGVGIVADM-AFDPER--DRNLRAIDAGHLFGSSTTRLGLRR 276 (313)
T ss_pred HHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHh----CCceEEeehh-hccccc--cCCeEEEECCCCCcceeEEEEEEC
Confidence 333322 233333344566788888999988 5444555443 222221 22444432 33334568899999
Q ss_pred CCCchHHHHHHHHhhhccchhHHHHHhhc
Q 003633 670 DSPLAVGMSTAILKLSENGMLQKLHEKWF 698 (806)
Q Consensus 670 ~spl~~~~n~~il~l~e~G~~~~i~~kw~ 698 (806)
+.++...+...+..+.+. +..++.++-+
T Consensus 277 ~~~~~~~~~~f~~~l~~~-~~~~~~~~~~ 304 (313)
T PRK12684 277 GAYLRGYVYTFIELFAPT-LNRKLVEQAL 304 (313)
T ss_pred CCcCCHHHHHHHHHHHHH-hCHHHHHHHh
Confidence 988777776666655442 4445544444
No 153
>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=93.17 E-value=2.1 Score=44.21 Aligned_cols=132 Identities=7% Similarity=-0.016 Sum_probs=76.5
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcH-HHHHHHHHHHHHc--CCeEEEEEEEcCCc--ccchHHHHHHHHHhC
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDS-QQMAAMADLIDFY--GWKEVIAIYVDDDY--GRNGISALSNMLEKN 81 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~-~q~~ai~~ll~~~--~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~ 81 (806)
...++|+|......+ + +.-+..+.+|. ..+..+++.+... |.++++++....++ .....+.+.+++++.
T Consensus 79 ~~~~ipvV~~~~~~~---~---~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~a~~~~ 152 (273)
T cd06310 79 KDAGIPVVLIDSGLN---S---DIAVSFVATDNVAAGKLAAEALAELLGKKGKVAVISFVPGSSTTDQREEGFLEGLKEY 152 (273)
T ss_pred HHCCCCEEEecCCCC---C---CcceEEEeeChHHHHHHHHHHHHHHcCCCceEEEEeCCCCCccHHHHHHHHHHHHHhC
Confidence 456899998743211 1 11122234444 4567777776665 89999999754433 334568888999988
Q ss_pred -CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeE-EEEecCcchHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 82 -MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRV-YVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 82 -g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rv-ivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
|+.+... .....+..+-...+.++.+..+++ .|++++...+..+++.+++.|+. ++...+..|
T Consensus 153 ~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~d~~a~g~~~~l~~~g~~-~di~vig~d 217 (273)
T cd06310 153 PGIEIVAT--QYSDSDYAKALDITEDLLTANPDLKGIFGANEGSAVGAARAVRQAGKA-GKVKVVGFD 217 (273)
T ss_pred CCcEEEec--ccCCcCHHHHHHHHHHHHHhCCCceEEEecCchhHHHHHHHHHhcCCC-CCeEEEEeC
Confidence 8765431 111122223333444543333333 34555567788899999999985 344444434
No 154
>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=93.07 E-value=4.7 Score=38.56 Aligned_cols=70 Identities=16% Similarity=0.208 Sum_probs=46.6
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++...++.+|.+|++|+++...... ...+. +.++....++++++.
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 455677888887765 34466654 2457889999999999998643221 22232 356777888888775
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (201)
T cd08420 81 DH 82 (201)
T ss_pred CC
Confidence 54
No 155
>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=93.04 E-value=5.1 Score=38.22 Aligned_cols=70 Identities=19% Similarity=0.206 Sum_probs=47.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+..++++.+.+..+ .+++++.. ++..++...|.+|++|+++..... ....+. ..++.+..++++++.
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~L~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 80 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVE-------YGGKKVEQAVLNGELDVGITVLPV---DEEEFD-SQPLCNEPLVAVLPR 80 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEE-------cCcHHHHHHHHcCCCCEEEEeccc---ccCCce-eEEeccccEEEEecC
Confidence 456788888888765 45566654 356889999999999999864322 122232 346677788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (197)
T cd08438 81 GH 82 (197)
T ss_pred CC
Confidence 55
No 156
>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=93.02 E-value=1.8 Score=44.71 Aligned_cols=135 Identities=13% Similarity=0.031 Sum_probs=78.4
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC--cccchHHHHHHHHHhC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD--YGRNGISALSNMLEKN 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~ 81 (806)
+...++|+|......+.. .+.+..+..++...+..+++.+... +=++++++....+ ......+.+.+++++.
T Consensus 77 l~~~~iPvv~~~~~~~~~----~~~~~~V~~d~~~~g~~~~~~l~~~~~~~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~ 152 (272)
T cd06301 77 ANAAGIPLVYVNRRPENA----PKGVAYVGSDEVVAGRLQAEYVADKLGGKGNVAILMGPLGQSAQIDRTKGVEEVLAKY 152 (272)
T ss_pred HHHCCCeEEEecCCCCCC----CCeeEEEecChHHHHHHHHHHHHHHhCCCccEEEEECCCCCccHHHHHHHHHHHHHHC
Confidence 356789999875432211 0223445666677777887876444 4579999875432 2345568899999988
Q ss_pred C-cEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 82 M-AKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 82 g-~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
| +++... .....+.......+.++.+ ..+++ |++.+...+..+++.+++.|...++...+.-|
T Consensus 153 ~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~~~~di~ivg~d 218 (272)
T cd06301 153 PDIKVVEE--QTANWSRAEAMDLMENWLSSGGKIDA-VVANNDEMALGAIMALKAAGKSDKDVPVAGID 218 (272)
T ss_pred CCcEEEec--CCCCccHHHHHHHHHHHHHhCCCCCE-EEECCCchHHHHHHHHHHcCCCCCCcEEEeeC
Confidence 8 444321 1112222222234444332 23554 45566677788999999999863344444433
No 157
>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=92.97 E-value=2 Score=44.62 Aligned_cols=125 Identities=9% Similarity=0.029 Sum_probs=77.3
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCCc--ccchHHHHHHHHHhC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDDY--GRNGISALSNMLEKN 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~ 81 (806)
+.+.+||+|.+....+ ....+.+....+++...+..+++.+... |.++++++..+.+. .....+.+.+.+++.
T Consensus 76 ~~~~~iPvV~~~~~~~---~~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~~~~~~~ 152 (272)
T cd06313 76 AIARGIPVIDMGTLIA---PLQINVHSFLAPDNYFMGASVAQALCNAMGGKGKIAMLQGALGHTGAQGRAQGFNDVIKKY 152 (272)
T ss_pred HHHCCCcEEEeCCCCC---CCCCceEEEECCCcHHHHHHHHHHHHHHcCCCceEEEEECCCCCcchhHHHHHHHHHHHhC
Confidence 3456899999855332 1111223335677777788888887666 89999999754332 344678899999887
Q ss_pred C-cEEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCC
Q 003633 82 M-AKVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQM 136 (806)
Q Consensus 82 g-~~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm 136 (806)
+ .++.. ......+.......+.++.+. .+++ |++.+...+..+++.+++.|+
T Consensus 153 ~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~nd~~a~g~~~al~~~g~ 207 (272)
T cd06313 153 PDIEVVD--EQPANWDVSKAARIWETWLTKYPQLDG-AFCHNDSMALAAYQIMKAAGR 207 (272)
T ss_pred CCCEEEe--ccCCCCCHHHHHHHHHHHHHhCCCCCE-EEECCCcHHHHHHHHHHHcCC
Confidence 5 65543 122122223333444444333 3444 555667788889999999997
No 158
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=92.81 E-value=5.3 Score=38.89 Aligned_cols=71 Identities=10% Similarity=0.174 Sum_probs=48.1
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++... ++.+++.++|.+|++|+++..... ....+++ .|+.+..+++++++
T Consensus 13 ~~~~~~l~~~~~~~P-~~~v~~~~~------~~~~~l~~~L~~g~lDl~i~~~~~---~~~~l~~-~~l~~~~~~lv~~~ 81 (203)
T cd08463 13 LFLPELVARFRREAP-GARLEIHPL------GPDFDYERALASGELDLVIGNWPE---PPEHLHL-SPLFSDEIVCLMRA 81 (203)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEeC------CcchhHHHHHhcCCeeEEEecccc---CCCCcEE-eEeecCceEEEEeC
Confidence 566788888888776 344666542 145789999999999999863221 1122333 56777888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~h 83 (203)
T cd08463 82 DH 83 (203)
T ss_pred CC
Confidence 65
No 159
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=92.79 E-value=1.2 Score=47.82 Aligned_cols=127 Identities=11% Similarity=0.122 Sum_probs=88.0
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEc--CCcccchHHHHHHHHHhCC
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVD--DDYGRNGISALSNMLEKNM 82 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d--~~~g~~~~~~l~~~l~~~g 82 (806)
...+.++|+|......+ ...+++ ...++..-+..+++.+...|-+++++|... ...+....+.+.+++++.|
T Consensus 132 ~l~~~~~P~V~i~~~~~---~~~~~~---V~~Dn~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~ 205 (333)
T COG1609 132 LLAAAGIPVVVIDRSPP---GLGVPS---VGIDNFAGAYLATEHLIELGHRRIAFIGGPLDSSASRERLEGYRAALREAG 205 (333)
T ss_pred HHHhcCCCEEEEeCCCc---cCCCCE---EEEChHHHHHHHHHHHHHCCCceEEEEeCCCccccHhHHHHHHHHHHHHCC
Confidence 45566899998765544 333444 457777778889999999999999999975 3456777899999999999
Q ss_pred cEE--EEEeccCCCCChhHHHHHHHhcCCCC---CeEEEEecCcchHHHHHHHHHHcCCccCC
Q 003633 83 AKV--SYKLPLPVQFNQHDITVLLNNSKPLG---PRVYVVHVSPDPGLRIFTTAQKLQMMTNN 140 (806)
Q Consensus 83 ~~i--~~~~~~~~~~~~~~~~~~l~~ik~~~---~rvivl~~~~~~~~~i~~~a~~~gm~~~~ 140 (806)
+.. .....-. .+..+-...+.++.... +++ |++++...|..+++++.+.|...++
T Consensus 206 ~~~~~~~i~~~~--~~~~~g~~~~~~ll~~~~~~ptA-if~~nD~~Alg~l~~~~~~g~~vP~ 265 (333)
T COG1609 206 LPINPEWIVEGD--FSEESGYEAAERLLARGEPRPTA-IFCANDLMALGALRALRELGLRVPE 265 (333)
T ss_pred CCCCcceEEecC--CChHHHHHHHHHHHhcCCCCCcE-EEEcCcHHHHHHHHHHHHcCCCCCC
Confidence 875 2221111 22334444444544332 444 5677788999999999999976544
No 160
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=92.74 E-value=5 Score=42.41 Aligned_cols=86 Identities=20% Similarity=0.226 Sum_probs=54.7
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
+++|||+.... ...+-.+++..+.+..+ .+++++.. .....++..|.+|++|+++..-
T Consensus 95 g~l~ig~~~~~--------------~~~~~~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 152 (305)
T CHL00180 95 GTLIIGASQTT--------------GTYLMPRLIGLFRQRYP-QINVQLQV-------HSTRRIAWNVANGQIDIAIVGG 152 (305)
T ss_pred ceEEEEEcCcc--------------hHhHHHHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHcCCccEEEEcC
Confidence 57899886311 12345577777777655 34466654 3578899999999999998632
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
.........+ ...++....++++++...
T Consensus 153 ~~~~~~~~~~-~~~~l~~~~~~~v~~~~~ 180 (305)
T CHL00180 153 EVPTELKKIL-EITPYVEDELALIIPKSH 180 (305)
T ss_pred ccCcccccce-eEEEeccCcEEEEECCCC
Confidence 2111111112 356777888888887765
No 161
>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=92.72 E-value=2.3 Score=43.99 Aligned_cols=136 Identities=7% Similarity=0.007 Sum_probs=82.9
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC--cccchHHHHHHHHHhC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD--YGRNGISALSNMLEKN 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~ 81 (806)
+...++|+|.+....+.. ...+++.++.+++...+..+++.+... |-++++++..+.+ ......+.+.+++++.
T Consensus 76 ~~~~~iPvV~~~~~~~~~--~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~ 153 (273)
T cd06309 76 AKAAGIPVILVDRGVDVK--DDSLYVTFIGSDFVEEGRRAADWLAKATGGKGNIVELQGTVGSSVAIDRKKGFAEVIKKY 153 (273)
T ss_pred HHHCCCCEEEEecCcCCc--cCcceeeEecCChHHHHHHHHHHHHHHcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHC
Confidence 456789999986432211 112456677888888888888887665 8899999975433 2234578889999987
Q ss_pred -CcEEEEEeccCCCCChhHHHHHHHhcCCC---CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 82 -MAKVSYKLPLPVQFNQHDITVLLNNSKPL---GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 82 -g~~i~~~~~~~~~~~~~~~~~~l~~ik~~---~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
+.++... .....+.++....+.++.+. .+++| ++.+...+..+++++++.|+..++-+-|++
T Consensus 154 ~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~aI-~~~~d~~a~g~~~a~~~~g~~ip~di~iig 219 (273)
T cd06309 154 PNMKIVAS--QTGDFTRAKGKEVMEALLKAHGDDIDAV-YAHNDEMALGAIQAIKAAGKKPGKDIKIVS 219 (273)
T ss_pred CCCEEeec--cCCcccHHHHHHHHHHHHHhCCCCccEE-EECCcHHHHHHHHHHHHcCCCCCCCeEEEe
Confidence 4554321 11112223333344444333 34543 444556677789999999986544444444
No 162
>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=92.62 E-value=7.6 Score=37.10 Aligned_cols=71 Identities=13% Similarity=0.068 Sum_probs=48.6
Q ss_pred EeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEe
Q 003633 382 QGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAP 461 (806)
Q Consensus 382 ~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~ 461 (806)
..+-.+++..+.+..+ .+++++.. ++..+++.+|.+|++|+++.... .....+ .+.|+....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~~~~ 79 (198)
T cd08412 12 PYYLPGLLRRFREAYP-GVEVRVVE-------GNQEELEEGLRSGELDLALTYDL---DLPEDI-AFEPLARLPPYVWLP 79 (198)
T ss_pred hhhhHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEcCC---CCCccc-ceeeeeccceEEEec
Confidence 3566788888888776 34566665 35688999999999999986321 112223 246777888888876
Q ss_pred ccC
Q 003633 462 INN 464 (806)
Q Consensus 462 ~~~ 464 (806)
...
T Consensus 80 ~~~ 82 (198)
T cd08412 80 ADH 82 (198)
T ss_pred CCC
Confidence 654
No 163
>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=92.48 E-value=1.3 Score=45.48 Aligned_cols=134 Identities=13% Similarity=0.049 Sum_probs=79.7
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~ 83 (806)
+...++|+|......+ .. .......++...+..+++.+...|-++++++..+.+ ......+.+.+.+++.|.
T Consensus 74 ~~~~~ipvv~~~~~~~---~~---~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~ 147 (268)
T cd01575 74 LRAAGIPVVEIMDLPP---DP---IDMAVGFSHAEAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGL 147 (268)
T ss_pred HHhcCCCEEEEecCCC---CC---CCCeEEeCcHHHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHHcCC
Confidence 3466899998743221 11 112345566677788888888889999999986542 444557788999998886
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
............+.......+.++.+. .+++|+ +++...+..+++.+++.|...++.+-+++
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~~p~di~vig 211 (268)
T cd01575 148 DPPLVVTTPEPSSFALGRELLAELLARWPDLDAVF-CSNDDLALGALFECQRRGISVPEDIAIAG 211 (268)
T ss_pred CCCceeEeccCCCHHHHHHHHHHHHhCCCCCCEEE-ECCcHHHHHHHHHHHHhCCCCCcceEEEe
Confidence 422111111112222333444444332 456544 45566777899999999975444443333
No 164
>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=92.40 E-value=8.8 Score=36.74 Aligned_cols=70 Identities=14% Similarity=0.168 Sum_probs=46.5
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. .+-..+...|.+|++|+++... ......+ -+.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~ 80 (198)
T cd08433 13 VLAVPLLRAVRRRYP-GIRLRIVE-------GLSGHLLEWLLNGRLDLALLYG---PPPIPGL-STEPLLEEDLFLVGPA 80 (198)
T ss_pred hcchHHHHHHHHHCC-CcEEEEEe-------cCcHHHHHHHhCCCCcEEEEeC---CCCCCCe-eEEEeccccEEEEecC
Confidence 455677888888765 45566664 2457889999999999998632 2222222 3457777888888866
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (198)
T cd08433 81 DA 82 (198)
T ss_pred CC
Confidence 54
No 165
>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=92.37 E-value=1.2 Score=45.75 Aligned_cols=123 Identities=11% Similarity=0.082 Sum_probs=75.1
Q ss_pred CCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEc--CCcccchHHHHHHHHHhCCcEEE
Q 003633 9 LKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVD--DDYGRNGISALSNMLEKNMAKVS 86 (806)
Q Consensus 9 ~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~ 86 (806)
.++|+|......+ . +.+.....++...++.+++.+..-|.++++++..+ +..+....+.|.+++++.|+.+.
T Consensus 76 ~~ipvv~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~~~~ 149 (267)
T cd06284 76 KLPPIVQACEYIP---G---LAVPSVSIDNVAAARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGLPAD 149 (267)
T ss_pred cCCCEEEEecccC---C---CCcceEEecccHHHHHHHHHHHHcCCceEEEEcCCccchhHHHHHHHHHHHHHHcCCCCC
Confidence 4899997642211 1 22233566667778888888777899999999764 23456678889999999885432
Q ss_pred EEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCcc
Q 003633 87 YKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMT 138 (806)
Q Consensus 87 ~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~ 138 (806)
.........+.++....+.++.+. .+++|+. ++...+..+++++++.|+..
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~~~~a~g~~~al~~~g~~~ 202 (267)
T cd06284 150 EELIQEGDFSLESGYAAARRLLALPDRPTAIFC-FSDEMAIGAISALKELGLRV 202 (267)
T ss_pred cceEEeCCCChHHHHHHHHHHHhCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCC
Confidence 111111111223333444444322 3555544 45566778899999998753
No 166
>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=92.32 E-value=1.5 Score=45.02 Aligned_cols=134 Identities=12% Similarity=0.026 Sum_probs=80.1
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC-c-c-cchHHHHHHHHHhCC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD-Y-G-RNGISALSNMLEKNM 82 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~-~-g-~~~~~~l~~~l~~~g 82 (806)
+...++|+|.+....+ ....++ ...++...+..+++.+...|-++++++..... . . ....+.+.+.+++.|
T Consensus 74 ~~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~~~~ 147 (267)
T cd06283 74 LAKNGKPVVLVDRKIP---ELGVDT---VTLDNYEAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALAEHG 147 (267)
T ss_pred HhcCCCCEEEEcCCCC---CCCCCE---EEeccHHHHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHHHcC
Confidence 4567899998754322 222333 34556666788888887889999999975433 1 1 345788899999887
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCCC--CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPLG--PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~~--~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.............+..+....+.++.+.. +++|+ +++...+..+++.+++.|+..++-+-|++
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~vp~di~v~g 212 (267)
T cd06283 148 IGVNEELIEIDDEDADELDERLRQLLNKPKKKTAIF-AANGLILLEVLKALKELGIRIPEDVGLIG 212 (267)
T ss_pred CCCCcceeEecccchHHHHHHHHHHHcCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCccceEEEE
Confidence 53221111111122234445566654443 45544 44566777889999999986444444443
No 167
>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=92.20 E-value=1.5 Score=44.26 Aligned_cols=127 Identities=7% Similarity=0.027 Sum_probs=90.3
Q ss_pred ccccCCCcEEecccCCCCcccCCCCce---E---EecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHH
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYF---I---RSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNML 78 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f---~---Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l 78 (806)
+....++=.|.|++|+-++-. +..-+ . ++..+-..-+.|+.+-++++|-|+++++. .|-....+.+.+.+
T Consensus 66 ll~~a~~dvi~~~cTsgs~~~-G~~~~~~~i~~~~~g~p~tt~~~A~~~AL~alg~~RIalvT---PY~~~v~~~~~~~l 141 (239)
T TIGR02990 66 ILPDEELDVVAYSCTSASVVI-GDDEVTRAINAAKPGTPVVTPSSAAVDGLAALGVRRISLLT---PYTPETSRPMAQYF 141 (239)
T ss_pred hcCCCCCCEEEEccchhheec-CHHHHHHHHHhcCCCCCeeCHHHHHHHHHHHcCCCEEEEEC---CCcHHHHHHHHHHH
Confidence 334467778999999876521 00000 0 11223334468888999999999999998 57778899999999
Q ss_pred HhCCcEEEEEeccCCC-------CChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHH-HcC
Q 003633 79 EKNMAKVSYKLPLPVQ-------FNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQ-KLQ 135 (806)
Q Consensus 79 ~~~g~~i~~~~~~~~~-------~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~-~~g 135 (806)
++.|++|.....+... .+.+.+...+.++...++|+|++.|..-....++.++. ++|
T Consensus 142 ~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAifisCTnLrt~~vi~~lE~~lG 206 (239)
T TIGR02990 142 AVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADALFLSCTALRAATCAQRIEQAIG 206 (239)
T ss_pred HhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEEEEeCCCchhHHHHHHHHHHHC
Confidence 9999999876544432 23456677777777789999999998877888887764 345
No 168
>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=92.18 E-value=1.2 Score=45.84 Aligned_cols=131 Identities=13% Similarity=0.142 Sum_probs=76.5
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCc--ccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDY--GRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~g~ 83 (806)
+.+.++|+|.+....+. ....+| +..++...++.+++.+...|-++++++..+..+ .....+.+.+.+++.|+
T Consensus 79 ~~~~~ipvV~~~~~~~~--~~~~~~---v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~ 153 (270)
T cd06294 79 LKEEKFPFVVIGKPEDD--KENITY---VDNDNIQAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDHGI 153 (270)
T ss_pred HHhcCCCEEEECCCCCC--CCCCCe---EEECcHHHHHHHHHHHHHcCCccEEEecCCcccHHHHHHHHHHHHHHHHcCC
Confidence 45678999987543211 012233 345566667777887766799999999754332 23457889999999885
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcE
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYV 142 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~ 142 (806)
.+..........+.......+.++.+. ++++|+. .+...+..+++++++.|+..++-+
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~iP~dv 213 (270)
T cd06294 154 PDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIVA-TDDLLALGVLKVLNELGLKVPEDL 213 (270)
T ss_pred CCCcceEEecCCchHHHHHHHHHHHhCCCCCCEEEE-CChHHHHHHHHHHHHcCCCCCcce
Confidence 321111111112223334445554333 3555444 456688889999999998644433
No 169
>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=92.12 E-value=1.3 Score=45.71 Aligned_cols=125 Identities=12% Similarity=0.072 Sum_probs=76.8
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~ 84 (806)
...++|+|.+....+ .+++ ...++..-+..+++.+...|-++++++..+.. .+....+.+.+.+++.|+.
T Consensus 75 ~~~~iPvv~~~~~~~-----~~~~---V~~d~~~ag~~a~~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~ 146 (265)
T cd06285 75 TRRGVPFVLVLRHAG-----TSPA---VTGDDVLGGRLATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAGIE 146 (265)
T ss_pred HHcCCCEEEEccCCC-----CCCE---EEeCcHHHHHHHHHHHHHCCCccEEEEeCCcccccHHHHHHHHHHHHHHcCCC
Confidence 456899998754321 2333 34455566677778887789999999985433 3455678899999998876
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCC
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNN 140 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~ 140 (806)
+.....+....+...-...+.++.+. .+++ |++++...+..+++.+++.|+..++
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~~l~~~g~~~p~ 203 (265)
T cd06285 147 VPPERIVYSGFDIEGGEAAAEKLLRSDSPPTA-IFAVNDFAAIGVMGAARDRGLRVPD 203 (265)
T ss_pred CChhhEEeCCCCHHHHHHHHHHHHcCCCCCCE-EEEcCcHHHHHHHHHHHHcCCCCCc
Confidence 43111111112222333445554333 3454 4455667778899999999975433
No 170
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=91.92 E-value=0.82 Score=47.13 Aligned_cols=102 Identities=12% Similarity=0.086 Sum_probs=62.5
Q ss_pred CCCCChhHhhhCCCceeEEeCchhHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHH-hhCCC
Q 003633 571 TSVKGIESLITNDWPIGYQVGSFAYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLF-LSNQT 649 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~-~~~~~ 649 (806)
.+|++++|| +|+++.+..++.....+ +.++ ...+ ..+..|.+.+|++ |.+|+++.....+..+ +.+-.
T Consensus 126 ~~i~s~~Dl--~G~kir~~~~~~~~~~~-~~~G---a~~v-~~~~~e~~~aL~~----G~vDg~~~~~~~~~~~~~~ev~ 194 (257)
T TIGR00787 126 KPITKPEDL--KGLKIRIPNSPMNEAQF-KALG---ANPE-PMAFSEVYTALQT----GVVDGQENPLSNVYSSKFYEVQ 194 (257)
T ss_pred CccCChHHh--CCCEEecCCCHHHHHHH-HHcC---Cccc-ccCHHHHHHHHHc----CCcccccCCHHHHhhcchhhhc
Confidence 579999999 79999887776666666 3343 2333 5577899999999 8999988765443221 11123
Q ss_pred CeEEeCCccccCCceeeecCC--CCchHHHHHHHHhh
Q 003633 650 DFGIIGQPFTRSGWGFAFQRD--SPLAVGMSTAILKL 684 (806)
Q Consensus 650 ~l~~~~~~~~~~~~~~~~~k~--spl~~~~n~~il~l 684 (806)
++..... .......+.+.++ ..|-+....+|...
T Consensus 195 ~y~~~~~-~~~~~~~~~~n~~~~~~L~~e~q~~i~~a 230 (257)
T TIGR00787 195 KYLSMTN-HGYLGYLVVVNKAFWKSLPPDLQAVVKEA 230 (257)
T ss_pred chheecC-CcccceEEEEeHHHHhcCCHHHHHHHHHH
Confidence 3222222 2234455667665 23555555555544
No 171
>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=91.90 E-value=1.5 Score=45.04 Aligned_cols=134 Identities=13% Similarity=0.100 Sum_probs=77.9
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~ 83 (806)
+.+.++|+|......+ ...++++ ..++..-+..+++.+...|-++|+++..... ......+.+.+++++.|+
T Consensus 74 l~~~~ipvV~~~~~~~---~~~~~~v---~~d~~~~~~~~~~~l~~~g~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~~~ 147 (265)
T cd06299 74 LLKRGIPVVFVDREIT---GSPIPFV---TSDPQPGMTEAVSLLVALGHKKIGYISGPQDTSTGRERLEAFRQACASLGL 147 (265)
T ss_pred HHhCCCCEEEEecccC---CCCCCEE---EECcHHHHHHHHHHHHHcCCCcEEEEeCCCCcccHHHHHHHHHHHHHHCCC
Confidence 3456899998755322 2334443 3344444556667776779999999965332 334456789999999885
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.+..........+.++-...+.++.+..+++ |++++...+..+++++++.|+..++-+.|++
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a-v~~~~d~~a~gv~~al~~~g~~vp~dv~v~g 209 (265)
T cd06299 148 EVNEDLVVLGGYSQESGYAGATKLLDQGATA-IIAGDSMMTIGAIRAIHDAGLVIGEDISLIG 209 (265)
T ss_pred CCChHhEEecCcchHHHHHHHHHHHcCCCCE-EEEcCcHHHHHHHHHHHHhCCCCCcceeEEE
Confidence 4321111111112223334455544334675 4556667788899999999986544454444
No 172
>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=91.87 E-value=1.4 Score=45.63 Aligned_cols=131 Identities=14% Similarity=0.085 Sum_probs=78.8
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC--C------cccchHHHHHHH
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD--D------YGRNGISALSNM 77 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~--~------~g~~~~~~l~~~ 77 (806)
+.+.++|+|.+....+ .+++ +.+++..-+..+++.+... .++++++..+. . .+....+.+.++
T Consensus 74 l~~~~iPvv~~~~~~~-----~~~~---v~~d~~~~g~~a~~~L~~~-~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~ 144 (269)
T cd06297 74 RLPTERPVVLVDAENP-----RFDS---FYLDNRLGGRLAGAYLADF-PGRIGAITVEEEPDRAFRRTVFAERRAGFQQA 144 (269)
T ss_pred HhhcCCCEEEEccCCC-----CCCE---EEECcHHHHHHHHHHHHHh-CCceEEEeCccccccccccccHHHHHHHHHHH
Confidence 4567899998754321 2333 3456666677777766555 79999886432 2 344568899999
Q ss_pred HHhCCcEEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 78 LEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 78 l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
+++.|+.+.....+....+..+....+.++.+. ++++ |++++...+..+++.+++.|...++-+-|++
T Consensus 145 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~~l~~~g~~vP~di~vvg 214 (269)
T cd06297 145 LKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLA-VFASADQQALGALQEAVELGLTVGEDVRVVG 214 (269)
T ss_pred HHHcCCCCChhhEEeCCCChhhHHHHHHHHHcCCCCCcE-EEEcCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 999887643211111111223334455555433 3444 4444666788999999999976555555544
No 173
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=91.85 E-value=6.5 Score=41.19 Aligned_cols=83 Identities=13% Similarity=0.151 Sum_probs=55.6
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
++++||++.. -...+-.+++..+.++.+ .+.+++.. .....++..|.+|++|+++...
T Consensus 91 ~~i~I~~~~~--------------~~~~~l~~~l~~~~~~~p-~~~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 148 (296)
T PRK11242 91 GSLRLAMTPT--------------FTAYLIGPLIDAFHARYP-GITLTIRE-------MSQERIEALLADDELDVGIAFA 148 (296)
T ss_pred eEEEEEeccc--------------hhhhhhHHHHHHHHHHCC-CCEEEEEe-------CCHHHHHHHHHCCCCcEEEEec
Confidence 4688888631 123455678888888765 45566654 3568899999999999998632
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
. .....+ .+.++....+++++++..
T Consensus 149 ~---~~~~~l-~~~~l~~~~~~~~~~~~~ 173 (296)
T PRK11242 149 P---VHSPEI-EAQPLFTETLALVVGRHH 173 (296)
T ss_pred C---CCCcce-eEEEeeeccEEEEEcCCC
Confidence 2 222223 346777888888887765
No 174
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=91.84 E-value=9.1 Score=36.58 Aligned_cols=72 Identities=18% Similarity=0.173 Sum_probs=47.2
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++..++..++.+|++|+++.... ...+...+. ..|+....++++++.
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 344577777777765 45566654 35688999999999999986321 111122333 357778888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 83 ~~ 84 (201)
T cd08435 83 GH 84 (201)
T ss_pred CC
Confidence 55
No 175
>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=91.84 E-value=0.23 Score=40.61 Aligned_cols=55 Identities=18% Similarity=0.410 Sum_probs=45.6
Q ss_pred ccchhhHHHHHHHhhhccC--cccccccchhhhHHHHHhhhhhhhccccceeeeeee
Q 003633 511 RRQIATMFLFSFSTLFKTN--QEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILT 565 (806)
Q Consensus 511 ~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt 565 (806)
..+..+++||++.++...| .-.|.+..+|++.+.+.++++.+.....+.+++.++
T Consensus 22 ~~~~~da~yfs~~t~tTvGyGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l~ 78 (79)
T PF07885_consen 22 KWSFIDALYFSFVTITTVGYGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVLT 78 (79)
T ss_dssp TTSHHHHHHHHHHHHTT---SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhcccCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5578999999999988665 347898889999999999999999988888777654
No 176
>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=91.80 E-value=2.7 Score=43.93 Aligned_cols=141 Identities=10% Similarity=0.058 Sum_probs=75.8
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHH----HcCC--eEEEEEEE-c--CCcccchHHHHH
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLID----FYGW--KEVIAIYV-D--DDYGRNGISALS 75 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~----~~~W--~~v~ii~~-d--~~~g~~~~~~l~ 75 (806)
.+...++|+|.+....+.-.....+.+-....++...+..+++.+. .-|+ ++++++.. . ........+.+.
T Consensus 74 ~~~~~~iPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~G~~ 153 (289)
T cd01540 74 KAKAYNMKVVAVDDRLVDADGKPMEDVPHVGMSATKIGEQVGEAIADEMKKRGWDPKEVGALRITYDELDTAKPRTDGAL 153 (289)
T ss_pred HHHhCCCeEEEecCCCcccCCCccccceEecCCHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecCCCCcchhhHHHHHH
Confidence 3556899999875432211100011122234455555555556443 3577 78888752 2 234566788899
Q ss_pred HHHHhCCcEEEEEeccCCC-CChhHHHHHHHhcCCC--CCeE-EEEecCcchHHHHHHHHHHcCCccCCcEEEE
Q 003633 76 NMLEKNMAKVSYKLPLPVQ-FNQHDITVLLNNSKPL--GPRV-YVVHVSPDPGLRIFTTAQKLQMMTNNYVWLA 145 (806)
Q Consensus 76 ~~l~~~g~~i~~~~~~~~~-~~~~~~~~~l~~ik~~--~~rv-ivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~ 145 (806)
+++++.|+........+.. .+.+.-...+.++.+. +++. +|++++...+..++.++++.|...++...|.
T Consensus 154 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~~d~~a~g~~~al~~~g~~~~di~vig 227 (289)
T cd01540 154 EALKAPGFPEANIFQAPQKTTDTEGAFDAAASTLTKNPNVKNWIIYGLNDETVLGAVRATEQSGIAAADVIGVG 227 (289)
T ss_pred HHHhcCCCCcceEecccccCcchhhHHHHHHHHHHhCCCcCeeEEEeCCcHHHHHHHHHHHHcCCCCcceEEEe
Confidence 9999888653211111111 1112222334444332 3454 5666677788899999999998643333333
No 177
>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=91.79 E-value=1.3 Score=45.55 Aligned_cols=131 Identities=14% Similarity=0.095 Sum_probs=78.7
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~ 84 (806)
...++|+|.+....+ ..+++ ...++...+..+++.+...|-++++++..... ........+.+.+++.|+.
T Consensus 71 ~~~~ipvV~~~~~~~----~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 143 (261)
T cd06272 71 IKLAIPVVSYGVDYD----LKYPI---VNVDNEKAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENGIS 143 (261)
T ss_pred HHcCCCEEEEcccCC----CCCCE---EEEChHHHHHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHHHcCCC
Confidence 456789887744322 22333 45566666788888877789999999975433 2344567889999998864
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCCC--CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEE
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPLG--PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLA 145 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~~--~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~ 145 (806)
+..........+.+.....+.++.+.. +++ |++++...+..+++.+++.|+..++-+-++
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~~vp~dv~vv 205 (261)
T cd06272 144 ISDSHIDVDGLSAEGGDNAAKKLLKESDLPTA-IICGSYDIALGVLSALNKQGISIPEDIEII 205 (261)
T ss_pred CCHHHeeeCCCCHHHHHHHHHHHHcCCCCCCE-EEECCcHHHHHHHHHHHHhCCCCCCceEEE
Confidence 321111111122223334445544333 444 555666778889999999998644444433
No 178
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=91.76 E-value=5.5 Score=38.21 Aligned_cols=70 Identities=16% Similarity=0.083 Sum_probs=46.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++.+.+...+.+|++|+++.... .....+ -+.++....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Di~i~~~~---~~~~~~-~~~~l~~~~~~lv~~~ 80 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRD-------LESDNLEAQLERGEVDLALTTPE---YAPDGL-RSRPLFEERYVCVTRR 80 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEee-------CCcccHHHHHhcCCCcEEEecCc---cCCccc-eeeeeecCcEEEEEcC
Confidence 455678888887765 34466654 24567899999999999985321 112223 2557777888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (198)
T cd08461 81 GH 82 (198)
T ss_pred CC
Confidence 54
No 179
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=91.72 E-value=8.9 Score=40.77 Aligned_cols=207 Identities=11% Similarity=0.129 Sum_probs=124.3
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
+.||||++. . -...+-.+++..+.+..+ .+++++.. ++.+.++++|.+|++|+++...
T Consensus 93 g~lrIg~~~--~------------~~~~~l~~~l~~f~~~~P-~i~l~l~~-------~~~~~~~~~L~~g~~Dl~i~~~ 150 (316)
T PRK12679 93 GVLTIATTH--T------------QARYSLPEVIKAFRELFP-EVRLELIQ-------GTPQEIATLLQNGEADIGIASE 150 (316)
T ss_pred ceEEEEech--H------------hhhcchHHHHHHHHHHCC-CeEEEEec-------CCHHHHHHHHHcCCCCEEEecc
Confidence 579999863 1 123556678888877765 34455554 3567899999999999998632
Q ss_pred EEecCccceeEecccccccceEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchh
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIA 515 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 515 (806)
... . ...+. +.++.....++++++..+...
T Consensus 151 ~~~-~-~~~l~-~~~l~~~~~~~v~~~~hpl~~----------------------------------------------- 180 (316)
T PRK12679 151 RLS-N-DPQLV-AFPWFRWHHSLLVPHDHPLTQ----------------------------------------------- 180 (316)
T ss_pred cCC-C-CCCce-EEEccCCcEEEEecCCCcccc-----------------------------------------------
Confidence 211 1 12233 357778888888876652110
Q ss_pred hHHHHHHHhhhccCcccccccchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCc-eeEEeCchh
Q 003633 516 TMFLFSFSTLFKTNQEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWP-IGYQVGSFA 594 (806)
Q Consensus 516 ~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~-ig~~~gs~~ 594 (806)
...-+++||. +.+ |.+..+...
T Consensus 181 -------------------------------------------------------~~~i~~~~L~--~~~~i~~~~~~~~ 203 (316)
T PRK12679 181 -------------------------------------------------------ITPLTLESIA--KWPLITYRQGITG 203 (316)
T ss_pred -------------------------------------------------------CCCCCHHHHh--CCCeEEecCCCcH
Confidence 1223778884 333 333344332
Q ss_pred H----HHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeC--CccccCCceeeec
Q 003633 595 Y----SYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIG--QPFTRSGWGFAFQ 668 (806)
Q Consensus 595 ~----~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~ 668 (806)
. .++ ...+.........++.+...+++.. |..-+++-.. .... . +...+..+. .......+.++.+
T Consensus 204 ~~~~~~~~-~~~~~~~~~~~~~~s~~~~~~~v~~----g~Gi~~lp~~-~~~~-~-~~~~L~~~~~~~~~~~~~~~l~~~ 275 (316)
T PRK12679 204 RSRIDDAF-ARKGLLADIVLSAQDSDVIKTYVAL----GLGIGLVAEQ-SSGE-Q-EESNLIRLDTRHLFDANTVWLGLK 275 (316)
T ss_pred HHHHHHHH-HHcCCCceEEEEeccHHHHHHHHHc----CCcEEEeccc-cccc-c-cCCcEEEEECcccCCCceEEEEEe
Confidence 2 233 2234333344556788888888888 5444555443 2332 2 333455443 2333456888999
Q ss_pred CCCCchHHHHHHHHhhhccchhHHHHHhhcC
Q 003633 669 RDSPLAVGMSTAILKLSENGMLQKLHEKWFC 699 (806)
Q Consensus 669 k~spl~~~~n~~il~l~e~G~~~~i~~kw~~ 699 (806)
++.+....+...+..+.+.--.+.|.++-..
T Consensus 276 ~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~ 306 (316)
T PRK12679 276 RGQLQRNYVWRFLELCNAGLSVEDIKRQVME 306 (316)
T ss_pred CCchhhHHHHHHHHHHhcccCHHHHHHHHhh
Confidence 9988888888888877777667777776553
No 180
>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=91.67 E-value=2.1 Score=44.12 Aligned_cols=128 Identities=10% Similarity=0.025 Sum_probs=78.2
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCc--ccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDY--GRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~g~ 83 (806)
+...++|+|.+....+ ...+++ ...++...++.+++.+...|-++++++..+... .....+.+.+.+++.|+
T Consensus 74 ~~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~ 147 (268)
T cd06270 74 LAAQVPPLVLINRHIP---GLADRC---IWLDNEQGGYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGI 147 (268)
T ss_pred HhhCCCCEEEEeccCC---CCCCCe---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCC
Confidence 3456889988754322 112333 456777778888888877799999999754322 33456788999998886
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCCC--CeEEEEecCcchHHHHHHHHHHcCCccCC
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPLG--PRVYVVHVSPDPGLRIFTTAQKLQMMTNN 140 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~~--~rvivl~~~~~~~~~i~~~a~~~gm~~~~ 140 (806)
.+..........+..+....+.++.+.. +++| ++++...+..+++.+++.|+..++
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~g~~~~l~~~g~~ip~ 205 (268)
T cd06270 148 ALDESLIIEGDFTEEGGYAAMQELLARGAPFTAV-FCANDEMAAGAISALREHGISVPQ 205 (268)
T ss_pred CCCcceEEECCCCHHHHHHHHHHHHhCCCCCCEE-EEcCcHHHHHHHHHHHHcCCCCCC
Confidence 5421111111223334445555554433 4544 445556778899999999975443
No 181
>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=91.62 E-value=7.7 Score=36.97 Aligned_cols=71 Identities=18% Similarity=0.142 Sum_probs=48.7
Q ss_pred EeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEe
Q 003633 382 QGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAP 461 (806)
Q Consensus 382 ~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~ 461 (806)
..+..+++..+.+..+ .+++++.. +...++..++.+|++|+++..... ....+ .+.|+....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~v~~ 79 (196)
T cd08415 12 LSLLPRAIARFRARHP-DVRISLHT-------LSSSTVVEAVLSGQADLGLASLPL---DHPGL-ESEPLASGRAVCVLP 79 (196)
T ss_pred ccccHHHHHHHHHHCC-CcEEEEEe-------cchHHHHHHHHcCCccEEEEeCCC---CCCcc-eeeeecccceEEEEc
Confidence 3566788888888765 34566665 356789999999999999863221 12222 356777788888887
Q ss_pred ccC
Q 003633 462 INN 464 (806)
Q Consensus 462 ~~~ 464 (806)
...
T Consensus 80 ~~~ 82 (196)
T cd08415 80 PGH 82 (196)
T ss_pred CCC
Confidence 654
No 182
>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=91.60 E-value=1.7 Score=44.82 Aligned_cols=133 Identities=8% Similarity=-0.038 Sum_probs=78.5
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~ 84 (806)
...++|+|......+ ..++++ ...++...++.+++.+...|-++++++....+ ......+.+.+.+++.|+.
T Consensus 76 ~~~~ipvV~i~~~~~---~~~~~~---V~~d~~~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 149 (269)
T cd06275 76 RYRHIPMVVMDWGPE---DDFADK---IQDNSEEGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLP 149 (269)
T ss_pred hcCCCCEEEEecccC---CCCCCe---EeeCcHHHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCC
Confidence 346899998754322 122333 34455556677778887789999999974322 2344568889999988876
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
+..........+.......++++.+. .+++ |++++...+..+++.+++.|...++-+-+++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~~l~~~g~~vp~di~vvg 212 (269)
T cd06275 150 VNPGWIVEGDFECEGGYEAMQRLLAQPKRPTA-VFCGNDLMAMGALCAAQEAGLRVPQDLSIIG 212 (269)
T ss_pred CCHHHhccCCCChHHHHHHHHHHHcCCCCCcE-EEECChHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 53111111112222333445555433 3444 4455566777889999999875444444443
No 183
>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=91.59 E-value=1.5 Score=45.19 Aligned_cols=131 Identities=12% Similarity=0.065 Sum_probs=77.2
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~ 83 (806)
+...++|+|.+....+. ...+++ ..+++...+..+++.+..-|.++++++..+.. ......+.+.+++++.++
T Consensus 74 ~~~~~ipvV~i~~~~~~--~~~~~~---v~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~ 148 (270)
T cd06296 74 LRRTGIPFVVVDPAGDP--DADVPS---VGATNWAGGLAATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAALAEAGI 148 (270)
T ss_pred HhcCCCCEEEEecccCC--CCCCCE---EEeCcHHHHHHHHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHHHHcCC
Confidence 35578999987654211 122343 45666666777788776779999999875332 334557889999998876
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcE
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYV 142 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~ 142 (806)
.+..........+.+.....+.++.+. .+++|+ +.+...+..+++.+++.|...++-+
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~~p~~i 208 (270)
T cd06296 149 PVDPALVREGDFSTESGFRAAAELLALPERPTAIF-AGNDLMALGVYEAARERGLRIPEDL 208 (270)
T ss_pred CCChHHheeCCCCHHHHHHHHHHHHhCCCCCcEEE-EcCcHHHHHHHHHHHHhCCCCCCce
Confidence 543211111112223333344444332 344444 4466677889999999997543333
No 184
>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=91.53 E-value=3.7 Score=42.38 Aligned_cols=132 Identities=9% Similarity=0.065 Sum_probs=80.0
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCCc--ccchHHHHHHHHHhC-
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDDY--GRNGISALSNMLEKN- 81 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~- 81 (806)
...++|+|.+....+ +.+ ++..+..++...+..+++.+... |-++++++..+... .....+.+.+++++.
T Consensus 78 ~~~~ipvV~~~~~~~---~~~--~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~g~~~~l~~~~ 152 (270)
T cd06308 78 YRAGIPVILLDRKIL---SDK--YTAYIGADNYEIGRQAGEYIANLLPGKGNILEIWGLEGSSPAIERHDGFKEALSKYP 152 (270)
T ss_pred HHCCCCEEEeCCCCC---Ccc--ceEEeecCcHHHHHHHHHHHHHHcCCCceEEEEECCCCCchHHHHHHHHHHHHHHCC
Confidence 457999998754221 211 23335567777777888877664 89999999754333 234578889999998
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
|+++.... ....+.++-...+.++.+ .++++ |++.+...+..+++++++.|+. .+...+.-|
T Consensus 153 ~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~a-I~~~~d~~a~g~~~al~~~g~~-~dv~vvg~d 216 (270)
T cd06308 153 KIKIVAQQ--DGDWLKEKAEEKMEELLQANPDIDL-VYAHNDPMALGAYLAAKRAGRE-KEIKFIGID 216 (270)
T ss_pred CCEEEEec--CCCccHHHHHHHHHHHHHhCCCCcE-EEeCCcHHHHHHHHHHHHcCCC-CCcEEEEec
Confidence 88765321 111222222233444322 24564 4555667788899999999986 444444444
No 185
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=91.52 E-value=2.5 Score=45.45 Aligned_cols=127 Identities=8% Similarity=-0.026 Sum_probs=76.2
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCc--ccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDY--GRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~g~ 83 (806)
+...++|+|...... ....+++ ...++...+..+++.|...|.++++++..+... .....+.+.+++++.|+
T Consensus 140 l~~~~iPvV~~~~~~---~~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~ 213 (342)
T PRK10014 140 AEEKGIPVVFASRAS---YLDDVDT---VRPDNMQAAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLKFGL 213 (342)
T ss_pred HhhcCCCEEEEecCC---CCCCCCE---EEeCCHHHHHHHHHHHHHCCCCEEEEEcCCcccccHHHHHHHHHHHHHHcCC
Confidence 456689999874321 1122333 455666667788888888899999999644332 23456789999999987
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccC
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTN 139 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~ 139 (806)
.+.....+....+.+.....+.++.+. .+++| ++.+...+..+++.+.+.|+..+
T Consensus 214 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~nd~~A~g~~~~l~~~g~~vp 270 (342)
T PRK10014 214 PFHSEWVLECTSSQKQAAEAITALLRHNPTISAV-VCYNETIAMGAWFGLLRAGRQSG 270 (342)
T ss_pred CCCcceEecCCCChHHHHHHHHHHHcCCCCCCEE-EECCcHHHHHHHHHHHHcCCCCC
Confidence 542111111111222223344444333 34554 45677788889999999997543
No 186
>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=91.51 E-value=6.2 Score=37.92 Aligned_cols=70 Identities=11% Similarity=0.204 Sum_probs=45.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++...++..|.+|++|+++..... ....+. ..++.+..++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 81 (200)
T cd08411 14 YLLPRLLPALRQAYP-KLRLYLRE-------DQTERLLEKLRSGELDAALLALPV---DEPGLE-EEPLFDEPFLLAVPK 81 (200)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEe-------CcHHHHHHHHHcCCccEEEEeccC---CCCCce-EEEeeccceEEEecC
Confidence 355677888877765 34566654 357889999999999999863221 112222 345667778888766
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~~ 83 (200)
T cd08411 82 DH 83 (200)
T ss_pred CC
Confidence 54
No 187
>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=91.50 E-value=2 Score=44.12 Aligned_cols=130 Identities=12% Similarity=0.069 Sum_probs=76.4
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC---CcccchHHHHHHHHHhCCc
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD---DYGRNGISALSNMLEKNMA 83 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~---~~g~~~~~~l~~~l~~~g~ 83 (806)
...++|+|.+....+ ..++| ..+++...+..+++.+...|.++++++.... .......+.+.+.+++.|+
T Consensus 72 ~~~gipvv~~~~~~~----~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~ 144 (265)
T cd06291 72 ENIDLPIVSFDRYLS----ENIPI---VSSDNYEGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGL 144 (265)
T ss_pred hcCCCCEEEEeCCCC----CCCCe---EeechHHHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHcCC
Confidence 456899998865432 22343 3445555667777877777999999997433 2345557889999999887
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCCC--CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEE
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPLG--PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLA 145 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~~--~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~ 145 (806)
.+.... .....+..+-...+.++.+.. +++| ++.+...+..+++..++.|...++-+-++
T Consensus 145 ~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~al~~~g~~vp~di~v~ 206 (265)
T cd06291 145 EVRIIE-IQENFDDAEKKEEIKELLEEYPDIDGI-FASNDLTAILVLKEAQQRGIRVPEDLQII 206 (265)
T ss_pred CCChhe-eeccccchHHHHHHHHHHhCCCCCCEE-EECChHHHHHHHHHHHHcCCCCCcceEEe
Confidence 642211 111111122233444443333 4443 34455577888999999997544333333
No 188
>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=91.37 E-value=2.5 Score=43.62 Aligned_cols=131 Identities=8% Similarity=0.001 Sum_probs=80.2
Q ss_pred CCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCc--ccchHHHHHHHHHhCCcEEE
Q 003633 9 LKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDY--GRNGISALSNMLEKNMAKVS 86 (806)
Q Consensus 9 ~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~g~~i~ 86 (806)
.++|+|......+. ...+ ...+++...+..+++.+...|-++++++..+... .....+.+.+++++.|..+.
T Consensus 77 ~~~pvV~i~~~~~~---~~~~---~V~~d~~~~~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~ 150 (269)
T cd06293 77 SYGNIVLVDEDVPG---AKVP---KVFCDNEQGGRLATRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIPEV 150 (269)
T ss_pred cCCCEEEECCCCCC---CCCC---EEEECCHHHHHHHHHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHHHcCCCCC
Confidence 47899987654322 1123 2557777888888888877899999999754332 33457889999999886432
Q ss_pred EEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 87 YKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 87 ~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.........+.+.....+.++.+ ..+++| ++++...+..+++++++.|...++-+-|++
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~g~~~al~~~g~~vp~di~i~g 211 (269)
T cd06293 151 PEYVCFGDYTREFGRAAAAQLLARGDPPTAI-FAASDEIAIGLLEVLRERGLSIPGDMSLVG 211 (269)
T ss_pred hheEEecCCCHHHHHHHHHHHHcCCCCCCEE-EEcCcHHHHHHHHHHHHcCCCCccceEEEe
Confidence 11111111222233344444432 345654 445667788899999999976555455544
No 189
>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=91.32 E-value=2.7 Score=43.22 Aligned_cols=133 Identities=12% Similarity=0.065 Sum_probs=78.9
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~ 84 (806)
...++|+|.+....+ ....++ ...++..-+..+++.+..-|-++++++..+.. ......+.+.+.+++.|+.
T Consensus 75 ~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (264)
T cd06274 75 QKAGLPVVALDRPGD---PSRFPS---VVSDNRDGAAELTRELLAAPPEEVLFLGGLPELSPSRERLAGFRQALADAGLP 148 (264)
T ss_pred HhcCCCEEEecCccC---CCCCCE---EEEccHHHHHHHHHHHHHCCCCcEEEEeCCCcccchHHHHHHHHHHHHHcCCC
Confidence 456899998744322 222343 34445555677788777789999999875433 3445578899999998864
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCC---CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPL---GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~---~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
+..........+.+.-...+.++.+. .+++|+ +++...+..+++++++.|+..++-+-|++
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~-~~~d~~A~g~~~al~~~g~~ip~dv~v~g 212 (264)
T cd06274 149 VQPDWIYAEGYSPESGYQLMAELLARLGRLPRALF-TTSYTLLEGVLRFLRERPGLAPSDLRIAT 212 (264)
T ss_pred CCcceeecCCCChHHHHHHHHHHHccCCCCCcEEE-EcChHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 32111111112222333344444322 356555 44666788899999999976555555554
No 190
>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=91.26 E-value=5.4 Score=38.56 Aligned_cols=68 Identities=13% Similarity=0.155 Sum_probs=44.0
Q ss_pred eeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEecc
Q 003633 384 YCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 384 ~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
+-..++..+.+..+ .+++++.. ++. ++++.|.+|++|++++.-.. ....+. ..|+....++++++..
T Consensus 14 ~l~~~i~~~~~~~P-~i~l~i~~-------~~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~ 80 (200)
T cd08462 14 LLPPVIERVAREAP-GVRFELLP-------PDD-QPHELLERGEVDLLIAPERF---MSDGHP-SEPLFEEEFVCVVWAD 80 (200)
T ss_pred HHHHHHHHHHHHCC-CCEEEEec-------CCh-hHHHHHhcCCeeEEEecCCC---CCCCce-eeeeeccceEEEEcCC
Confidence 44567777777665 34466654 244 89999999999999863211 112233 3467778888888766
Q ss_pred C
Q 003633 464 N 464 (806)
Q Consensus 464 ~ 464 (806)
.
T Consensus 81 h 81 (200)
T cd08462 81 N 81 (200)
T ss_pred C
Confidence 5
No 191
>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=91.26 E-value=10 Score=35.98 Aligned_cols=70 Identities=21% Similarity=0.301 Sum_probs=46.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-..++..+.+..+ .+++++.. +....++.++.+|++|+++.... .....+. ..++.+..+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~l~-~~~l~~~~~~~v~~~ 80 (195)
T cd08434 13 SLVPDLIRAFRKEYP-NVTFELHQ-------GSTDELLDDLKNGELDLALCSPV---PDEPDIE-WIPLFTEELVLVVPK 80 (195)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEec-------CcHHHHHHHHHcCCccEEEEccC---CCCCCee-EEEeecceEEEEecC
Confidence 445567777777764 24455554 35678899999999999986322 2223333 356777788888766
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (195)
T cd08434 81 DH 82 (195)
T ss_pred CC
Confidence 54
No 192
>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=91.25 E-value=1.9 Score=44.12 Aligned_cols=130 Identities=15% Similarity=0.098 Sum_probs=80.1
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEc-CC--cccchHHHHHHHHHhCC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVD-DD--YGRNGISALSNMLEKNM 82 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d-~~--~g~~~~~~l~~~l~~~g 82 (806)
+.+.++|+|.+....+ ..++ +..+....+..+++.+..-|-++++++... ++ .+....+.+.+.+++.|
T Consensus 74 ~~~~~ipvv~~~~~~~-----~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~v~~~~~~~~~~~~r~~gf~~~~~~~~ 145 (259)
T cd01542 74 IKKLNVPVVVVGQDYP-----GISS---VVYDDYGAGYELGEYLAQQGHKNIAYLGVSESDIAVGILRKQGYLDALKEHG 145 (259)
T ss_pred HhcCCCCEEEEeccCC-----CCCE---EEECcHHHHHHHHHHHHHcCCCcEEEEcCCcccchhHHHHHHHHHHHHHHcC
Confidence 4556899998754221 2232 456677778888888877899999998643 22 33456788999999988
Q ss_pred c-EEEEEeccCCCCChhHHHHHHHhcCCCC-CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 83 A-KVSYKLPLPVQFNQHDITVLLNNSKPLG-PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 83 ~-~i~~~~~~~~~~~~~~~~~~l~~ik~~~-~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
. .+... ....+...-...+.++.+.. +++|+. ++...+..+++.+++.|+..++.+.+++-
T Consensus 146 ~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~i~~-~~d~~a~g~~~~l~~~g~~vp~di~v~g~ 208 (259)
T cd01542 146 ICPPNIV---ETDFSYESAYEAAQELLEPQPPDAIVC-ATDTIALGAMKYLQELGRRIPEDISVAGF 208 (259)
T ss_pred CChHHee---eccCchhhHHHHHHHHhcCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCceEEEec
Confidence 7 21111 11112223334444444333 555444 44567788999999999875555666553
No 193
>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=91.24 E-value=2.2 Score=44.12 Aligned_cols=134 Identities=16% Similarity=0.099 Sum_probs=80.4
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~ 84 (806)
...++|+|.+....+. ...+++ ...++...+..+++.+...|-++++++....+ ......+.+.+++++.|+.
T Consensus 80 ~~~~ipvV~i~~~~~~--~~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 154 (273)
T cd06292 80 AERGLPVVLVNGRAPP--PLKVPH---VSTDDALAMRLAVRHLVALGHRRIGFASGPGRTVPRRRKIAGFRAALEEAGLE 154 (273)
T ss_pred HhCCCCEEEEcCCCCC--CCCCCE---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCC
Confidence 4568999988654322 112343 45677777888888887789999999875432 2445578899999998854
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
...........+.+.-...+.++....+++|+ +++...+..+++..++.|+..++-+-|++
T Consensus 155 ~~~~~i~~~~~~~~~~~~~~~~~l~~~~~ai~-~~~d~~a~g~~~~l~~~g~~ip~di~ii~ 215 (273)
T cd06292 155 PPEALVARGMFSVEGGQAAAVELLGSGPTAIV-AASDLMALGAIRAARRRGLRVPEDVSVVG 215 (273)
T ss_pred CChhheEeCCCCHHHHHHHHHHHhcCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCcceEEEe
Confidence 21100111112222223334444333467544 55667778899999999975444444443
No 194
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=91.21 E-value=4.7 Score=38.79 Aligned_cols=70 Identities=17% Similarity=0.143 Sum_probs=47.6
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.++.+ .+++++.. ++...+..+|.+|++|+++... ......+ -+.|+....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~-~~~~l~~~~~~lv~~~ 80 (200)
T cd08466 13 LLLPRLLARLKQLAP-NISLRESP-------SSEEDLFEDLRLQEVDLVIDYV---PFRDPSF-KSELLFEDELVCVARK 80 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec-------CchHhHHHHHHcCCccEEEecc---cCCCCCc-eeeeecccceEEEEeC
Confidence 455677778877765 34566654 3577899999999999998632 1112223 2457778888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (200)
T cd08466 81 DH 82 (200)
T ss_pred CC
Confidence 65
No 195
>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=91.20 E-value=2 Score=44.15 Aligned_cols=121 Identities=10% Similarity=0.010 Sum_probs=74.3
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~ 83 (806)
+...++|+|.+....+ .. .+....+++...+..+++.+...|-++|+++..+.. ......+.+.+.+++.|.
T Consensus 73 ~~~~~ipvV~~~~~~~---~~---~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~ 146 (266)
T cd06278 73 CRRNGIPVVLINRYVD---GP---GVDAVCSDNYEAGRLAAELLLAKGCRRIAFIGGPADTSTSRERERGFRDALAAAGV 146 (266)
T ss_pred HhhcCCCEEEECCccC---CC---CCCEEEEChHHHHHHHHHHHHHCCCceEEEEcCCCcccchHHHHHHHHHHHHHcCC
Confidence 4567999999854322 11 223366777777888888887789999999985443 344567889999998887
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcC
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQ 135 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~g 135 (806)
.+... ... ..+..+....+.++.+. .+++|+. .+...+..+++..++.+
T Consensus 147 ~~~~~-~~~-~~~~~~~~~~~~~~l~~~~~~~~i~~-~~~~~a~~~~~~l~~~~ 197 (266)
T cd06278 147 PVVVE-EAG-DYSYEGGYEAARRLLASRPRPDAIFC-ANDLLAIGVMDAARQEG 197 (266)
T ss_pred Chhhh-ccC-CCCHHHHHHHHHHHHhcCCCCCEEEE-cCcHHHHHHHHHHHHhc
Confidence 64321 111 12223333444444333 3454443 34456677778877753
No 196
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=91.16 E-value=8.5 Score=37.08 Aligned_cols=71 Identities=14% Similarity=0.134 Sum_probs=47.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. +....+.+.|.+|++|+++..... .....+. +.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~~ 81 (198)
T cd08413 13 YVLPPVIAAFRKRYP-KVKLSLHQ-------GTPSQIAEMVLKGEADIAIATEAL--DDHPDLV-TLPCYRWNHCVIVPP 81 (198)
T ss_pred hhccHHHHHHHHhCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEEccCC--CCCCCcE-EEEeeeeeEEEEecC
Confidence 455678888888776 34566654 357889999999999999853211 1112233 467777888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~h 83 (198)
T cd08413 82 GH 83 (198)
T ss_pred CC
Confidence 55
No 197
>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=90.98 E-value=1.5 Score=45.01 Aligned_cols=129 Identities=11% Similarity=0.073 Sum_probs=75.2
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~ 83 (806)
+...++|+|.+....+. ...+| ..+++...+..+++.+...|-++|+++..+.+ ......+.+.+.+++.|.
T Consensus 75 ~~~~~ipvV~~~~~~~~---~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~l~~~~~ 148 (268)
T cd06289 75 LAESGIPVVLVAREVAG---APFDY---VGPDNAAGARLATEHLISLGHRRIAFIGGLEDSSTRRERLAGYRAALAEAGL 148 (268)
T ss_pred HHhcCCCEEEEeccCCC---CCCCE---EeecchHHHHHHHHHHHHCCCCCEEEecCCccccchHHHHHHHHHHHHHcCC
Confidence 45678999987433221 12232 44566666777888777779999998874332 445667899999998885
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCc
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNY 141 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~ 141 (806)
.+.....++...+.+.....+.++... .+++|+ +.+...+..+++++++.|+..++-
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~~~~a~~~~~al~~~g~~~p~d 207 (268)
T cd06289 149 PFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAIV-CFNDLVAFGAMSGLRRAGLTPGRD 207 (268)
T ss_pred CCCchhEEecCcchhhHHHHHHHHHcCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCcc
Confidence 322111111111222233344443333 345544 445556778899999999764333
No 198
>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=90.94 E-value=3 Score=44.08 Aligned_cols=137 Identities=13% Similarity=0.064 Sum_probs=79.3
Q ss_pred cccCCCcEEecccCCCCccc-------CCC-CceEEecCCcHHHHHHHHHHHHHcCCeE--------EEEEEEcC--Ccc
Q 003633 6 ANGLKVPLVSFAATDPTLSA-------LQF-PYFIRSTQSDSQQMAAMADLIDFYGWKE--------VIAIYVDD--DYG 67 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~-------~~~-p~f~Rt~psd~~q~~ai~~ll~~~~W~~--------v~ii~~d~--~~g 67 (806)
+...++|+|.+....+.... ..+ +++-...+++...++.+++.+...|-++ ++++..+. ...
T Consensus 78 ~~~~giPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~g~~~~~~~g~~~i~~i~~~~~~~~~ 157 (305)
T cd06324 78 AEGAGVKLFLVNSGLTEAQARELGPPREKFPDWLGQLLPNDEEAGYLMAEALISQARSVQAPGGRIDLLAISGDPTTPAA 157 (305)
T ss_pred HHhCCCeEEEEecCCCcchhhcccccccccCceeeeeccCcHHHHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCChHH
Confidence 45678999988654332110 112 2234566677777788888877666664 66665332 223
Q ss_pred cchHHHHHHHHHhCC-cEEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEE
Q 003633 68 RNGISALSNMLEKNM-AKVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWL 144 (806)
Q Consensus 68 ~~~~~~l~~~l~~~g-~~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi 144 (806)
....+.+.+++++.| ..+.. .+....+.+.-...+.++.+. ++++|+ +.+...+..+++++++.|+..++-+-|
T Consensus 158 ~~R~~Gf~~~~~~~g~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~g~~~al~~~g~~vp~di~v 234 (305)
T cd06324 158 ILREAGLRRALAEHPDVRLRQ--VVYAGWSEDEAYEQAENLLKRYPDVRLIW-AANDQMAFGALRAAKEAGRKPGRDVLF 234 (305)
T ss_pred HHHHHHHHHHHHHCCCceEee--eecCCCCHHHHHHHHHHHHHHCCCccEEE-ECCchHHHHHHHHHHHcCCCcCCCEEE
Confidence 455788899999887 33321 122222333333444554332 455544 556677888999999999864433333
Q ss_pred E
Q 003633 145 A 145 (806)
Q Consensus 145 ~ 145 (806)
+
T Consensus 235 i 235 (305)
T cd06324 235 G 235 (305)
T ss_pred E
Confidence 3
No 199
>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=90.92 E-value=6.1 Score=37.90 Aligned_cols=70 Identities=21% Similarity=0.207 Sum_probs=46.5
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. .+.+.+...|.+|++|+++.... .....+ -..|+....++++++.
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 445567777777664 33455543 35789999999999999986322 222223 2467788888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (200)
T cd08417 81 DH 82 (200)
T ss_pred CC
Confidence 54
No 200
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=90.76 E-value=4.5 Score=42.50 Aligned_cols=125 Identities=14% Similarity=0.129 Sum_probs=71.4
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHH-HcCCe-EEEEEEEcC--CcccchHHHHHHHHHh
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLID-FYGWK-EVIAIYVDD--DYGRNGISALSNMLEK 80 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~-~~~W~-~v~ii~~d~--~~g~~~~~~l~~~l~~ 80 (806)
.+...++|+|.+....+ ..+.+....+++..-+..+++.+. ..+.+ +++++..+. .......+.+.+++++
T Consensus 102 ~~~~~~ipvV~~~~~~~-----~~~~~~~V~~D~~~~g~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~R~~gf~~al~~ 176 (295)
T PRK10653 102 MANQANIPVITLDRGAT-----KGEVVSHIASDNVAGGKMAGDFIAKKLGEGAKVIQLEGIAGTSAARERGEGFKQAVAA 176 (295)
T ss_pred HHHHCCCCEEEEccCCC-----CCceeeEEccChHHHHHHHHHHHHHHhCCCceEEEEEccCCCccHHHHHHHHHHHHhh
Confidence 34557899998853211 112233444444444677777654 44653 566555322 2344667889999999
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEE-EEecCcchHHHHHHHHHHcCC
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVY-VVHVSPDPGLRIFTTAQKLQM 136 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvi-vl~~~~~~~~~i~~~a~~~gm 136 (806)
.|+.+... .....+..+....+.++.+..++.- +++.+...+..+++++++.|+
T Consensus 177 ~g~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~A~g~l~al~~~G~ 231 (295)
T PRK10653 177 HKFNVLAS--QPADFDRTKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK 231 (295)
T ss_pred CCCEEEEe--cCCCCCHHHHHHHHHHHHHhCCCcCEEEECCChhHHHHHHHHHHcCC
Confidence 99876422 1112232334444555554444433 444555666778999999996
No 201
>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=90.63 E-value=4.8 Score=42.15 Aligned_cols=137 Identities=14% Similarity=0.057 Sum_probs=76.2
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCCc--ccchHHHHHHHHHhC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDDY--GRNGISALSNMLEKN 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~ 81 (806)
+...++|+|.+....+...... +++.-+..++..-+..+++.+... |-++++++..+.+. .....+.+.+.+++.
T Consensus 77 ~~~~~iPvV~~~~~~~~~~~~~-~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~l~~~ 155 (294)
T cd06316 77 VAEAGIKLVFMDNVPSGLEHGK-DYAGIVTDDNYGNGQIAADALAKALPGKGKVGLIYHGADYFVTNQRDQGFKETIKKN 155 (294)
T ss_pred HHHcCCcEEEecCCCcccccCc-ceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCcccHHHHHHHHHHHHHHh
Confidence 4457899998765443322111 222334455555567788877665 88999999754443 334468888888876
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
+..+....... ..+.......++++.+. .+++|+ +.+...+..+++.+++.|+ .+-..+.-|
T Consensus 156 ~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~--~di~vvg~d 219 (294)
T cd06316 156 YPDITIVAEKG-IDGPSKAEDIANAMLTQNPDLKGIY-AVWDVPAEGVIAALRAAGR--DDIKVTTVD 219 (294)
T ss_pred CCCcEEEeecC-CcchhHHHHHHHHHHHhCCCeeEEE-eCCCchhHHHHHHHHHcCC--CCceEEEeC
Confidence 53322111111 11111222334444333 345444 4556778899999999996 333444433
No 202
>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=90.53 E-value=5 Score=41.48 Aligned_cols=125 Identities=8% Similarity=0.016 Sum_probs=72.9
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC-cccchHHHHHHHHHhCC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD-YGRNGISALSNMLEKNM 82 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~g 82 (806)
+...+||+|.+....+ +.. .....+.+++...+..+++++... |-++|+++..+.. ......+.+.+.+++.+
T Consensus 81 ~~~~gIpvV~~d~~~~---~~~-~~~~~V~~d~~~~g~~aa~~l~~~~~g~~~i~~~~g~~~~~~~~R~~gf~~~l~~~~ 156 (274)
T cd06311 81 AKKAGIFVVVVDRGLS---SPG-AQDLYVAGDNYGMGRVAGEYIATKLGGNGNIVVLRGIPTPIDNERVDAFDAAIAKYP 156 (274)
T ss_pred HHHCCCeEEEEcCCCC---CCc-ccceEEcCCcHHHHHHHHHHHHHHhCCCCeEEEEECCCCcchhHHHHHHHHHHhhCC
Confidence 3467899998754321 111 111224556666677777876555 8899999975332 22344688999999988
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCc
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~ 137 (806)
+++... .....+.+.-...+.++.+ .++++| ++.+...+..+++++++.|..
T Consensus 157 ~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~g~~~al~~~g~~ 210 (274)
T cd06311 157 IKILDR--QYANWNRDDAFSVMQDLLTKFPKIDAV-WAHDDDMAVGVLAAIKQAGRT 210 (274)
T ss_pred cEEEec--cCCCCcHHHHHHHHHHHHHhCCCcCEE-EECCCcHHHHHHHHHHHcCCC
Confidence 765432 2222222222333444322 234554 344555678889999998864
No 203
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=90.52 E-value=7.6 Score=41.10 Aligned_cols=84 Identities=14% Similarity=0.182 Sum_probs=54.6
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
..|+||+.. . -...+-.+++..+.+..+ .+++++.. ++.+.++..|.+|++|++++..
T Consensus 93 g~l~Ig~~~--~------------~~~~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~ 150 (309)
T PRK12682 93 GTLTIATTH--T------------QARYVLPRVVAAFRKRYP-KVNLSLHQ-------GSPDEIARMVISGEADIGIATE 150 (309)
T ss_pred CeEEEeeCc--h------------HHHHHHHHHHHHHHHhCC-CeEEEEec-------CCHHHHHHHHHcCCccEEEecC
Confidence 468998863 1 112455677778777765 34455554 3568899999999999998632
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
.. .....++ +.|+.....+++++...
T Consensus 151 ~~--~~~~~l~-~~~l~~~~~~~~~~~~~ 176 (309)
T PRK12682 151 SL--ADDPDLA-TLPCYDWQHAVIVPPDH 176 (309)
T ss_pred cc--cCCCcce-EEEeeeeeEEEEecCCC
Confidence 21 1122333 35778888888887665
No 204
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=90.46 E-value=7.2 Score=41.70 Aligned_cols=85 Identities=14% Similarity=0.085 Sum_probs=54.1
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
.++||||++.. + ...+-.+++..+.+..+ .+++++.. ++.+.++..|.+|++|+++..
T Consensus 92 ~g~l~Ig~~~~--~------------~~~~l~~~l~~f~~~~P-~i~i~i~~-------~~~~~~~~~L~~g~iDl~i~~ 149 (324)
T PRK12681 92 KGSLYIATTHT--Q------------ARYALPPVIKGFIERYP-RVSLHMHQ-------GSPTQIAEAAAKGNADFAIAT 149 (324)
T ss_pred CCeEEEEechh--H------------HHHhhHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCCCEEEec
Confidence 46899998631 1 12345567777777765 45566654 467899999999999999863
Q ss_pred EEEecCccceeEecccccccceEEEEeccC
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
... .....+. ..|+.....+++++...
T Consensus 150 ~~~--~~~~~l~-~~~l~~~~~~~v~~~~h 176 (324)
T PRK12681 150 EAL--HLYDDLI-MLPCYHWNRSVVVPPDH 176 (324)
T ss_pred Ccc--cCCCCeE-EEEeccceeEEEeCCCC
Confidence 211 1122233 34666777777776554
No 205
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=90.46 E-value=14 Score=39.19 Aligned_cols=84 Identities=18% Similarity=0.196 Sum_probs=53.5
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
++|+||+... . ...+-..+++.+.+..+ .+++++.. +++++++..|.+|++|+++...
T Consensus 93 g~l~Ig~~~~--~------------~~~~l~~~i~~f~~~~P-~i~l~~~~-------~~~~~~~~~L~~~~~D~~i~~~ 150 (309)
T PRK12683 93 GHLTVATTHT--Q------------ARYALPKVVRQFKEVFP-KVHLALRQ-------GSPQEIAEMLLNGEADIGIATE 150 (309)
T ss_pred ceEEEEeccc--h------------HHHHHHHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHcCCccEEEecC
Confidence 6799998631 1 11334467777777664 34466655 3689999999999999998532
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
.. .....+.+ .|+....++++++...
T Consensus 151 ~~--~~~~~l~~-~~l~~~~~~~v~~~~h 176 (309)
T PRK12683 151 AL--DREPDLVS-FPYYSWHHVVVVPKGH 176 (309)
T ss_pred CC--CCCCCceE-EEcccCeEEEEecCCC
Confidence 11 11223444 3677778888887655
No 206
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=90.39 E-value=2.2 Score=45.89 Aligned_cols=132 Identities=9% Similarity=0.054 Sum_probs=77.7
Q ss_pred CCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEc--CCcccchHHHHHHHHHhCCcEEE
Q 003633 9 LKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVD--DDYGRNGISALSNMLEKNMAKVS 86 (806)
Q Consensus 9 ~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~ 86 (806)
.++|+|.+....+ +..++.+ ..+++...+..+++.+...|-+++++|..+ +..+....+.+.+++++.|+.+.
T Consensus 138 ~~iPvV~~d~~~~---~~~~~~~--v~~d~~~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~~~ 212 (341)
T PRK10703 138 RHIPMVVMDWGEA---KADFTDA--IIDNAFEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVP 212 (341)
T ss_pred CCCCEEEEecccC---CcCCCCe--EEECcHHHHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHHcCCCCC
Confidence 6899998754322 1122222 334444556777777766799999998643 23445567889999999997653
Q ss_pred EEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 87 YKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 87 ~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.........+.++....+.++.+. .+++|+ +++...+..+++++.+.|..-++-+.|++
T Consensus 213 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~a~g~~~al~~~g~~ip~dv~vvg 273 (341)
T PRK10703 213 EEWIVQGDFEPESGYEAMQQILSQKHRPTAVF-CGGDIMAMGAICAADEMGLRVPQDISVIG 273 (341)
T ss_pred hHHeEeCCCCHHHHHHHHHHHHhCCCCCCEEE-ECCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 211111112223333445454333 455554 45667778899999999975444444443
No 207
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=90.38 E-value=1.6 Score=46.54 Aligned_cols=68 Identities=16% Similarity=0.063 Sum_probs=46.0
Q ss_pred CCCChhHhhhCCCceeEEeCchhHHHhh---hhcccccccceeC-CCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHh
Q 003633 572 SVKGIESLITNDWPIGYQVGSFAYSYLS---DSLRIQKSRLISL-GSPEDYERALRQGPRNGGVAAIVDELPYVQLFL 645 (806)
Q Consensus 572 ~i~s~~dL~~~~~~ig~~~gs~~~~~l~---~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~ 645 (806)
+|++++|| .|++||+..++.....+. +..+.+...+... -.+.+...+|.+ |.+||++...++.....
T Consensus 113 ~I~s~~DL--kGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~Al~~----G~VDAa~~~~p~~~~~~ 184 (320)
T PRK11480 113 TISKPEDL--IGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQPPAIIAAWQR----GDIDGAYVWAPAVNALE 184 (320)
T ss_pred CCCChHHc--CCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECCcHHHHHHHHc----CCcCEEEEcchHHHHHH
Confidence 59999999 799999987765443322 3344443333222 236778899999 99999988877765443
No 208
>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=90.33 E-value=14 Score=35.58 Aligned_cols=71 Identities=18% Similarity=0.193 Sum_probs=48.1
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
++-.+++..+.+..+ .+++++.. ++...+++.|.+|++|+++..-.. .....+ .+.++....++++++.
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 566778888888765 34566654 356789999999999999863211 111223 2467777888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~h 83 (198)
T cd08444 82 GH 83 (198)
T ss_pred CC
Confidence 65
No 209
>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=90.28 E-value=3.6 Score=42.57 Aligned_cols=125 Identities=10% Similarity=-0.008 Sum_probs=69.7
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc-CC--eEEEEEEEcCC--cccchHHHHHHHHHh
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY-GW--KEVIAIYVDDD--YGRNGISALSNMLEK 80 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~-~W--~~v~ii~~d~~--~g~~~~~~l~~~l~~ 80 (806)
+.+.++|+|.+....+. ....+| +..++..-+..+++.+... |. ++++++..+.. ......+.+.+++++
T Consensus 79 ~~~~~ipvV~~~~~~~~--~~~~~~---V~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~~a~~~ 153 (275)
T cd06307 79 LAAAGVPVVTLVSDLPG--SPRAGY---VGIDNRAAGRTAAWLIGRFLGRRPGKVAVLAGSHRFRGHEEREMGFRSVLRE 153 (275)
T ss_pred HHHCCCcEEEEeCCCCC--CceeeE---EccChHHHHHHHHHHHHHHhCCCCCeEEEEecCCCCcchHHHHHHHHHHHHh
Confidence 34578999987543221 111122 3444445555666665443 54 69998875433 234456889999988
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCc
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~ 137 (806)
.+..+..........+.++-...++++.+ .++++|+.... . +..+++.+++.|+.
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d-~-~~g~~~al~~~g~~ 210 (275)
T cd06307 154 EFPGLRVLETLEGLDDPARAYEATRKLLARHPDLVGIYNAGG-G-NRGVIRALREAGRA 210 (275)
T ss_pred hCCCcEEEeeccCCCChHHHHHHHHHHHHhCCCceEEEECCC-C-hHHHHHHHHHcCCC
Confidence 77554332222222222333344445432 34666665543 3 46889999999974
No 210
>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=90.27 E-value=5.6 Score=38.52 Aligned_cols=70 Identities=13% Similarity=0.141 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
++-.+++..+.++.+ .+++++.. ++..+++++|.+|++|++++..... ...++. .+..+..++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~-------~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~lv~~~ 80 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQ-------ASREAMLAQVADGEIDLALGVFPEL---PEELHA-ETLFEERFVCLADR 80 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEec-------CChHhHHHHHHCCCccEEEeccccC---CcCeeE-EEeeeccEEEEEeC
Confidence 555677777777655 35566654 3678999999999999998633221 122333 46667788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~h 82 (200)
T cd08465 81 AT 82 (200)
T ss_pred CC
Confidence 54
No 211
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=90.01 E-value=13 Score=38.69 Aligned_cols=83 Identities=14% Similarity=0.187 Sum_probs=52.6
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
..++||+... ....+-.+++..+.+..+ .+++++.. +...+++..+.+|++|+++...
T Consensus 89 g~l~i~~~~~--------------~~~~~~~~~l~~~~~~~P-~i~i~v~~-------~~~~~~~~~l~~g~~Di~i~~~ 146 (290)
T PRK10837 89 GALRIYASST--------------IGNYILPAMIARYRRDYP-QLPLELSV-------GNSQDVINAVLDFRVDIGLIEG 146 (290)
T ss_pred CeEEEEecch--------------hHhhhhHHHHHHHHHHCC-CceEEEEE-------CCHHHHHHHHHhCCceEEEecC
Confidence 5789988731 112445567777777764 34566654 3567899999999999998632
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
... ...+ ...|+....++++++...
T Consensus 147 ~~~---~~~~-~~~~l~~~~~~lv~~~~h 171 (290)
T PRK10837 147 PCH---SPEL-ISEPWLEDELVVFAAPDS 171 (290)
T ss_pred CCC---CCce-eEEEeecceEEEEEcCCC
Confidence 211 1222 235666777888877554
No 212
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=90.01 E-value=9.9 Score=40.03 Aligned_cols=86 Identities=8% Similarity=0.110 Sum_probs=56.5
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
..+|+||++.. -...+-.+++..+.+..+ .+++++.. ++..++..+|.+|++|+++..
T Consensus 94 ~g~l~I~~~~~--------------~~~~~l~~~l~~~~~~~p-~i~~~~~~-------~~~~~~~~~l~~g~~Di~i~~ 151 (302)
T PRK09791 94 AGQINIGMGAS--------------IARSLMPAVISRFHQQHP-QVKVRIME-------GQLVSMINELRQGELDFTINT 151 (302)
T ss_pred ceEEEEEechH--------------HHHhhhHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHCCCccEEEEe
Confidence 36799998742 122455677777777766 44555554 356899999999999999862
Q ss_pred EEEecCccceeEecccccccceEEEEeccC
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
..-. .....+.+ .|+....+++++++..
T Consensus 152 ~~~~-~~~~~~~~-~~l~~~~~~l~~~~~~ 179 (302)
T PRK09791 152 YYQG-PYDHEFTF-EKLLEKQFAVFCRPGH 179 (302)
T ss_pred cCCc-ccccceeE-EEeccceEEEEEcCCC
Confidence 2111 11223444 6888889999887665
No 213
>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=89.97 E-value=6 Score=41.14 Aligned_cols=110 Identities=6% Similarity=-0.032 Sum_probs=67.3
Q ss_pred ecCCcHHHHHHHHHHHHH--cCCeEEEEEEEcC-CcccchHHHHHHHHHhC-CcEEEEEeccCCCCChhHHHHHHHhcCC
Q 003633 34 STQSDSQQMAAMADLIDF--YGWKEVIAIYVDD-DYGRNGISALSNMLEKN-MAKVSYKLPLPVQFNQHDITVLLNNSKP 109 (806)
Q Consensus 34 t~psd~~q~~ai~~ll~~--~~W~~v~ii~~d~-~~g~~~~~~l~~~l~~~-g~~i~~~~~~~~~~~~~~~~~~l~~ik~ 109 (806)
+.+++..-+..+++.+.. .|-++++++.... ..+....+.+.+++++. |+.+... +....+..+-...+.++.+
T Consensus 109 V~~d~~~~g~~~~~~L~~~~~g~~~i~~l~~~~~~~~~~R~~gf~~al~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~ 186 (280)
T cd06303 109 VGFDHAAGARLLADYFIKRYPNHARYAMLYFSPGYISTARGDTFIDCVHARNNWTLTSE--FYTDATRQKAYQATSDILS 186 (280)
T ss_pred eCCCHHHHHHHHHHHHHHhcCCCcEEEEEECCCCcchhHHHHHHHHHHHhCCCceEEEe--ecCCCCHHHHHHHHHHHHH
Confidence 455555566777887665 7999999997533 22344578889999988 7664322 2222233333344444433
Q ss_pred CC--CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 110 LG--PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 110 ~~--~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
.. +++ |++++...+..+++++++.|+. ++...+.-|
T Consensus 187 ~~~~~~a-i~~~nd~~A~g~l~al~~~G~~-~dv~vvg~d 224 (280)
T cd06303 187 NNPDVDF-IYACSTDIALGASDALKELGRE-DDILINGWG 224 (280)
T ss_pred hCCCCcE-EEECCcHHHHHHHHHHHHcCCC-CCcEEEecC
Confidence 33 444 4466677888999999999985 333344333
No 214
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=89.97 E-value=3.2 Score=44.27 Aligned_cols=131 Identities=8% Similarity=-0.002 Sum_probs=76.5
Q ss_pred CCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHHhCCcEEE
Q 003633 9 LKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD--DYGRNGISALSNMLEKNMAKVS 86 (806)
Q Consensus 9 ~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~--~~g~~~~~~l~~~l~~~g~~i~ 86 (806)
.++|+|...... ....++ ....++..-+..+++.+...|-+++++|..+. .......+.+.+++++.|+.+.
T Consensus 135 ~~iPvV~i~~~~---~~~~~~---~v~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~ 208 (327)
T PRK10423 135 PSVPTVMMDWAP---FDGDSD---LIQDNSLLGGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIP 208 (327)
T ss_pred CCCCEEEECCcc---CCCCCC---EEEEChHHHHHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCCC
Confidence 378998875321 111112 13333344467777888888999999996432 2345567889999999987642
Q ss_pred EEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 87 YKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 87 ~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
....+....+.+.-...+.++.+. .+++ |++++...+..+++.+++.|+..++-+-|++
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~A~g~~~~l~~~g~~vP~dvsvig 269 (327)
T PRK10423 209 DGYEVTGDFEFNGGFDAMQQLLALPLRPQA-VFTGNDAMAVGVYQALYQAGLSVPQDIAVIG 269 (327)
T ss_pred cceEEeCCCChHHHHHHHHHHhcCCCCCCE-EEEcCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 111111111222222344444333 3454 4456667788899999999976555444444
No 215
>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=89.85 E-value=11 Score=36.15 Aligned_cols=70 Identities=13% Similarity=0.054 Sum_probs=45.2
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
++-..++..+.+..+ .+++++.. ++...+...|.+|++|+++..... . ...+ -+.++....++++++.
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 455677777777765 35566654 245788899999999999853211 1 1222 2457777777777765
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (200)
T cd08464 81 QQ 82 (200)
T ss_pred CC
Confidence 44
No 216
>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=89.84 E-value=16 Score=34.91 Aligned_cols=72 Identities=10% Similarity=0.032 Sum_probs=48.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. .+...+.+.|.+|++|+++.... .......++ ..++.+..++++++.
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 455678888888876 45566665 35788999999999999986321 111222333 457777888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 83 ~h 84 (198)
T cd08437 83 DH 84 (198)
T ss_pred CC
Confidence 54
No 217
>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=89.80 E-value=5.4 Score=40.86 Aligned_cols=130 Identities=11% Similarity=0.096 Sum_probs=79.7
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCc--ccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDY--GRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~g~~ 84 (806)
...++|+|.+.... . ...++ ...++..-+..+++.+...|-++|+++..+... .....+.+.+++++.|+.
T Consensus 76 ~~~~ipvv~~~~~~-~---~~~~~---v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~ 148 (264)
T cd01574 76 APADVPVVFVDGSP-S---PRVST---VSVDQEGGARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIA 148 (264)
T ss_pred HhcCCCEEEEeccC-C---CCCCE---EEeCcHHHHHHHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHHHHCCCC
Confidence 35689999986432 1 22333 456667778888888878899999999754332 234567788899888876
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCCC-CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPLG-PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~~-~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
+... +....+.+.-...+.++.+.. +++ |++++...+..+++++++.|...++-+-|++
T Consensus 149 ~~~~--~~~~~~~~~~~~~~~~~l~~~~~~a-i~~~~d~~a~g~~~~~~~~g~~ip~~i~ii~ 208 (264)
T cd01574 149 PPPV--LEGDWSAESGYRAGRELLREGDPTA-VFAANDQMALGVLRALHELGLRVPDDVSVVG 208 (264)
T ss_pred ccee--eecCCCHHHHHHHHHHHHhCCCCcE-EEEcCcHHHHHHHHHHHHcCCCCccceEEec
Confidence 5422 211122233334444544333 555 4455667788899999999864443344443
No 218
>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=89.75 E-value=13 Score=35.52 Aligned_cols=69 Identities=10% Similarity=0.086 Sum_probs=45.0
Q ss_pred eeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEecc
Q 003633 384 YCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 384 ~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
+-..++..+.+..+- +++++.. ++...+..+|.+|++|+++..-.. ....+. ..++....++++++..
T Consensus 14 ~~~~~l~~~~~~~P~-i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~ 81 (198)
T cd08441 14 WLMPVLDQFRERWPD-VELDLSS-------GFHFDPLPALLRGELDLVITSDPL---PLPGIA-YEPLFDYEVVLVVAPD 81 (198)
T ss_pred hhHHHHHHHHHhCCC-eEEEEEe-------CCchhHHHHHHcCCceEEEecCCc---CCCCcE-EEEccCCcEEEEEcCC
Confidence 445777788777653 4466654 356789999999999999863221 112232 3466777888877665
Q ss_pred C
Q 003633 464 N 464 (806)
Q Consensus 464 ~ 464 (806)
.
T Consensus 82 ~ 82 (198)
T cd08441 82 H 82 (198)
T ss_pred C
Confidence 4
No 219
>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=89.72 E-value=18 Score=34.54 Aligned_cols=70 Identities=10% Similarity=0.072 Sum_probs=46.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++...+..++.+|++|+++..... ....+. +.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 80 (199)
T cd08426 13 ELLPSLIARFRQRYP-GVFFTVDV-------ASTADVLEAVLSGEADIGLAFSPP---PEPGIR-VHSRQPAPIGAVVPP 80 (199)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEe-------CCcHHHHHHHHCCCccEEEecCCC---CCCCeE-EEeeccCcEEEEecC
Confidence 445677777777765 34455654 256889999999999999863221 112233 467778888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~h 82 (199)
T cd08426 81 GH 82 (199)
T ss_pred CC
Confidence 54
No 220
>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=89.68 E-value=6.2 Score=40.48 Aligned_cols=129 Identities=9% Similarity=0.030 Sum_probs=75.0
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC-cccchHHHHHHHHHhC-
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD-YGRNGISALSNMLEKN- 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~- 81 (806)
+...++|+|.+....+ ..+.+....+++..-+..+++.+... |-+++++++..+. ......+.+.+++++.
T Consensus 76 ~~~~~ipvV~~~~~~~-----~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~ 150 (267)
T cd06322 76 AKKAGIPVITVDIAAE-----GVAVVSHVATDNYAGGVLAGELAAKVLNGKGQVAIIDYPTVQSVVDRVRGFKEALADYP 150 (267)
T ss_pred HHHCCCCEEEEcccCC-----CCceEEEEecChHHHHHHHHHHHHHHhCCCceEEEEecCCCccHHHHHHHHHHHHHhCC
Confidence 3467899999853221 11222334555555567777776554 8889999974322 2344578889999988
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
|+.+... ....+.+.....+.++.. .++++ |++++...+..+++++++.|. +.+.|++
T Consensus 151 ~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~al~~~g~---~di~vvg 210 (267)
T cd06322 151 NIKIVAV---QPGITRAEALTAAQNILQANPDLDG-IFAFGDDAALGAVSAIKAAGR---DNVKVIG 210 (267)
T ss_pred CcEEEEe---cCCCChHHHHHHHHHHHHhCCCCCE-EEEcCCcHHHHHHHHHHHCCC---CCeEEEE
Confidence 8876421 111122222333444432 23554 445556677888899999997 3344444
No 221
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=89.64 E-value=11 Score=39.54 Aligned_cols=86 Identities=13% Similarity=0.152 Sum_probs=55.6
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
.++|+||++.. -...+-.+++..+.+..+ .+++.+.. .+...++.++.+|++|++++.
T Consensus 92 ~~~l~I~~~~~--------------~~~~~~~~~l~~~~~~~P-~~~i~~~~-------~~~~~~~~~l~~g~~D~~i~~ 149 (300)
T TIGR02424 92 GPTVRIGALPT--------------VAARLMPEVVKRFLARAP-RLRVRIMT-------GPNAYLLDQLRVGALDLVVGR 149 (300)
T ss_pred CceEEEecccH--------------HHHhhhHHHHHHHHHhCC-CcEEEEEe-------CchHHHHHHHHCCCCCEEEEe
Confidence 46799998631 112345567777777766 45566665 356889999999999999864
Q ss_pred EEEecCccceeEecccccccceEEEEeccC
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
.... .....+. ..|+.....+++++...
T Consensus 150 ~~~~-~~~~~~~-~~~l~~~~~~~~~~~~h 177 (300)
T TIGR02424 150 LGAP-ETMQGLS-FEHLYNEPVVFVVRAGH 177 (300)
T ss_pred cCCc-cccccee-eeeecCCceEEEEcCCC
Confidence 3221 1122232 45777888888887654
No 222
>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=89.55 E-value=5.4 Score=38.49 Aligned_cols=70 Identities=16% Similarity=0.149 Sum_probs=46.8
Q ss_pred EeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEe
Q 003633 382 QGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAP 461 (806)
Q Consensus 382 ~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~ 461 (806)
..+-.+++..+.++.+ .+++++.. ++. .++++|.+|++|++++.... ....+. ..|+.+..++++++
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 3556678888888765 44566653 234 78899999999999863221 112233 46777788888887
Q ss_pred ccC
Q 003633 462 INN 464 (806)
Q Consensus 462 ~~~ 464 (806)
...
T Consensus 79 ~~h 81 (200)
T cd08460 79 AGH 81 (200)
T ss_pred CCC
Confidence 665
No 223
>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=89.55 E-value=16 Score=34.66 Aligned_cols=71 Identities=18% Similarity=0.164 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++...+..++.+|++|+++..... .....+. ..++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~~~~~ 81 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQ-------AGSDDLLAAVREGRLDLAFVGLPE--RRPPGLA-SRELAREPLVAVVAP 81 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCHHHHHHHHHcCCccEEEEecCC--CCCCCcE-EEEeecceEEEEecC
Confidence 455677788877765 45566654 356789999999999999864322 1222232 356677778887766
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~~ 83 (194)
T cd08436 82 DH 83 (194)
T ss_pred CC
Confidence 54
No 224
>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=89.38 E-value=3.6 Score=42.22 Aligned_cols=126 Identities=9% Similarity=0.003 Sum_probs=75.1
Q ss_pred CCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHHhCCcEEE
Q 003633 9 LKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD--DYGRNGISALSNMLEKNMAKVS 86 (806)
Q Consensus 9 ~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~--~~g~~~~~~l~~~l~~~g~~i~ 86 (806)
.++|+|.+....+ ....++ ...++..-+..+++.+...|-++++++..+. .......+.+.+.+++.|+.+.
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 3799998765422 122333 4456666677788877667999999997542 2334567888899988876542
Q ss_pred EEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCc
Q 003633 87 YKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNY 141 (806)
Q Consensus 87 ~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~ 141 (806)
....+....+...-...+.++.+. .+++| ++++...+..+++.+++.|+..++.
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai-i~~~~~~a~~~~~~l~~~g~~ip~d 205 (265)
T cd06290 150 PDLIVQGDFEEESGLEAVEELLQRGPDFTAI-FAANDQTAYGARLALYRRGLRVPED 205 (265)
T ss_pred HHHEEecCCCHHHHHHHHHHHHcCCCCCCEE-EEcCcHHHHHHHHHHHHcCCCCCcc
Confidence 111111111222223344444332 35554 4567777888999999999754433
No 225
>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=89.17 E-value=5 Score=41.55 Aligned_cols=133 Identities=8% Similarity=-0.001 Sum_probs=80.8
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD--DYGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~--~~g~~~~~~l~~~l~~~g~~ 84 (806)
.+.++|+|......+. ...+++ +..++...+..+++.+...|-+++++|.... ..+......+.+++++.|+.
T Consensus 76 ~~~~iPvV~i~~~~~~--~~~~~~---V~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~ 150 (269)
T cd06287 76 RQRGIPVVSIGRPPGD--RTDVPY---VDLQSAATARMLLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHGMP 150 (269)
T ss_pred HHcCCCEEEeCCCCCC--CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcCCC
Confidence 4558899987543210 122343 3445566667777888788999999996432 23445678899999998875
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
..... .....+.++-...++++.+. .+++|+ +++...+..+++.+++.|+..++-+=|++
T Consensus 151 ~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~gvl~al~~~gl~vP~dvsvig 212 (269)
T cd06287 151 PVVLR-VDEAGGEEAGYAACAQLLAQHPDLDALC-VPVDAFAVGAVRAATELGRAVPDQLRVVT 212 (269)
T ss_pred cceeE-ecCCCChHHHHHHHHHHHhCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 32211 11112222323444554332 455544 55778889999999999987655554444
No 226
>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=89.11 E-value=4.4 Score=41.81 Aligned_cols=132 Identities=12% Similarity=0.035 Sum_probs=78.7
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC-------cccchHHHHHHHH
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD-------YGRNGISALSNML 78 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~-------~g~~~~~~l~~~l 78 (806)
+...++|+|...... .+..+++ ...++...+..+++.+...|-++++++..... ......+.+.+++
T Consensus 70 ~~~~~~pvV~~~~~~---~~~~~~~---v~~D~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~R~~gf~~~~ 143 (270)
T cd01544 70 LAKLNPNLVFVDSNP---APDGFDS---VVPDFEQAVEKALDYLLELGHTRIGFIGGEEKTTDGHEYIEDPRETAFREYM 143 (270)
T ss_pred HHhhCCCEEEECCCC---CCCCCCE---EEECHHHHHHHHHHHHHHcCCCcEEEECCCcccccccchhhhHHHHHHHHHH
Confidence 345688999875432 2223443 45666777777888877789999999985432 3344578899999
Q ss_pred HhCCcE-EEEEeccCCCCChhHHHHHHHhcC-CC---CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 79 EKNMAK-VSYKLPLPVQFNQHDITVLLNNSK-PL---GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 79 ~~~g~~-i~~~~~~~~~~~~~~~~~~l~~ik-~~---~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
++.|.. ... .+....+..+-...+.++. +. .+++ |++++...+..+++.+++.|+..++-+-|++
T Consensus 144 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~~~a-i~~~~d~~a~g~~~~l~~~g~~vp~di~v~g 213 (270)
T cd01544 144 KEKGLYDPEL--IYIGDFTVESGYQLMKEALKSLGDNLPTA-FFIASDPMAIGALRALQEAGIKVPEDVSVIS 213 (270)
T ss_pred HHcCCCChhe--EeeCCCCHHHHHHHHHHHHhccCCCCCCE-EEEcCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 998841 111 1111112222233344432 22 2454 4456677888999999999986444444443
No 227
>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=89.04 E-value=21 Score=33.85 Aligned_cols=70 Identities=16% Similarity=0.245 Sum_probs=46.2
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+..+++..+.+..+ .+++++.. +....+..++.+|++|+++...... ...+ ...++....++++++.
T Consensus 12 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 79 (197)
T cd08419 12 YFAPRLLGAFCRRHP-GVEVSLRV-------GNREQVLERLADNEDDLAIMGRPPE---DLDL-VAEPFLDNPLVVIAPP 79 (197)
T ss_pred hHhhHHHHHHHHHCC-CceEEEEE-------CCHHHHHHHHhcCCccEEEecCCCC---CCCe-EEEEeccCCEEEEecC
Confidence 355677778877764 34566664 3567889999999999998532211 1112 3457777888888875
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 80 ~~ 81 (197)
T cd08419 80 DH 81 (197)
T ss_pred CC
Confidence 54
No 228
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=88.97 E-value=6.8 Score=41.77 Aligned_cols=131 Identities=10% Similarity=0.069 Sum_probs=79.7
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~ 84 (806)
.+.++|+|......+ ...+++ ...++...+..+++.+-..|-++++++....+ .+....+.+.+++++.|+.
T Consensus 138 ~~~~iPvV~v~~~~~---~~~~~~---V~~d~~~~~~~a~~~L~~~G~r~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~ 211 (328)
T PRK11303 138 QNDGLPIIALDRALD---REHFTS---VVSDDQDDAEMLAESLLKFPAESILLLGALPELSVSFEREQGFRQALKDDPRE 211 (328)
T ss_pred HhcCCCEEEECCCCC---CCCCCE---EEeCCHHHHHHHHHHHHHCCCCeEEEEeCccccccHHHHHHHHHHHHHHcCCC
Confidence 356889988643221 222333 34666666777888777789999999975433 3455678899999999875
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
+... .....+.++-...+.++.+. .+++|+ +++...+..+++++.+.|+..++-+-|++
T Consensus 212 ~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~g~~~al~~~g~~vP~disv~g 272 (328)
T PRK11303 212 VHYL--YANSFEREAGAQLFEKWLETHPMPDALF-TTSYTLLQGVLDVLLERPGELPSDLAIAT 272 (328)
T ss_pred ceEE--EeCCCChHHHHHHHHHHHcCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 4322 11112222333344454333 456544 45566788899999999976554444443
No 229
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=88.74 E-value=2.8 Score=45.96 Aligned_cols=88 Identities=7% Similarity=-0.065 Sum_probs=67.1
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc-
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP- 121 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~- 121 (806)
..+.+.++.+|.+++.+++...-...+..+.+.+.|++.|+.+.....+.++.+.+++...+..+++.++|+||-.+..
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 5567788999999999888543334557889999999999987655556667778889999999999999999976653
Q ss_pred -chHHHHHHH
Q 003633 122 -DPGLRIFTT 130 (806)
Q Consensus 122 -~~~~~i~~~ 130 (806)
-++.+.+..
T Consensus 100 ~iD~AK~ia~ 109 (383)
T PRK09860 100 PHDCAKGIAL 109 (383)
T ss_pred HHHHHHHHHH
Confidence 355555544
No 230
>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=88.58 E-value=4.2 Score=42.33 Aligned_cols=127 Identities=13% Similarity=0.065 Sum_probs=77.3
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC-------------------Cc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD-------------------DY 66 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~-------------------~~ 66 (806)
+...++|+|.+....+ ...+ ....++...+..+++.+...|-++++++..+. ..
T Consensus 75 ~~~~~ipvV~~~~~~~----~~~~---~v~~d~~~~g~~~~~~L~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 147 (283)
T cd06279 75 LLRRGLPVVVVDQPLP----PGVP---SVGIDDRAAAREAARHLLDLGHRRIGILGLRLGRDRNTGRVTDERLASATFSV 147 (283)
T ss_pred HHHcCCCEEEEecCCC----CCCC---EEeeCcHHHHHHHHHHHHHcCCCcEEEecCccccccccccccccccccccccc
Confidence 3457899998754321 1223 24566677788888888888999999997532 12
Q ss_pred ccchHHHHHHHHHhCCcEEEEEeccC-CCCChhHHHHHHHhcCCCC--CeEEEEecCcchHHHHHHHHHHcCCccCC
Q 003633 67 GRNGISALSNMLEKNMAKVSYKLPLP-VQFNQHDITVLLNNSKPLG--PRVYVVHVSPDPGLRIFTTAQKLQMMTNN 140 (806)
Q Consensus 67 g~~~~~~l~~~l~~~g~~i~~~~~~~-~~~~~~~~~~~l~~ik~~~--~rvivl~~~~~~~~~i~~~a~~~gm~~~~ 140 (806)
.....+.+.+++++.|+.+.....+. ...+.+.....+.++.+.. +++ |++++...+..+++++++.|+..++
T Consensus 148 ~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~gv~~al~~~g~~ip~ 223 (283)
T cd06279 148 ARERLEGYLEALEEAGIDISDVPIWEIPENDRASGEEAARELLDASPRPTA-ILCMSDVLALGALQVARELGLRVPE 223 (283)
T ss_pred HHHHHHHHHHHHHHcCCCCChheEEecCCCchHHHHHHHHHHHcCCCCCcE-EEECCcHHHHHHHHHHHHcCCCCCC
Confidence 33457888899998885431111111 1122233444555554333 444 4455667778899999999985443
No 231
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=88.43 E-value=13 Score=35.29 Aligned_cols=70 Identities=11% Similarity=0.109 Sum_probs=46.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. +....+.+++.+|++|+++..... ....+. +.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~ 80 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHT-------RDSPTVEQWLSAQQCDLGLVSTLH---EPPGIE-RERLLRIDGVCVLPP 80 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEecCC---CCCCee-EEEeeccCeEEEecC
Confidence 456678888888875 45577765 356788999999999999863211 122232 456677788877766
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (196)
T cd08456 81 GH 82 (196)
T ss_pred CC
Confidence 54
No 232
>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=88.39 E-value=3.7 Score=42.83 Aligned_cols=127 Identities=8% Similarity=0.044 Sum_probs=82.3
Q ss_pred CCcEEecccCCCCcccC-CCCceEEecCCcHHHHHHHHHHHHHcCCeE-EEEEEEcCCc--ccchHHHHHHHHHhCCcEE
Q 003633 10 KVPLVSFAATDPTLSAL-QFPYFIRSTQSDSQQMAAMADLIDFYGWKE-VIAIYVDDDY--GRNGISALSNMLEKNMAKV 85 (806)
Q Consensus 10 ~vP~Is~~at~p~Ls~~-~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~-v~ii~~d~~~--g~~~~~~l~~~l~~~g~~i 85 (806)
++|+|...... ... .+|++ ..++..-+..+++.+...|-|+ ++++..+.+. +....+.+.+++++.|+.+
T Consensus 79 ~iPvV~~~~~~---~~~~~~~~V---~~D~~~a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~ 152 (279)
T PF00532_consen 79 GIPVVLIDRYI---DNPEGVPSV---YIDNYEAGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPI 152 (279)
T ss_dssp TSEEEEESS-S---CTTCTSCEE---EEEHHHHHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCE
T ss_pred CCCEEEEEecc---CCcccCCEE---EEcchHHHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCC
Confidence 89999865432 112 34443 2334444567778888999999 9999986654 4556778999999999965
Q ss_pred EEEeccCCCCChhHHHHHHHhcCCCCCeE-EEEecCcchHHHHHHHHHHcC-CccCCcE
Q 003633 86 SYKLPLPVQFNQHDITVLLNNSKPLGPRV-YVVHVSPDPGLRIFTTAQKLQ-MMTNNYV 142 (806)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~l~~ik~~~~rv-ivl~~~~~~~~~i~~~a~~~g-m~~~~~~ 142 (806)
..........+.++-...++++.+..|++ .|++++...|..+++++++.| ...++-+
T Consensus 153 ~~~~i~~~~~~~~~g~~~~~~ll~~~p~idai~~~nd~~A~ga~~~l~~~gr~~ip~di 211 (279)
T PF00532_consen 153 DEEWIFEGDFDYESGYEAARELLESHPDIDAIFCANDMMAIGAIRALRERGRLKIPEDI 211 (279)
T ss_dssp EEEEEEESSSSHHHHHHHHHHHHHTSTT-SEEEESSHHHHHHHHHHHHHTT-TCTTTEE
T ss_pred CcccccccCCCHHHHHHHHHHHHhhCCCCEEEEEeCHHHHHHHHHHHHHcCCcccChhh
Confidence 44333332233344345555555555552 466777788999999999999 6555444
No 233
>PF13377 Peripla_BP_3: Periplasmic binding protein-like domain; PDB: 3K9C_B 3BIL_B 3JVD_B 1ZAY_A 1VPW_A 1DBQ_A 2PUA_A 1QQA_A 1PNR_A 1JHZ_A ....
Probab=88.37 E-value=1.4 Score=41.32 Aligned_cols=99 Identities=10% Similarity=0.086 Sum_probs=63.0
Q ss_pred HHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHH-HhcCCCCCeEEEEecCcc
Q 003633 46 ADLIDFYGWKEVIAIYVDD--DYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLL-NNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 46 ~~ll~~~~W~~v~ii~~d~--~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l-~~ik~~~~rvivl~~~~~ 122 (806)
++.+...|-+++++|..+. .+.....+.+.+++++.|+.......... ....+..... ..+++..+++|++ ++..
T Consensus 1 ~~~L~~~G~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~pdaii~-~~~~ 78 (160)
T PF13377_consen 1 VDYLIERGHRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFEELIFFSD-DDSEDAREAQLLWLRRLRPDAIIC-SNDR 78 (160)
T ss_dssp HHHHHHTT-SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEEGEEEEES-SSHHHHHHHHHHHHHTCSSSEEEE-SSHH
T ss_pred ChHHHHCCCCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCCeeEeecC-CcchhHHHHHHHHHhcCCCcEEEE-cCHH
Confidence 4567778999999999333 34456688899999999998554333322 2222232222 2233336676554 7778
Q ss_pred hHHHHHHHHHHcCCccCCcEEEEc
Q 003633 123 PGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 123 ~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.+..++..+.+.|+..++-+.|++
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 899999999999986554444444
No 234
>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=88.22 E-value=21 Score=33.97 Aligned_cols=70 Identities=13% Similarity=0.125 Sum_probs=47.1
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-..++..+.+..+ .+++++.. ....++...|.+|++|+++.... .....+ ...++.+..++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~ 81 (197)
T cd08425 14 YLIGPLIDRFHARYP-GIALSLRE-------MPQERIEAALADDRLDLGIAFAP---VRSPDI-DAQPLFDERLALVVGA 81 (197)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEE-------CcHHHHHHHHHcCCccEEEEecC---CCCCCc-EEEEeccccEEEEecC
Confidence 344678888887765 45566665 24678999999999999986322 122223 2456777788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~~ 83 (197)
T cd08425 82 TH 83 (197)
T ss_pred CC
Confidence 55
No 235
>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=88.09 E-value=4.8 Score=41.56 Aligned_cols=133 Identities=14% Similarity=0.201 Sum_probs=79.9
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC-cccchHHHHHHHHHhCCcEE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD-YGRNGISALSNMLEKNMAKV 85 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~g~~i 85 (806)
...++|+|.+....+. ...+ .+..++..-+..+++.+...|.++++++...++ .+....+.+.+.+++.|..+
T Consensus 80 ~~~~ipvV~~~~~~~~---~~~~---~V~~D~~~~g~~~~~~l~~~G~~~i~~l~~~~~~~~~~r~~g~~~~l~~~~~~~ 153 (273)
T cd01541 80 EKLGIPYVFINASYEE---LNFP---SLVLDDEKGGYKATEYLIELGHRKIAGIFKADDLQGVKRMKGFIKAYREHGIPF 153 (273)
T ss_pred HHCCCCEEEEecCCCC---CCCC---EEEECcHHHHHHHHHHHHHcCCcCEEEecCCCcccHHHHHHHHHHHHHHcCCCC
Confidence 4568999987544221 1222 356667777788888887889999998874322 34455678899999888642
Q ss_pred EEE--eccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 86 SYK--LPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 86 ~~~--~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
... ...............+.++.+ ..+++| ++.+...+..+++++++.|+..++-+-|++
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av-~~~~d~~a~g~~~al~~~g~~~p~dv~vvg 217 (273)
T cd01541 154 NPSNVITYTTEEKEEKLFEKIKEILKRPERPTAI-VCYNDEIALRVIDLLKELGLKIPEDISVVG 217 (273)
T ss_pred ChHHEEeccccchhhHHHHHHHHHHcCCCCCCEE-EEcCcHHHHHHHHHHHHcCCCCCCcEEEEE
Confidence 111 011111111223344444433 345654 456667788899999999986554444443
No 236
>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=88.00 E-value=7.7 Score=39.97 Aligned_cols=122 Identities=7% Similarity=-0.076 Sum_probs=74.3
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCC-----eEEEEEEEcCC--cccchHHHHHHHH
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGW-----KEVIAIYVDDD--YGRNGISALSNML 78 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W-----~~v~ii~~d~~--~g~~~~~~l~~~l 78 (806)
+...++|+|.+....+ +.. .......++...++.+++.+...+- ++++++....+ ......+.+.+++
T Consensus 77 ~~~~giPvV~~~~~~~---~~~--~~~~V~~d~~~~g~~~~~~l~~~g~~~~~~~~i~~l~g~~~~~~~~~R~~g~~~~~ 151 (268)
T cd06306 77 QVAASIPVIALVNDIN---SPD--ITAKVGVSWYEMGYQAGEYLAQRHPKGSKPAKVAWFPGPKGAGWVKAVEKGFRDAL 151 (268)
T ss_pred HHHCCCCEEEeccCCC---Ccc--eeEEecCChHHHHHHHHHHHHHHhhcCCCCceEEEEeCCCCCchHHHHHHHHHHHH
Confidence 3457899998743211 111 1123455555567788888766665 89999975433 3455678899999
Q ss_pred HhCCcEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCC
Q 003633 79 EKNMAKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQM 136 (806)
Q Consensus 79 ~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm 136 (806)
++.++++... .....+.+.-...+.++.+ .++++|+. ....+..+++.+++.|+
T Consensus 152 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~--~d~~a~~~~~~l~~~g~ 207 (268)
T cd06306 152 AGSAIEISAI--KYGDTGKEVQRKLVEEALEAHPDIDYIVG--SAVAAEAAVGILRQRGL 207 (268)
T ss_pred hhcCcEEeee--ccCCccHHHHHHHHHHHHHhCCCcCEEee--cchhhhHHHHHHHhcCC
Confidence 9999876532 1111222333344444432 34677653 46777888999999996
No 237
>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=87.86 E-value=7.1 Score=39.99 Aligned_cols=129 Identities=10% Similarity=0.100 Sum_probs=79.1
Q ss_pred cCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC-CcccchHHHHHHHHHhCCcEEE
Q 003633 8 GLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD-DYGRNGISALSNMLEKNMAKVS 86 (806)
Q Consensus 8 ~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~-~~g~~~~~~l~~~l~~~g~~i~ 86 (806)
..++|+|.+....+ ...++++ ..++..-+..+++.+...|-++++++..+. .........+.+++++.|+...
T Consensus 75 ~~~iPvV~~~~~~~---~~~~~~v---~~d~~~~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~ 148 (263)
T cd06280 75 RLSFPVVLIDRAGP---AGRVDAV---VLDNRAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAPD 148 (263)
T ss_pred hcCCCEEEECCCCC---CCCCCEE---EECcHHHHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHHcCCCCC
Confidence 45889988754432 2234542 345666677777888788999999987532 2234557888999998887643
Q ss_pred EEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 87 YKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 87 ~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.. ... .+.++....+.++... .+++ |++++...+..+++.+++.|+..++-+.|++
T Consensus 149 ~~-~~~--~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~~l~~~g~~~p~di~iig 206 (263)
T cd06280 149 AR-FVA--PTAEAAEAALAAWLAAPERPEA-LVASNGLLLLGALRAVRAAGLRIPQDLALAG 206 (263)
T ss_pred hh-hcc--cCHHHHHHHHHHHhcCCCCCcE-EEECCcHHHHHHHHHHHHcCCCCCCcEEEEE
Confidence 21 111 2222323344444322 4555 4556677788999999999986554444443
No 238
>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=87.52 E-value=17 Score=35.07 Aligned_cols=70 Identities=11% Similarity=0.064 Sum_probs=46.5
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.++.+ .+++++.. +....+...|.+|++|+++.... .....+. ..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~ 80 (200)
T cd08467 13 ALLPRLAPRLRERAP-GLDLRLCP-------IGDDLAERGLEQGTIDLAVGRFA---VPPDGLV-VRRLYDDGFACLVRH 80 (200)
T ss_pred HHHHHHHHHHHhhCC-CCEEEEec-------CCcccHHHHhhCCCcCEEEecCC---CCCccce-eEEeeeccEEEEEcC
Confidence 455677888877765 34566664 24568999999999999985321 1112233 356778888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~h 82 (200)
T cd08467 81 GH 82 (200)
T ss_pred CC
Confidence 54
No 239
>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=87.41 E-value=28 Score=33.39 Aligned_cols=72 Identities=14% Similarity=0.144 Sum_probs=47.8
Q ss_pred EeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEe
Q 003633 382 QGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAP 461 (806)
Q Consensus 382 ~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~ 461 (806)
..+-.+++..+.+..+ .+++++.. ++...+...+.+|++|+++..... .....+. +.++....++++++
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 4566778888887765 34455554 356789999999999999863211 1112233 45677788888877
Q ss_pred ccC
Q 003633 462 INN 464 (806)
Q Consensus 462 ~~~ 464 (806)
...
T Consensus 81 ~~h 83 (198)
T cd08443 81 RDH 83 (198)
T ss_pred CCC
Confidence 655
No 240
>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=87.25 E-value=7.8 Score=37.06 Aligned_cols=107 Identities=11% Similarity=0.107 Sum_probs=70.9
Q ss_pred EEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC--CcEEEEEeccCCCCChhHHHHHHHhcCC
Q 003633 32 IRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN--MAKVSYKLPLPVQFNQHDITVLLNNSKP 109 (806)
Q Consensus 32 ~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~--g~~i~~~~~~~~~~~~~~~~~~l~~ik~ 109 (806)
-|+.++ .....+.+.+..-++ ++.++-.+.+ .++.+...|++. |+.|+... ++..+..+...+++.|++
T Consensus 29 ~rv~g~--dl~~~l~~~~~~~~~-~ifllG~~~~----~~~~~~~~l~~~yP~l~ivg~~--~g~f~~~~~~~i~~~I~~ 99 (172)
T PF03808_consen 29 ERVTGS--DLFPDLLRRAEQRGK-RIFLLGGSEE----VLEKAAANLRRRYPGLRIVGYH--HGYFDEEEEEAIINRINA 99 (172)
T ss_pred cccCHH--HHHHHHHHHHHHcCC-eEEEEeCCHH----HHHHHHHHHHHHCCCeEEEEec--CCCCChhhHHHHHHHHHH
Confidence 344443 334666666666666 6666665444 566777777776 66666443 222356778899999999
Q ss_pred CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcCccc
Q 003633 110 LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATDWLS 150 (806)
Q Consensus 110 ~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~~~ 150 (806)
++||+|++.+..+....++.+.++.. ... +||..++..
T Consensus 100 ~~pdiv~vglG~PkQE~~~~~~~~~l--~~~-v~i~vG~~~ 137 (172)
T PF03808_consen 100 SGPDIVFVGLGAPKQERWIARHRQRL--PAG-VIIGVGGAF 137 (172)
T ss_pred cCCCEEEEECCCCHHHHHHHHHHHHC--CCC-EEEEECchh
Confidence 99999999998887777776665533 233 777776544
No 241
>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=87.24 E-value=9.9 Score=39.09 Aligned_cols=130 Identities=9% Similarity=-0.048 Sum_probs=76.7
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC-cccchHHHHHHHHHhC-C
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD-YGRNGISALSNMLEKN-M 82 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~-g 82 (806)
.+.++|+|.+....+ . ..+ .+..++...++.+++.+... |.++++++..+.. ......+.+.+.+++. +
T Consensus 79 ~~~~ipvv~~~~~~~---~-~~~---~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~g~~~~~~~~R~~g~~~~~~~~~~ 151 (271)
T cd06321 79 QAAGIVVVAVDVAAE---G-ADA---TVTTDNVQAGEISCQYLADRLGGKGNVAILNGPPVSAVLDRVAGCKAALAKYPG 151 (271)
T ss_pred HHCCCeEEEecCCCC---C-ccc---eeeechHHHHHHHHHHHHHHhCCCceEEEEeCCCCchHHHHHHHHHHHHHhCCC
Confidence 456899999865432 1 112 24566666777888887766 9999999975432 2344567888889887 6
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
+++.... .....+...-...+.++.+ ..+++ |++.+...+..+++++++.|+ .+...+..|
T Consensus 152 ~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~al~~~g~--~di~v~g~d 214 (271)
T cd06321 152 IKLLSDD-QNGKGSRDGGLRVMQGLLTRFPKLDG-VFAINDPTAIGADLAAKQAGR--NDIKITSVD 214 (271)
T ss_pred cEEEeee-cCCCCChhhHHHHHHHHHHhCCCCCE-EEECCchhHHHHHHHHHHcCC--CCcEEEEec
Confidence 6532111 1111121121233444432 34565 444566678889999999997 344455444
No 242
>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=87.05 E-value=4.6 Score=41.24 Aligned_cols=134 Identities=11% Similarity=0.092 Sum_probs=80.3
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHH-cCC-eEEEEEEEcCCc--ccchHHHHHHHHHh-
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDF-YGW-KEVIAIYVDDDY--GRNGISALSNMLEK- 80 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~-~~W-~~v~ii~~d~~~--g~~~~~~l~~~l~~- 80 (806)
+...+||+|++... .....+...-..++....+..+++++.. .+= .+|+++....++ .....+.+.+.+++
T Consensus 76 ~~~~gIpvv~~d~~----~~~~~~~~~~v~~d~~~~G~~~a~~l~~~~~~~~~v~~~~~~~~~~~~~~r~~g~~~~l~~~ 151 (257)
T PF13407_consen 76 AKAAGIPVVTVDSD----EAPDSPRAAYVGTDNYEAGKLAAEYLAEKLGAKGKVLILSGSPGNPNTQERLEGFRDALKEY 151 (257)
T ss_dssp HHHTTSEEEEESST----HHTTSTSSEEEEE-HHHHHHHHHHHHHHHHTTTEEEEEEESSTTSHHHHHHHHHHHHHHHHC
T ss_pred HhhcCceEEEEecc----ccccccceeeeeccHHHHHHHHHHHHHHHhccCceEEeccCCCCchHHHHHHHHHHHHHhhc
Confidence 45678999997544 1112234445667778888999988644 333 677777544433 33467888889988
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.++++... .+....+.+.....+.++.+.++-..|+.++...+..+.++.++.|+.+ .+++.+
T Consensus 152 ~~~~~~~~-~~~~~~~~~~a~~~~~~~l~~~~~~~i~~~~~~~~~g~~~al~~~g~~~--~~~v~g 214 (257)
T PF13407_consen 152 PGVEIVDE-YEYTDWDPEDARQAIENLLQANPVDAIIACNDGMALGAAQALQQAGRAG--KVIVVG 214 (257)
T ss_dssp TTEEEEEE-EEECTTSHHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHHHHHHTTCTT--TSEEEE
T ss_pred ceeeeeee-eeccCCCHHHHHHHHHHhhhcCCceEEEeCCChHHHHHHHHHHHcCCcc--cceeec
Confidence 46666542 2222344455555555554444422345566677777899999999843 344444
No 243
>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=87.01 E-value=6.4 Score=40.44 Aligned_cols=135 Identities=10% Similarity=0.070 Sum_probs=79.6
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC-cccchHHHHHHHHHhCCcE
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD-YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~g~~ 84 (806)
+...++|+|.+....+. .. +-.+..++...+..+++.+...|-++++++..... ......+.+.+++++.|+.
T Consensus 67 l~~~~~PvV~~~~~~~~---~~---~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~ 140 (265)
T cd01543 67 LQKLGIPVVDVSGSREK---PG---IPRVTTDNAAIGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAGYE 140 (265)
T ss_pred HhhCCCCEEEEeCccCC---CC---CCEEeeCHHHHHHHHHHHHHHCCCcEEEEEcCCCCHHHHHHHHHHHHHHHHcCCc
Confidence 34568999987543221 12 23456677777788888888889999999874433 1233467889999999987
Q ss_pred EEEEeccCC--CCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccC-CcEEEEcC
Q 003633 85 VSYKLPLPV--QFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTN-NYVWLATD 147 (806)
Q Consensus 85 i~~~~~~~~--~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~-~~~wi~t~ 147 (806)
+........ ..+.++-...+.++.+. .+++ |++++...+..+++.+++.|+..+ +...+.-|
T Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~~l~~~g~~vp~di~vigfd 207 (265)
T cd01543 141 CSFFYRGLSTDAQSWEEEQEELAQWLQSLPKPVG-IFACTDARARQLLEACRRAGIAVPEEVAVLGVD 207 (265)
T ss_pred cccccCccccccccHHHHHHHHHHHHhcCCCCcE-EEecChHHHHHHHHHHHHhCCCCCCceEEEeeC
Confidence 521111110 11112223334443222 3454 555577788889999999997533 33444434
No 244
>PRK15454 ethanol dehydrogenase EutG; Provisional
Probab=86.71 E-value=4.1 Score=44.79 Aligned_cols=88 Identities=7% Similarity=-0.070 Sum_probs=65.8
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
+.+.++++.+|.+++.++....-...+..+.+.+.|++.|+.+.....+.++.+.+++...+...++.++|+||-.+...
T Consensus 38 ~~l~~~~~~~g~~~~lvv~~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~P~~~~v~~~~~~~r~~~~D~IiavGGGS 117 (395)
T PRK15454 38 SSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLAVKGIAMTLWPCPVGEPCITDVCAAVAQLRESGCDGVIAFGGGS 117 (395)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCcCEEEEeCChH
Confidence 55677888999998887764433445668889999999999876554556666677888999999999999999888654
Q ss_pred --hHHHHHHH
Q 003633 123 --PGLRIFTT 130 (806)
Q Consensus 123 --~~~~i~~~ 130 (806)
++.+.+..
T Consensus 118 ~iD~AKaia~ 127 (395)
T PRK15454 118 VLDAAKAVAL 127 (395)
T ss_pred HHHHHHHHHH
Confidence 44544433
No 245
>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=86.69 E-value=7.5 Score=41.43 Aligned_cols=130 Identities=11% Similarity=0.088 Sum_probs=76.9
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcE
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~ 84 (806)
...++|+|......+ +..+++ ...++..-+..+++.+-..|-++++++....+ ......+.+.+++++.|+.
T Consensus 137 ~~~~iPvV~~~~~~~---~~~~~~---V~~dn~~~~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~ 210 (327)
T TIGR02417 137 QNEGLPVVALDRSLD---DEHFCS---VISDDVDAAAELIERLLSQHADEFWYLGAQPELSVSRDRLAGFRQALKQATLE 210 (327)
T ss_pred HhcCCCEEEEccccC---CCCCCE---EEeCcHHHHHHHHHHHHHCCCCeEEEEeCcccchhHHHHHHHHHHHHHHcCCC
Confidence 346789987754322 122333 34455555666667777789999999975433 3455678899999998875
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCC---CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPL---GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~---~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
+... +....+.++-...+.++.+. .+++| ++.+...+..+++++++.| ..++-+-|++
T Consensus 211 ~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~~Ai-~~~~D~~A~g~~~al~~~g-~vP~dvsvig 271 (327)
T TIGR02417 211 VEWV--YGGNYSRESGYQMFAKLCARLGRLPQAL-FTTSYTLLEGVLDYMLERP-LLDSQLHLAT 271 (327)
T ss_pred hHhE--EeCCCChHHHHHHHHHHHhcCCCCCcEE-EEcCcHHHHHHHHHHHHcC-CCCCcceEEE
Confidence 3211 11111222223344454332 35654 4456677889999999999 5554444443
No 246
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=86.52 E-value=18 Score=38.27 Aligned_cols=71 Identities=13% Similarity=0.270 Sum_probs=47.5
Q ss_pred eeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEecc
Q 003633 384 YCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 384 ~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
+-.+++..+.+..+ .+++++.. ++..+++.+|.+|++|+++...... .....+ -..|+....++++++..
T Consensus 111 ~l~~~l~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~l-~~~~l~~~~~~lv~~~~ 180 (312)
T PRK10341 111 FMSDMINKFKEVFP-KAQVSMYE-------AQLSSFLPAIRDGRLDFAIGTLSNE-MKLQDL-HVEPLFESEFVLVASKS 180 (312)
T ss_pred hHHHHHHHHHHhCC-CCEEEEEe-------CCHHHHHHHHHcCCCcEEEecCCcc-cccCCe-eEEEEecccEEEEEcCC
Confidence 44577777777665 35566665 3578999999999999998632211 111222 34677778888888765
Q ss_pred C
Q 003633 464 N 464 (806)
Q Consensus 464 ~ 464 (806)
.
T Consensus 181 ~ 181 (312)
T PRK10341 181 R 181 (312)
T ss_pred C
Confidence 4
No 247
>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=86.44 E-value=13 Score=39.10 Aligned_cols=133 Identities=11% Similarity=0.015 Sum_probs=69.1
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCe---------EE--EEEEEcCC--cccch
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWK---------EV--IAIYVDDD--YGRNG 70 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~---------~v--~ii~~d~~--~g~~~ 70 (806)
+...++|+|.+....+.......+-+..+.+++..-+...++++... |-+ ++ +++..+.. .....
T Consensus 78 ~~~~giPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~a~~l~~~~~~~~~~~~~~~~g~~~i~~~~g~~~~~~~~~R 157 (303)
T cd01539 78 AKQKNIPVIFFNREPEEEDIKSYDKAYYVGTDAEQSGILQGKLIADYWNANKDALDKNGDGIIQYVMLKGEPGHPDAIAR 157 (303)
T ss_pred HHHCCCCEEEeCCCCcccccccccccceeeecHHHHHHHHHHHHHHHhhccccccccCCCCceEEEEEEcCCCCchhhhh
Confidence 34569999987653221111111222335566666667777776443 221 23 44443222 22344
Q ss_pred HHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCC---CCeEEEEecCcchHHHHHHHHHHcCCccC
Q 003633 71 ISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPL---GPRVYVVHVSPDPGLRIFTTAQKLQMMTN 139 (806)
Q Consensus 71 ~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~---~~rvivl~~~~~~~~~i~~~a~~~gm~~~ 139 (806)
.+.+.+++++.++.+..........+.+.-...++++... ++++ |++.+...+..+++++++.|...+
T Consensus 158 ~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~~a-i~~~~d~~a~g~~~al~~~g~~~p 228 (303)
T cd01539 158 TKYSIETLNDAGIKTEELASDTANWDRAQAKDKMDALLLKYGDKIEA-VIANNDAMALGAIEALQKYGYNKG 228 (303)
T ss_pred hhhHHHHHHhcCCCeEEEEeecCCCCHHHHHHHHHHHHHhcCCCccE-EEECCchHHHHHHHHHHHcCCCcC
Confidence 6778899998887653222222222223333344444322 2444 444556667788899999887543
No 248
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=86.38 E-value=27 Score=37.33 Aligned_cols=84 Identities=11% Similarity=0.089 Sum_probs=56.3
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
+++|||+... -...+-.++++.+.+..+ .+.+++.. ++.+.++++|.+|++|+++...
T Consensus 93 g~lrIg~~~~--------------~~~~~l~~~l~~f~~~~P-~v~i~l~~-------~~~~~~~~~l~~g~~Dl~i~~~ 150 (327)
T PRK12680 93 GQLTLTTTHT--------------QARFVLPPAVAQIKQAYP-QVSVHLQQ-------AAESAALDLLGQGDADIAIVST 150 (327)
T ss_pred eEEEEEecch--------------hHHHhhHHHHHHHHHHCC-CcEEEEEe-------CChHHHHHHHHCCCCcEEEEec
Confidence 5799998741 112445678888888776 34566665 3578999999999999998532
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
.. ....... ..|+....++++++...
T Consensus 151 ~~--~~~~~~~-~~~l~~~~~~l~~~~~h 176 (327)
T PRK12680 151 AG--GEPSAGI-AVPLYRWRRLVVVPRGH 176 (327)
T ss_pred CC--CCCCcce-EEEeeccceEEEEeCCC
Confidence 11 1111222 46788888888887665
No 249
>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=86.36 E-value=16 Score=37.75 Aligned_cols=134 Identities=12% Similarity=0.038 Sum_probs=76.2
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHH-HHcCCe--EEEEEEEcC--CcccchHHHHHHHHHh
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLI-DFYGWK--EVIAIYVDD--DYGRNGISALSNMLEK 80 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W~--~v~ii~~d~--~~g~~~~~~l~~~l~~ 80 (806)
+.+.++|+|.+....+ .. .+.+-.+..++...+..+++.+ +..|-+ +++++..+. ..+....+.+.+.+++
T Consensus 76 ~~~~~iPvV~~~~~~~---~~-~~~~~~v~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~~~l~~ 151 (282)
T cd06318 76 AKAAGVPVVVVDSSIN---LE-AGVVTQVQSSNAKNGNLVGEWVVGELGDKPMKIILLSGDAGNLVGQARRDGFLLGVSE 151 (282)
T ss_pred HHHCCCCEEEecCCCC---CC-cCeEEEEecCcHHHHHHHHHHHHHHhCCCCceEEEEECCCCCchHhHHHHhHHHHHhh
Confidence 3457899998864321 10 1223345666677788888876 446865 888887532 3456667889999998
Q ss_pred CCcE------EEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 81 NMAK------VSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 81 ~g~~------i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.|+. +..........+..+-...+.++... ++++ |++.+...+..+++++++.|+. +-+-+++
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~al~~~g~~--~dv~vvg 222 (282)
T cd06318 152 AQLRKYGKTNFTIVAQGYGDWTREGGLKAMEDLLVAHPDINV-VYSENDDMALGAMRVLAEAGKT--DDVKVAA 222 (282)
T ss_pred CcccccccCCeEEEecCCCCCCHHHHHHHHHHHHHhCCCcCE-EEECCcchHHHHHHHHHHcCCC--CCeEEEe
Confidence 8642 11111011112222323334443322 3444 4455566778899999999974 3344443
No 250
>cd08192 Fe-ADH7 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to CoA-dependent thiolysis to yield acetyl-CoA and 6-C8-SPC-CoA. The major laundry surfactant in worldwide use is commercial linear alkylbenzenesulfonate (LAS) which contains 20 congeners of linear alkanes (C10 to C13). LAS is fully biodegradable in oxic environments. Degradation involves microbial communities. Parvibaculum lavamentivorans DS-1T is a representative member of many heterotrophic, LAS-degrading communities, in which it catalyzes the first steps of LAS degradation. Strain DS-1T is a small heterotrophic bacterium able to omega-oxygenate the comm
Probab=86.19 E-value=5.2 Score=43.70 Aligned_cols=89 Identities=8% Similarity=-0.062 Sum_probs=66.6
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc-
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP- 121 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~- 121 (806)
..+.++++.+|.+++.+++.......+..+.+.+.|++.|+++.....+.+..+.+++...+...+..++|.||-.+..
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 4567788889999999888544444446788999999999987654456666777888899999999999999976653
Q ss_pred -chHHHHHHHH
Q 003633 122 -DPGLRIFTTA 131 (806)
Q Consensus 122 -~~~~~i~~~a 131 (806)
-+..+++...
T Consensus 93 viD~aK~ia~~ 103 (370)
T cd08192 93 ALDLAKAVALM 103 (370)
T ss_pred HHHHHHHHHHH
Confidence 3556555443
No 251
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=86.15 E-value=6.3 Score=42.58 Aligned_cols=91 Identities=5% Similarity=0.010 Sum_probs=73.2
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
+.+.+.++.+|++++-+|.+..-...+..+.+.+.|++.|+.+.....+.++.+.+....-+..+++.++|.||-.+-.+
T Consensus 18 ~~l~~~~~~~g~~r~liVTd~~~~~~g~~~~v~~~L~~~~i~~~if~~v~p~P~~~~v~~~~~~~~~~~~D~iIalGGGS 97 (377)
T COG1454 18 KELGEEVKRLGAKRALIVTDRGLAKLGLLDKVLDSLDAAGIEYEVFDEVEPEPTIETVEAGAEVAREFGPDTIIALGGGS 97 (377)
T ss_pred HHHHHHHHhcCCCceEEEECCccccchhHHHHHHHHHhcCCeEEEecCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 56667788899999999997666667789999999999998877777777777888888899999999999999877543
Q ss_pred --hHHHHHHHHHH
Q 003633 123 --PGLRIFTTAQK 133 (806)
Q Consensus 123 --~~~~i~~~a~~ 133 (806)
++.+.+....+
T Consensus 98 ~~D~AK~i~~~~~ 110 (377)
T COG1454 98 VIDAAKAIALLAE 110 (377)
T ss_pred HHHHHHHHHHHhh
Confidence 55555544443
No 252
>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=86.05 E-value=28 Score=32.88 Aligned_cols=72 Identities=21% Similarity=0.165 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++.+.+++.+.+|++|+++..-... .....+ .+.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~-~~~~l~~~~~~~v~~~ 82 (195)
T cd08427 13 GLLPRALARLRRRHP-DLEVHIVP-------GLSAELLARVDAGELDAAIVVEPPF-PLPKDL-VWTPLVREPLVLIAPA 82 (195)
T ss_pred HHhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCCCEEEEcCCCC-ccccCc-eEEEcccCcEEEEECC
Confidence 455677888877775 34566654 3568999999999999998632111 101223 2456777888888776
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 83 ~~ 84 (195)
T cd08427 83 EL 84 (195)
T ss_pred CC
Confidence 54
No 253
>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=86.04 E-value=5.5 Score=40.98 Aligned_cols=128 Identities=7% Similarity=-0.029 Sum_probs=73.4
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~ 83 (806)
+.+.++|+|......+ ...++ ...++..-+..+++.+...|-++++++..... .+....+.+.+++++.|+
T Consensus 75 ~~~~~ipvV~i~~~~~----~~~~~---V~~d~~~~g~~a~~~l~~~G~~~i~~l~~~~~~~~~~~R~~Gf~~~~~~~~~ 147 (269)
T cd06281 75 LASLDLPIVLLDRDMG----GGADA---VLFDHAAGMRQAVEYLISLGHRRIALVGGGSNTRPGRERLEGYKAAFAAAGL 147 (269)
T ss_pred HHhCCCCEEEEecccC----CCCCE---EEECcHHHHHHHHHHHHHCCCcEEEEecCccccccHHHHHHHHHHHHHHcCC
Confidence 3456889988754432 12233 34444444466667666679999999975332 234456888999999887
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcE
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYV 142 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~ 142 (806)
.+.....+.... .+.-...+.++.+ ..+++|+ +.+...+..+++++++.|+..++-+
T Consensus 148 ~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~ip~dv 206 (269)
T cd06281 148 PPDPALVRLSTP-AASGFDATRALLALPDRPTAII-AGGTQVLVGVLRALREAGLRIPRDL 206 (269)
T ss_pred CCCHHHeecCcH-HHHHHHHHHHHHcCCCCCcEEE-EcCcHHHHHHHHHHHHcCCCCCcce
Confidence 542110111111 1222233444332 3467765 4566677789999999997544433
No 254
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=85.91 E-value=27 Score=33.12 Aligned_cols=73 Identities=14% Similarity=0.048 Sum_probs=47.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEe--cCccceeEecccccccceEEEE
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIV--TNRTKIVDFSQPYISTGLVIVA 460 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it--~~r~~~vdft~p~~~~~~~~~v 460 (806)
.+-.+++..+.+..+ .+++++.. ++...+..++.+|++|+++...... ......+ .+.++....+++++
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 445677788887765 45566664 3567899999999999998632111 1122223 35667788888888
Q ss_pred eccC
Q 003633 461 PINN 464 (806)
Q Consensus 461 ~~~~ 464 (806)
+...
T Consensus 84 ~~~~ 87 (200)
T cd08423 84 PADH 87 (200)
T ss_pred cCCC
Confidence 7655
No 255
>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=85.89 E-value=33 Score=32.72 Aligned_cols=70 Identities=14% Similarity=0.171 Sum_probs=46.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.++.+ .+++++.. ++..++...+.+|++|+++...... ...+ -+.++.+..++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~ 80 (196)
T cd08458 13 SFMSGVIQTFIADRP-DVSVYLDT-------VPSQTVLELVSLQHYDLGISILAGD---YPGL-TTEPVPSFRAVCLLPP 80 (196)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEec-------cChHHHHHHHHcCCCCEEEEeccCC---CCCc-eEEEeccCceEEEecC
Confidence 445677888888776 34566654 3567789999999999998633221 1222 2356777788888766
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~h 82 (196)
T cd08458 81 GH 82 (196)
T ss_pred CC
Confidence 54
No 256
>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=85.82 E-value=7.5 Score=40.07 Aligned_cols=124 Identities=11% Similarity=-0.010 Sum_probs=67.8
Q ss_pred cccC-CCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHH-cCCeEEEEEEEcCC-cccchHHHHHHHHHhCC
Q 003633 6 ANGL-KVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDF-YGWKEVIAIYVDDD-YGRNGISALSNMLEKNM 82 (806)
Q Consensus 6 ~~~~-~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~-~~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~g 82 (806)
..++ ++|++......+.. ...+ +...++..-+..++.++.. .|-++++++..+.. ......+.+.+.+++.|
T Consensus 76 ~~~~~~~PiV~i~~~~~~~--~~~~---~v~~d~~~a~~~a~~ll~~~~G~~~I~~i~~~~~~~~~~r~~gf~~~~~~~g 150 (265)
T cd06354 76 AKQYPDQKFAIIDAVVDDP--PNVA---SIVFKEEEGSFLAGYLAALMTKTGKVGFIGGMDIPLIRRFEAGFEAGVKYVN 150 (265)
T ss_pred HHHCCCCEEEEEecccCCC--CcEE---EEEecchhHHHHHHHHHHhhcCCCeEEEEecccChHHHHHHHHHHHHHHHHh
Confidence 3444 78999875422110 1112 2333343334444556654 39999999975332 12222467888898888
Q ss_pred ---cEEEEEeccCCCCC-hhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcC
Q 003633 83 ---AKVSYKLPLPVQFN-QHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQ 135 (806)
Q Consensus 83 ---~~i~~~~~~~~~~~-~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~g 135 (806)
..+..........+ .++-...+.++.+..+++ |++.+...+..+++++++.|
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~pda-I~~~nd~~A~gv~~al~~~g 206 (265)
T cd06354 151 PGVPDIEVLVQYAGSFNDPAKGKEIAQAMYDQGADV-IFAAAGGTGNGVFQAAKEAG 206 (265)
T ss_pred ccCCCceEEEEEcCcccCHHHHHHHHHHHHHCCCcE-EEECCCCCchHHHHHHHhcC
Confidence 64332111111111 123334445544445776 55557778889999999987
No 257
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=85.20 E-value=1.6 Score=45.75 Aligned_cols=210 Identities=12% Similarity=0.065 Sum_probs=111.8
Q ss_pred HHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeE-ecccccccceEEEEeccC
Q 003633 386 IDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVD-FSQPYISTGLVIVAPINN 464 (806)
Q Consensus 386 idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vd-ft~p~~~~~~~~~v~~~~ 464 (806)
..+.+.+.++.|-++++++.+.+.- +....+++.|.+|.+|++.........+...+. +..||......
T Consensus 16 ~~fa~~v~e~t~G~v~i~v~~~g~l---g~~~e~~~~v~~G~vdm~~~~~~~~~~~~p~~~~~~lP~~~~~~~------- 85 (286)
T PF03480_consen 16 EKFAEEVEERTGGRVKIEVFPAGQL---GKEAEVLEAVQDGAVDMAVVSPSYLAGFVPEFGVFDLPFLFRDYE------- 85 (286)
T ss_dssp HHHHHHHHHHTTTSEEEEEEETTSS---SSHHHHHHHHHTTSSSEEEEEGGGGTTTSGGGGGGGSTTTSSSHH-------
T ss_pred HHHHHHHHHHcCCeEEEEEecCccc---CCHHHHHHHHhCCCccEEeecchhhhhhchhheeeeCCCCCCCHH-------
Confidence 6788889999999988888875421 367899999999999999764433333322211 33343331100
Q ss_pred CCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchhhHHHHHHHhhhccCcccccccchhhhHHH
Q 003633 465 HKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIATMFLFSFSTLFKTNQEATVSSLGRFVMVV 544 (806)
Q Consensus 465 ~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~ 544 (806)
++.. ++-. . ..+.+.--
T Consensus 86 ------------------------------------------------~~~~-~~~~---~-----------~~~~l~~~ 102 (286)
T PF03480_consen 86 ------------------------------------------------ELDR-VMDS---G-----------YGPELREE 102 (286)
T ss_dssp ------------------------------------------------HHHH-HHHS---H-----------HHHHHHHH
T ss_pred ------------------------------------------------HHHH-HHhC---c-----------HHHHHHHH
Confidence 0000 0000 0 00000000
Q ss_pred HHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCchhHHHhhhhcccccccceeCCCHhHHHHHHhc
Q 003633 545 WLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGSFAYSYLSDSLRIQKSRLISLGSPEDYERALRQ 624 (806)
Q Consensus 545 w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~ 624 (806)
.---.+.+...|..-...+.+. ..+|++++|| +|.++.+..+.....++ +.+|. ..+.. ...|.+.+|++
T Consensus 103 ~~~~g~~~L~~~~~g~~~~~~~---~~pi~s~~Dl--kG~kiR~~~~~~~~~~~-~~lGa---~pv~i-p~~evy~aLq~ 172 (286)
T PF03480_consen 103 LEEKGIKLLGWFPGGPRQFFST---KKPIRSPEDL--KGLKIRVPGSPVMSDFF-EALGA---SPVPI-PWSEVYQALQQ 172 (286)
T ss_dssp HHHTTEEEEEEEEEEEEEEEES---SS--SSGGGG--TTEEEEETSSHHHHHHH-HHCTS---EEEE--TGGGHHHHHHT
T ss_pred HHhhceEEEEEecCCceEEEec---ccCCccHhhH--hhCeEEecCCHHHHHHH-HHcCC---eeecC-cHHHHHHHHhc
Confidence 0000122223344444444442 3589999999 78888876455555555 45553 23333 45689999999
Q ss_pred CCCCCCeEEEEeCchhHHHH-hhCCCCeEEeCCccccCCceeeecCCCC--chHHHHHHHHh
Q 003633 625 GPRNGGVAAIVDELPYVQLF-LSNQTDFGIIGQPFTRSGWGFAFQRDSP--LAVGMSTAILK 683 (806)
Q Consensus 625 ~~~~g~~~a~i~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~k~sp--l~~~~n~~il~ 683 (806)
|.+|+.......+... +.+.+++..... ....++.+++.+..= |-+....+|.+
T Consensus 173 ----G~vDg~~~~~~~~~~~~~~ev~~y~~~~~-~~~~~~~~~~n~~~w~~L~~e~q~~l~~ 229 (286)
T PF03480_consen 173 ----GVVDGAENSASSIYSLGLYEVAKYFTDTN-HGWSPYAVIMNKDWWDSLPDEDQEALDD 229 (286)
T ss_dssp ----TSSSEEEEEHHHHHHTTGGGTSSEEEEEE-EEEEEEEEEEEHHHHHHS-HHHHHHHHH
T ss_pred ----CCcCeEecCHHHHHhcChhhhCCeeEeec-ccCcceEEEEcHHHHhcCCHHHHHHHHH
Confidence 8999999877665332 223456444333 444556666766531 44444444433
No 258
>cd08190 HOT Hydroxyacid-oxoacid transhydrogenase (HOT) involved in gamma-hydroxybutyrate metabolism. Hydroxyacid-oxoacid transhydrogenase (HOT), also known as D-2-hydroxyglutarate transhydrogenase. It catalyzes the conversion of gamma-hydroxybutyrate (GHB) to succinic semialdehyde (SSA), coupled to the stoichiometric conversion of alpha-ketoglutarate to D-2-hydroxyglutarate in gamma-Hydroxybutyrate catabolism. Unlike many other alcohols, which are oxidized by NAD-linked dehydrogenases, gamma-hydroxybutyrate is metabolized to succinate semialdehyde by hydroxyacid-oxoacid transhydrogenase which does not require free NAD or NADP, but instead using alpha -ketoglutarate as an acceptor, converting it to d-2-hydroxyglutarate. Alpha-ketoglutarate serves as an intermediate acceptor to regenerate NAD(P) required for the oxidation of GHB. HOT also catalyzes the reversible oxidation of a hydroxyacid obligatorily coupled to the reduction of an oxoacid, and requires no cofactor. In mammals, the HOT
Probab=85.19 E-value=6.1 Score=43.79 Aligned_cols=87 Identities=9% Similarity=-0.046 Sum_probs=66.2
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
+.+.++++.+|.+++.+++...-+..+..+.+.+.|++.|+.+.....+.++.+.+.+...+..+++.++|+||-.+...
T Consensus 12 ~~l~~~l~~~g~~~vlivt~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 91 (414)
T cd08190 12 AEVGMDLKNLGARRVCLVTDPNLAQLPPVKVVLDSLEAAGINFEVYDDVRVEPTDESFKDAIAFAKKGQFDAFVAVGGGS 91 (414)
T ss_pred HHHHHHHHHcCCCeEEEEECcchhhcchHHHHHHHHHHcCCcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 55667888999999999986555545567889999999998876544555566777888888999999999999887643
Q ss_pred --hHHHHHH
Q 003633 123 --PGLRIFT 129 (806)
Q Consensus 123 --~~~~i~~ 129 (806)
+..+.+.
T Consensus 92 viD~AKaia 100 (414)
T cd08190 92 VIDTAKAAN 100 (414)
T ss_pred HHHHHHHHH
Confidence 4555443
No 259
>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=85.09 E-value=35 Score=32.30 Aligned_cols=72 Identities=15% Similarity=0.092 Sum_probs=46.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-..++..+.+..+ .+++++.. +...+++..|.+|++|++++...... +...+. ..++....++++++.
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 455677888887765 35566654 35788999999999999986332210 122232 356677778888765
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 83 ~~ 84 (197)
T cd08449 83 EH 84 (197)
T ss_pred CC
Confidence 54
No 260
>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=84.96 E-value=17 Score=38.22 Aligned_cols=127 Identities=6% Similarity=-0.108 Sum_probs=71.4
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc-C-CeEEEEEEEcCC--cccchHHHHHHHHHhC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY-G-WKEVIAIYVDDD--YGRNGISALSNMLEKN 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~-~-W~~v~ii~~d~~--~g~~~~~~l~~~l~~~ 81 (806)
+...++|+|.+....+. +. .-+.....++...+..+++.+... + -++++++..+.. ......+.+.++++++
T Consensus 77 ~~~~~iPvV~v~~~~~~-~~---~~~~~v~~D~~~~g~~a~~~l~~~~~~~~~I~~l~g~~~~~~~~~R~~Gf~~~l~~~ 152 (298)
T cd06302 77 AREAGIKVVTHDSDVQP-DN---RDYDIEQADNKAIGETLMDSLAEQMGGKGEYAIFVGSLTATNQNAWIDAAKAYQKEK 152 (298)
T ss_pred HHHCCCeEEEEcCCCCC-Cc---ceeEEeccCHHHHHHHHHHHHHHHcCCCCEEEEEeCCCCCcchHHHHHHHHHHHhhc
Confidence 35679999987543211 01 112233456666677778876554 4 369999875433 2344568899999998
Q ss_pred Cc-EEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCc
Q 003633 82 MA-KVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 82 g~-~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~ 137 (806)
|. .+..........+.+.-...+.++.+. .+++ |++++...+..+++++++.|+.
T Consensus 153 g~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~D~~A~g~~~al~~~g~~ 210 (298)
T cd06302 153 YYPMLELVDRQYGDDDADKSYQTAQELLKAYPDLKG-IIGPTSVGIPGAARAVEEAGLK 210 (298)
T ss_pred CCCCeEEeCcccCCCCHHHHHHHHHHHHHhCCCceE-EEECCCcchhHHHHHHHhcCCC
Confidence 72 122111222222222222334443322 3444 4445567888899999999975
No 261
>PRK09701 D-allose transporter subunit; Provisional
Probab=84.93 E-value=18 Score=38.28 Aligned_cols=128 Identities=13% Similarity=0.032 Sum_probs=75.0
Q ss_pred ccCCCcEEecccCCCC--cccCCCCceEEecCCcHHHHHHHHHHH-HHcCC--eEEEEEEEcCC--cccchHHHHHHHHH
Q 003633 7 NGLKVPLVSFAATDPT--LSALQFPYFIRSTQSDSQQMAAMADLI-DFYGW--KEVIAIYVDDD--YGRNGISALSNMLE 79 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~--Ls~~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W--~~v~ii~~d~~--~g~~~~~~l~~~l~ 79 (806)
.+.+||+|.+....+. +....-....-+..++...+..+++.+ +..|- ++++++..+.. ......+.+.+.++
T Consensus 104 ~~~giPvV~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~aa~~L~~~~g~~~~~i~~l~g~~~~~~~~~R~~Gf~~al~ 183 (311)
T PRK09701 104 WKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAFK 183 (311)
T ss_pred HHCCCcEEEeCCCCCcccccccCCceEEEeccchHHHHHHHHHHHHHHhCCCCCEEEEEECCCCCccHHHHHHHHHHHHH
Confidence 4678999998644321 111111122234566666777888865 54564 79988864333 34455788999998
Q ss_pred hCC-cEEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCc
Q 003633 80 KNM-AKVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 80 ~~g-~~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~ 137 (806)
+.| +++... .....+.++-...+.++.+. ++++ |++.+...+..++.++++.|..
T Consensus 184 ~~~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~~-I~~~~d~~A~g~~~al~~~G~~ 241 (311)
T PRK09701 184 KASQIKLVAS--QPADWDRIKALDVATNVLQRNPNIKA-IYCANDTMAMGVAQAVANAGKT 241 (311)
T ss_pred hCCCcEEEEe--cCCCCCHHHHHHHHHHHHHhCCCCCE-EEECCcchHHHHHHHHHHcCCC
Confidence 887 765432 11112222223444444332 3454 5566677888999999999974
No 262
>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=84.81 E-value=24 Score=34.49 Aligned_cols=70 Identities=9% Similarity=0.035 Sum_probs=47.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+..+++..+.+..+ .+++++.. .+...+.+.|.+|++|++++... .....+. ..|+....++++++.
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 445667777777665 34566654 35678999999999999986322 1223343 457777888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (221)
T cd08469 81 DH 82 (221)
T ss_pred CC
Confidence 55
No 263
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=84.80 E-value=16 Score=37.93 Aligned_cols=121 Identities=10% Similarity=0.085 Sum_probs=62.5
Q ss_pred CCCCChhHhhhCCCceeEEeCc-hhHHHhh--hhccc--------------------ccccceeCCCHhHHHHHHhcCCC
Q 003633 571 TSVKGIESLITNDWPIGYQVGS-FAYSYLS--DSLRI--------------------QKSRLISLGSPEDYERALRQGPR 627 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs-~~~~~l~--~~~~~--------------------~~~~~~~~~~~~~~~~~l~~~~~ 627 (806)
..|+|++||. .|.+|++.... .....+. ++.+. ..-++++. ...+...++.+
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 KKIKSLDELQ-DGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVEL-EAPQLPRSLDD--- 193 (271)
T ss_pred cCCCCHHHhc-CCCEEEecCCCccHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEEC-cHHHHHHhccc---
Confidence 4799999993 48899988632 2222121 22111 11233333 45567778877
Q ss_pred CCCeEEEEeCchhHHHHhhCC-CCeEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccchhHHHHHhh
Q 003633 628 NGGVAAIVDELPYVQLFLSNQ-TDFGIIGQPFTRSGWGFAFQRDSPLAVGMSTAILKLSENGMLQKLHEKW 697 (806)
Q Consensus 628 ~g~~~a~i~~~~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~il~l~e~G~~~~i~~kw 697 (806)
|++|+++...+++.....+. .+-......-..+-..+++++..-=.+.+.+.+.-++....-+.|.++|
T Consensus 194 -g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~~~~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~~~ 263 (271)
T PRK11063 194 -AQIALAVINTTYASQIGLTPAKDGIFVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANKVF 263 (271)
T ss_pred -ccccEEEEChHHHHHcCCCCCCCeeEECCCCCCeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 89999999888876543222 1212222111122234566655333344444444444444445555554
No 264
>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=84.64 E-value=33 Score=32.93 Aligned_cols=70 Identities=10% Similarity=0.024 Sum_probs=46.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++...++++|.+|++|+++.... .....++ +.++....++++++.
T Consensus 14 ~~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~l~~~l~~g~~D~~~~~~~---~~~~~~~-~~~l~~~~~~lv~~~ 81 (198)
T cd08486 14 RSLPLLLRAFLTSTP-TATVSLTH-------MTKDEQVEGLLAGTIHVGFSRFF---PRHPGIE-IVNIAQEDLYLAVHR 81 (198)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEE-------CCHHHHHHHHHcCCceEEEecCC---CCCCceE-EEEEeeccEEEEecC
Confidence 445677777777765 45566655 36789999999999999985321 1112232 456667788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~h 83 (198)
T cd08486 82 SQ 83 (198)
T ss_pred CC
Confidence 54
No 265
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=84.64 E-value=35 Score=36.05 Aligned_cols=83 Identities=14% Similarity=0.065 Sum_probs=51.2
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
..++||++.. -...+-.+++..+.+..+ .+++++... +-..+...|.+|++|+++...
T Consensus 94 g~l~I~~~~~--------------~~~~~l~~~l~~~~~~~P-~v~i~i~~~-------~~~~~~~~l~~~~~Dl~i~~~ 151 (309)
T PRK11013 94 GQLSIACLPV--------------FSQSLLPGLCQPFLARYP-DVSLNIVPQ-------ESPLLEEWLSAQRHDLGLTET 151 (309)
T ss_pred CcEEEEEcHH--------------HHHhhHHHHHHHHHHHCC-CCeEEEEeC-------CHHHHHHHHHcCCCCEEEEcC
Confidence 5788887631 112455677777777764 355666652 456788999999999998632
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
... ...+. ..++.....+++++...
T Consensus 152 ~~~---~~~~~-~~~l~~~~~~~~~~~~~ 176 (309)
T PRK11013 152 LHT---PAGTE-RTELLTLDEVCVLPAGH 176 (309)
T ss_pred CCC---CCCce-eeeecceeEEEEEcCCC
Confidence 211 11222 33555666677776554
No 266
>PRK09526 lacI lac repressor; Reviewed
Probab=84.62 E-value=16 Score=39.26 Aligned_cols=128 Identities=6% Similarity=-0.005 Sum_probs=77.5
Q ss_pred CCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcEEE
Q 003633 9 LKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAKVS 86 (806)
Q Consensus 9 ~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~i~ 86 (806)
.++|+|.+... + ....++ ...++..-+..+++.+...|-++++++..+.. ......+.+.+++++.|+.+.
T Consensus 143 ~~iPvV~~d~~-~---~~~~~~---V~~d~~~~~~~a~~~L~~~G~~~I~~l~g~~~~~~~~~R~~Gf~~al~~~gi~~~ 215 (342)
T PRK09526 143 ADVPCLFLDVS-P---QSPVNS---VSFDPEDGTRLGVEHLVELGHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQPI 215 (342)
T ss_pred CCCCEEEEecc-C---CCCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEeCCCccccHHHHHHHHHHHHHHcCCCcc
Confidence 47888876432 1 112232 45566666778888887789999999974322 334557889999999998643
Q ss_pred EEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 87 YKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 87 ~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.. +....+.++-...+.++... .+++ |++++...+..+++++++.|+..++-+-|++
T Consensus 216 ~~--~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~A~g~~~al~~~g~~vP~disvig 274 (342)
T PRK09526 216 AV--REGDWSAMSGYQQTLQMLREGPVPSA-ILVANDQMALGVLRALHESGLRVPGQISVIG 274 (342)
T ss_pred eE--EeCCCchHHHHHHHHHHhcCCCCCcE-EEEcCcHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 21 11112222222334444332 3454 4456667788999999999986555444443
No 267
>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=84.56 E-value=9.2 Score=39.28 Aligned_cols=127 Identities=9% Similarity=0.035 Sum_probs=74.8
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCc--ccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDY--GRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~g~ 83 (806)
+...++|+|......+ ....++ ...++...+..+++.+...|.++++++..+.+. .....+.+.+.+++.|+
T Consensus 76 l~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~ 149 (268)
T cd06277 76 IKELGIPFVLVDHYIP---NEKADC---VLTDNYSGAYAATEYLIEKGHRKIGFVGDPLYSPSFEERYEGYKKALLDHGI 149 (268)
T ss_pred HhhcCCCEEEEccCCC---CCCCCE---EEecchHHHHHHHHHHHHCCCCcEEEECCCCCCcchHHHHHHHHHHHHHcCC
Confidence 4556899998754332 122333 334555556666677777799999999765442 23456788999999887
Q ss_pred EEEEEeccC-CCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCC
Q 003633 84 KVSYKLPLP-VQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNN 140 (806)
Q Consensus 84 ~i~~~~~~~-~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~ 140 (806)
.+.....+. ...........+..+. ..+++ |++++...+..+++++++.|+..++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~a-i~~~~d~~a~g~~~a~~~~g~~~p~ 205 (268)
T cd06277 150 PFNEDYDITEKEEDEEDIGKFIDELK-PLPTA-FFCSNDGVAFLLIKVLKEMGIRVPE 205 (268)
T ss_pred CCCcceEEEcchhHHHHHHHHHhcCC-CCCCE-EEECCcHHHHHHHHHHHHcCCCCCC
Confidence 643211111 0112233444444432 23555 4455666777888888999975433
No 268
>PRK09492 treR trehalose repressor; Provisional
Probab=84.44 E-value=11 Score=39.79 Aligned_cols=99 Identities=11% Similarity=0.025 Sum_probs=65.0
Q ss_pred ecCCcHHHHHHHHHHHHHcCCeEEEEEEEc-C--CcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCC
Q 003633 34 STQSDSQQMAAMADLIDFYGWKEVIAIYVD-D--DYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPL 110 (806)
Q Consensus 34 t~psd~~q~~ai~~ll~~~~W~~v~ii~~d-~--~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~ 110 (806)
...++..-+..+++.+...|-++++++... . ..+....+.+.+++++.|+.+... .. ..+...-...+.++...
T Consensus 155 V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~-~~~~~~~~~~~~~~l~~ 231 (315)
T PRK09492 155 VCYDDEGAIKLLMQRLYDQGHRHISYLGVDHSDVTTGKRRHQAYLAFCKQHKLTPVAA--LG-GLSMQSGYELVAKVLTP 231 (315)
T ss_pred EEECcHHHHHHHHHHHHHcCCCeEEEEcCCcccchhHHHHHHHHHHHHHHcCCCceee--cC-CCCchHHHHHHHHHhhc
Confidence 455666667777787777899999999632 2 234567889999999999875421 11 11222222334444445
Q ss_pred CCeEEEEecCcchHHHHHHHHHHcCC
Q 003633 111 GPRVYVVHVSPDPGLRIFTTAQKLQM 136 (806)
Q Consensus 111 ~~rvivl~~~~~~~~~i~~~a~~~gm 136 (806)
++++|+ +++...+..+++++++.|+
T Consensus 232 ~~~ai~-~~~D~~A~g~~~al~~~g~ 256 (315)
T PRK09492 232 ETTALV-CATDTLALGASKYLQEQGR 256 (315)
T ss_pred CCCEEE-EcCcHHHHHHHHHHHHcCC
Confidence 677665 5556788889999999996
No 269
>PRK10624 L-1,2-propanediol oxidoreductase; Provisional
Probab=84.41 E-value=6.5 Score=43.10 Aligned_cols=87 Identities=8% Similarity=0.014 Sum_probs=64.6
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.+.++.+|.+++.+++...-+-.+..+.+.+.|++.|+++.....+.++.+.+++...+..+++.++|+||-.+...
T Consensus 19 ~~l~~~~~~~g~~~~lvvtd~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 98 (382)
T PRK10624 19 GALTDEVKRRGFKKALIVTDKTLVKCGVVAKVTDVLDAAGLAYEIYDGVKPNPTIEVVKEGVEVFKASGADYLIAIGGGS 98 (382)
T ss_pred HHHHHHHHhcCCCEEEEEeCcchhhCcchHHHHHHHHHCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCChH
Confidence 55778888899999998885444434478889999999998876544565566677888888899999999999766533
Q ss_pred --hHHHHHH
Q 003633 123 --PGLRIFT 129 (806)
Q Consensus 123 --~~~~i~~ 129 (806)
+..+++.
T Consensus 99 ~iD~aK~ia 107 (382)
T PRK10624 99 PQDTCKAIG 107 (382)
T ss_pred HHHHHHHHH
Confidence 5555443
No 270
>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=84.34 E-value=6.7 Score=42.84 Aligned_cols=89 Identities=6% Similarity=-0.041 Sum_probs=66.8
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc-
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP- 121 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~- 121 (806)
+.+.++++.++.+++.+++....+.....+.+.+.|++.|+++.....+....+.+++...+..++..++|+||-.+..
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 5667778889999999998544433467788999999999887654456666677889999999998999999977654
Q ss_pred -chHHHHHHHH
Q 003633 122 -DPGLRIFTTA 131 (806)
Q Consensus 122 -~~~~~i~~~a 131 (806)
-+..+++...
T Consensus 92 ~~D~AK~va~~ 102 (370)
T cd08551 92 VLDTAKAIALL 102 (370)
T ss_pred HHHHHHHHHHH
Confidence 3555555443
No 271
>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=84.33 E-value=7 Score=42.75 Aligned_cols=89 Identities=11% Similarity=0.001 Sum_probs=66.3
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc-
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP- 121 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~- 121 (806)
+.+.+.++.+|-+++.+++...-...+..+.+.+.|++.|+.+.....+.++.+.+++...+..+++.++|+||-.+..
T Consensus 15 ~~l~~~l~~~g~~~~lvvt~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS 94 (374)
T cd08189 15 AQLPAAISQLGVKKVLIVTDKGLVKLGLLDKVLEALEGAGIEYAVYDGVPPDPTIENVEAGLALYRENGCDAILAVGGGS 94 (374)
T ss_pred HHHHHHHHhcCCCeEEEEeCcchhhcccHHHHHHHHHhcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 4567778889989999888544443446788999999999887655556666777888899999999999999976653
Q ss_pred -chHHHHHHHH
Q 003633 122 -DPGLRIFTTA 131 (806)
Q Consensus 122 -~~~~~i~~~a 131 (806)
-++.+++...
T Consensus 95 ~~D~aK~ia~~ 105 (374)
T cd08189 95 VIDCAKAIAAR 105 (374)
T ss_pred HHHHHHHHHHH
Confidence 3555555443
No 272
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=84.22 E-value=19 Score=37.99 Aligned_cols=69 Identities=19% Similarity=0.134 Sum_probs=44.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+...++..+.+..+ .+++.+.. +....+...|.+|++|+++..-... ...+ ...|+.+..++++++.
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 344567788877764 34466654 2457889999999999998532111 1222 3457777888887765
Q ss_pred c
Q 003633 463 N 463 (806)
Q Consensus 463 ~ 463 (806)
.
T Consensus 173 ~ 173 (305)
T PRK11233 173 D 173 (305)
T ss_pred c
Confidence 4
No 273
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=84.14 E-value=10 Score=40.53 Aligned_cols=133 Identities=9% Similarity=-0.004 Sum_probs=77.7
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC-cccchHHHHHHHHHhCCcE
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD-YGRNGISALSNMLEKNMAK 84 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~g~~ 84 (806)
+...++|+|....... . .... -...++..-+..+++.+...|-++++++....+ ........+.+++++.|+.
T Consensus 138 l~~~~iPvV~~~~~~~---~-~~~~--~V~~Dn~~~~~~a~~~L~~~Gh~~I~~i~~~~~~~~~~R~~Gf~~al~~~g~~ 211 (331)
T PRK14987 138 IEVAGIPVVELMDSQS---P-CLDI--AVGFDNFEAARQMTTAIIARGHRHIAYLGARLDERTIIKQKGYEQAMLDAGLV 211 (331)
T ss_pred HHhCCCCEEEEecCCC---C-CCCc--eEEeCcHHHHHHHHHHHHHCCCceEEEEcCCCcccHHHHHHHHHHHHHHcCCC
Confidence 3456899987532111 1 1112 245566666777788887889999999964322 2334568889999999863
Q ss_pred EEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 85 VSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 85 i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.. ...+....+.+.-...+.++.+. .+++ |++++...+..+++++++.|+..++-+-|++
T Consensus 212 ~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~nD~~A~g~~~al~~~g~~vP~disvig 273 (331)
T PRK14987 212 PY-SVMVEQSSSYSSGIELIRQARREYPQLDG-VFCTNDDLAVGAAFECQRLGLKVPDDMAIAG 273 (331)
T ss_pred cc-ceeecCCCChhhHHHHHHHHHhcCCCCCE-EEECCcHHHHHHHHHHHHcCCCCCCccEEEe
Confidence 11 01111111111222344444333 3555 4456777888999999999987665555554
No 274
>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=84.04 E-value=43 Score=32.47 Aligned_cols=71 Identities=14% Similarity=0.119 Sum_probs=45.1
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++...++..|.+|++|+++........-...+ ...|+....++++++.
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 455677777777765 35566665 47899999999999999985332111100111 2447777777777654
No 275
>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=83.94 E-value=40 Score=32.04 Aligned_cols=70 Identities=19% Similarity=0.163 Sum_probs=45.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. +...++...+.+|++|+++.... .....+. ..++.+..++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~~~~~ 80 (196)
T cd08457 13 GFLPRFLAAFLRLRP-NLHLSLMG-------LSSSQVLEAVASGRADLGIADGP---LEERQGF-LIETRSLPAVVAVPM 80 (196)
T ss_pred cccHHHHHHHHHHCC-CeEEEEEe-------cCcHHHHHHHHcCCccEEEeccC---CCCCCcE-EEEeccCCeEEEeeC
Confidence 456688888888776 44566654 23468889999999999986322 1122232 345667777777765
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (196)
T cd08457 81 GH 82 (196)
T ss_pred CC
Confidence 44
No 276
>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=83.93 E-value=7.3 Score=42.61 Aligned_cols=88 Identities=13% Similarity=0.076 Sum_probs=66.1
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.++++.++.+++.+++...-...+..+.+.+.|++.|+.+.....+.++.+.+++...+..+++.++|.||-.+...
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 45667788889999998885443344567889999999998876555566666778888999999999999999887643
Q ss_pred --hHHHHHHH
Q 003633 123 --PGLRIFTT 130 (806)
Q Consensus 123 --~~~~i~~~ 130 (806)
++.+++..
T Consensus 95 ~iD~aK~ia~ 104 (376)
T cd08193 95 SMDVAKLVAV 104 (376)
T ss_pred HHHHHHHHHH
Confidence 55555544
No 277
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=83.65 E-value=6.2 Score=42.49 Aligned_cols=112 Identities=4% Similarity=-0.098 Sum_probs=68.0
Q ss_pred ecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCC-
Q 003633 34 STQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPL- 110 (806)
Q Consensus 34 t~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~- 110 (806)
...++..-+..+++.+...|-+++++|..+.. ......+.+.+++++.|+.+..........+...-...+.++.+.
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 34555566666777777789999999975433 345567889999999987542111111111222222334444333
Q ss_pred -CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 111 -GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 111 -~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.+++| ++.+...+..++++++++|+..++-+-|++
T Consensus 236 ~~~~ai-~~~nD~~A~g~~~al~~~G~~vP~disVig 271 (343)
T PRK10727 236 RNFTAV-ACYNDSMAAGAMGVLNDNGIDVPGEISLIG 271 (343)
T ss_pred CCCCEE-EEcCcHHHHHHHHHHHHcCCCCCcceeEEe
Confidence 34544 456777888999999999986554444443
No 278
>PF13685 Fe-ADH_2: Iron-containing alcohol dehydrogenase; PDB: 3CE9_C.
Probab=83.60 E-value=7.8 Score=39.44 Aligned_cols=99 Identities=12% Similarity=0.188 Sum_probs=61.0
Q ss_pred HHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch
Q 003633 44 AMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP 123 (806)
Q Consensus 44 ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~ 123 (806)
.+.++++.++.+++.+|...+-| .-..+.+.+.|++.|+++..........+.+++..+..+++..++++||-.+....
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 35678888899999999966554 33557788899999999874433333355667778888888889999888887653
Q ss_pred HHHHH-HHHHHcCCccCCcEEEEcC
Q 003633 124 GLRIF-TTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 124 ~~~i~-~~a~~~gm~~~~~~wi~t~ 147 (806)
..+. ..|.++| ..|+-+-|.
T Consensus 88 -~D~~K~~A~~~~---~p~isVPTa 108 (250)
T PF13685_consen 88 -IDIAKYAAFELG---IPFISVPTA 108 (250)
T ss_dssp -HHHHHHHHHHHT-----EEEEES-
T ss_pred -HHHHHHHHHhcC---CCEEEeccc
Confidence 2333 3555666 467777775
No 279
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=83.56 E-value=28 Score=33.71 Aligned_cols=130 Identities=11% Similarity=0.043 Sum_probs=85.3
Q ss_pred hcccccCCCcEEecccCCCCccc-CCCCceE--Ee----cCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHH
Q 003633 3 SEVANGLKVPLVSFAATDPTLSA-LQFPYFI--RS----TQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALS 75 (806)
Q Consensus 3 ~~i~~~~~vP~Is~~at~p~Ls~-~~~p~f~--Rt----~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~ 75 (806)
+......+|=+|.|++|+.++.- .+|.-=+ |+ --+-..-+.|+++-++.+|-+++.++. .|-....+.-.
T Consensus 60 Al~Lada~vdvI~Y~CtsgS~i~G~~~d~ei~~~ie~~~~v~vvTts~Avv~aL~al~a~ri~vlT---PY~~evn~~e~ 136 (238)
T COG3473 60 ALELADAGVDVIVYGCTSGSLIGGPGYDKEIAQRIEEAKGVPVVTTSTAVVEALNALGAQRISVLT---PYIDEVNQREI 136 (238)
T ss_pred HHhcCccccCEEEEeccceeeecCCchhHHHHHHHHhccCCceeechHHHHHHHHhhCcceEEEec---cchhhhhhHHH
Confidence 34566778999999999988875 2331000 00 000001136777888999999999997 57777888889
Q ss_pred HHHHhCCcEEEEEeccCCCC-------ChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHH-HcC
Q 003633 76 NMLEKNMAKVSYKLPLPVQF-------NQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQ-KLQ 135 (806)
Q Consensus 76 ~~l~~~g~~i~~~~~~~~~~-------~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~-~~g 135 (806)
+.++++|++|+....+-... +....-..-+++...++|.+++.|..-.+..++.... +.|
T Consensus 137 ef~~~~Gfeiv~~~~Lgi~dn~eigr~~P~~~y~lAk~~~~~~~DaiFiSCTnlRt~eii~~lE~~~G 204 (238)
T COG3473 137 EFLEANGFEIVDFKGLGITDNLEIGRQEPWAVYRLAKEVFTPDADAIFISCTNLRTFEIIEKLERDTG 204 (238)
T ss_pred HHHHhCCeEEEEeeccCCcccchhcccChHHHHHHHHHhcCCCCCeEEEEeeccccHHHHHHHHHHhC
Confidence 99999999998665443211 1223345556777889999999887666666665443 344
No 280
>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=83.28 E-value=42 Score=31.82 Aligned_cols=66 Identities=12% Similarity=0.067 Sum_probs=40.8
Q ss_pred eHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEecc
Q 003633 385 CIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 385 ~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
...++..+.+. + .+++++.. ++.+.+..++.+|++|+++..- ......+ .+.++.+...+++++..
T Consensus 15 l~~~l~~f~~~-~-~v~l~l~~-------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~~ 80 (195)
T cd08428 15 FLPALAPVLKR-E-RILLDLIV-------DDEDRTHDLLRDGEVVGCISTQ---AQPMQGC-RSDYLGSMDYLLVASPD 80 (195)
T ss_pred hHHHHHHHHhC-c-CeEEEEEe-------CCchhHHHHHHcCcceEEEEec---CCCCCCc-eeEEeeeeeEEEEECCc
Confidence 44566777776 3 56666665 3567899999999999877421 1111222 34566666777666543
No 281
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=83.21 E-value=5.3 Score=42.86 Aligned_cols=73 Identities=19% Similarity=0.175 Sum_probs=50.7
Q ss_pred CCCCChhHhhhCCCceeEEeCch-hHHHhh---hhcccccccce-eCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHh
Q 003633 571 TSVKGIESLITNDWPIGYQVGSF-AYSYLS---DSLRIQKSRLI-SLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFL 645 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs~-~~~~l~---~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~ 645 (806)
.+|++++|| .|+++|+..++. ....+. .+.+...+.+. ..-.+.+...++.. |.+||++...++.....
T Consensus 126 ~~i~~~adl--kGk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~----g~vda~~~~ep~~~~~~ 199 (335)
T COG0715 126 SGIKSVADL--KGKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAA----GQVDAFVVWEPWNAAAE 199 (335)
T ss_pred CCcccccCC--CCceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhc----CCcceEEecCCchhhhh
Confidence 588899999 799999998875 333332 23344444332 22345588889988 99999999888887766
Q ss_pred hCCC
Q 003633 646 SNQT 649 (806)
Q Consensus 646 ~~~~ 649 (806)
.+..
T Consensus 200 ~~~~ 203 (335)
T COG0715 200 GEGG 203 (335)
T ss_pred ccCC
Confidence 6643
No 282
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=83.07 E-value=10 Score=40.47 Aligned_cols=132 Identities=10% Similarity=-0.008 Sum_probs=75.2
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCc
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMA 83 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~ 83 (806)
+...++|+|......+ ...+++ ...++..-+..+++.+...|.++++++..+.. ........+.+++++.|+
T Consensus 132 l~~~~~pvV~~~~~~~---~~~~~~---V~~D~~~~~~~a~~~l~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~g~ 205 (327)
T PRK10339 132 ASALTDNICFIDFHEP---GSGYDA---VDIDLARISKEIIDFYINQGVNRIGFIGGEDEPGKADIREVAFAEYGRLKQV 205 (327)
T ss_pred HHhcCCCEEEEeCCCC---CCCCCE---EEECHHHHHHHHHHHHHHCCCCeEEEeCCccccchhhHHHHHHHHHHHHcCC
Confidence 3456789887643221 122332 45555555677778877789999999964332 233446778888888876
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEE
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLA 145 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~ 145 (806)
. .....+....+.++-...+.++.+ ..+++ |++++...+..++++++++|...++-+-|+
T Consensus 206 ~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~D~~A~g~~~al~~~g~~vP~di~vi 267 (327)
T PRK10339 206 V-REEDIWRGGFSSSSGYELAKQMLAREDYPKA-LFVASDSIAIGVLRAIHERGLNIPQDISLI 267 (327)
T ss_pred C-ChhheeecCcChhHHHHHHHHHHhCCCCCCE-EEECCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 1 100011111122222334444432 23554 555667788899999999997544434333
No 283
>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=82.84 E-value=7.4 Score=39.72 Aligned_cols=109 Identities=11% Similarity=-0.012 Sum_probs=68.2
Q ss_pred ecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCC--
Q 003633 34 STQSDSQQMAAMADLIDFYGWKEVIAIYVDD--DYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKP-- 109 (806)
Q Consensus 34 t~psd~~q~~ai~~ll~~~~W~~v~ii~~d~--~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~-- 109 (806)
..+++...+..+++.+...|-++++++..+. .......+.+.+.+++.|+.+.....+....+..+-...+.++.+
T Consensus 94 v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~ 173 (260)
T cd06286 94 VYIDHYEAFYEALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLLKMK 173 (260)
T ss_pred EEECChHHHHHHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCCCChHheEeCCCCHHHHHHHHHHHHcCC
Confidence 4566677778888888888999999997543 344455788999999988654211111111122232334444433
Q ss_pred CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEE
Q 003633 110 LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVW 143 (806)
Q Consensus 110 ~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~w 143 (806)
..+++| ++++...+..+++.++++|+..++-+-
T Consensus 174 ~~~~ai-~~~~d~~a~~~~~~l~~~g~~ip~di~ 206 (260)
T cd06286 174 DRPDAI-FTGSDEVAAGIITEAKKQGIRVPEDLA 206 (260)
T ss_pred CCCCEE-EEcchHHHHHHHHHHHHcCCCCCcceE
Confidence 345644 466667788999999999975443333
No 284
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=82.84 E-value=40 Score=35.39 Aligned_cols=86 Identities=13% Similarity=0.128 Sum_probs=53.0
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
.+.++||+... + ...+..+++..+.+..+ .+++.+.. ++..++++.|.+|++|++++.
T Consensus 91 ~g~l~Ig~~~~--~------------~~~~l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~ 148 (300)
T PRK11074 91 RGQLSIAVDNI--V------------RPDRTRQLIVDFYRHFD-DVELIIRQ-------EVFNGVWDALADGRVDIAIGA 148 (300)
T ss_pred CceEEEEEcCc--c------------chhHHHHHHHHHHHhCC-CceEEEEe-------hhhhHHHHHHHCCCCCEEEec
Confidence 36899998641 1 12344577777777766 33455554 346789999999999999973
Q ss_pred EEEecCccceeEecccccccceEEEEeccC
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
.... .....+ -..++....+++++++..
T Consensus 149 ~~~~-~~~~~l-~~~~l~~~~~~~v~~~~h 176 (300)
T PRK11074 149 TRAI-PVGGRF-AFRDMGMLSWACVVSSDH 176 (300)
T ss_pred CccC-Cccccc-ceeecccceEEEEEcCCC
Confidence 2211 111112 244567778888887655
No 285
>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=82.63 E-value=9.3 Score=41.76 Aligned_cols=87 Identities=9% Similarity=-0.014 Sum_probs=65.7
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.++++.++.+++.+|+..+-+..+..+.+.+.|++.|+.+.....+.++.+.+++...+..++..++|+||-.+...
T Consensus 12 ~~l~~~~~~~~~~r~livt~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 91 (375)
T cd08194 12 DETGAVLADLGGKRPLIVTDKVMVKLGLVDKLTDSLKKEGIESAIFDDVVSEPTDESVEEGVKLAKEGGCDVIIALGGGS 91 (375)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhcchHHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 45566777788899999985544544567889999999999876555666677778889999999999999999777543
Q ss_pred --hHHHHHH
Q 003633 123 --PGLRIFT 129 (806)
Q Consensus 123 --~~~~i~~ 129 (806)
+..+.+.
T Consensus 92 ~~D~AKaia 100 (375)
T cd08194 92 PIDTAKAIA 100 (375)
T ss_pred HHHHHHHHH
Confidence 5555544
No 286
>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=82.55 E-value=16 Score=36.30 Aligned_cols=70 Identities=9% Similarity=-0.032 Sum_probs=39.0
Q ss_pred eeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeCCcc-ccCCceeeecCCCCchHHHHHHHHhh
Q 003633 610 ISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIGQPF-TRSGWGFAFQRDSPLAVGMSTAILKL 684 (806)
Q Consensus 610 ~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~~~k~spl~~~~n~~il~l 684 (806)
....+..+..+.+.+ |++++.+......... ........+++.. ....+++++.|+++-.+.-.+.|..+
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 8999887654332211 1223333444432 23346889999887544444444333
No 287
>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=82.49 E-value=44 Score=31.50 Aligned_cols=70 Identities=16% Similarity=0.181 Sum_probs=46.2
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+..+++..+.+..+ .+++++.. ++...+..++.+|++|+++..... ....+. ..|+....++++++.
T Consensus 13 ~~l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 80 (197)
T cd08414 13 GLLPRLLRRFRARYP-DVELELRE-------MTTAEQLEALRAGRLDVGFVRPPP---DPPGLA-SRPLLREPLVVALPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHcCCccEEEEcCCC---CCCCee-EEEEeeccEEEEecC
Confidence 445677777777764 34566654 356889999999999999863222 122232 356777888888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (197)
T cd08414 81 DH 82 (197)
T ss_pred CC
Confidence 54
No 288
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=82.37 E-value=16 Score=38.70 Aligned_cols=84 Identities=12% Similarity=0.114 Sum_probs=55.4
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
++.++||+.. + ...++-.+++..+.+..+ .+++++.. ++...++.+|.+|++|+++..
T Consensus 111 ~~~i~i~~~~--~------------~~~~~l~~~l~~f~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Di~i~~ 168 (314)
T PRK09508 111 ERVFNLCICS--P------------LDIRLTSQIYNRIEQIAP-NIHVVFKS-------SLNQNIEHQLRYQETEFVISY 168 (314)
T ss_pred ccEEEEEech--h------------HHHHHHHHHHHHHHHhCC-CcEEEEEe-------CcchhHHHHHhcCCccEEEec
Confidence 4678888752 1 112466788888888876 34566654 356889999999999999874
Q ss_pred EEEecCccceeEecccccccceEEEEeccC
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
... ....+.+ .++....++++++...
T Consensus 169 ~~~---~~~~l~~-~~l~~~~~~lv~~~~h 194 (314)
T PRK09508 169 EEF---DRPEFTS-VPLFKDELVLVASKNH 194 (314)
T ss_pred CCC---Cccccce-eeeecCceEEEEcCCC
Confidence 321 1222333 3667788888887665
No 289
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=82.28 E-value=36 Score=36.13 Aligned_cols=82 Identities=9% Similarity=0.052 Sum_probs=53.6
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
.++++||+.... ...+-..++..+.+..+ .++++.. ..++++..|.+|++|++++.
T Consensus 116 ~~~l~Ig~~~~~--------------~~~~l~~~l~~f~~~~P-~i~i~~~---------~~~~~~~~l~~g~~Dl~i~~ 171 (317)
T PRK11482 116 QRTITIATTPSV--------------GALVMPVIYQAIKTHYP-QLLLRNI---------PISDAENQLSQFQTDLIIDT 171 (317)
T ss_pred CceEEEEecHHH--------------HHHHHHHHHHHHHHHCC-CCEEEEe---------cchhHHHHHHCCCcCEEEec
Confidence 357999987311 12345667777777776 3444332 34678999999999999864
Q ss_pred EEEecCccceeEecccccccceEEEEeccC
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
... ....+.+ .|+....++++++...
T Consensus 172 ~~~---~~~~~~~-~~l~~~~~~lv~~~~h 197 (317)
T PRK11482 172 HSC---SNRTIQH-HVLFTDNVVLVCRQGH 197 (317)
T ss_pred cCC---CCCceEE-EEEecCcEEEEEeCCC
Confidence 322 2233443 5778888888887765
No 290
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=82.12 E-value=8 Score=40.76 Aligned_cols=112 Identities=11% Similarity=0.060 Sum_probs=69.6
Q ss_pred ecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCc--ccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCC-
Q 003633 34 STQSDSQQMAAMADLIDFYGWKEVIAIYVDDDY--GRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPL- 110 (806)
Q Consensus 34 t~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~- 110 (806)
...++...+..+++.+...|-++++++..+... .....+.|.+.+++.|+.+..........+.+.....+.++.+.
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 344556667777787777899999999754332 34457889999999887643111111112223334455555433
Q ss_pred -CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 111 -GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 111 -~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.+++|+. ++...+..++++.++.|+..++-++|++
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 3666554 5667777899999999975444455554
No 291
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=81.78 E-value=49 Score=31.49 Aligned_cols=73 Identities=15% Similarity=0.145 Sum_probs=46.4
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. +....+..+|.+|++|+++............+ -+.|.....++++++.
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 455677777777664 34566654 35678999999999999986322111011222 2466777788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 84 ~h 85 (200)
T cd08453 84 AW 85 (200)
T ss_pred CC
Confidence 55
No 292
>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=81.40 E-value=12 Score=38.28 Aligned_cols=120 Identities=8% Similarity=-0.070 Sum_probs=67.8
Q ss_pred CCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc-CCeEEEEEEEcC-CcccchHHHHHHHHHhCCcEEEE
Q 003633 10 KVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY-GWKEVIAIYVDD-DYGRNGISALSNMLEKNMAKVSY 87 (806)
Q Consensus 10 ~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~-~W~~v~ii~~d~-~~g~~~~~~l~~~l~~~g~~i~~ 87 (806)
++|++......+. ....++ ...++..-++.++.++... |-+++++|..+. .......+.+.+++++.|..+..
T Consensus 80 ~ipvv~~~~~~~~--~~~~~~---v~~d~~~~~~~a~~l~~~~~g~~~I~~i~~~~~~~~~~R~~Gf~~~~~~~~~~~~~ 154 (260)
T cd06304 80 DVKFAIIDGVVDA--PPNVAS---YVFREYEGSYLAGVLAALMTKTGKVGFVGGMPIPEVNRFINGFAAGAKSVNPDITV 154 (260)
T ss_pred CCEEEEecCccCC--CCCeee---eecchHHHHHHHHHHHHHhccCCceEEEeccccHHHHHHHHHHHHHHHHhCCCcEE
Confidence 6788876443211 011221 2333333344444556555 999999997532 22344477889999998864332
Q ss_pred EeccCCCC-ChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcC
Q 003633 88 KLPLPVQF-NQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQ 135 (806)
Q Consensus 88 ~~~~~~~~-~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~g 135 (806)
........ +.+.-...++++.+..+++| ++.+...+..++.++++.|
T Consensus 155 ~~~~~~~~~~~~~~~~~~~~~l~~~~~ai-~~~~d~~A~gv~~al~~~g 202 (260)
T cd06304 155 LVIYTGSFFDPAKGKEAALALIDQGADVI-FAAAGGTGPGVIQAAKEAG 202 (260)
T ss_pred EEEEecCccCcHHHHHHHHHHHhCCCCEE-EEcCCCCchHHHHHHHHcC
Confidence 11111111 11223344555544557765 6677788889999999988
No 293
>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=81.26 E-value=11 Score=41.38 Aligned_cols=87 Identities=7% Similarity=-0.051 Sum_probs=64.6
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCC-cccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDD-YGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
..+.++++.+| +++.+|+.... ...+..+.+.+.|++.|+++.....+.++.+.+++...+..+++.++|+||-.+..
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 45667777788 89988885443 24567788999999999987655556666777888888888999999999976654
Q ss_pred c--hHHHHHHH
Q 003633 122 D--PGLRIFTT 130 (806)
Q Consensus 122 ~--~~~~i~~~ 130 (806)
. ++.+.+..
T Consensus 94 S~iD~aK~ia~ 104 (380)
T cd08185 94 SSMDTAKAIAF 104 (380)
T ss_pred cHHHHHHHHHH
Confidence 3 55555544
No 294
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=81.18 E-value=4.4 Score=43.22 Aligned_cols=65 Identities=6% Similarity=-0.007 Sum_probs=45.2
Q ss_pred HHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccce-eEecccccc
Q 003633 386 IDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKI-VDFSQPYIS 453 (806)
Q Consensus 386 idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~-vdft~p~~~ 453 (806)
..+-+.+.++.|-.+++++.|.+. -|.=..++++|..|.+|+.+.+......+... --|+.||..
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 346677888999997666666432 13568999999999999998876655554433 335666655
No 295
>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=81.08 E-value=4.4 Score=44.21 Aligned_cols=89 Identities=8% Similarity=0.044 Sum_probs=68.4
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
+.+.+.++.+| ++.+|+...-...+..+.+.+.|++.|+++.....+....+.+++...+..++..++|+||..+...
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 45667788888 9999986633334478999999999999987766677777888999999999999999999888754
Q ss_pred --hHHHHHHHHHH
Q 003633 123 --PGLRIFTTAQK 133 (806)
Q Consensus 123 --~~~~i~~~a~~ 133 (806)
++.+++.....
T Consensus 90 ~~D~aK~va~~~~ 102 (366)
T PF00465_consen 90 VMDAAKAVALLLA 102 (366)
T ss_dssp HHHHHHHHHHHHT
T ss_pred cCcHHHHHHhhcc
Confidence 55666555444
No 296
>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=80.72 E-value=10 Score=41.51 Aligned_cols=87 Identities=8% Similarity=0.024 Sum_probs=64.0
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.+.++.+|.+++.+++...-.-.+..+.+.+.|++.|+.+.....+.++.+.+.+......+++.++|+||-.+...
T Consensus 18 ~~l~~~l~~~g~~r~lvvt~~~~~~~g~~~~v~~~L~~~~i~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiaiGGGS 97 (379)
T TIGR02638 18 EDIVDEVKRRGFKKALVVTDKDLIKFGVADKVTDLLDEAGIAYELFDEVKPNPTITVVKAGVAAFKASGADYLIAIGGGS 97 (379)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhccchHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCChH
Confidence 45667788899999998885443333467889999999998876554555566677888888889999999999777543
Q ss_pred --hHHHHHH
Q 003633 123 --PGLRIFT 129 (806)
Q Consensus 123 --~~~~i~~ 129 (806)
++.+.+.
T Consensus 98 viD~aKaia 106 (379)
T TIGR02638 98 PIDTAKAIG 106 (379)
T ss_pred HHHHHHHHH
Confidence 4554443
No 297
>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=80.56 E-value=22 Score=37.62 Aligned_cols=118 Identities=15% Similarity=0.060 Sum_probs=73.0
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEc-C--CcccchHHHHHHHHHhCCc
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVD-D--DYGRNGISALSNMLEKNMA 83 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d-~--~~g~~~~~~l~~~l~~~g~ 83 (806)
...++|+|...... ..++ ...+++..-+..+++.+...|-+++++|..+ . ..+....+.+.+++++.|+
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 34567777654311 1122 2445666666677777777899999999732 2 2455678889999999998
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCC
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQM 136 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm 136 (806)
.... .....+.++-...+.++...++++| ++++...+..+++.+.+.|.
T Consensus 205 ~~~~---~~~~~~~~~~~~~~~~~l~~~~tAi-~~~~D~~A~g~~~~l~~~g~ 253 (311)
T TIGR02405 205 EPIY---QTGQLSHESGYVLTDKVLKPETTAL-VCATDTLALGAAKYLQELDR 253 (311)
T ss_pred Ccee---eeCCCCHHHHHHHHHHHHhcCCCEE-EECCcHHHHHHHHHHHHcCC
Confidence 6321 1111122222233444333456655 57777888999999999885
No 298
>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=80.52 E-value=55 Score=31.30 Aligned_cols=70 Identities=14% Similarity=0.198 Sum_probs=46.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++..+++.++.+|++|++++..... ...+. +.|+....++++++.
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 566778888877765 34566654 2568999999999999998632211 12232 446677788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~h 83 (203)
T cd08445 82 GH 83 (203)
T ss_pred CC
Confidence 54
No 299
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=80.51 E-value=12 Score=40.15 Aligned_cols=111 Identities=4% Similarity=-0.131 Sum_probs=67.6
Q ss_pred cCCcHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCC--C
Q 003633 35 TQSDSQQMAAMADLIDFYGWKEVIAIYVDDD--YGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKP--L 110 (806)
Q Consensus 35 ~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~--~ 110 (806)
..++..-+..+++.+...|-+++++|....+ .+....+.+.+++++.|+.+..........+...-...+.++.+ .
T Consensus 157 ~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 236 (346)
T PRK10401 157 CLDNVSGARMATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRNL 236 (346)
T ss_pred EECcHHHHHHHHHHHHHCCCCeEEEEeCCCcCcchHHHHHHHHHHHHHcCCCCChhheecCCCChHHHHHHHHHHHcCCC
Confidence 3445554566667777789999999975332 34566888999999999754211111111122222233444432 2
Q ss_pred CCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 111 GPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 111 ~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.+++|+ +++...+..+++++++.|+..++-+-|++
T Consensus 237 ~~~ai~-~~nd~~A~g~~~al~~~G~~vP~disvig 271 (346)
T PRK10401 237 QLTAVF-AYNDNMAAGALTALKDNGIAIPLHLSIIG 271 (346)
T ss_pred CCcEEE-ECCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 456544 56777888999999999986554444443
No 300
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=80.49 E-value=20 Score=38.56 Aligned_cols=130 Identities=8% Similarity=-0.051 Sum_probs=75.1
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc-----CCeEEEEEEEcCC--cccchHHHHHHHH
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY-----GWKEVIAIYVDDD--YGRNGISALSNML 78 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~-----~W~~v~ii~~d~~--~g~~~~~~l~~~l 78 (806)
+.+.++|+|.+....+ +.. .......++...+...++.+... |-++++++..+.. ......+.+.+.+
T Consensus 124 ~~~~giPvV~~~~~~~---~~~--~~~~V~~D~~~~g~~aa~~L~~~~~~~~g~~~i~~i~g~~~~~~~~~R~~Gf~~~l 198 (343)
T PRK10936 124 LQAANIPVIALVNGID---SPQ--VTTRVGVSWYQMGYQAGRYLAQWHPKGSKPLNVALLPGPEGAGGSKAVEQGFRAAI 198 (343)
T ss_pred HHHCCCCEEEecCCCC---Ccc--ceEEEecChHHHHHHHHHHHHHHHHhcCCCceEEEEECCCCCchHHHHHHHHHHHH
Confidence 3466899997632211 111 11224556666677777765443 5789999874322 3334577889999
Q ss_pred HhCCcEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 79 EKNMAKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 79 ~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
++.|+++.... .. ..+.+.-...++++.+ .++++|+ ++...+..+++.+++.|+. +-+.|++
T Consensus 199 ~~~~i~~~~~~-~~-~~~~~~~~~~~~~~l~~~~~~~ai~--~~d~~A~ga~~al~~~g~~--~di~Vvg 262 (343)
T PRK10936 199 AGSDVRIVDIA-YG-DNDKELQRNLLQELLERHPDIDYIA--GSAVAAEAAIGELRGRNLT--DKIKLVS 262 (343)
T ss_pred hcCCCEEEEee-cC-CCcHHHHHHHHHHHHHhCCCccEEE--eCCHHHHHHHHHHHhcCCC--CCeEEEE
Confidence 98898865421 11 1222222233444322 3467765 4556777788999999973 4455554
No 301
>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=79.80 E-value=14 Score=40.54 Aligned_cols=87 Identities=8% Similarity=-0.077 Sum_probs=63.7
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
+.+.++++.+|.+++.+++...-.-.+..+.+.+.|++.|+.+.....+.++.+.+++...+..+++.++|+||-.+...
T Consensus 17 ~~l~~~l~~~g~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs 96 (377)
T cd08188 17 KLAGRYARRLGAKKVLLVSDPGVIKAGWVDRVIESLEEAGLEYVVFSDVSPNPRDEEVMAGAELYLENGCDVIIAVGGGS 96 (377)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 55677788899999998885443333467889999999998776544455556677788888889999999999877543
Q ss_pred --hHHHHHH
Q 003633 123 --PGLRIFT 129 (806)
Q Consensus 123 --~~~~i~~ 129 (806)
+..+.+.
T Consensus 97 viD~AK~ia 105 (377)
T cd08188 97 PIDCAKGIG 105 (377)
T ss_pred HHHHHHHHH
Confidence 5554443
No 302
>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=79.76 E-value=55 Score=30.82 Aligned_cols=70 Identities=10% Similarity=-0.021 Sum_probs=47.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++..++...+.+|++|+++... ......+ .+.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Di~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~ 80 (197)
T cd08448 13 RGLPRILRAFRAEYP-GIEVALHE-------MSSAEQIEALLRGELDLGFVHS---RRLPAGL-SARLLHREPFVCCLPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe-------CCHHHHHHHHHcCCcceEEEeC---CCCCcCc-eEEEEecCcEEEEeeC
Confidence 455678888888775 34566664 3678999999999999998532 1222223 2456777788887766
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~h 82 (197)
T cd08448 81 GH 82 (197)
T ss_pred CC
Confidence 54
No 303
>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=79.04 E-value=59 Score=30.74 Aligned_cols=71 Identities=20% Similarity=0.140 Sum_probs=47.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.++.+ .+++++.. ++...+..++.+|++|+++...... ....+. ..++.+..++++++.
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 555678888888875 34566665 3678899999999999998632111 112232 356677777777765
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~~ 83 (199)
T cd08430 82 IA 83 (199)
T ss_pred Cc
Confidence 54
No 304
>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=78.77 E-value=37 Score=35.31 Aligned_cols=126 Identities=5% Similarity=-0.020 Sum_probs=71.0
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc------CCeEEEEEEEcCCc--ccchHHHHHHH
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY------GWKEVIAIYVDDDY--GRNGISALSNM 77 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~------~W~~v~ii~~d~~~--g~~~~~~l~~~ 77 (806)
+...++|+|.+....+. ...+++ +..++...+..+++.+... |-++++++..+.+. .....+.+.++
T Consensus 76 l~~~~ipvV~~~~~~~~---~~~~~~--v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~~~ 150 (288)
T cd01538 76 AADAGIPVIAYDRLILN---SNVDYY--VSFDNEKVGELQGQALVDGLGAKGKPPGNIELIAGSPTDNNAKLFFNGAMSV 150 (288)
T ss_pred HHHCCCCEEEECCCCCC---CCcceE--EEeChHHHHHHHHHHHHHHHhhcCCCCceEEEEECCCCCchHHHHHHHHHHH
Confidence 34568999988654332 122222 3344444566666665444 88999999754332 33446778899
Q ss_pred HHhCC----cEEEEEeccCCCCChhHHHHHHHhcCCC---CCeEEEEecCcchHHHHHHHHHHcCCcc
Q 003633 78 LEKNM----AKVSYKLPLPVQFNQHDITVLLNNSKPL---GPRVYVVHVSPDPGLRIFTTAQKLQMMT 138 (806)
Q Consensus 78 l~~~g----~~i~~~~~~~~~~~~~~~~~~l~~ik~~---~~rvivl~~~~~~~~~i~~~a~~~gm~~ 138 (806)
+++.+ +.+... ......+...-...+.++.+. .+++| ++.+...+..++.++++.|+..
T Consensus 151 l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~I-~~~~d~~a~g~~~al~~~g~~~ 216 (288)
T cd01538 151 LKPLIDSGKITIVGE-VATPDWDPETAQKRMENALTANYNKVDGV-LAANDGTAGGAIAALKAAGLAG 216 (288)
T ss_pred HHhccccCCeeEEec-cccCCCCHHHHHHHHHHHHHhCCCCccEE-EeCCcHHHHHHHHHHHHcCCCC
Confidence 99887 544322 122122222223344444333 33443 3445667788899999999754
No 305
>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=78.56 E-value=16 Score=39.72 Aligned_cols=86 Identities=7% Similarity=0.022 Sum_probs=63.3
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcc-cchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYG-RNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g-~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
+.+.++++.+| +++.+++....+- .+..+.+.+.|++.|+++.....+.++.+.+++...+..+++.++|+||-.+..
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 44567788888 8888887544423 345688999999999987655556666777888899999999999999988765
Q ss_pred c--hHHHHHH
Q 003633 122 D--PGLRIFT 129 (806)
Q Consensus 122 ~--~~~~i~~ 129 (806)
. +..+.+.
T Consensus 94 SviD~aK~ia 103 (357)
T cd08181 94 SPLDAAKAIA 103 (357)
T ss_pred hHHHHHHHHH
Confidence 4 5555443
No 306
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=78.46 E-value=37 Score=35.20 Aligned_cols=122 Identities=11% Similarity=0.077 Sum_probs=64.5
Q ss_pred cCCCCChhHhhhCCCceeEEe--CchhHHHh-hhhc---------cc-----------ccccceeCCCHhHHHHHHhcCC
Q 003633 570 STSVKGIESLITNDWPIGYQV--GSFAYSYL-SDSL---------RI-----------QKSRLISLGSPEDYERALRQGP 626 (806)
Q Consensus 570 ~~~i~s~~dL~~~~~~ig~~~--gs~~~~~l-~~~~---------~~-----------~~~~~~~~~~~~~~~~~l~~~~ 626 (806)
..+++|++||. .|.+|++.+ +...+.++ .+.. +. .+-++++. ...+...+|.+
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 SKKIKTVAQIK-EGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMEL-EGAQLPRVLDD-- 194 (272)
T ss_pred ccCCCCHHHcC-CCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEc-CHHHhHhhccC--
Confidence 35799999994 588899986 33333322 1111 11 11222222 34567777777
Q ss_pred CCCCeEEEEeCchhHHHHhhCC-CCeEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccchhHHHHHhh
Q 003633 627 RNGGVAAIVDELPYVQLFLSNQ-TDFGIIGQPFTRSGWGFAFQRDSPLAVGMSTAILKLSENGMLQKLHEKW 697 (806)
Q Consensus 627 ~~g~~~a~i~~~~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~il~l~e~G~~~~i~~kw 697 (806)
|++|+++...+++...-.+. .+-......-..+...++++.+..=.+.+.+.+..++....-+.|.++|
T Consensus 195 --g~vD~a~i~~~~~~~ag~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 264 (272)
T PRK09861 195 --PKVDVAIISTTYIQQTGLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETIF 264 (272)
T ss_pred --cccCEEEEchhHHHHcCCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 88999988887765311111 1111221111112234555554335566666666666665556666664
No 307
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=78.29 E-value=46 Score=34.84 Aligned_cols=86 Identities=13% Similarity=0.155 Sum_probs=51.4
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
..||||+... ...++-.+++..+.+..+ .+++++.. ++.+.+..+|.+|++|+++...
T Consensus 93 g~l~i~~~~~--------------~~~~~l~~~l~~f~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~ 150 (296)
T PRK11062 93 LLFDVGVADA--------------LSKRLVSRVLLTAVPEDE-SIHLRCFE-------STHEMLLEQLSQHKLDMILSDC 150 (296)
T ss_pred eEEEEEecch--------------hhHhhHHHHHHHHHhcCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEecC
Confidence 4689988631 123566677777766554 34455543 3678999999999999988532
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
.........+ ...|+....++++++.+.
T Consensus 151 ~~~~~~~~~l-~~~~l~~~~~~~~~~~~~ 178 (296)
T PRK11062 151 PVDSTQQEGL-FSKKLGECGVSFFCTNPL 178 (296)
T ss_pred CCccccccch-hhhhhhccCcceEecCCC
Confidence 2111111122 234666667766665443
No 308
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=78.28 E-value=82 Score=33.20 Aligned_cols=70 Identities=14% Similarity=0.191 Sum_probs=45.9
Q ss_pred eHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEeccC
Q 003633 385 CIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 385 ~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
-.+++..+.++.+. +++.+.. ++..++.+.|.+|++|++++-.. .......+. ..++....++++++...
T Consensus 108 l~~~l~~~~~~~P~-i~l~l~~-------~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~-~~~l~~~~~~~v~~~~h 177 (308)
T PRK10094 108 VAQLLAWLNERYPF-TQFHISR-------QIYMGVWDSLLYEGFSLAIGVTG-TEALANTFS-LDPLGSVQWRFVMAADH 177 (308)
T ss_pred HHHHHHHHHHhCCC-cEEEEEe-------ehhhhHHHHHhCCCccEEEeccc-CccccCCee-EEEecceeEEEEECCCC
Confidence 45778888887774 4566654 35678899999999999986211 111122333 34777788888886654
No 309
>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=78.04 E-value=56 Score=33.45 Aligned_cols=120 Identities=7% Similarity=0.060 Sum_probs=67.2
Q ss_pred CCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC--cccchHHHHHHHHHhCCcEE
Q 003633 10 KVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD--YGRNGISALSNMLEKNMAKV 85 (806)
Q Consensus 10 ~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~--~g~~~~~~l~~~l~~~g~~i 85 (806)
++|+|......+. ...++| ...++..-+..+++.+... +-.+++++..... ......+.+.+++++.|+++
T Consensus 79 ~ipvV~~~~~~~~--~~~~~~---V~~D~~~~g~~a~~~l~~~~~~g~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~~ 153 (271)
T cd06314 79 GIKLITTDSDAPD--SGRYVY---IGTDNYAAGRTAGEIMKKALPGGGKVAIFVGSLGADNAKERIQGIKDAIKDSKIEI 153 (271)
T ss_pred CCCEEEecCCCCc--cceeEE---EccChHHHHHHHHHHHHHHcCCCCEEEEEecCCCCCCHHHHHHHHHHHHhcCCcEE
Confidence 8999997543211 111222 3444555567777776443 2345666654322 34456788999999999876
Q ss_pred EEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHHHHcCCc
Q 003633 86 SYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a~~~gm~ 137 (806)
.... ....+.++....+.++.+. .+++|+ +.+...+..++..+++.|+.
T Consensus 154 ~~~~--~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~d~~a~~~~~al~~~g~~ 204 (271)
T cd06314 154 VDTR--GDEEDFAKAKSNAEDALNAHPDLKCMF-GLYAYNGPAIAEAVKAAGKL 204 (271)
T ss_pred EEEe--cCccCHHHHHHHHHHHHHhCCCccEEE-ecCCccHHHHHHHHHHcCCC
Confidence 5321 1112223334455555333 345543 44555666788888888875
No 310
>KOG3857 consensus Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=77.77 E-value=20 Score=37.41 Aligned_cols=96 Identities=15% Similarity=0.008 Sum_probs=76.5
Q ss_pred CCCceEEecCCcHHHHHHHH----HHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHH
Q 003633 27 QFPYFIRSTQSDSQQMAAMA----DLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITV 102 (806)
Q Consensus 27 ~~p~f~Rt~psd~~q~~ai~----~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~ 102 (806)
..+|-|-++||....++++. +-++..|.|++.++.+-+---....+..++.|++.|+.+.......+..+..++..
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 35677778888888766543 34788999999999966655566788899999999999887666666777888999
Q ss_pred HHHhcCCCCCeEEEEecCcc
Q 003633 103 LLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 103 ~l~~ik~~~~rvivl~~~~~ 122 (806)
.|.-.|..+.|.+|-.+...
T Consensus 119 alefak~~~fDs~vaiGGGS 138 (465)
T KOG3857|consen 119 ALEFAKKKNFDSFVAIGGGS 138 (465)
T ss_pred HHHHHHhcccceEEEEcCcc
Confidence 99888989999988877643
No 311
>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=77.67 E-value=17 Score=39.99 Aligned_cols=87 Identities=11% Similarity=0.058 Sum_probs=60.7
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.++++.+| +++.+++...-+..+..+.+.+.|++.|+++.....+.+..+..+....+...++.++|+||-.+...
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 89888884333334678889999999998876444444344556677777777888999999877643
Q ss_pred --hHHHHHHH
Q 003633 123 --PGLRIFTT 130 (806)
Q Consensus 123 --~~~~i~~~ 130 (806)
++.+++..
T Consensus 91 ~iD~aK~ia~ 100 (386)
T cd08191 91 CIDLAKIAGL 100 (386)
T ss_pred HHHHHHHHHH
Confidence 55555543
No 312
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=77.12 E-value=62 Score=34.32 Aligned_cols=69 Identities=12% Similarity=0.067 Sum_probs=45.6
Q ss_pred eeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEecc
Q 003633 384 YCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 384 ~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
+-.+++..+.+..+ .+++++.. ..-.++...|.+|++|+++..-. .....+.+ .++....++++++..
T Consensus 103 ~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~L~~g~~Dl~i~~~~---~~~~~~~~-~~l~~~~~~lv~~~~ 170 (317)
T PRK15421 103 WLTPALENFHKNWP-QVEMDFKS-------GVTFDPQPALQQGELDLVMTSDI---LPRSGLHY-SPMFDYEVRLVLAPD 170 (317)
T ss_pred HHHHHHHHHHHHCC-CceEEEEe-------CccHHHHHHHHCCCcCEEEecCc---ccCCCceE-EEeccceEEEEEcCC
Confidence 34567777776655 45566654 24578899999999999986322 12223443 677788888888766
Q ss_pred C
Q 003633 464 N 464 (806)
Q Consensus 464 ~ 464 (806)
.
T Consensus 171 h 171 (317)
T PRK15421 171 H 171 (317)
T ss_pred C
Confidence 5
No 313
>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=77.10 E-value=67 Score=30.33 Aligned_cols=70 Identities=14% Similarity=0.217 Sum_probs=47.2
Q ss_pred eeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEecc
Q 003633 384 YCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 384 ~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
+-.++++.+.+..+ .+.+++.. ++..++...+.+|++|+++...... ....+ .+.++....++++++..
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 55678888888776 34466654 3568899999999999998633211 11222 34677788888888665
Q ss_pred C
Q 003633 464 N 464 (806)
Q Consensus 464 ~ 464 (806)
.
T Consensus 84 ~ 84 (199)
T cd08451 84 H 84 (199)
T ss_pred C
Confidence 4
No 314
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=76.80 E-value=33 Score=35.78 Aligned_cols=122 Identities=18% Similarity=0.098 Sum_probs=83.5
Q ss_pred CCcEEecccCCCCccc--C--CCCceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC-cccchHHHHHHHHHhCC
Q 003633 10 KVPLVSFAATDPTLSA--L--QFPYFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD-YGRNGISALSNMLEKNM 82 (806)
Q Consensus 10 ~vP~Is~~at~p~Ls~--~--~~p~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~g 82 (806)
++|+|-.+.|+|.=.. . .-|---=|.-||..-...-++++++. +-|+++++|.-++ .....++.|+..+++.|
T Consensus 109 ~iPVV~aavtd~v~a~Lv~~~~~pg~NvTGvsD~~~v~q~i~lik~~~Pnak~Igv~Y~p~E~ns~~l~eelk~~A~~~G 188 (322)
T COG2984 109 TIPVVFAAVTDPVGAKLVKSLEQPGGNVTGVSDLLPVAQQIELIKALLPNAKSIGVLYNPGEANSVSLVEELKKEARKAG 188 (322)
T ss_pred CCCEEEEccCchhhccCCccccCCCCceeecCCcchHHHHHHHHHHhCCCCeeEEEEeCCCCcccHHHHHHHHHHHHHCC
Confidence 4899977777654221 1 12333346677877677777887764 8999999997554 77888999999999999
Q ss_pred cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch---HHHHHHHHHHcCC
Q 003633 83 AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP---GLRIFTTAQKLQM 136 (806)
Q Consensus 83 ~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~---~~~i~~~a~~~gm 136 (806)
++|.-.. ++ +..|+...++.+. .++|+|+.-++... ...++..|.+.+.
T Consensus 189 l~vve~~-v~---~~ndi~~a~~~l~-g~~d~i~~p~dn~i~s~~~~l~~~a~~~ki 240 (322)
T COG2984 189 LEVVEAA-VT---SVNDIPRAVQALL-GKVDVIYIPTDNLIVSAIESLLQVANKAKI 240 (322)
T ss_pred CEEEEEe-cC---cccccHHHHHHhc-CCCcEEEEecchHHHHHHHHHHHHHHHhCC
Confidence 9987432 32 2335555566555 78899998887543 3445667776553
No 315
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=76.50 E-value=67 Score=32.70 Aligned_cols=83 Identities=20% Similarity=0.071 Sum_probs=53.1
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
+.++||++... ...+..+++..+.+..+ .+++++.. ++..++..+|.+|++|+++...
T Consensus 67 ~~l~I~~~~~~--------------~~~~~~~~l~~~~~~~p-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~ 124 (269)
T PRK11716 67 GELSLFCSVTA--------------AYSHLPPILDRFRAEHP-LVEIKLTT-------GDAADAVEKVQSGEADLAIAAK 124 (269)
T ss_pred ceEEEEecchH--------------HHHHHHHHHHHHHHHCC-CeEEEEEE-------CCHHHHHHHHHCCCccEEEEec
Confidence 56888876311 12455678888888765 34566665 3567899999999999998632
Q ss_pred EEecCccceeEecccccccceEEEEecc
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
.. .....+. ..++....++++++..
T Consensus 125 ~~--~~~~~~~-~~~l~~~~~~~v~~~~ 149 (269)
T PRK11716 125 PE--TLPASVA-FSPIDEIPLVLIAPAL 149 (269)
T ss_pred CC--CCCcceE-EEEcccceEEEEEcCC
Confidence 21 1111232 3566777778877655
No 316
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=76.12 E-value=8.9 Score=38.23 Aligned_cols=104 Identities=11% Similarity=0.177 Sum_probs=48.3
Q ss_pred CCCceeEEeCchhHHHhhhhccccccc--ceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEe--CC-
Q 003633 582 NDWPIGYQVGSFAYSYLSDSLRIQKSR--LISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGII--GQ- 656 (806)
Q Consensus 582 ~~~~ig~~~gs~~~~~l~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~--~~- 656 (806)
.|.+||+-..|.....+.+.. +.... +++. +..++++.|.+ |.+||.+....-+. .+.-++... ..
T Consensus 113 dGmRVGiD~~S~Dq~~LT~~~-~~gk~Ve~Vei-~Y~q~~~~l~~----g~IDA~IWN~d~i~---~~~~~l~~~~l~~~ 183 (232)
T PF14503_consen 113 DGMRVGIDPSSIDQKILTEAE-FEGKNVEFVEI-PYNQLLELLRS----GEIDAAIWNYDEIE---DKNFGLKYVPLKDD 183 (232)
T ss_dssp ---EEEE-TT-HHHHHHHHHH-HTTS--EEEE---HHHHHHHHHH----TS--EEEEE--HHC---CHHCTEEEEE--SS
T ss_pred eeeEeecCCCCccHHHHHHHH-hCCCceEEEEe-cHHHHHHHHHC----CCccEEEECCcccc---cccCCeeEEeCCch
Confidence 578899998888777775433 23333 3333 46789999999 99999998776221 111233322 21
Q ss_pred -cc-ccCCceeeecCCCC-chHHHHHHHHhhhccchhHHHHHhhc
Q 003633 657 -PF-TRSGWGFAFQRDSP-LAVGMSTAILKLSENGMLQKLHEKWF 698 (806)
Q Consensus 657 -~~-~~~~~~~~~~k~sp-l~~~~n~~il~l~e~G~~~~i~~kw~ 698 (806)
.. ....-.++++|+.+ +...+++ +.....+-++.++-.
T Consensus 184 ~~~~~~seAVivi~~~~~~i~~ll~~----~id~~~vl~iQ~~V~ 224 (232)
T PF14503_consen 184 PMSKDASEAVIVIRKDNEPIKALLRK----LIDVEKVLEIQKKVL 224 (232)
T ss_dssp CHHHHTT-EEEEEETT-HHHHHHHHH----H--HHHHHHHHHHHH
T ss_pred HHHHhcCeeEEEEeCCCHHHHHHHHH----hcCHHHHHHHHHHHH
Confidence 11 12234577788875 4333333 333344445555544
No 317
>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=76.11 E-value=36 Score=33.17 Aligned_cols=103 Identities=14% Similarity=0.118 Sum_probs=63.7
Q ss_pred CCCCChhHhhhCCCceeE-EeCchhHHHhhhhc---ccccccceeC----CCHhHHHHHHhcCCCCCCeEEEEeCchhHH
Q 003633 571 TSVKGIESLITNDWPIGY-QVGSFAYSYLSDSL---RIQKSRLISL----GSPEDYERALRQGPRNGGVAAIVDELPYVQ 642 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~-~~gs~~~~~l~~~~---~~~~~~~~~~----~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~ 642 (806)
..|++++||.+.+.++.- ..||-...++...+ ++....+..| .+-.+...++.. |..|+-+.....++
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 379999999776665433 35776666664332 3344444433 466688888888 89999987655554
Q ss_pred HHhhCCCCeEEeCCccccCCceeeecCCCCchHHHHHHHHh
Q 003633 643 LFLSNQTDFGIIGQPFTRSGWGFAFQRDSPLAVGMSTAILK 683 (806)
Q Consensus 643 ~~~~~~~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~il~ 683 (806)
.+ ..-+|..+ ....|-++++|..-..+.+...|.-
T Consensus 157 ~~--~gL~Fvpl----~~E~~dlv~~~~~~~~~~vq~ll~~ 191 (193)
T PF12727_consen 157 EF--YGLDFVPL----AEERYDLVIRREDLEDPAVQALLDF 191 (193)
T ss_pred hh--cCCCcEEc----cccceEEEEEhhHcCCHHHHHHHHH
Confidence 21 12234433 3356778888877666666555543
No 318
>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=76.11 E-value=19 Score=39.19 Aligned_cols=86 Identities=14% Similarity=0.099 Sum_probs=63.0
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
+.+.++++.+|.+++.+|+....+ ..+.+.+.|++.|+.+.....+.++.+.+++...+..+++.++|+||-.+...
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 456677888899999999854443 45677888888888766555566666677888888889989999999777543
Q ss_pred --hHHHHHHHH
Q 003633 123 --PGLRIFTTA 131 (806)
Q Consensus 123 --~~~~i~~~a 131 (806)
+..+++...
T Consensus 89 ~~D~aK~ia~~ 99 (367)
T cd08182 89 VLDTAKALAAL 99 (367)
T ss_pred HHHHHHHHHHH
Confidence 556555443
No 319
>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=76.04 E-value=16 Score=39.99 Aligned_cols=87 Identities=8% Similarity=0.001 Sum_probs=63.5
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.+.++.+|-+++.+++...-+-.+..+.+.+.|++.|+.+.....+.++.+.+.+...+..++..++|+||-.+...
T Consensus 17 ~~l~~~l~~~g~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGGS 96 (377)
T cd08176 17 KEIGDELKNLGFKKALIVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVKPNPTITNVKDGLAVFKKEGCDFIISIGGGS 96 (377)
T ss_pred HHHHHHHHHhCCCeEEEECCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCcH
Confidence 45667788888889888874333323567889999999998876554565566777888889999999999999777643
Q ss_pred --hHHHHHH
Q 003633 123 --PGLRIFT 129 (806)
Q Consensus 123 --~~~~i~~ 129 (806)
++.+.+.
T Consensus 97 ~iD~aK~ia 105 (377)
T cd08176 97 PHDCAKAIG 105 (377)
T ss_pred HHHHHHHHH
Confidence 4454443
No 320
>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=75.21 E-value=9.6 Score=41.26 Aligned_cols=84 Identities=10% Similarity=0.060 Sum_probs=61.8
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.++++.++ +++.+|+....+ ....+.+.+.|++.|+.+.+. .+....+.+++...+..+++.++|+||-.+...
T Consensus 12 ~~l~~~~~~~~-~r~livt~~~~~-~~~~~~v~~~L~~~~i~~~~~-~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGGS 88 (351)
T cd08170 12 DELGEYLARLG-KRALIIADEFVL-DLVGAKIEESLAAAGIDARFE-VFGGECTRAEIERLAEIARDNGADVVIGIGGGK 88 (351)
T ss_pred HHHHHHHHHhC-CeEEEEECHHHH-HHHHHHHHHHHHhCCCeEEEE-EeCCcCCHHHHHHHHHHHhhcCCCEEEEecCch
Confidence 44667777776 898888843333 367888999999999987644 355566778888889999999999999877644
Q ss_pred --hHHHHHH
Q 003633 123 --PGLRIFT 129 (806)
Q Consensus 123 --~~~~i~~ 129 (806)
+..+++.
T Consensus 89 ~iD~aK~ia 97 (351)
T cd08170 89 TLDTAKAVA 97 (351)
T ss_pred hhHHHHHHH
Confidence 4444443
No 321
>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=74.44 E-value=37 Score=35.50 Aligned_cols=127 Identities=10% Similarity=-0.055 Sum_probs=70.8
Q ss_pred CCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHH-cC----CeEEEEEEEcCC--cccchHHHHHHHHHhC
Q 003633 9 LKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDF-YG----WKEVIAIYVDDD--YGRNGISALSNMLEKN 81 (806)
Q Consensus 9 ~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~-~~----W~~v~ii~~d~~--~g~~~~~~l~~~l~~~ 81 (806)
.++|+|.+..-.+ .. ..+-.+..++..-+..+++.+.. +. -++++++....+ ......+.+.+++++.
T Consensus 80 ~~iPvV~~~~~~~---~~--~~~~~V~~D~~~~g~~~~~~L~~~~~~~~g~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~ 154 (295)
T TIGR02955 80 KSIPVFALVNQID---SN--QVKGRVGVDWYQMGYQAGEYLAQRHPKGSGPTTLAWLPGPKNRGGTKPVTQGFRAALEGS 154 (295)
T ss_pred cCCCEEEEecCCC---cc--ceeEEEeecHHHHHHHHHHHHHHhcccCCCCeeEEEEeCCCcCCchhHHHHHHHHHHhcC
Confidence 3889887522111 11 11222344444445666776544 22 346999975433 3455688899999999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCC--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKP--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
|+++... .....+...-...+.++.+ .++++| +++...+..+++++++.|+. +-+.+++
T Consensus 155 g~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~d~i--~~~d~~a~g~l~al~~~g~~--~dv~vvg 215 (295)
T TIGR02955 155 DVEISAI--LWADNDKELQRNLLQDLLKKHPDIDYL--VGSAVAAEAAISELRSLHMT--QQIKLVS 215 (295)
T ss_pred CcEEEEE--ecCCCcHHHHHHHHHHHHHhCCCcCEE--EeccHHHHHHHHHHHhhCcc--CCeEEEE
Confidence 9877532 2212222232334444432 345653 55666778888998888862 4455554
No 322
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=74.14 E-value=49 Score=35.30 Aligned_cols=129 Identities=12% Similarity=0.052 Sum_probs=66.5
Q ss_pred cccCCCcEEecccCCCCccc-CCCCceEEecCCcHHHHHHHHHHH-HHc-----------CCeEEEEEEEcC--Ccccch
Q 003633 6 ANGLKVPLVSFAATDPTLSA-LQFPYFIRSTQSDSQQMAAMADLI-DFY-----------GWKEVIAIYVDD--DYGRNG 70 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~-~~~p~f~Rt~psd~~q~~ai~~ll-~~~-----------~W~~v~ii~~d~--~~g~~~ 70 (806)
+...++|+|.+....+ ... ...+-...+..++..-++.+++++ ++. |-.++++|.... ......
T Consensus 102 l~~~giPvV~vd~~~~-~~~~~~~~~~~~V~~D~~~ag~~a~~~l~~~~~~~~~~~~~~~g~~~i~~i~g~~~~~~~~~R 180 (330)
T PRK15395 102 ARGQDVPVVFFNKEPS-RKALDSYDKAYYVGTDSKESGIIQGDLIAKHWKANPAWDLNKDGKIQYVLLKGEPGHPDAEAR 180 (330)
T ss_pred HHHCCCcEEEEcCCcc-ccccccccceeEEccChHHHHHHHHHHHHHHHhhccccccCCCCceEEEEEecCCCCchHHHH
Confidence 3456899999865321 111 011111223445555555555544 332 333445454322 223445
Q ss_pred HHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCC----CCeEEEEecCcchHHHHHHHHHHcCC
Q 003633 71 ISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPL----GPRVYVVHVSPDPGLRIFTTAQKLQM 136 (806)
Q Consensus 71 ~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~----~~rvivl~~~~~~~~~i~~~a~~~gm 136 (806)
.+.+.+++++.|+.+..........+.+.-...+.++.+. ++++ |++++...+..+++++++.|+
T Consensus 181 ~~G~~~al~~~g~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~a-i~~~~d~~A~gvl~al~~~Gl 249 (330)
T PRK15395 181 TTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEV-VIANNDAMAMGAVEALKAHNK 249 (330)
T ss_pred HHHHHHHHHhcCCCeeeeecccCCcCHHHHHHHHHHHHhhCcCCCeeE-EEECCchHHHHHHHHHHhcCC
Confidence 7888999999887654321111111222222344444332 3444 445566778899999999986
No 323
>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=73.95 E-value=23 Score=35.40 Aligned_cols=194 Identities=15% Similarity=0.087 Sum_probs=111.6
Q ss_pred EeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcC-cccEEEeeEEEecCc---cceeE--ecccccccc
Q 003633 382 QGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVAND-VFDAAVGDIAIVTNR---TKIVD--FSQPYISTG 455 (806)
Q Consensus 382 ~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g-~~D~~~~~~~it~~r---~~~vd--ft~p~~~~~ 455 (806)
.+..-++.+...+..+.++++.+. .-..+...|..| ++|+.+.+-....++ ...++ -..|+..+.
T Consensus 10 ~~~~~~l~~~f~~~~g~~v~v~~~---------~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~ 80 (230)
T PF13531_consen 10 APALEELAEAFEKQPGIKVEVSFG---------GSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLARSP 80 (230)
T ss_dssp HHHHHHHHHHHHHHHCEEEEEEEE---------CHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEEEE
T ss_pred HHHHHHHHHHHHhccCCeEEEEEC---------ChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCcccccccCc
Confidence 345567888887788866444333 357788888877 689887743221111 12333 567888888
Q ss_pred eEEEEeccCCCCCcceeecCcchhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchhhHHHHHHHhhhccCcccccc
Q 003633 456 LVIVAPINNHKASAWVFLKPFTVEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIATMFLFSFSTLFKTNQEATVS 535 (806)
Q Consensus 456 ~~~~v~~~~~~~~~~~~l~PF~~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s 535 (806)
++++++...+
T Consensus 81 ~vl~~~~~~~---------------------------------------------------------------------- 90 (230)
T PF13531_consen 81 LVLAVPKGNP---------------------------------------------------------------------- 90 (230)
T ss_dssp EEEEEETTST----------------------------------------------------------------------
T ss_pred eEEEeccCcc----------------------------------------------------------------------
Confidence 9999887761
Q ss_pred cchhhhHHHHHhhhhhhhccccceeeeeeeeccccCCCCChhHhhhCCCceeEEeCc------hhHHHhhhhcc------
Q 003633 536 SLGRFVMVVWLFLLMVITSSYTASLSSILTVQQLSTSVKGIESLITNDWPIGYQVGS------FAYSYLSDSLR------ 603 (806)
Q Consensus 536 ~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~ig~~~gs------~~~~~l~~~~~------ 603 (806)
..+.+++||.+.+.+|++.... .....+.+ .+
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 3678899998777788887632 11222211 11
Q ss_pred cccccce-eCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCC--eEEeCCcccc--CCceeeecCCCCchHHHH
Q 003633 604 IQKSRLI-SLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTD--FGIIGQPFTR--SGWGFAFQRDSPLAVGMS 678 (806)
Q Consensus 604 ~~~~~~~-~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~--l~~~~~~~~~--~~~~~~~~k~spl~~~~n 678 (806)
.-..++. ..++..+....+.. |+.++.+.....+.+. ....+ +..+++.... ..+.+++.++++-.+.-.
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 0112333 45677888888988 8899888765544222 22233 3344444442 457788888886555555
Q ss_pred HHHHhhhccchhHHHHHh
Q 003633 679 TAILKLSENGMLQKLHEK 696 (806)
Q Consensus 679 ~~il~l~e~G~~~~i~~k 696 (806)
..+..|... .-+++..+
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 555555543 33444433
No 324
>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=73.56 E-value=1.1e+02 Score=31.26 Aligned_cols=69 Identities=14% Similarity=0.183 Sum_probs=45.6
Q ss_pred eeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEecc
Q 003633 384 YCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 384 ~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
+-.+++..+.+..+ .+++++.. ++..+++..|.+|++|+++...... ...+. ..|+....++++++..
T Consensus 98 ~~~~~l~~~~~~~p-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~lv~s~~ 165 (279)
T TIGR03339 98 YVLDLVARFRQRYP-GIEVSVRI-------GNSQEVLQALQSYRVDVAVSSEVVD---DPRLD-RVVLGNDPLVAVVHRQ 165 (279)
T ss_pred HHHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEecccC---CCceE-EEEcCCceEEEEECCC
Confidence 44567777777655 34466654 3568899999999999998632222 12232 3567778888888765
Q ss_pred C
Q 003633 464 N 464 (806)
Q Consensus 464 ~ 464 (806)
.
T Consensus 166 ~ 166 (279)
T TIGR03339 166 H 166 (279)
T ss_pred C
Confidence 5
No 325
>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=73.14 E-value=39 Score=33.50 Aligned_cols=111 Identities=15% Similarity=0.107 Sum_probs=71.9
Q ss_pred CCCcEEecccC--CCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEE
Q 003633 9 LKVPLVSFAAT--DPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVS 86 (806)
Q Consensus 9 ~~vP~Is~~at--~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~ 86 (806)
.++..|-.-+| -|.|...+ | +.-++...-..++.++.. .++++|....+ -.+...+..+..+..+.
T Consensus 86 ~G~d~illlCTG~F~~l~~~~-~----lleP~ril~~lV~al~~~---~~vGVivP~~e----Q~~~~~~kW~~l~~~~~ 153 (221)
T PF07302_consen 86 QGYDVILLLCTGEFPGLTARN-P----LLEPDRILPPLVAALVGG---HQVGVIVPLPE----QIAQQAEKWQPLGNPVV 153 (221)
T ss_pred CCCCEEEEeccCCCCCCCCCc-c----eeehHHhHHHHHHHhcCC---CeEEEEecCHH----HHHHHHHHHHhcCCCeE
Confidence 34444444444 34555433 3 233444444555555544 89999997655 44555566677777777
Q ss_pred EEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC--cchHHHHHHHH
Q 003633 87 YKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS--PDPGLRIFTTA 131 (806)
Q Consensus 87 ~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~--~~~~~~i~~~a 131 (806)
+...-|...+.+++...-++++..++|+|+++|- ....+.+++++
T Consensus 154 ~a~asPy~~~~~~l~~Aa~~L~~~gadlIvLDCmGYt~~~r~~~~~~ 200 (221)
T PF07302_consen 154 VAAASPYEGDEEELAAAARELAEQGADLIVLDCMGYTQEMRDIVQRA 200 (221)
T ss_pred EEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEECCCCCHHHHHHHHHH
Confidence 6665665467788999999999999999999884 44556666654
No 326
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=73.12 E-value=67 Score=33.53 Aligned_cols=82 Identities=15% Similarity=0.075 Sum_probs=51.6
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
++++||++.. . ...+...++..+.+.- .+++++.. +.-..++..+.+|++|+++..-
T Consensus 90 g~l~I~~~~~--~------------~~~~l~~~l~~f~~~~--~i~i~l~~-------~~~~~~~~~l~~~~~d~~i~~~ 146 (294)
T PRK03635 90 LTLSIAVNAD--S------------LATWFLPALAPVLARS--GVLLDLVV-------EDQDHTAELLRRGEVVGAVTTE 146 (294)
T ss_pred eEEEEeecch--h------------HHHHHHHHHHHHHhCC--CcEEEEEe-------cCcHHHHHHHhCCCceEEEecc
Confidence 5789998631 1 1123345666666653 55566665 2456889999999999998532
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
. .....+ .+.|+....++++++...
T Consensus 147 ~---~~~~~l-~~~~l~~~~~~lv~~~~~ 171 (294)
T PRK03635 147 P---QPVQGC-RVDPLGAMRYLAVASPAF 171 (294)
T ss_pred C---CCCCCc-eeeecccceEEEEEcchH
Confidence 1 122222 467788888888887543
No 327
>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=72.35 E-value=25 Score=38.52 Aligned_cols=88 Identities=6% Similarity=0.065 Sum_probs=63.0
Q ss_pred HHHHHHHHHc---CCeEEEEEEEcCCcc-cchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEe
Q 003633 43 AAMADLIDFY---GWKEVIAIYVDDDYG-RNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVH 118 (806)
Q Consensus 43 ~ai~~ll~~~---~W~~v~ii~~d~~~g-~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~ 118 (806)
+.+.++++.+ |.+++.+++...... .+..+.+.+.|++.|+.+.....+.++.+.+++...+..++..++|+||-.
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 889999888544333 344688999999999877655456666677888888999998999999977
Q ss_pred cCc--chHHHHHHH
Q 003633 119 VSP--DPGLRIFTT 130 (806)
Q Consensus 119 ~~~--~~~~~i~~~ 130 (806)
+.. -+..+++..
T Consensus 92 GGGS~iD~aK~ia~ 105 (383)
T cd08186 92 GGGSPIDSAKSAAI 105 (383)
T ss_pred CCccHHHHHHHHHH
Confidence 653 355555544
No 328
>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=72.06 E-value=7.9 Score=39.48 Aligned_cols=78 Identities=13% Similarity=0.099 Sum_probs=58.6
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC-cchHHHHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS-PDPGLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~-~~~~~~i~~~a~~ 133 (806)
|++|.. ++.|.......+.+++++.|+.+... .+...+.......+.++.+.++|.||+... ++....+++++.+
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 344543 45688888999999999999998765 333345566667788887889999888755 5567789999999
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|+
T Consensus 79 ~gI 81 (257)
T PF13407_consen 79 AGI 81 (257)
T ss_dssp TTS
T ss_pred cCc
Confidence 886
No 329
>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=71.87 E-value=14 Score=40.55 Aligned_cols=86 Identities=9% Similarity=0.032 Sum_probs=62.0
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCc-ccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDY-GRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~-g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
+.+.++++.++ +++.+|.....+ ..+..+.+.+.|++.|+++.....+.++.+.+++...+..+++.++|+||-.+..
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 45667777775 888888743333 2355788999999999987655556666667788888999999999999977754
Q ss_pred c--hHHHHHH
Q 003633 122 D--PGLRIFT 129 (806)
Q Consensus 122 ~--~~~~i~~ 129 (806)
. ++.+++.
T Consensus 97 S~iD~aK~ia 106 (382)
T cd08187 97 SVIDSAKAIA 106 (382)
T ss_pred HHHHHHHHHH
Confidence 3 5555443
No 330
>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=71.73 E-value=25 Score=37.61 Aligned_cols=100 Identities=6% Similarity=-0.006 Sum_probs=66.0
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.+.++.+|.+++.+|+.... .....+.+.+.|++. +++.......++.+.+++...+..+++.++|+||..+...
T Consensus 12 ~~l~~~~~~~g~~~~liv~~~~~-~~~~~~~v~~~l~~~-~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs 89 (332)
T cd07766 12 EKIGEEIKRGGFDRALVVSDEGV-VKGVGEKVADSLKKL-IAVHIFDGVGPNPTFEEVKEAVERARAAEVDAVIAVGGGS 89 (332)
T ss_pred HHHHHHHHhcCCCeEEEEeCCch-hhhHHHHHHHHHHhc-CcEEEeCCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCch
Confidence 34566778889999999984333 336778888899887 6654443344445667888888888888999999777543
Q ss_pred --hHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 123 --PGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 123 --~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
+..+++......| ..++-|-|.
T Consensus 90 ~~D~aK~ia~~~~~~---~p~i~iPTt 113 (332)
T cd07766 90 TLDTAKAVAALLNRG---LPIIIVPTT 113 (332)
T ss_pred HHHHHHHHHHHhcCC---CCEEEEeCC
Confidence 5555554433223 234555543
No 331
>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=70.48 E-value=97 Score=29.21 Aligned_cols=72 Identities=14% Similarity=0.158 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
++-.+++..+.+..+ .+++++.. +....+...+.+|++|+++..... ......+ -+.++....++++++.
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 556678888888775 34566654 245778999999999999863221 0011222 2456777788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 83 ~h 84 (199)
T cd08416 83 TS 84 (199)
T ss_pred CC
Confidence 54
No 332
>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=70.43 E-value=57 Score=31.06 Aligned_cols=100 Identities=12% Similarity=0.048 Sum_probs=63.3
Q ss_pred HHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC--CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEE
Q 003633 39 SQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN--MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYV 116 (806)
Q Consensus 39 ~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~--g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rviv 116 (806)
......+.+.....+ .+|.++-...+ .++.+.+.+++. |++|+....-+ ....+-..++.+|++.+||+|+
T Consensus 32 ~dl~~~ll~~~~~~~-~~v~llG~~~~----~~~~~~~~l~~~yp~l~i~g~~~g~--~~~~~~~~i~~~I~~~~pdiv~ 104 (171)
T cd06533 32 SDLMPALLELAAQKG-LRVFLLGAKPE----VLEKAAERLRARYPGLKIVGYHHGY--FGPEEEEEIIERINASGADILF 104 (171)
T ss_pred HHHHHHHHHHHHHcC-CeEEEECCCHH----HHHHHHHHHHHHCCCcEEEEecCCC--CChhhHHHHHHHHHHcCCCEEE
Confidence 334566666655555 45666665444 455555666654 77777543222 2334444588999999999999
Q ss_pred EecCcchHHHHHHHHHHcCCccCCcEEEEcCc
Q 003633 117 VHVSPDPGLRIFTTAQKLQMMTNNYVWLATDW 148 (806)
Q Consensus 117 l~~~~~~~~~i~~~a~~~gm~~~~~~wi~t~~ 148 (806)
+.+..+....++.+.++.. +.-+++..++
T Consensus 105 vglG~PkQE~~~~~~~~~l---~~~v~~~vG~ 133 (171)
T cd06533 105 VGLGAPKQELWIARHKDRL---PVPVAIGVGG 133 (171)
T ss_pred EECCCCHHHHHHHHHHHHC---CCCEEEEece
Confidence 9999888788777666543 2345666554
No 333
>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=70.26 E-value=68 Score=30.78 Aligned_cols=86 Identities=10% Similarity=-0.009 Sum_probs=57.5
Q ss_pred HHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhC--CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEE
Q 003633 39 SQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKN--MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYV 116 (806)
Q Consensus 39 ~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~--g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rviv 116 (806)
...+..+.+....-+| +|.++-...+ .++.+.+.+++. |++|+.. ....++++-..++.+|.++++|+++
T Consensus 34 ~dl~~~l~~~~~~~~~-~vfllG~~~~----v~~~~~~~l~~~yP~l~i~g~---~g~f~~~~~~~i~~~I~~s~~dil~ 105 (177)
T TIGR00696 34 PDLMEELCQRAGKEKL-PIFLYGGKPD----VLQQLKVKLIKEYPKLKIVGA---FGPLEPEERKAALAKIARSGAGIVF 105 (177)
T ss_pred HHHHHHHHHHHHHcCC-eEEEECCCHH----HHHHHHHHHHHHCCCCEEEEE---CCCCChHHHHHHHHHHHHcCCCEEE
Confidence 3445666666666674 6666664433 566667777654 7787765 2223445556789999999999999
Q ss_pred EecCcchHHHHHHHHH
Q 003633 117 VHVSPDPGLRIFTTAQ 132 (806)
Q Consensus 117 l~~~~~~~~~i~~~a~ 132 (806)
+.+..+....++.+.+
T Consensus 106 VglG~PkQE~~~~~~~ 121 (177)
T TIGR00696 106 VGLGCPKQEIWMRNHR 121 (177)
T ss_pred EEcCCcHhHHHHHHhH
Confidence 9998887777665543
No 334
>PRK10537 voltage-gated potassium channel; Provisional
Probab=70.08 E-value=6.6 Score=42.96 Aligned_cols=54 Identities=20% Similarity=0.348 Sum_probs=40.9
Q ss_pred CCccchhhHHHHHHHhhhccC--cccccccchhhhHHHHHhhhhhhhccccceeee
Q 003633 509 PPRRQIATMFLFSFSTLFKTN--QEATVSSLGRFVMVVWLFLLMVITSSYTASLSS 562 (806)
Q Consensus 509 ~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s 562 (806)
+...++.+++||++.++...+ ...|.+..+|++.+++.++++.+.....+.++.
T Consensus 164 ~~~~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~ 219 (393)
T PRK10537 164 PPIESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFG 219 (393)
T ss_pred cCCCCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445689999999998887544 447888899999999999888766554444444
No 335
>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=69.91 E-value=17 Score=39.23 Aligned_cols=86 Identities=10% Similarity=0.126 Sum_probs=60.7
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
.-+.+.++.++ +++.+|+....+ ....+.+.+.|++.|+.+.....+..+.+.+++.......++.++|+||-.+...
T Consensus 12 ~~l~~~~~~~~-~r~liv~d~~~~-~~~~~~v~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~iiavGGGs 89 (345)
T cd08171 12 KKIPEVCEKYG-KKVVVIGGKTAL-AAAKDKIKAALEQSGIEITDFIWYGGESTYENVERLKKNPAVQEADMIFAVGGGK 89 (345)
T ss_pred HHHHHHHHhcC-CEEEEEeCHHHH-HHHHHHHHHHHHHCCCeEEEEEecCCCCCHHHHHHHHHHHhhcCCCEEEEeCCcH
Confidence 45666777788 888888754333 3457778888999998776444555566677788888888889999999777543
Q ss_pred --hHHHHHHH
Q 003633 123 --PGLRIFTT 130 (806)
Q Consensus 123 --~~~~i~~~ 130 (806)
+..+++..
T Consensus 90 ~~D~aK~ia~ 99 (345)
T cd08171 90 AIDTVKVLAD 99 (345)
T ss_pred HHHHHHHHHH
Confidence 44554443
No 336
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=69.82 E-value=70 Score=32.83 Aligned_cols=112 Identities=18% Similarity=0.203 Sum_probs=63.4
Q ss_pred ChhHhhh-CCCceeEEe------CchhHHHhhhhccc---ccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHH
Q 003633 575 GIESLIT-NDWPIGYQV------GSFAYSYLSDSLRI---QKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLF 644 (806)
Q Consensus 575 s~~dL~~-~~~~ig~~~------gs~~~~~l~~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~ 644 (806)
++++|.+ .+.++++.+ |-+....|. .++. ...+++...+.++.+..+.. |+.|+.+.-...+..
T Consensus 126 ~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~-~~g~~~~~~~k~v~~~~v~~~l~~V~~----G~ad~g~vy~sd~~~- 199 (258)
T COG0725 126 SLEDLLERPDVRLAIGDPKTVPAGKYAKEALE-LLGLWYTLKDKLVLATNVRQALAYVET----GEADAGFVYVSDALL- 199 (258)
T ss_pred cHHHHhcCcCcEEEecCCCCCCchHHHHHHHH-HhchhhhccccEEecCcHHHHHHHHHc----CCCCeEEEEEEhhhc-
Confidence 3667765 355677654 445555553 2222 23467777888899999999 899877665443222
Q ss_pred hhCCCC-eEEeCCcccc-CCceeeecCCCCc---hHHHHHHHHhhhccchhHHHHHhh
Q 003633 645 LSNQTD-FGIIGQPFTR-SGWGFAFQRDSPL---AVGMSTAILKLSENGMLQKLHEKW 697 (806)
Q Consensus 645 ~~~~~~-l~~~~~~~~~-~~~~~~~~k~spl---~~~~n~~il~l~e~G~~~~i~~kw 697 (806)
...-+ +..+++.... ..|..++.+++.- ...|-+.++. ..-+++.++|
T Consensus 200 -~~~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s----~~a~~il~~~ 252 (258)
T COG0725 200 -SKKVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLS----PEAQEILEKY 252 (258)
T ss_pred -cCCceEEEEcccccCCCeEEEEEEEcCCCCHHHHHHHHHHHhC----HHHHHHHHHc
Confidence 11222 4444443332 4577888887664 5555555544 2334454444
No 337
>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=67.55 E-value=1.1e+02 Score=28.76 Aligned_cols=71 Identities=14% Similarity=0.115 Sum_probs=46.5
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. .+.+.++.+|.+|++|+++...... ....+ .+.++....++++++.
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 556788888888876 34566654 2457889999999999998632111 11122 3456667777877766
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~h 83 (195)
T cd08431 82 NH 83 (195)
T ss_pred CC
Confidence 54
No 338
>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=67.05 E-value=36 Score=37.16 Aligned_cols=83 Identities=10% Similarity=0.070 Sum_probs=59.6
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.++++.++ +++.+|+..... ..+.+.+.|++.|+.+.... +..+.+.+++...+..++..++|+||-.+...
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 888888843332 67788889999998765443 44456667788888889999999999877653
Q ss_pred --hHHHHHHH
Q 003633 123 --PGLRIFTT 130 (806)
Q Consensus 123 --~~~~i~~~ 130 (806)
++.+++..
T Consensus 87 ~~D~aK~ia~ 96 (374)
T cd08183 87 VIDAGKAIAA 96 (374)
T ss_pred HHHHHHHHHH
Confidence 55555544
No 339
>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=66.94 E-value=1.1e+02 Score=28.63 Aligned_cols=70 Identities=17% Similarity=0.188 Sum_probs=46.9
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.++++.+.+..+ .+++++.. ++...+...|.+|++|+++...... ...+. +.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~~~ 80 (196)
T cd08450 13 QWLPEVLPILREEHP-DLDVELSS-------LFSPQLAEALMRGKLDVAFMRPEIQ---SDGID-YQLLLKEPLIVVLPA 80 (196)
T ss_pred hhHHHHHHHHHhhCC-CcEEEEEe-------cChHHHHHHHhcCCccEEEEeCCCC---CCCcE-EEEEEccceEEEecC
Confidence 455678888888766 34566665 3567899999999999998532211 12232 456777788888876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (196)
T cd08450 81 DH 82 (196)
T ss_pred CC
Confidence 54
No 340
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=66.90 E-value=1.6e+02 Score=30.48 Aligned_cols=70 Identities=13% Similarity=0.134 Sum_probs=48.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+..+++..+.+..+ .+.+.+.. .+.++++..+.+|++|+++..... ....+++ .|+....+++++++
T Consensus 103 ~~l~~~~~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~~-~~l~~~~~~~v~~~ 170 (296)
T PRK09906 103 NLLPKVLPMFRLRHP-DTLIELVS-------LITTQQEEKLRRGELDVGFMRHPV---YSDEIDY-LELLDEPLVVVLPV 170 (296)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe-------CCcHHHHHHHHcCCeeEEEecCCC---CCCCceE-EEEecccEEEEecC
Confidence 445577777777765 45566654 246889999999999999864332 2233443 68888899999876
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 171 ~~ 172 (296)
T PRK09906 171 DH 172 (296)
T ss_pred CC
Confidence 65
No 341
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=66.55 E-value=1.1e+02 Score=31.81 Aligned_cols=121 Identities=21% Similarity=0.227 Sum_probs=72.7
Q ss_pred CCCCChhHhhhC----C--CceeEE-eCch---hHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchh
Q 003633 571 TSVKGIESLITN----D--WPIGYQ-VGSF---AYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPY 640 (806)
Q Consensus 571 ~~i~s~~dL~~~----~--~~ig~~-~gs~---~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~ 640 (806)
.+++|++||++. . ..+|.. .|+. ....+.+..+.. .+.++|+...+.+.+|.. |.+|+.+.....
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 588999998742 2 234543 2332 223344555543 467889999999999999 999998887654
Q ss_pred HHHHhhC-CCC-eEEeC--------------Cc----c-ccCCceeeecCCCC--chHHHHHHHHhhhccchhHHHHHh
Q 003633 641 VQLFLSN-QTD-FGIIG--------------QP----F-TRSGWGFAFQRDSP--LAVGMSTAILKLSENGMLQKLHEK 696 (806)
Q Consensus 641 ~~~~~~~-~~~-l~~~~--------------~~----~-~~~~~~~~~~k~sp--l~~~~n~~il~l~e~G~~~~i~~k 696 (806)
..-++.. .-+ +.+.+ |. + .....+++.|||-| .++.+..++.+..++-.+++..++
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 4443332 111 11111 11 0 11225889999998 999999999999999877655554
No 342
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=66.17 E-value=5.6 Score=48.58 Aligned_cols=55 Identities=7% Similarity=0.260 Sum_probs=46.9
Q ss_pred cchhhHHHHHHHhhhccC--cccccccchhhhHHHHHhhhhhhhccccceeeeeeee
Q 003633 512 RQIATMFLFSFSTLFKTN--QEATVSSLGRFVMVVWLFLLMVITSSYTASLSSILTV 566 (806)
Q Consensus 512 ~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~s~Yta~L~s~Lt~ 566 (806)
.+...++||++.|+..-| ...|.+..+|++.++|.++++++.+...+++++++..
T Consensus 249 ~~Yi~slYwai~TmtTVGYGDi~p~t~~E~i~~i~~ml~g~~~~a~~ig~i~~li~~ 305 (823)
T PLN03192 249 IRYISAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE 305 (823)
T ss_pred HHHHHHHHHHHHHHhhccCCCcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346678999999988654 4479999999999999999999999999999988754
No 343
>PLN02245 ATP phosphoribosyl transferase
Probab=65.99 E-value=39 Score=36.63 Aligned_cols=104 Identities=12% Similarity=0.069 Sum_probs=58.1
Q ss_pred CCCChhHhhh-------CCCceeEEeCchhHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHH
Q 003633 572 SVKGIESLIT-------NDWPIGYQVGSFAYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLF 644 (806)
Q Consensus 572 ~i~s~~dL~~-------~~~~ig~~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~ 644 (806)
.+++++||.. ...+|+..--.....||.+ .+.....++...-.-|. +-.. |-.|++++-.....-+
T Consensus 178 ~~~s~~dL~g~~~~~~~~~~RIATkYp~ltr~ff~~-~Gv~~v~Iv~l~GAvE~--AP~l----GlADaIvDIVsTGtTL 250 (403)
T PLN02245 178 NINSLKELAQMPQWTEERPLRVVTGFTYLGPKFMKD-NGFKHVTFSTADGALEA--APAM----GIADAILDLVSSGTTL 250 (403)
T ss_pred ccCCHHHhcccccccccCceEEEeCCHHHHHHHHHH-cCCCeEEEEECcCceec--cccc----CchhhhcchhccHHHH
Confidence 5788888842 1157877777778888844 45544455555433333 2222 6677777765555444
Q ss_pred hhCCCCeEEeC-CccccCCceeeecCCCC-----chHHHHHHHHhh
Q 003633 645 LSNQTDFGIIG-QPFTRSGWGFAFQRDSP-----LAVGMSTAILKL 684 (806)
Q Consensus 645 ~~~~~~l~~~~-~~~~~~~~~~~~~k~sp-----l~~~~n~~il~l 684 (806)
..+ +|.+++ +.+....-.+...|++. -++.+...+.++
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 577775 34444444455566653 223444444444
No 344
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=64.83 E-value=22 Score=38.71 Aligned_cols=84 Identities=12% Similarity=0.075 Sum_probs=60.5
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.+.++.+| +++.+|+....+ ....+.+.+.|++.|+++.+. .++...+.+.+...+..+++.++|+||-.+...
T Consensus 19 ~~l~~~l~~~g-~~~livtd~~~~-~~~~~~v~~~l~~~~~~~~~~-~~~~ep~~~~v~~~~~~~~~~~~d~IIavGGGs 95 (366)
T PRK09423 19 ARLGEYLKPLG-KRALVIADEFVL-GIVGDRVEASLKEAGLTVVFE-VFNGECSDNEIDRLVAIAEENGCDVVIGIGGGK 95 (366)
T ss_pred HHHHHHHHHcC-CEEEEEEChhHH-HHHHHHHHHHHHhCCCeEEEE-EeCCCCCHHHHHHHHHHHHhcCCCEEEEecChH
Confidence 55667788889 898888843333 346788888899999887544 355556667888888888888999999877643
Q ss_pred --hHHHHHH
Q 003633 123 --PGLRIFT 129 (806)
Q Consensus 123 --~~~~i~~ 129 (806)
+..+++.
T Consensus 96 v~D~aK~iA 104 (366)
T PRK09423 96 TLDTAKAVA 104 (366)
T ss_pred HHHHHHHHH
Confidence 4454444
No 345
>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=64.76 E-value=1.3e+02 Score=28.56 Aligned_cols=70 Identities=13% Similarity=0.079 Sum_probs=44.3
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++-++++.+|.+|++|+++...... ...+. +.++.+..++++++.
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 445677777777654 45566654 3567899999999999998632111 12232 346667777776654
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~~ 83 (198)
T cd08485 82 SR 83 (198)
T ss_pred CC
Confidence 43
No 346
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=64.53 E-value=24 Score=36.13 Aligned_cols=77 Identities=4% Similarity=-0.037 Sum_probs=53.1
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc-chHHHHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP-DPGLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~-~~~~~i~~~a~~ 133 (806)
|+++.. ++.|.......+.+++++.|.++.... ...+.......+..+.+.+.|.+|+.... .....+++++.+
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~~~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~~~i~~~~~ 78 (273)
T cd06305 2 IAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYD---AGGDDAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRALD 78 (273)
T ss_pred eEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEEC---CCCCHHHHHHHHHHHHHcCCCEEEEecCChhhhHHHHHHHHH
Confidence 566654 566778889999999999999987532 12233444566666666789999887543 334566778887
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|+
T Consensus 79 ~~i 81 (273)
T cd06305 79 AGI 81 (273)
T ss_pred cCC
Confidence 774
No 347
>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=63.25 E-value=62 Score=32.79 Aligned_cols=120 Identities=7% Similarity=0.040 Sum_probs=74.1
Q ss_pred ccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHH--cCCeEEEEEEEcC-CcccchHHHHHHHHHhCCc
Q 003633 7 NGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDF--YGWKEVIAIYVDD-DYGRNGISALSNMLEKNMA 83 (806)
Q Consensus 7 ~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~--~~W~~v~ii~~d~-~~g~~~~~~l~~~l~~~g~ 83 (806)
++.++|++...-..+. ...+++ ...++..-+..+++.+.. .|-+++++|.... ..++...+.+.+++++.|+
T Consensus 73 ~~~~~PvV~i~~~~~~--~~~~~~---V~~D~~~~~~~a~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l~~~g~ 147 (247)
T cd06276 73 KIPKEKLLILDHSIPE--GGEYSS---VAQDFEKAIYNALQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFCKDYNI 147 (247)
T ss_pred ccCCCCEEEEcCcCCC--CCCCCe---EEEccHHHHHHHHHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHHHHcCC
Confidence 4467888876543221 112333 344555556677777767 8999999997543 3456668889999999997
Q ss_pred EEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEE
Q 003633 84 KVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLA 145 (806)
Q Consensus 84 ~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~ 145 (806)
.... .. ... . ..+ ..++ .|++++...+..+++.+++.|+..++-+=|+
T Consensus 148 ~~~~---~~-~~~--~--~~~-----~~~~-ai~~~~d~~A~g~~~~l~~~g~~iP~disvi 195 (247)
T cd06276 148 ETEI---IN-DYE--N--REI-----EKGD-LYIILSDTDLVFLIKKARESGLLLGKDIGII 195 (247)
T ss_pred Cccc---cc-ccc--h--hhc-----cCCc-EEEEeCHHHHHHHHHHHHHcCCcCCceeEEE
Confidence 6431 11 000 1 001 1234 4667778888999999999998655443333
No 348
>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=63.17 E-value=44 Score=36.84 Aligned_cols=80 Identities=8% Similarity=-0.024 Sum_probs=58.2
Q ss_pred HcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc--chHHHHH
Q 003633 51 FYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP--DPGLRIF 128 (806)
Q Consensus 51 ~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~--~~~~~i~ 128 (806)
..+.+++.+|+...-...+..+.+.+.|++.|+++.....+.++.+.+.+...+..++..++|+||-.+.. -+..+++
T Consensus 18 ~~~~~k~liVtd~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS~iD~AK~i 97 (398)
T cd08178 18 LKGKKRAFIVTDRFMVKLGYVDKVIDVLKRRGVETEVFSDVEPDPSLETVRKGLELMNSFKPDTIIALGGGSPMDAAKIM 97 (398)
T ss_pred hcCCCeEEEEcChhHHhCccHHHHHHHHHHCCCeEEEecCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHHH
Confidence 34668988888433333447788999999999887655556666677788888888999999999976654 3556555
Q ss_pred HH
Q 003633 129 TT 130 (806)
Q Consensus 129 ~~ 130 (806)
..
T Consensus 98 A~ 99 (398)
T cd08178 98 WL 99 (398)
T ss_pred HH
Confidence 43
No 349
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=62.37 E-value=15 Score=40.65 Aligned_cols=89 Identities=11% Similarity=0.220 Sum_probs=68.7
Q ss_pred hhhHHHHHHHHHHHHHHhhhhccccCCCCCCCCccchhhHHHHHHHhhhcc--CcccccccchhhhHHHHHhhhhhhhcc
Q 003633 478 VEMWCVTAASFVMIAVVIWILEHRVNDDFRGPPRRQIATMFLFSFSTLFKT--NQEATVSSLGRFVMVVWLFLLMVITSS 555 (806)
Q Consensus 478 ~~~W~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~s~~~R~v~~~w~~~~lil~s~ 555 (806)
...|..-++.+++.++++++.|.....+-........-.++||..-|+..- |...|..+.+|++..++.++++-+-+.
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 357888999999999999999998544322223346889999999888754 456899999999999998888877777
Q ss_pred ccceeeeeeee
Q 003633 556 YTASLSSILTV 566 (806)
Q Consensus 556 Yta~L~s~Lt~ 566 (806)
=.+.|-|=++.
T Consensus 314 PAGILGSGfAL 324 (654)
T KOG1419|consen 314 PAGILGSGFAL 324 (654)
T ss_pred ccccccchhhh
Confidence 66677666554
No 350
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=62.34 E-value=29 Score=35.06 Aligned_cols=76 Identities=8% Similarity=-0.088 Sum_probs=54.5
Q ss_pred EEEEEEc--CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYVD--DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++..+ +.|.......+.+++++.|+.+.... ...+.......++++.+.+++.+++......... ++.+.+.
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 4566643 77888889999999999998877542 2233344566677777789999998777665555 7777776
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 78 ~i 79 (264)
T cd06267 78 GI 79 (264)
T ss_pred CC
Confidence 64
No 351
>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=62.03 E-value=1.2e+02 Score=31.74 Aligned_cols=125 Identities=7% Similarity=-0.082 Sum_probs=69.3
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCe-EEEEEEEcCC--cccchHHHHHHHHHhC-
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWK-EVIAIYVDDD--YGRNGISALSNMLEKN- 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~-~v~ii~~d~~--~g~~~~~~l~~~l~~~- 81 (806)
+.+.++|+|.+....+ . .+....+..++..-++.+++.+...+-+ +++++..+.. ......+.+.+.+++.
T Consensus 75 ~~~~~iPvV~~d~~~~---~--~~~~~~V~~d~~~~g~~~~~~L~~~g~~~~i~~i~g~~~~~~~~~R~~g~~~~~~~~~ 149 (302)
T TIGR02634 75 AKDEGIKVVAYDRLIN---D--ADIDFYLSFDNEKVGEMQARAVLEAAPKGNYFLMGGSPTDNNAKLLRGGQMKVLQPAI 149 (302)
T ss_pred HHHCCCeEEEecCcCC---C--CCccEEEecCHHHHHHHHHHHHHhhCCCCCEEEEeCCCCCcchHHHHHHHHHHHhhhc
Confidence 4567899998754321 1 1122234455566677778877666555 7887764322 2333456777777763
Q ss_pred ---CcEEEEEeccCCCCChhHHHHHHHhcCC---CCCeEEEEecCcchHHHHHHHHHHcCCc
Q 003633 82 ---MAKVSYKLPLPVQFNQHDITVLLNNSKP---LGPRVYVVHVSPDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 82 ---g~~i~~~~~~~~~~~~~~~~~~l~~ik~---~~~rvivl~~~~~~~~~i~~~a~~~gm~ 137 (806)
++.+... ......+..+....+.++.. ..+++ |++++...+..+++++++.|+.
T Consensus 150 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~ll~~~~~~~~a-I~~~~D~~A~g~~~al~~~g~~ 209 (302)
T TIGR02634 150 DSGDIKIVGD-QWVDGWLPENALRIMENALTANDNKVDA-VVASNDATAGGAIQALTAQGLA 209 (302)
T ss_pred cCCCeEEecC-cCCCCCCHHHHHHHHHHHHHhCCCCccE-EEECCCchHHHHHHHHHHCCCC
Confidence 3554311 11111222333455555432 23555 4445566777899999999973
No 352
>PF14981 FAM165: FAM165 family
Probab=61.56 E-value=19 Score=25.24 Aligned_cols=33 Identities=21% Similarity=0.054 Sum_probs=28.6
Q ss_pred cccchhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 003633 718 LISFWGLYLLCGTITFTAFLVFLLRMVCQYVRY 750 (806)
Q Consensus 718 l~~~~g~F~il~~g~~lal~vf~~E~~~~~~~~ 750 (806)
++++--++||++.-.++.++.|..--+|+++|.
T Consensus 3 L~~vPlLlYILaaKtlilClaFAgvK~yQ~krl 35 (51)
T PF14981_consen 3 LDNVPLLLYILAAKTLILCLAFAGVKMYQRKRL 35 (51)
T ss_pred hhhchHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 567888999999999999999998888888765
No 353
>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=61.14 E-value=26 Score=35.85 Aligned_cols=78 Identities=9% Similarity=0.034 Sum_probs=54.9
Q ss_pred EEEEEEEc--CCcccchHHHHHHHHHh-CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc-hHHHHHHHH
Q 003633 56 EVIAIYVD--DDYGRNGISALSNMLEK-NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD-PGLRIFTTA 131 (806)
Q Consensus 56 ~v~ii~~d--~~~g~~~~~~l~~~l~~-~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~-~~~~i~~~a 131 (806)
+|++|..+ +.|.......+.+++++ .|.++.+... ..+.+.....+.++.+.+.|.+|+..... ....++.++
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~l 77 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFEDA---KNDVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVKAA 77 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEeCC---CCCHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHHHH
Confidence 36677753 66888888999999999 8998876432 23345566777777778899998876543 345667777
Q ss_pred HHcCC
Q 003633 132 QKLQM 136 (806)
Q Consensus 132 ~~~gm 136 (806)
.+.|+
T Consensus 78 ~~~~i 82 (272)
T cd06301 78 NAAGI 82 (272)
T ss_pred HHCCC
Confidence 77664
No 354
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=61.04 E-value=1.3e+02 Score=31.10 Aligned_cols=84 Identities=14% Similarity=0.052 Sum_probs=56.0
Q ss_pred CCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 355 ARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 355 g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
++.++||+... ....+-.+++..+.+..+ .+++++.. +....++..|.+|++|+++..
T Consensus 88 ~~~l~Ig~~~~--------------~~~~~l~~~l~~f~~~~P-~v~v~~~~-------~~~~~~~~~l~~g~~Dl~i~~ 145 (275)
T PRK03601 88 HNELSIGASAS--------------LWECMLTPWLGRLYQNQE-ALQFEARI-------AQRQSLVKQLHERQLDLLITT 145 (275)
T ss_pred CceEEEeccHH--------------HHHHHHHHHHHHHHHhCC-CcEEEEEE-------CChHHHHHHHHcCCCCEEEEc
Confidence 35789888631 123556677778777655 34566655 356889999999999999964
Q ss_pred EEEecCccceeEecccccccceEEEEeccC
Q 003633 435 IAIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 435 ~~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
.... . ..+ ...|+....++++++...
T Consensus 146 ~~~~--~-~~l-~~~~l~~~~~~~v~~~~~ 171 (275)
T PRK03601 146 EAPK--M-DEF-SSQLLGHFTLALYTSAPS 171 (275)
T ss_pred CCCc--c-CCc-cEEEecceeEEEEecCch
Confidence 3222 1 223 345778888888887654
No 355
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=61.00 E-value=27 Score=35.23 Aligned_cols=77 Identities=13% Similarity=0.051 Sum_probs=53.1
Q ss_pred EEEEEEc--CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYVD--DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
++++... +.++......+++++++.|+++.+... ..+.+.....++++.+.+++.+|+..........+..+.+.
T Consensus 2 ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~~---~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~l~~~ 78 (264)
T cd01537 2 IGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLANS---QNDAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARKA 78 (264)
T ss_pred eEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEecCCCcchhHHHHhhhc
Confidence 5677754 667888899999999999998765432 22344566677777777899888877554443356666665
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 79 ~i 80 (264)
T cd01537 79 GI 80 (264)
T ss_pred CC
Confidence 53
No 356
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=60.98 E-value=1.2e+02 Score=32.59 Aligned_cols=125 Identities=9% Similarity=0.022 Sum_probs=64.0
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHH-c--CCeEEEEEEEcCC--cccchHHHHHHHHHh
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDF-Y--GWKEVIAIYVDDD--YGRNGISALSNMLEK 80 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~-~--~W~~v~ii~~d~~--~g~~~~~~l~~~l~~ 80 (806)
+...+||+|++.+..+. +.. -+++- .-++...+..+++++.+ . +-.+|+++..... ......+.+.+.+++
T Consensus 101 a~~~gIpVV~~d~~~~~--~~~-~~~V~-~~~~~~~G~~~~~~l~~~l~~g~gki~il~g~~~~~~~~~r~~g~~~~l~~ 176 (336)
T PRK15408 101 AMQRGVKVLTWDSDTKP--ECR-SYYIN-QGTPEQLGSMLVEMAAKQVGKDKAKVAFFYSSPTVTDQNQWVKEAKAKIAK 176 (336)
T ss_pred HHHCCCeEEEeCCCCCC--ccc-eEEEe-cCCHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCCccHHHHHHHHHHHHHh
Confidence 45679999998653221 111 12221 12334556666666544 3 4568888874322 122335667777754
Q ss_pred --CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchH-HHHHHHHHHcCC
Q 003633 81 --NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPG-LRIFTTAQKLQM 136 (806)
Q Consensus 81 --~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~-~~i~~~a~~~gm 136 (806)
.+++++.. .....+.+.-....+++.+..+|+=.+++..+.+ ...+++.++.|+
T Consensus 177 ~~p~~~vv~~--~~~~~d~~~a~~~~~~lL~~~pdi~aI~~~~~~~~~Ga~~Al~~~g~ 233 (336)
T PRK15408 177 EHPGWEIVTT--QFGYNDATKSLQTAEGILKAYPDLDAIIAPDANALPAAAQAAENLKR 233 (336)
T ss_pred hCCCCEEEee--cCCCCcHHHHHHHHHHHHHHCCCCcEEEECCCccHHHHHHHHHhCCC
Confidence 35565532 1212222333335555555555554444444444 457888888885
No 357
>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=60.83 E-value=55 Score=33.58 Aligned_cols=85 Identities=13% Similarity=0.065 Sum_probs=57.2
Q ss_pred EEEEEEE----cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHH
Q 003633 56 EVIAIYV----DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTA 131 (806)
Q Consensus 56 ~v~ii~~----d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a 131 (806)
+|++++. |..|.....+.+.+..++.|+++.+.+..+ +.+++.+.+.++.+.+.++||.++. .....+.+.|
T Consensus 1 kva~l~~g~~~D~~~n~~~~~G~~~~~~~~gv~~~~~e~~~---~~~~~~~~i~~~~~~g~dlIi~~g~-~~~~~~~~vA 76 (258)
T cd06353 1 KVAFVYVGPIGDQGWNYAHDEGRKAAEKALGVEVTYVENVP---EGADAERVLRELAAQGYDLIFGTSF-GFMDAALKVA 76 (258)
T ss_pred CEEEEEeCCCCccchhHHHHHHHHHHHHhcCCeEEEEecCC---chHhHHHHHHHHHHcCCCEEEECch-hhhHHHHHHH
Confidence 4777875 334555567888888888899988877553 3568888899888889999998543 2333444555
Q ss_pred HHcCCccCCcEEEEcCc
Q 003633 132 QKLQMMTNNYVWLATDW 148 (806)
Q Consensus 132 ~~~gm~~~~~~wi~t~~ 148 (806)
.+- ++-.|+..+.
T Consensus 77 ~~~----p~~~F~~~d~ 89 (258)
T cd06353 77 KEY----PDVKFEHCSG 89 (258)
T ss_pred HHC----CCCEEEECCC
Confidence 543 3556666553
No 358
>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=59.18 E-value=33 Score=37.03 Aligned_cols=84 Identities=10% Similarity=0.106 Sum_probs=56.8
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.++++.+| +++.+|+.... .....+.+.+.|++.|+.+.+.. +....+.+.+...+..+++.++|+||-.+...
T Consensus 12 ~~l~~~~~~~g-~~~liv~~~~~-~~~~~~~v~~~l~~~~i~~~~~~-~~~~p~~~~v~~~~~~~~~~~~d~IIavGGGs 88 (349)
T cd08550 12 KEIAAILSTFG-SKVAVVGGKTV-LKKSRPRFEAALAKSIIVVDVIV-FGGECSTEEVVKALCGAEEQEADVIIGVGGGK 88 (349)
T ss_pred HHHHHHHHHcC-CeEEEEEChHH-HHHHHHHHHHHHHhcCCeeEEEE-cCCCCCHHHHHHHHHHHHhcCCCEEEEecCcH
Confidence 45667788889 88877774333 23556788888998887654332 44344566788888888888999998777543
Q ss_pred --hHHHHHH
Q 003633 123 --PGLRIFT 129 (806)
Q Consensus 123 --~~~~i~~ 129 (806)
+..+++.
T Consensus 89 ~~D~aK~ia 97 (349)
T cd08550 89 TLDTAKAVA 97 (349)
T ss_pred HHHHHHHHH
Confidence 4444443
No 359
>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=58.36 E-value=16 Score=34.48 Aligned_cols=101 Identities=17% Similarity=0.183 Sum_probs=57.1
Q ss_pred CCCChhHhhhCCCceeEEeCchhHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCe
Q 003633 572 SVKGIESLITNDWPIGYQVGSFAYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDF 651 (806)
Q Consensus 572 ~i~s~~dL~~~~~~ig~~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l 651 (806)
++++++||.+ +.+|+..--.....||.+ .+.+ .+++.....-|..- .. |-.|++++-.....-+..+ +|
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-VEIIKLSGSVELAP--PL----GLADAIVDIVETGTTLRAN--GL 125 (163)
T ss_dssp CGCCGGGGSS-TEEEEES-HHHHHHHHHH-CT-E-EEEEE-SS-TTHHH--HT----TSSSEEEEEESSSHHHHHT--TE
T ss_pred CCCCHHHhcc-CCEEEECCHHHHHHHHHH-cCCc-EEEEEccCCccccC--CC----CCCCEEEEeccCcHHHHHC--CC
Confidence 4778899932 778888777788888854 3433 44554443334332 23 6789999877776655555 46
Q ss_pred EEeCCccccCCceeeecCCCC--chHHHHHHHHhh
Q 003633 652 GIIGQPFTRSGWGFAFQRDSP--LAVGMSTAILKL 684 (806)
Q Consensus 652 ~~~~~~~~~~~~~~~~~k~sp--l~~~~n~~il~l 684 (806)
.+++..+.+ .-.+...+.+- -.+.++..+.+|
T Consensus 126 ~~i~~i~~s-~a~LI~n~~~~~~k~~~i~~l~~~l 159 (163)
T PF01634_consen 126 KEIETILES-SARLIANKASLKEKEEKIDELVTRL 159 (163)
T ss_dssp EEEEEEEEE-EEEEEEEHHHHHHCHHHHHHHHHHH
T ss_pred EEeEEEEEE-EEEEEEcCccchhhHHHHHHHHHHH
Confidence 666555543 33444444442 223455555444
No 360
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=57.95 E-value=2.3e+02 Score=29.22 Aligned_cols=85 Identities=15% Similarity=0.141 Sum_probs=53.5
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeE
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDI 435 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~ 435 (806)
+.++||+.... ...+..+++..+.+..+ .+.+.+.. .+-++++.+|.+|++|+++...
T Consensus 97 ~~l~I~~~~~~--------------~~~~l~~~l~~f~~~~p-~i~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~ 154 (294)
T PRK09986 97 GRIEIGIVGTA--------------LWGRLRPAMRHFLKENP-NVEWLLRE-------LSPSMQMAALERRELDAGIWRM 154 (294)
T ss_pred ceEEEEEehHH--------------hHHHHHHHHHHHHHhCC-CeEEEEEe-------CCHHHHHHHHHcCCCCEEEecC
Confidence 57899986311 12344667777777766 34455554 2457889999999999998521
Q ss_pred EEecCccceeEecccccccceEEEEeccC
Q 003633 436 AIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 436 ~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
. .......+.+ .|+....+++++++..
T Consensus 155 ~-~~~~~~~l~~-~~l~~~~~~~v~~~~~ 181 (294)
T PRK09986 155 A-DLEPNPGFTS-RRLHESAFAVAVPEEH 181 (294)
T ss_pred C-ccCCCCCeEE-EEeecccEEEEEcCCC
Confidence 1 0112233444 5667788888887765
No 361
>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=57.58 E-value=28 Score=36.00 Aligned_cols=79 Identities=13% Similarity=0.113 Sum_probs=51.1
Q ss_pred EEEEEEc---CCcccchHHHHHHHHHhCCcEEEEEeccCCC-CChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHH
Q 003633 57 VIAIYVD---DDYGRNGISALSNMLEKNMAKVSYKLPLPVQ-FNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQ 132 (806)
Q Consensus 57 v~ii~~d---~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~-~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~ 132 (806)
|++|..+ ++|....++.+.+++++.|.++......+.. .+.......+..+.+.++|.+|+..........++.+.
T Consensus 2 Igvi~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIv~~~~~~~~~~~~~l~ 81 (280)
T cd06303 2 IAVIYPGQQISDYWVRNIASFTARLEELNIPYELTQFSSRPGIDHRLQSQQLNEALQSKPDYLIFTLDSLRHRKLIERVL 81 (280)
T ss_pred eeEEecCccHHHHHHHHHHHHHHHHHHcCCcEEEEEeccCcccCHHHHHHHHHHHHHcCCCEEEEcCCchhhHHHHHHHH
Confidence 6777764 4677778899999999999877654222111 12334456677788889999988754333344556666
Q ss_pred HcC
Q 003633 133 KLQ 135 (806)
Q Consensus 133 ~~g 135 (806)
+.+
T Consensus 82 ~~~ 84 (280)
T cd06303 82 ASG 84 (280)
T ss_pred hCC
Confidence 655
No 362
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=56.67 E-value=1.6e+02 Score=31.44 Aligned_cols=132 Identities=7% Similarity=-0.083 Sum_probs=75.4
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcC---CcccchHHHHHHHHHhC-
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDD---DYGRNGISALSNMLEKN- 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~---~~g~~~~~~l~~~l~~~- 81 (806)
+...++|+|.+.... .... ......+++...++.+++.+...|-++++++.... ..+....+.+.+.+++.
T Consensus 102 ~~~~~iPvV~id~~~---~~~~--~~~~V~~D~~~~g~~a~~~L~~~g~~~i~~i~~g~~~~~~~~~R~~gf~~~l~~~~ 176 (330)
T PRK10355 102 AKQEGIKVLAYDRMI---NNAD--IDFYISFDNEKVGELQAKALVDKVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYI 176 (330)
T ss_pred HHHCCCeEEEECCCC---CCCC--ccEEEecCHHHHHHHHHHHHHHhcCCCCEEEEeCCCCCccHHHHHHHHHHHHhhhc
Confidence 345689999874432 1112 22246677777888888988777778877665322 23344567788888763
Q ss_pred --C-cEEEEEeccCCCCChhHHHHHHHhcC-C--CCCeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 82 --M-AKVSYKLPLPVQFNQHDITVLLNNSK-P--LGPRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 82 --g-~~i~~~~~~~~~~~~~~~~~~l~~ik-~--~~~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
| +.+....... ..+..+-...+.++. + ..+++ |++.+...+..+++.++++|+. +-+.|++
T Consensus 177 ~~~~i~~~~~~~~~-~~~~~~~~~~~~~lL~~~~~~~~a-I~~~nD~~A~g~l~al~~~g~~--~di~IiG 243 (330)
T PRK10355 177 DSGKIKVVGDQWVD-GWLPENALKIMENALTANNNKIDA-VVASNDATAGGAIQALSAQGLS--GKVAISG 243 (330)
T ss_pred cCCCeEEecccCCC-CCCHHHHHHHHHHHHHhCCCCccE-EEECCCchHHHHHHHHHHCCCC--CCceEEc
Confidence 4 4432111111 112222223333332 2 23554 5566777888899999999975 3455554
No 363
>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=56.64 E-value=2e+02 Score=29.86 Aligned_cols=131 Identities=8% Similarity=-0.059 Sum_probs=65.8
Q ss_pred cccCCCcEEecccCCCCcccCCCCceEEecCCcHHH-HHHHHHHH-HHc-CCeEEEEEEEcCCc--ccchHHHHHHHHHh
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQ-MAAMADLI-DFY-GWKEVIAIYVDDDY--GRNGISALSNMLEK 80 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q-~~ai~~ll-~~~-~W~~v~ii~~d~~~--g~~~~~~l~~~l~~ 80 (806)
+.+.+||+|.+....+. . +........|..+ ++..++.+ +++ +-++|+++..+... .....+.+.+.+++
T Consensus 77 ~~~~giPvV~~~~~~~~--~---~~~~~v~~~Dn~~~g~~aa~~l~~~l~~~~~I~~i~g~~~~~~~~~r~~g~~~~~~~ 151 (302)
T TIGR02637 77 AMKRGIKVVTWDSGVAP--E---GRNLFLNQASADLIGRTQVQLAAEQIGNGGEIAILSAASTATNQNAWIEIMKKELKD 151 (302)
T ss_pred HHHCCCEEEEeCCCCCC--C---ceeEEEecCCHHHHHHHHHHHHHHHcCCCcEEEEEECCCCCccHHHHHHHHHHHHhh
Confidence 45568999987543221 1 1223344444443 34445543 332 23789988754322 22345777777776
Q ss_pred CC---cEEEEEeccCCCCChhHHHHHHHhcCCCC--CeEEEEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 81 NM---AKVSYKLPLPVQFNQHDITVLLNNSKPLG--PRVYVVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 81 ~g---~~i~~~~~~~~~~~~~~~~~~l~~ik~~~--~rvivl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.| +++... .....+.+.-...+.++.+.. +++|+. .+...+..+++++++.|+. +.+.|.+
T Consensus 152 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~~ai~~-~~d~~a~ga~~al~~~g~~--~~i~vvg 217 (302)
T TIGR02637 152 PKYPKVKLVAT--VYGDDDAQKSYQEAQGLLKSYPNLKGIIA-PTTVGIKAAAQAVSDAKLI--GKVKLTG 217 (302)
T ss_pred ccCCCCEEEee--ecCCchHHHHHHHHHHHHHhCCCccEEEe-CCCchHHHHHHHHHhcCCC--CCEEEEE
Confidence 53 344221 111122223333444443333 444443 3456677788888888864 3344443
No 364
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=56.08 E-value=1.1e+02 Score=28.75 Aligned_cols=65 Identities=20% Similarity=0.137 Sum_probs=36.4
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
++-..++..+.+..+ .+++++... +.+. .+.+|++|+++.... .....+. +.++.+..++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~~---------~~~~-~~~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~ 78 (201)
T cd08471 14 LHVLPIITDFLDAYP-EVSVRLLLL---------DRVV-NLLEEGVDVAVRIGH---LPDSSLV-ATRVGSVRRVVCASP 78 (201)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEEc---------Cccc-hhhcccccEEEEecC---CCCCCeE-EEEccccceEEEECH
Confidence 455577888888776 455665531 1223 355789999985221 1112233 346666667776643
No 365
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=55.84 E-value=1.2e+02 Score=30.68 Aligned_cols=88 Identities=9% Similarity=0.056 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh-CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEE
Q 003633 39 SQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK-NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVV 117 (806)
Q Consensus 39 ~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~-~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl 117 (806)
...+..+.+.....| .+|.++-.+.+ .++.+.+.+++ .|+.|+.... . ..+.++...++.+|.+++||++++
T Consensus 91 ~dl~~~ll~~~~~~~-~~v~llG~~~~----v~~~a~~~l~~~y~l~i~g~~~-G-yf~~~e~~~i~~~I~~s~~dil~V 163 (243)
T PRK03692 91 ADLWEALMARAGKEG-TPVFLVGGKPE----VLAQTEAKLRTQWNVNIVGSQD-G-YFTPEQRQALFERIHASGAKIVTV 163 (243)
T ss_pred HHHHHHHHHHHHhcC-CeEEEECCCHH----HHHHHHHHHHHHhCCEEEEEeC-C-CCCHHHHHHHHHHHHhcCCCEEEE
Confidence 344566666666667 56666664443 45555555543 3777764332 1 123455667899999999999999
Q ss_pred ecCcchHHHHHHHHHH
Q 003633 118 HVSPDPGLRIFTTAQK 133 (806)
Q Consensus 118 ~~~~~~~~~i~~~a~~ 133 (806)
.+..+.-..++...++
T Consensus 164 glG~PkQE~~~~~~~~ 179 (243)
T PRK03692 164 AMGSPKQEIFMRDCRL 179 (243)
T ss_pred ECCCcHHHHHHHHHHH
Confidence 9988776666655444
No 366
>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=55.60 E-value=17 Score=32.11 Aligned_cols=86 Identities=20% Similarity=0.096 Sum_probs=47.7
Q ss_pred eEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcC--CCCCeEEEEecCcchHHHHHHHHH
Q 003633 55 KEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSK--PLGPRVYVVHVSPDPGLRIFTTAQ 132 (806)
Q Consensus 55 ~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik--~~~~rvivl~~~~~~~~~i~~~a~ 132 (806)
|+++++-..++-+.- ...+.+.|.+.|.+|... .+..+.-+=......+. -..+|.++++..++....+++++.
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 567777755543433 334555555688776532 22221100001122233 368899999999999999999999
Q ss_pred HcCCccCCcEEEEcC
Q 003633 133 KLQMMTNNYVWLATD 147 (806)
Q Consensus 133 ~~gm~~~~~~wi~t~ 147 (806)
++| .+.+|+.++
T Consensus 77 ~~g---~~~v~~~~g 88 (116)
T PF13380_consen 77 ALG---VKAVWLQPG 88 (116)
T ss_dssp HHT----SEEEE-TT
T ss_pred HcC---CCEEEEEcc
Confidence 998 478999988
No 367
>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=55.60 E-value=1.8e+02 Score=27.26 Aligned_cols=70 Identities=13% Similarity=0.112 Sum_probs=46.7
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
++-.+++..+.+..+ .+++++.. +.+..+..+|.+|++|+++..... ....+ -+.++....++++++.
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 345677888877765 45566654 367889999999999999863221 11222 2456677788888776
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 82 ~~ 83 (198)
T cd08446 82 SH 83 (198)
T ss_pred CC
Confidence 55
No 368
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=54.90 E-value=83 Score=34.10 Aligned_cols=101 Identities=9% Similarity=-0.025 Sum_probs=62.9
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEE--eccCCCCChhHHHHHHHhcCCCC---CeEEEE
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYK--LPLPVQFNQHDITVLLNNSKPLG---PRVYVV 117 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~--~~~~~~~~~~~~~~~l~~ik~~~---~rvivl 117 (806)
+.+.+.++.++++++.+++. ........+.+.+.|++.|+.+... ....+..+.+++...+..+++.+ .|.||.
T Consensus 20 ~~l~~~l~~~~~~~~livtd-~~~~~~~~~~v~~~L~~~gi~~~~~~~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~IIa 98 (358)
T PRK00002 20 SELGELLAPLKGKKVAIVTD-ETVAPLYLEKLRASLEAAGFEVDVVVLPDGEQYKSLETLEKIYDALLEAGLDRSDTLIA 98 (358)
T ss_pred HHHHHHHHhcCCCeEEEEEC-CchHHHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCCEEEE
Confidence 45666777778899998884 4434457788888999888865521 12333345567777777776654 488887
Q ss_pred ecCcc--hHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 118 HVSPD--PGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 118 ~~~~~--~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
.+... +...++......| ..++-|-|.
T Consensus 99 vGGGsv~D~aK~iA~~~~~g---ip~i~IPTT 127 (358)
T PRK00002 99 LGGGVIGDLAGFAAATYMRG---IRFIQVPTT 127 (358)
T ss_pred EcCcHHHHHHHHHHHHhcCC---CCEEEcCch
Confidence 77543 5555555433333 234444444
No 369
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=54.40 E-value=2.6e+02 Score=28.93 Aligned_cols=65 Identities=11% Similarity=-0.006 Sum_probs=41.1
Q ss_pred HHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEeccC
Q 003633 387 DILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPINN 464 (806)
Q Consensus 387 dl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~~ 464 (806)
..+..+.+.- .+.+++.. +..+++..+|.+|++|+++..... ....+. +.|+....++++++...
T Consensus 107 ~~l~~~~~~~--~i~i~~~~-------~~~~~~~~~L~~~~~d~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~~ 171 (294)
T PRK13348 107 PALAAVLAGE--RILLELIV-------DDQDHTFALLERGEVVGCVSTQPK---PMRGCL-AEPLGTMRYRCVASPAF 171 (294)
T ss_pred HHHHHHHhCC--CeEEEEEE-------cchHHHHHHHhcCCeEEEEecCCc---ccCCcc-cccccccceEEEEccch
Confidence 3444444442 44466554 356889999999999998753221 223344 57788888888876543
No 370
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=54.25 E-value=43 Score=34.34 Aligned_cols=79 Identities=10% Similarity=0.046 Sum_probs=52.7
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|++++. ++.|....+..+.+++++.|.++.....-. ..+.+.....+..+.+.++|.||+.....+....+.++.+.
T Consensus 2 Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~-~~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~~ 80 (268)
T cd06306 2 LCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGG-YPNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVAA 80 (268)
T ss_pred eEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCCC-CCCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHHC
Confidence 566665 356777888999999999999887542211 11233445667777788999999876544433246777776
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|+
T Consensus 81 gi 82 (268)
T cd06306 81 SI 82 (268)
T ss_pred CC
Confidence 64
No 371
>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=54.04 E-value=45 Score=36.40 Aligned_cols=79 Identities=5% Similarity=-0.065 Sum_probs=56.5
Q ss_pred cCCeEEEEEEEcCCcc-cchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc--hHHHHH
Q 003633 52 YGWKEVIAIYVDDDYG-RNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD--PGLRIF 128 (806)
Q Consensus 52 ~~W~~v~ii~~d~~~g-~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~--~~~~i~ 128 (806)
++-+++.+|+....+- .+..+.+.+.|++.|+.+.....+.++.+.+.+...+..+++.++|.||-.+... ++.+.+
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 3458888887433332 3456788999999999876555555567778888999999999999999877643 555554
Q ss_pred HH
Q 003633 129 TT 130 (806)
Q Consensus 129 ~~ 130 (806)
..
T Consensus 101 a~ 102 (375)
T cd08179 101 WI 102 (375)
T ss_pred HH
Confidence 43
No 372
>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=53.84 E-value=46 Score=33.80 Aligned_cols=77 Identities=9% Similarity=0.023 Sum_probs=51.9
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
+++|.. .+.|.......+.+++++.|.++... ....+.......++++.+.++|.+++..........++++.+.
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 455554 45677778889999999999887543 2122334455677778788899988876544444567777776
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 79 ~i 80 (268)
T cd06289 79 GI 80 (268)
T ss_pred CC
Confidence 64
No 373
>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=53.57 E-value=52 Score=33.59 Aligned_cols=75 Identities=8% Similarity=-0.068 Sum_probs=49.8
Q ss_pred EEEEEEc-----CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHH
Q 003633 57 VIAIYVD-----DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTA 131 (806)
Q Consensus 57 v~ii~~d-----~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a 131 (806)
|+++..+ +.|.....+.+++++++.|.++..... . .+.+.....+..+.+.++|.||+....... .+..+
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~--~~~~l 76 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKFV-S--DEDEEEFELPSFLEDGKVDGIILLGGISTE--YIKEI 76 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEeC-C--CChHHHHHHHHHHHHCCCCEEEEeCCCChH--HHHHH
Confidence 5666655 678888899999999999988765432 2 222333445556667789999987754432 36666
Q ss_pred HHcCC
Q 003633 132 QKLQM 136 (806)
Q Consensus 132 ~~~gm 136 (806)
.+.|.
T Consensus 77 ~~~~i 81 (268)
T cd06277 77 KELGI 81 (268)
T ss_pred hhcCC
Confidence 66664
No 374
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=53.49 E-value=94 Score=31.08 Aligned_cols=92 Identities=17% Similarity=0.168 Sum_probs=51.0
Q ss_pred CCCChhHhhh--------CC--CceeEEeCchhHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhH
Q 003633 572 SVKGIESLIT--------ND--WPIGYQVGSFAYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYV 641 (806)
Q Consensus 572 ~i~s~~dL~~--------~~--~~ig~~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~ 641 (806)
.+++++||.. .+ .+|+..-......|+.+ .+.....++...-.-|.. -.. |-.|++++-....
T Consensus 110 ~~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf~~-~Gv~~~~Iv~l~GsvEla--P~~----GlAD~IvDivsTG 182 (228)
T PRK13583 110 DVDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFLSQ-KGVQDYRIVESLGATEGA--PAN----GSAEIIVDITSTG 182 (228)
T ss_pred ccCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHHHH-cCCceeEEEECCCceecc--ccc----Ccchhhhhhhchh
Confidence 4677777741 12 46777777778888843 454433455544333331 122 6677777765555
Q ss_pred HHHhhCCCCeEEeC-CccccCCceeeecCCCC
Q 003633 642 QLFLSNQTDFGIIG-QPFTRSGWGFAFQRDSP 672 (806)
Q Consensus 642 ~~~~~~~~~l~~~~-~~~~~~~~~~~~~k~sp 672 (806)
.-+..+ +|.+++ +.+....-.+...+.|.
T Consensus 183 ~TLr~N--gL~~i~~~~Il~SsA~LI~n~~s~ 212 (228)
T PRK13583 183 ETLRAN--HLKILSDGVILRSQACLVRARKAD 212 (228)
T ss_pred HHHHHC--CCEEecCceEEEEEEEEEEecccc
Confidence 444333 577775 34444444556677764
No 375
>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=53.49 E-value=1.4e+02 Score=31.18 Aligned_cols=104 Identities=14% Similarity=0.128 Sum_probs=60.3
Q ss_pred CcEEecccCCCCccc----CCCC--ceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCCc-ccchHHHHHHHHHhC
Q 003633 11 VPLVSFAATDPTLSA----LQFP--YFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDDY-GRNGISALSNMLEKN 81 (806)
Q Consensus 11 vP~Is~~at~p~Ls~----~~~p--~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~~-g~~~~~~l~~~l~~~ 81 (806)
+|+|-.+.++|.-+. ...| .+.=+. +..-.+...++++.+ +-++++++|++++- +....+.+.+.+++.
T Consensus 82 iPVVf~~V~dp~~~~l~~~~~~~~~nvTGv~--~~~~~~~~l~l~~~l~P~~k~igvl~~~~~~~~~~~~~~~~~~a~~~ 159 (294)
T PF04392_consen 82 IPVVFCGVSDPVGAGLVDSLDRPGKNVTGVS--ERPPIEKQLELIKKLFPDAKRIGVLYDPSEPNSVAQIEQLRKAAKKL 159 (294)
T ss_dssp S-EEEECES-TTTTTS-S-SSS--SSEEEEE--E---HHHHHHHHHHHSTT--EEEEEEETT-HHHHHHHHHHHHHHHHT
T ss_pred cEEEEEeccChhhhhccccccCCCCCEEEEE--CCcCHHHHHHHHHHhCCCCCEEEEEecCCCccHHHHHHHHHHHHHHc
Confidence 999887777776433 2233 443333 444456666666664 46999999976653 456678888889999
Q ss_pred CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 82 MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 82 g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
|+++.... + .+.+++...+.++. .+.+++++..+.
T Consensus 160 g~~l~~~~-v---~~~~~~~~~~~~l~-~~~da~~~~~~~ 194 (294)
T PF04392_consen 160 GIELVEIP-V---PSSEDLEQALEALA-EKVDALYLLPDN 194 (294)
T ss_dssp T-EEEEEE-E---SSGGGHHHHHHHHC-TT-SEEEE-S-H
T ss_pred CCEEEEEe-c---CcHhHHHHHHHHhh-ccCCEEEEECCc
Confidence 99876543 2 23567888888875 456887776543
No 376
>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=53.40 E-value=1.6e+02 Score=27.53 Aligned_cols=65 Identities=17% Similarity=0.087 Sum_probs=39.3
Q ss_pred eeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEecc
Q 003633 384 YCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 384 ~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
+-..++..+.+..+ .+++++... + .+.++.+|++|+++.... .....+ .+.++....++++++..
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~~---------~-~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~~ 78 (194)
T cd08432 14 WLIPRLARFQARHP-DIDLRLSTS---------D-RLVDFAREGIDLAIRYGD---GDWPGL-EAERLMDEELVPVCSPA 78 (194)
T ss_pred HHHHHhHHHHHHCC-CeEEEEEec---------C-CccccccccccEEEEecC---CCCCCc-ceEEccCCcEEEecCHH
Confidence 44566677777665 455666541 1 456788999999985321 111222 35567777887777643
No 377
>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=53.37 E-value=50 Score=35.63 Aligned_cols=85 Identities=8% Similarity=0.162 Sum_probs=56.7
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCC--CChhHHHHHHHhcCCCCCeEEEEecC
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQ--FNQHDITVLLNNSKPLGPRVYVVHVS 120 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~--~~~~~~~~~l~~ik~~~~rvivl~~~ 120 (806)
+.+.++++.++.+++.+|+....+ ....+.+.+.|++.|+.+......... .+.+.+...+..+++ ++|+||-.+.
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 446677888898999888833222 223577888999999866433333332 556677777777777 8999987775
Q ss_pred cc--hHHHHHH
Q 003633 121 PD--PGLRIFT 129 (806)
Q Consensus 121 ~~--~~~~i~~ 129 (806)
.. +..+++.
T Consensus 90 Gs~~D~aK~vA 100 (348)
T cd08175 90 GTINDITKYVS 100 (348)
T ss_pred cHHHHHHHHHH
Confidence 43 5555554
No 378
>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=53.36 E-value=64 Score=31.05 Aligned_cols=74 Identities=22% Similarity=0.236 Sum_probs=46.5
Q ss_pred CCCChhHhhhCCCceeEEeCchhHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCe
Q 003633 572 SVKGIESLITNDWPIGYQVGSFAYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDF 651 (806)
Q Consensus 572 ~i~s~~dL~~~~~~ig~~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l 651 (806)
++++.+|| .+.+|+..-......|+. +.+.+ ..+++..-.-|.. -.. |-.|++++-.....-+..+ +|
T Consensus 100 ~~~~~~~l--~~~rIATkyp~i~~~~f~-~~Gi~-v~ii~l~GsvE~a--P~~----GlaD~IvDiv~TG~TL~~N--gL 167 (182)
T TIGR00070 100 DISSVEDL--KGKRIATKYPNLARRYFE-KKGID-VEIIKLNGSVELA--PLL----GLADAIVDIVSTGTTLREN--GL 167 (182)
T ss_pred CCCChHHh--CCCEEEECCHHHHHHHHH-HcCCe-EEEEECcceeecc--cCC----CceeEEEEEeCCHHHHHHC--CC
Confidence 56788998 588899887778888884 34543 4455544333321 113 7889998877666655554 34
Q ss_pred EEeCCc
Q 003633 652 GIIGQP 657 (806)
Q Consensus 652 ~~~~~~ 657 (806)
.++.+.
T Consensus 168 ~~ie~i 173 (182)
T TIGR00070 168 RIIEVI 173 (182)
T ss_pred EEeeEE
Confidence 444433
No 379
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=53.14 E-value=59 Score=34.91 Aligned_cols=82 Identities=13% Similarity=0.047 Sum_probs=58.4
Q ss_pred CCeEEEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHH
Q 003633 53 GWKEVIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFT 129 (806)
Q Consensus 53 ~W~~v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~ 129 (806)
.-.+++++.. +++|.....+.+++++++.|+++.+.. +...+...-...+..+.+.+++.|++...... ....++
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 4457888875 567888888999999999999987532 22223333346677777889999998765433 356788
Q ss_pred HHHHcCC
Q 003633 130 TAQKLQM 136 (806)
Q Consensus 130 ~a~~~gm 136 (806)
+|.+.|.
T Consensus 100 ~a~~~gI 106 (336)
T PRK15408 100 RAMQRGV 106 (336)
T ss_pred HHHHCCC
Confidence 8888875
No 380
>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=53.06 E-value=45 Score=34.17 Aligned_cols=79 Identities=14% Similarity=0.123 Sum_probs=53.5
Q ss_pred EEEEEEEc---CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHH
Q 003633 56 EVIAIYVD---DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTA 131 (806)
Q Consensus 56 ~v~ii~~d---~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a 131 (806)
+|+++..+ +.|.....+.+.+++++.|..+.....- ..+.+.....+.++...++|.+|+...... ....++.+
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~~~--~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~l~~~ 78 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRGPE--TFDVADMARLIEAAIAAKPDGIVVTIPDPDALDPAIKRA 78 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEECCC--CCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHHHH
Confidence 35666643 5688888999999999999988754221 113445566777777789999888764332 34566777
Q ss_pred HHcCC
Q 003633 132 QKLQM 136 (806)
Q Consensus 132 ~~~gm 136 (806)
.+.|+
T Consensus 79 ~~~~i 83 (271)
T cd06312 79 VAAGI 83 (271)
T ss_pred HHCCC
Confidence 77663
No 381
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=53.02 E-value=1.2e+02 Score=29.95 Aligned_cols=108 Identities=17% Similarity=0.187 Sum_probs=64.1
Q ss_pred CCCCChhHhhhCCCce-eEEeCchhHHHhhhh---cccccccceeCC----CHhHHHHHHhcCCCCCCeEEEEeCchhHH
Q 003633 571 TSVKGIESLITNDWPI-GYQVGSFAYSYLSDS---LRIQKSRLISLG----SPEDYERALRQGPRNGGVAAIVDELPYVQ 642 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~i-g~~~gs~~~~~l~~~---~~~~~~~~~~~~----~~~~~~~~l~~~~~~g~~~a~i~~~~~~~ 642 (806)
..|++++||.+.+.++ -=.+||-....+.+. ++.....+.-|. +-.....++.. |+.||-+.-+..++
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 3589999998665442 223577666655433 333444444443 34456777888 99999998554443
Q ss_pred HHhhCCCCeEEeCCccccCCceeeecCCCCchHHHHHHHHhhhccch
Q 003633 643 LFLSNQTDFGIIGQPFTRSGWGFAFQRDSPLAVGMSTAILKLSENGM 689 (806)
Q Consensus 643 ~~~~~~~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~il~l~e~G~ 689 (806)
. -.-+|.. +....|-|+.+|+.-=.+.+...+..|...++
T Consensus 163 ~---~gL~Fip----l~~E~YD~virke~~~~~~vr~fi~~L~s~~~ 202 (223)
T COG1910 163 K---YGLDFIP----LGDEEYDFVIRKERLDKPVVRAFIKALKSEGF 202 (223)
T ss_pred H---cCCceEE----cccceEEEEEehhHccCHHHHHHHHHhccccc
Confidence 2 1224444 34557778888876555555555555555433
No 382
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=52.61 E-value=99 Score=31.67 Aligned_cols=70 Identities=19% Similarity=0.156 Sum_probs=39.1
Q ss_pred HHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCc-ccEEEeeEEEecCcc---cee-Eec-ccccccceEEE
Q 003633 386 IDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDV-FDAAVGDIAIVTNRT---KIV-DFS-QPYISTGLVIV 459 (806)
Q Consensus 386 idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~-~D~~~~~~~it~~r~---~~v-dft-~p~~~~~~~~~ 459 (806)
-++.+.+.+..|.+ +.+.. +.-..+..++..|. +|+.+.+-.-..++. ..+ ..+ .+|....++++
T Consensus 42 ~~l~~~Fe~~~g~~--v~~~~-------~~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~n~lvl~ 112 (257)
T PRK10677 42 QDIAAQYKKEKGVD--VVSSF-------ASSSTLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLGNSLVVV 112 (257)
T ss_pred HHHHHHHHhhhCCe--EEEEe-------cccHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeecCEEEEE
Confidence 34555555666655 43332 12346778888877 899887542211111 112 121 35777788888
Q ss_pred EeccC
Q 003633 460 APINN 464 (806)
Q Consensus 460 v~~~~ 464 (806)
+++..
T Consensus 113 ~~~~~ 117 (257)
T PRK10677 113 APKAS 117 (257)
T ss_pred EECCC
Confidence 88764
No 383
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=52.41 E-value=2.2e+02 Score=30.04 Aligned_cols=136 Identities=8% Similarity=0.069 Sum_probs=75.6
Q ss_pred ccccCCCcEEecccCCCCcccCCCCceEEecCCcHHHHHHHHHHH-HHcCC-eEEEEEEEcC--CcccchHHHHHHHHHh
Q 003633 5 VANGLKVPLVSFAATDPTLSALQFPYFIRSTQSDSQQMAAMADLI-DFYGW-KEVIAIYVDD--DYGRNGISALSNMLEK 80 (806)
Q Consensus 5 i~~~~~vP~Is~~at~p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll-~~~~W-~~v~ii~~d~--~~g~~~~~~l~~~l~~ 80 (806)
-+...+||+|.+....+.- . ....-...+....+...++.+ ++++- -+++++.... .......+.+.+.+++
T Consensus 111 ~a~~aGIpVv~~d~~~~~~--~--~~~~~vg~dn~~~G~~~a~~l~~~~~~~g~v~~~~g~~~~~~~~~R~~G~~~~l~~ 186 (322)
T COG1879 111 KAKAAGIPVVTVDSDIPGP--G--DRVAYVGSDNYKAGRLAAEYLAKALGGKGKVVVLVGSPGNSSAEERVKGFRDALKE 186 (322)
T ss_pred HHHHCCCcEEEEecCCCCC--C--ceeEEEecCcHHHHHHHHHHHHHHhCCCCeEEEEecCCCCchHHHHHhhHHHHHHh
Confidence 3567899999985543322 1 121222234444455556654 44432 3455555333 2345568889999998
Q ss_pred CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC-cchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 81 NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS-PDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 81 ~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~-~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
.+.++........+.+.+.-......+.+..+++-.+++. ...+....+++++.|... .+.+++
T Consensus 187 ~~~~~~v~~~~~~~~~~~~a~~~~~~~L~~~pdi~~i~~~~d~~a~ga~~A~~~~g~~~--~v~v~g 251 (322)
T COG1879 187 HPPDIEVVDVQTGDWDRDKALEVMEDLLAANPDIDGIYAANDGMALGAIQALKAAGRKG--DVVVVG 251 (322)
T ss_pred CCCcEEEeeccCCcccHHHHHHHHHHHHHhCCCceEEEECCchhHHHHHHHHHHcCCCC--ceEEEE
Confidence 8753222232332333344445666677777787666655 445556667777788654 455554
No 384
>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=52.38 E-value=57 Score=33.07 Aligned_cols=77 Identities=3% Similarity=-0.058 Sum_probs=52.0
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++.. ++.|.......+.+++++.|..+..... ..+.+.....++++.+.++|.+|+..........+..+.+.
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATT---DYDAEREADAVETLLRQRVDGLILTVADAATSPALDLLDAE 78 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeC---CCCHHHHHHHHHHHHhcCCCEEEEecCCCCchHHHHHHhhC
Confidence 455553 4567778889999999999998875432 23344555677777778899998865433333467777777
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 79 ~i 80 (266)
T cd06282 79 RV 80 (266)
T ss_pred CC
Confidence 74
No 385
>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=52.19 E-value=48 Score=33.17 Aligned_cols=78 Identities=12% Similarity=0.049 Sum_probs=54.4
Q ss_pred EEEEEEEc---CCcccchHHHHHHHHHh--CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHH
Q 003633 56 EVIAIYVD---DDYGRNGISALSNMLEK--NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTT 130 (806)
Q Consensus 56 ~v~ii~~d---~~~g~~~~~~l~~~l~~--~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~ 130 (806)
+|+++..+ +.++....+.+.+++++ .++++.+... ..+.++....+.++...+++.+++.........+...
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~ 77 (269)
T cd01391 1 KIGVLLPLSGSAPFGAQLLAGIELAAEEIGRGLEVILADS---QSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVEL 77 (269)
T ss_pred CceEEeecCCCcHHHHHHHHHHHHHHHHhCCceEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEecCCCHHHHHHHHH
Confidence 35667753 46788888999999999 7777765432 2233456677777777789999988776665556777
Q ss_pred HHHcCC
Q 003633 131 AQKLQM 136 (806)
Q Consensus 131 a~~~gm 136 (806)
+.+.|.
T Consensus 78 ~~~~~i 83 (269)
T cd01391 78 AAAAGI 83 (269)
T ss_pred HHHcCC
Confidence 776664
No 386
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=52.18 E-value=69 Score=33.77 Aligned_cols=79 Identities=16% Similarity=0.101 Sum_probs=45.8
Q ss_pred CCCCChhHhhhCCCceeEEe-CchhHHH---hhhhccccccccee--CCCHhHHHHHHhcCCCCCCeEEEEeCchh---H
Q 003633 571 TSVKGIESLITNDWPIGYQV-GSFAYSY---LSDSLRIQKSRLIS--LGSPEDYERALRQGPRNGGVAAIVDELPY---V 641 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~-gs~~~~~---l~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~g~~~a~i~~~~~---~ 641 (806)
..|+++.|| .|++|.+.. ||-.+.. +.+.+++....... .-...+..+++++ |.+||++.-... .
T Consensus 127 ~~Ikti~DL--~GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~~~~~~a~~~~~l~~----g~iDA~~~~~G~p~~a 200 (321)
T COG2358 127 AGIKTIADL--KGKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAESADALKN----GTIDAAFYVAGVPNPA 200 (321)
T ss_pred CCcceehhc--CCCEEeecCCCCccHHHHHHHHHHcCCCCcchhhhhhcCchhhHHHhhC----CcccEEEEecCCCCcc
Confidence 479999999 799988763 3322222 22445544333322 1123355778888 899988874421 1
Q ss_pred HHHhhCCCCeEEeC
Q 003633 642 QLFLSNQTDFGIIG 655 (806)
Q Consensus 642 ~~~~~~~~~l~~~~ 655 (806)
-..+...|++.+++
T Consensus 201 i~el~~~~~i~lv~ 214 (321)
T COG2358 201 ISELATTCDIVLVP 214 (321)
T ss_pred HHHHHhhCCeEEEe
Confidence 23445567766654
No 387
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=52.14 E-value=1.7e+02 Score=34.54 Aligned_cols=67 Identities=13% Similarity=0.107 Sum_probs=46.1
Q ss_pred cCCeEEEEEEEcCCc---------c---cchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEec
Q 003633 52 YGWKEVIAIYVDDDY---------G---RNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHV 119 (806)
Q Consensus 52 ~~W~~v~ii~~d~~~---------g---~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~ 119 (806)
|..-+|++|..-|+- | ......+...+++.|.++.....++ .+.+.+...+.+..+ ++|+||..+
T Consensus 184 ~~~prv~vi~tG~El~~~~~~~~~g~i~dsn~~~l~~~l~~~g~~~~~~~~v~--Dd~~~i~~~l~~~~~-~~D~iIttG 260 (633)
T PRK14498 184 YKKPRVGIISTGDELVEPGEPLKPGKIYDVNSYTLAAAVEEAGGEPVRYGIVP--DDEEELEAALRKALK-ECDLVLLSG 260 (633)
T ss_pred ecCcEEEEEecCccccCCCCCCCCCEEEEChHHHHHHHHHHCCCEEEEEEEeC--CCHHHHHHHHHHHHh-cCCEEEECC
Confidence 445678888775541 2 2345678888999999887766665 345667777777654 789998877
Q ss_pred Cc
Q 003633 120 SP 121 (806)
Q Consensus 120 ~~ 121 (806)
..
T Consensus 261 G~ 262 (633)
T PRK14498 261 GT 262 (633)
T ss_pred CC
Confidence 54
No 388
>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=51.98 E-value=1.9e+02 Score=26.42 Aligned_cols=99 Identities=8% Similarity=-0.111 Sum_probs=60.4
Q ss_pred HHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccC----CCCChhHH-HHHHHhcCCCCCeEEEEec
Q 003633 45 MADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLP----VQFNQHDI-TVLLNNSKPLGPRVYVVHV 119 (806)
Q Consensus 45 i~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~----~~~~~~~~-~~~l~~ik~~~~rvivl~~ 119 (806)
+.+.+...+-....-+|.+.... .....+.++|++.|.++....... .+..+..+ ...+..+...+.+.||+.+
T Consensus 29 l~~~~~~~~~~~~~r~y~~~~~~-~~~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvS 107 (149)
T cd06167 29 LLEFLRDGGEIVLARAYGNWTSP-ERQRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVS 107 (149)
T ss_pred HHHHHHhCCeEEEEEEEEecCCc-hhHHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEE
Confidence 33333333333444445433221 457889999999999987665331 12222222 2344444455789999999
Q ss_pred CcchHHHHHHHHHHcCCccCCcEEEEcCc
Q 003633 120 SPDPGLRIFTTAQKLQMMTNNYVWLATDW 148 (806)
Q Consensus 120 ~~~~~~~i~~~a~~~gm~~~~~~wi~t~~ 148 (806)
...+-..+++.+++.| ..+++++..
T Consensus 108 gD~Df~~~i~~lr~~G----~~V~v~~~~ 132 (149)
T cd06167 108 GDSDFVPLVERLRELG----KRVIVVGFE 132 (149)
T ss_pred CCccHHHHHHHHHHcC----CEEEEEccC
Confidence 9999999999999987 345665543
No 389
>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=51.81 E-value=53 Score=33.43 Aligned_cols=77 Identities=8% Similarity=-0.022 Sum_probs=52.0
Q ss_pred EEEEEEc--CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHHHH
Q 003633 57 VIAIYVD--DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a~~ 133 (806)
|+++..| +.|.....+.+.+++++.|.++.... ...+.+.....+.++.+.++|.+|+...... ....+.++.+
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~---~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSI---ANQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKK 78 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEec---CCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHH
Confidence 4555543 56777889999999999998876432 1223444566677777789999988665333 3456677777
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|+
T Consensus 79 ~~i 81 (267)
T cd06322 79 AGI 81 (267)
T ss_pred CCC
Confidence 664
No 390
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=50.86 E-value=2.1e+02 Score=26.69 Aligned_cols=70 Identities=14% Similarity=0.160 Sum_probs=45.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++.+.+..++.+|++|+++... ......+ .+.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~-------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~v~~~ 80 (198)
T cd08447 13 SFLPRLLAAARAALP-DVDLVLRE-------MVTTDQIEALESGRIDLGLLRP---PFARPGL-ETRPLVREPLVAAVPA 80 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHcCCceEEEecC---CCCCCCe-eEEEeecCceEEEecC
Confidence 456678888888765 34455554 3678999999999999998532 1112222 2356667777777765
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~~ 82 (198)
T cd08447 81 GH 82 (198)
T ss_pred CC
Confidence 44
No 391
>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=50.33 E-value=1.7e+02 Score=25.48 Aligned_cols=79 Identities=13% Similarity=0.107 Sum_probs=40.8
Q ss_pred HHHcCCeEEEEEEEcCC-cccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC-cchHHH
Q 003633 49 IDFYGWKEVIAIYVDDD-YGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS-PDPGLR 126 (806)
Q Consensus 49 l~~~~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~-~~~~~~ 126 (806)
+...|.|.|+=+-.|++ -+....+.+.+.+++.|+...+.-......+.+++......+.+..- -|++||- ..-+..
T Consensus 23 la~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y~~iPv~~~~~~~~~v~~f~~~l~~~~~-Pvl~hC~sG~Ra~~ 101 (110)
T PF04273_consen 23 LAAQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQYVHIPVDGGAITEEDVEAFADALESLPK-PVLAHCRSGTRASA 101 (110)
T ss_dssp HHHCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EEEE----TTT--HHHHHHHHHHHHTTTT-SEEEE-SCSHHHHH
T ss_pred HHHCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeEEEeecCCCCCCHHHHHHHHHHHHhCCC-CEEEECCCChhHHH
Confidence 45589999988887755 45566777889999999997754333333455666555555554443 3555555 444444
Q ss_pred HH
Q 003633 127 IF 128 (806)
Q Consensus 127 i~ 128 (806)
+.
T Consensus 102 l~ 103 (110)
T PF04273_consen 102 LW 103 (110)
T ss_dssp HH
T ss_pred HH
Confidence 33
No 392
>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=50.31 E-value=82 Score=29.52 Aligned_cols=66 Identities=24% Similarity=0.153 Sum_probs=38.5
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
++-.+++..+.+..+ .+++++.. .+.+. .+.+|++|+++... ......+. +.++....++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~-~l~~~~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~ 78 (197)
T cd08422 14 LHLAPLLAEFLARYP-DVRLELVL---------SDRLV-DLVEEGFDLAIRIG---ELPDSSLV-ARRLGPVRRVLVASP 78 (197)
T ss_pred HHHHHHHHHHHHhCC-ceEEEEec---------Ccccc-chhhcCccEEEEeC---CCCCcchh-hhhhhccCcEEEECH
Confidence 455677888888775 44455543 12233 45668899998632 11222232 456677777777764
Q ss_pred c
Q 003633 463 N 463 (806)
Q Consensus 463 ~ 463 (806)
.
T Consensus 79 ~ 79 (197)
T cd08422 79 A 79 (197)
T ss_pred H
Confidence 3
No 393
>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=50.14 E-value=55 Score=33.13 Aligned_cols=77 Identities=4% Similarity=-0.088 Sum_probs=51.5
Q ss_pred EEEEEEEc--CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHHH
Q 003633 56 EVIAIYVD--DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTAQ 132 (806)
Q Consensus 56 ~v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a~ 132 (806)
+|++|..+ +.|.....+.+.+++++.|+++..... ..+.+.....++++...+.+.+|+...... ....+..+.
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~~~~~~l~ 77 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDA---QNDVSKQIQQIEDLIAQGVDGIIISPVDSAALTPALKKAN 77 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEeCCCchhHHHHHHHHH
Confidence 36777754 568888899999999999988775422 123344456677777778998888764433 233566666
Q ss_pred HcC
Q 003633 133 KLQ 135 (806)
Q Consensus 133 ~~g 135 (806)
+.+
T Consensus 78 ~~~ 80 (267)
T cd01536 78 AAG 80 (267)
T ss_pred HCC
Confidence 655
No 394
>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=49.88 E-value=63 Score=34.69 Aligned_cols=97 Identities=9% Similarity=0.018 Sum_probs=63.4
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
+.+.+.++.+|.+++.+++...-+-. ..+.+.+.|++.+..+ + ..+.+..+.+.+...+..++..++|.||-.+...
T Consensus 12 ~~l~~~l~~~g~~~~livt~~~~~~~-~~~~v~~~l~~~~~~~-~-~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs 88 (337)
T cd08177 12 AALAAELERLGASRALVLTTPSLATK-LAERVASALGDRVAGT-F-DGAVMHTPVEVTEAAVAAAREAGADGIVAIGGGS 88 (337)
T ss_pred HHHHHHHHHcCCCeEEEEcChHHHHH-HHHHHHHHhccCCcEE-e-CCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCcH
Confidence 55677889999999998884433333 6667788887765432 2 3344455667788888888888999999777643
Q ss_pred --hHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 123 --PGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 123 --~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
+..+++.... + ..++-|-|.
T Consensus 89 ~iD~aK~ia~~~--~---~p~i~IPTt 110 (337)
T cd08177 89 TIDLAKAIALRT--G---LPIIAIPTT 110 (337)
T ss_pred HHHHHHHHHHHh--c---CCEEEEcCC
Confidence 4555544322 2 345555554
No 395
>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=49.73 E-value=76 Score=33.98 Aligned_cols=78 Identities=6% Similarity=-0.028 Sum_probs=52.5
Q ss_pred HHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc--hHHHH
Q 003633 50 DFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD--PGLRI 127 (806)
Q Consensus 50 ~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~--~~~~i 127 (806)
..++.+++.+|+...-+-.+..+.+.+.|++. +.+.....+.++.+.+.+...+..+++.++|+||-.+... +..+.
T Consensus 18 ~~~~~~~~lvv~~~~~~~~g~~~~v~~~l~~~-~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IiaiGGGs~~D~aKa 96 (332)
T cd08180 18 KELKNKRVLIVTDPFMVKSGMLDKVTDHLDSS-IEVEIFSDVVPDPPIEVVAKGIKKFLDFKPDIVIALGGGSAIDAAKA 96 (332)
T ss_pred HHhCCCeEEEEeCchhhhCccHHHHHHHHHhc-CcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEECCchHHHHHHH
Confidence 45556899888843333334677888888876 6554333455555667788888888889999999776543 44544
Q ss_pred H
Q 003633 128 F 128 (806)
Q Consensus 128 ~ 128 (806)
+
T Consensus 97 ~ 97 (332)
T cd08180 97 I 97 (332)
T ss_pred H
Confidence 4
No 396
>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=49.51 E-value=70 Score=32.52 Aligned_cols=78 Identities=3% Similarity=-0.144 Sum_probs=50.5
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++.. ++.|.....+.+.+++++.|.++.....-. .........+..+.+.+.+.+|+..........+..+.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 79 (270)
T cd01545 2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCDS--GSPDLAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEA 79 (270)
T ss_pred EEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCCC--CchHHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHHhc
Confidence 455654 467888889999999999998876543221 1222445566667778889888765433234556666666
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 80 ~i 81 (270)
T cd01545 80 GV 81 (270)
T ss_pred CC
Confidence 53
No 397
>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=49.16 E-value=2.3e+02 Score=26.62 Aligned_cols=70 Identities=16% Similarity=0.102 Sum_probs=45.8
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-.+++..+.+..+ .+++++.. ++..++..+|.+|++|+++..- ......+. +.++....++++++.
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 344577788877765 34566654 3578899999999999998521 22222333 356667777777766
Q ss_pred cC
Q 003633 463 NN 464 (806)
Q Consensus 463 ~~ 464 (806)
..
T Consensus 81 ~h 82 (197)
T cd08452 81 QH 82 (197)
T ss_pred CC
Confidence 54
No 398
>PRK09189 uroporphyrinogen-III synthase; Validated
Probab=48.30 E-value=52 Score=33.26 Aligned_cols=88 Identities=8% Similarity=-0.056 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHHc--CCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEE
Q 003633 39 SQQMAAMADLIDFY--GWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYV 116 (806)
Q Consensus 39 ~~q~~ai~~ll~~~--~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rviv 116 (806)
...++.+++++... .-++|.++. |..+.+.|.+.|++.|+.|.....|.......+.......+++.+.|+|+
T Consensus 101 ~~~~e~L~~~~~~~~~~~~~vL~~r-----g~~~r~~l~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~l~~~~~d~i~ 175 (240)
T PRK09189 101 GGDGVRLAETVAAALAPTARLLYLA-----GRPRAPVFEDRLAAAGIPFRVAECYDMLPVMYSPATLSAILGGAPFDAVL 175 (240)
T ss_pred CCCHHHHHHHHHHhcCCCCcEEEec-----cCcccchhHHHHHhCCCeeEEEEEEEeecCCCChHHHHHHHhcCCCCEEE
Confidence 34577788776442 335555554 33445788899999998876544442211111222334455556677766
Q ss_pred EecCcchHHHHHHHHH
Q 003633 117 VHVSPDPGLRIFTTAQ 132 (806)
Q Consensus 117 l~~~~~~~~~i~~~a~ 132 (806)
+.+ +..+..+++...
T Consensus 176 f~S-~~~~~~f~~~~~ 190 (240)
T PRK09189 176 LYS-RVAARRFFALMR 190 (240)
T ss_pred EeC-HHHHHHHHHHHh
Confidence 655 456677776654
No 399
>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=47.93 E-value=77 Score=32.85 Aligned_cols=77 Identities=10% Similarity=-0.010 Sum_probs=54.0
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc-chHHHHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP-DPGLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~-~~~~~i~~~a~~ 133 (806)
|+++.. ++.|.....+.+.+++++.|.++..... ..+.......++.+.+.++|.||+.... +.....++++.+
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 566664 3567778889999999999999775432 2234445677777778899998887643 334567778877
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|.
T Consensus 79 ~~i 81 (288)
T cd01538 79 AGI 81 (288)
T ss_pred CCC
Confidence 664
No 400
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=47.86 E-value=57 Score=34.90 Aligned_cols=63 Identities=14% Similarity=0.129 Sum_probs=42.2
Q ss_pred cCCCCCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEE
Q 003633 352 ADNARPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAA 431 (806)
Q Consensus 352 ~~~g~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~ 431 (806)
|..|+++++++.. |.. .-+.-.+++.+.+.+||++. ++.+. +-.-+...|.+|.+|+.
T Consensus 25 ~~~~~~V~~~~~~---W~~-----------~~~~t~v~~~iLe~~GY~V~-e~~~~-------~~~~~~~ala~GdiDv~ 82 (331)
T PRK11119 25 PGKGITVQPAQST---IAE-----------ETFQTLLVSRALEKLGYDVN-KPKEV-------DYNVFYTSIANGDATFT 82 (331)
T ss_pred CCCCeEEEEeecC---ccH-----------HHHHHHHHHHHHHHcCCcee-eeccc-------CcHHHHHHHHcCCCeEe
Confidence 4468899998873 321 12445678888888998750 33332 23677888999999998
Q ss_pred EeeEE
Q 003633 432 VGDIA 436 (806)
Q Consensus 432 ~~~~~ 436 (806)
+....
T Consensus 83 ~~~W~ 87 (331)
T PRK11119 83 AVNWF 87 (331)
T ss_pred hhhcc
Confidence 76443
No 401
>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=47.46 E-value=84 Score=31.85 Aligned_cols=76 Identities=11% Similarity=-0.033 Sum_probs=53.1
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++.. +++|-....+.+.+++++.|+.+..... ..+.+.....+..+.+.+.|.||+....... ..++++.+.
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 4567778889999999999998875432 2234455577788888899999887654333 346777776
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 78 ~i 79 (265)
T cd06299 78 GI 79 (265)
T ss_pred CC
Confidence 63
No 402
>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=47.44 E-value=1.5e+02 Score=32.00 Aligned_cols=101 Identities=11% Similarity=-0.040 Sum_probs=63.3
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEe--ccCCCCChhHHHHHHHhcCCCCCe---EEEE
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKL--PLPVQFNQHDITVLLNNSKPLGPR---VYVV 117 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~--~~~~~~~~~~~~~~l~~ik~~~~r---vivl 117 (806)
.-+.++++.++-+++.++++.+-+ ....+.+.+.|++.|+.+.... ...+..+.+.+...+..+++.++| +||.
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 345567777788899888854433 3466788899999888653221 222233456777888888877777 7776
Q ss_pred ecCcc--hHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 118 HVSPD--PGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 118 ~~~~~--~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
.+... +...++......| ..++.|-|.
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 66543 5555554433233 356666664
No 403
>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=47.43 E-value=1.3e+02 Score=32.41 Aligned_cols=84 Identities=13% Similarity=0.061 Sum_probs=56.0
Q ss_pred HHHHHHHHHcCC--eEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCC---CCeEEEE
Q 003633 43 AAMADLIDFYGW--KEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPL---GPRVYVV 117 (806)
Q Consensus 43 ~ai~~ll~~~~W--~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~---~~rvivl 117 (806)
..+.++++.+|. +++.+++ |...-. +.+.+.|++.|+.+.....+.++.+.+++....+..++. ++|+||-
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 456677777764 5666666 433211 567788888888755445566677777888888888876 8999997
Q ss_pred ecCcc--hHHHHHHH
Q 003633 118 HVSPD--PGLRIFTT 130 (806)
Q Consensus 118 ~~~~~--~~~~i~~~ 130 (806)
.+... ++.+.+..
T Consensus 88 iGGGS~iD~AKaia~ 102 (347)
T cd08184 88 IGGGSTLDVAKAVSN 102 (347)
T ss_pred eCCcHHHHHHHHHHH
Confidence 77543 55554443
No 404
>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=47.26 E-value=74 Score=34.09 Aligned_cols=98 Identities=10% Similarity=0.086 Sum_probs=61.1
Q ss_pred HHHHHHHHHcCC-eEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEe-ccCCCCChhHHHHHHHhcCCCCCeEEEEecC
Q 003633 43 AAMADLIDFYGW-KEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKL-PLPVQFNQHDITVLLNNSKPLGPRVYVVHVS 120 (806)
Q Consensus 43 ~ai~~ll~~~~W-~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~-~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~ 120 (806)
..+.++++.++. +++.+|.....+-. ..+.+.+.|++.|+++.... ...+..+.+.+...+..+++ +.|+||-.+.
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 445667777876 78888875444333 34788888998887654321 22233456677788888887 8999988776
Q ss_pred cc--hHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 121 PD--PGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 121 ~~--~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
.. +...++. ...| -.++-|-|.
T Consensus 90 Gsv~D~aK~iA--~~~g---ip~I~VPTT 113 (332)
T cd08549 90 GTIIDLVKFVS--FKVG---KPFISVPTA 113 (332)
T ss_pred cHHHHHHHHHH--HHcC---CCEEEeCCC
Confidence 43 5555554 2233 345555554
No 405
>cd08479 PBP2_CrgA_like_9 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=46.98 E-value=1.9e+02 Score=27.05 Aligned_cols=65 Identities=12% Similarity=0.058 Sum_probs=38.0
Q ss_pred eeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 383 GYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 383 G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
.+-..++..+.++.+ .+++++... .....+.+|++|+++.. .......+. +.++.....+++++.
T Consensus 14 ~~l~~~l~~f~~~~P-~i~i~~~~~----------~~~~~l~~g~~Dl~i~~---~~~~~~~l~-~~~l~~~~~~~~~~~ 78 (198)
T cd08479 14 RHIAPALSDFAKRYP-ELEVQLELT----------DRPVDLVEEGFDLDIRV---GDLPDSSLI-ARKLAPNRRILCASP 78 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEec----------CccccccccCccEEEEc---CCCCCccce-eeeccCCceEEEECH
Confidence 555678888888776 455665531 12357889999999852 112222333 335556666666543
No 406
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=46.62 E-value=64 Score=33.16 Aligned_cols=77 Identities=6% Similarity=-0.102 Sum_probs=51.8
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a~~ 133 (806)
|+++.. .+.|.......+.+++++.|..+..... ..+.+.....+..+...++|.||+...... ....++.+.+
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 455553 3567778889999999999998865321 223334456777788889999988754332 2456677777
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|.
T Consensus 79 ~~i 81 (282)
T cd06318 79 AGV 81 (282)
T ss_pred CCC
Confidence 664
No 407
>cd00757 ThiF_MoeB_HesA_family ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1).
Probab=46.61 E-value=2e+02 Score=28.79 Aligned_cols=89 Identities=12% Similarity=0.099 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHcCCeEEEEEE---------------EcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHH
Q 003633 41 QMAAMADLIDFYGWKEVIAIY---------------VDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLN 105 (806)
Q Consensus 41 q~~ai~~ll~~~~W~~v~ii~---------------~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~ 105 (806)
.+..+++.+...|..++.++- ..++-|+.-++.+.+.+++.+..+... .++...+.+++.+.+
T Consensus 32 lGs~va~~La~~Gvg~i~lvD~D~ve~sNL~Rq~l~~~~diG~~Ka~~~~~~l~~~np~~~i~-~~~~~i~~~~~~~~~- 109 (228)
T cd00757 32 LGSPAAEYLAAAGVGKLGLVDDDVVELSNLQRQILHTEADVGQPKAEAAAERLRAINPDVEIE-AYNERLDAENAEELI- 109 (228)
T ss_pred HHHHHHHHHHHcCCCEEEEEcCCEEcCcccccccccChhhCCChHHHHHHHHHHHhCCCCEEE-EecceeCHHHHHHHH-
Confidence 456777888888999998873 334678888999999999876543322 122222334444443
Q ss_pred hcCCCCCeEEEEecCcchHHHHH-HHHHHcC
Q 003633 106 NSKPLGPRVYVVHVSPDPGLRIF-TTAQKLQ 135 (806)
Q Consensus 106 ~ik~~~~rvivl~~~~~~~~~i~-~~a~~~g 135 (806)
.+.|+||.+.....+...+ +.+.+.+
T Consensus 110 ----~~~DvVi~~~d~~~~r~~l~~~~~~~~ 136 (228)
T cd00757 110 ----AGYDLVLDCTDNFATRYLINDACVKLG 136 (228)
T ss_pred ----hCCCEEEEcCCCHHHHHHHHHHHHHcC
Confidence 2478998888776666655 4556555
No 408
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=46.10 E-value=3.1e+02 Score=28.44 Aligned_cols=104 Identities=8% Similarity=-0.076 Sum_probs=50.0
Q ss_pred CCChhHhhhCCCcee-EEeCchhHHHhhhhcccc---cccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCC
Q 003633 573 VKGIESLITNDWPIG-YQVGSFAYSYLSDSLRIQ---KSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQ 648 (806)
Q Consensus 573 i~s~~dL~~~~~~ig-~~~gs~~~~~l~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~ 648 (806)
.-+++||. +.++. ...+.....++.+ .+.. ......+++.+...+++.. |..-+++. ...........
T Consensus 180 ~i~~~dL~--~~p~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~v~~----g~gi~~lp-~~~~~~~~~~~ 251 (297)
T PRK11139 180 LKTPEDLA--RHTLLHDDSREDWRAWFRA-AGLDDLNVQQGPIFSHSSMALQAAIH----GQGVALGN-RVLAQPEIEAG 251 (297)
T ss_pred CCCHHHhh--cCceEeecCcccHHHHHHH-hCCCCcCcccceeeCCHHHHHHHHHh----CCCeEecc-hhhhHHHHHCC
Confidence 34778884 44433 2222334444432 2221 1122446777777777777 44444444 33333333332
Q ss_pred CCeEEeCCcc-ccCCceeeecCCCCchHHHHHHHHhh
Q 003633 649 TDFGIIGQPF-TRSGWGFAFQRDSPLAVGMSTAILKL 684 (806)
Q Consensus 649 ~~l~~~~~~~-~~~~~~~~~~k~spl~~~~n~~il~l 684 (806)
.-...+.+.. ....+.++.+|+.+....+...+..+
T Consensus 252 ~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 288 (297)
T PRK11139 252 RLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWL 288 (297)
T ss_pred ceecccccCcCCCccEEEEeccccccChhHHHHHHHH
Confidence 1112222222 23467888888776555555544433
No 409
>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=46.06 E-value=68 Score=32.75 Aligned_cols=80 Identities=13% Similarity=0.165 Sum_probs=51.6
Q ss_pred EEEEEEEc--CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchH-HHHHHHHH
Q 003633 56 EVIAIYVD--DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPG-LRIFTTAQ 132 (806)
Q Consensus 56 ~v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~-~~i~~~a~ 132 (806)
||++|..+ +.|-......+.+++++.|.++.....-. ..+.......+.++...+.|.+|+....... ...+..+.
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 46767644 56777888999999999999877543211 1233445566777777789988886543332 44666666
Q ss_pred HcCC
Q 003633 133 KLQM 136 (806)
Q Consensus 133 ~~gm 136 (806)
+.|+
T Consensus 80 ~~~i 83 (273)
T cd06310 80 DAGI 83 (273)
T ss_pred HCCC
Confidence 6553
No 410
>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=45.90 E-value=1e+02 Score=31.53 Aligned_cols=78 Identities=6% Similarity=-0.047 Sum_probs=49.7
Q ss_pred CCeEEEEEEE---------cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch
Q 003633 53 GWKEVIAIYV---------DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP 123 (806)
Q Consensus 53 ~W~~v~ii~~---------d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~ 123 (806)
..+.|++|.. ++.|.....+.+.+.+++.|+.+.+... +.. +.......+.+.++|.||+......
T Consensus 2 ~s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~~---~~~--~~~~~~~~l~~~~~dgiii~~~~~~ 76 (275)
T cd06295 2 RTDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSFV---SSP--DRDWLARYLASGRADGVILIGQHDQ 76 (275)
T ss_pred CceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEeC---Cch--hHHHHHHHHHhCCCCEEEEeCCCCC
Confidence 3567888884 3446677788899999999998775421 111 2334444555678998888654322
Q ss_pred HHHHHHHHHHcCC
Q 003633 124 GLRIFTTAQKLQM 136 (806)
Q Consensus 124 ~~~i~~~a~~~gm 136 (806)
...++++.+.|.
T Consensus 77 -~~~~~~~~~~~i 88 (275)
T cd06295 77 -DPLPERLAETGL 88 (275)
T ss_pred -hHHHHHHHhCCC
Confidence 244677777664
No 411
>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=45.68 E-value=53 Score=26.50 Aligned_cols=42 Identities=26% Similarity=0.250 Sum_probs=34.3
Q ss_pred HHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEE
Q 003633 44 AMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVS 86 (806)
Q Consensus 44 ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~ 86 (806)
...++++.+ -++|.+.+++|+-|+..+..+.+.+.+.|..+.
T Consensus 34 ~~~~~L~~~-~~~vii~~D~D~aG~~a~~~~~~~l~~~g~~~~ 75 (79)
T cd03364 34 EQAELLKRL-AKEVILAFDGDEAGQKAALRALELLLKLGLNVR 75 (79)
T ss_pred HHHHHHHhc-CCeEEEEECCCHHHHHHHHHHHHHHHHCCCeEE
Confidence 345666655 689999998888899999999999999988764
No 412
>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=45.30 E-value=60 Score=33.58 Aligned_cols=76 Identities=14% Similarity=0.156 Sum_probs=52.5
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc-chHHHHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP-DPGLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~-~~~~~i~~~a~~ 133 (806)
|++|.. ++.|.......+.+++++.|..+... ... +.+.....+.++.+.++|.+|+.... .....+++++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~---~~~-~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~~~~ 77 (289)
T cd01540 2 IGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKI---DVP-DGEKVLSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAKA 77 (289)
T ss_pred eeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEc---cCC-CHHHHHHHHHHHHHcCCCEEEEccCchhhhHHHHHHHHh
Confidence 556664 35577788899999999999887643 222 33444566777888899998887643 344567788887
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|.
T Consensus 78 ~~i 80 (289)
T cd01540 78 YNM 80 (289)
T ss_pred CCC
Confidence 764
No 413
>TIGR00249 sixA phosphohistidine phosphatase SixA.
Probab=45.12 E-value=92 Score=28.93 Aligned_cols=98 Identities=7% Similarity=-0.118 Sum_probs=58.4
Q ss_pred ecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCe
Q 003633 34 STQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPR 113 (806)
Q Consensus 34 t~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~r 113 (806)
.++.-..|++.+++.++..+..--.++.+.-.-.+..++.+.+.+.. ...+.....+.+..+..++...+.++.....+
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 34555678999999888766544344444433334444444433321 12344344455444556667777776654566
Q ss_pred EEEEecCcchHHHHHHHHH
Q 003633 114 VYVVHVSPDPGLRIFTTAQ 132 (806)
Q Consensus 114 vivl~~~~~~~~~i~~~a~ 132 (806)
.++++++.+....++...-
T Consensus 102 ~vliVgH~P~i~~l~~~l~ 120 (152)
T TIGR00249 102 SVLLVSHLPLVGYLVAELC 120 (152)
T ss_pred EEEEEeCCCCHHHHHHHHh
Confidence 7888888888888887764
No 414
>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents uroporphyrinogen III synthase (4.2.1.75 from EC) which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the inversion of the final pyrrole unit (ring D) of the linear tetrapyrrole molecule, linking it to the first pyrrole unit (ring A), thereby generating a large macrocyclic structure called uroporphyrinogen III []. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains []. Congenital erythropoietic porphyria (CEP) is an autosomal recessive inborn error of metabolism that results from the markedly deficient activity of uroporphyrinogen III synthase []. ; GO: 0004852 uroporphyrinogen-III synthase activity, 0033014 tetrapyrrole biosynthetic process; PDB: 1WD7_B 1WCX_A 1WCW_A 3D8R_A 3D8T_B 3D8S_A 3D8N_A 3RE1_A 3MW8_A 3P9Z_A ....
Probab=44.37 E-value=26 Score=35.17 Aligned_cols=92 Identities=16% Similarity=0.090 Sum_probs=57.6
Q ss_pred cCCcHHHHHHHHHHHHH-cCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCe
Q 003633 35 TQSDSQQMAAMADLIDF-YGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPR 113 (806)
Q Consensus 35 ~psd~~q~~ai~~ll~~-~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~r 113 (806)
+|++...++.+++.+.. ..-++|.++.. ....+.|.+.|++.|++|.....|.. ............+...+.+
T Consensus 97 ~~~~~~~s~~L~~~l~~~~~~~~vl~~~g-----~~~~~~l~~~L~~~g~~v~~~~vY~~-~~~~~~~~~~~~l~~~~~~ 170 (231)
T PF02602_consen 97 VPSSEGSSEGLAELLKEQLRGKRVLILRG-----EGGRPDLPEKLREAGIEVTEVIVYET-PPEELSPELKEALDRGEID 170 (231)
T ss_dssp E-TTSSSHHHHHGGHHHCCTTEEEEEEES-----SSSCHHHHHHHHHTTEEEEEEECEEE-EEHHHHHHHHHHHHHTTTS
T ss_pred cCCCCCCHHHHHHHHHhhCCCCeEEEEcC-----CCccHHHHHHHHHCCCeEEEEEEeec-ccccchHHHHHHHHcCCCC
Confidence 56656667888887763 44478777663 33467788999999999877666653 2222333444555555666
Q ss_pred EEEEecCcchHHHHHHHHHH
Q 003633 114 VYVVHVSPDPGLRIFTTAQK 133 (806)
Q Consensus 114 vivl~~~~~~~~~i~~~a~~ 133 (806)
+ |+++++..+..++....+
T Consensus 171 ~-v~ftS~~~~~~~~~~~~~ 189 (231)
T PF02602_consen 171 A-VVFTSPSAVRAFLELLKK 189 (231)
T ss_dssp E-EEESSHHHHHHHHHHSSG
T ss_pred E-EEECCHHHHHHHHHHhHh
Confidence 5 455566667777766554
No 415
>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=44.21 E-value=72 Score=33.70 Aligned_cols=87 Identities=11% Similarity=0.111 Sum_probs=58.3
Q ss_pred EEEEEEE----cCCcccchHHHHHHHHHhC-CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHH
Q 003633 56 EVIAIYV----DDDYGRNGISALSNMLEKN-MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTT 130 (806)
Q Consensus 56 ~v~ii~~----d~~~g~~~~~~l~~~l~~~-g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~ 130 (806)
+++++.. |..|.+...+.+.+.-++. |+++.+.+..+. +..++...+..+.+.+.|+||+++..- ...+...
T Consensus 3 ~v~~~~~g~~~D~g~n~~~~~G~~~~~~~~~~i~~~~~e~~~~--~~~~~~~~~~~~~~~g~dlIi~~g~~~-~~~~~~v 79 (306)
T PF02608_consen 3 KVALLDPGGINDKGFNQSAYEGLKRAEKELDGIEIIYVENVPE--TDADYEEAIRQLADQGYDLIIGHGFEY-SDALQEV 79 (306)
T ss_dssp EEEEESSS-CCCSSHHHHHHHHHHHHHHHCTTEEEEEEES-S---TCHHHHHHHHHHHHTT-SEEEEESGGG-HHHHHHH
T ss_pred EEEEEECCCCCCccHHHHHHHHHHHHHHHcCCceEEEEecCCc--cHHHHHHHHHHHHHcCCCEEEEccHHH-HHHHHHH
Confidence 4555553 4556677788888888888 999998887652 457888899999889999999987643 2344444
Q ss_pred HHHcCCccCCcEEEEcCcc
Q 003633 131 AQKLQMMTNNYVWLATDWL 149 (806)
Q Consensus 131 a~~~gm~~~~~~wi~t~~~ 149 (806)
|.+- ++-.|+..++.
T Consensus 80 A~~y----Pd~~F~~~d~~ 94 (306)
T PF02608_consen 80 AKEY----PDTKFIIIDGY 94 (306)
T ss_dssp HTC-----TTSEEEEESS-
T ss_pred HHHC----CCCEEEEEecC
Confidence 5432 45567766643
No 416
>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=44.07 E-value=3.3e+02 Score=27.93 Aligned_cols=132 Identities=11% Similarity=0.013 Sum_probs=64.9
Q ss_pred cccCCCcEEecccCCCCcccCCCC-ceEEecCCcHHHHHHHHHHHHHc--CCeEEEEEEEcCC-cccchHHHHHHHHHhC
Q 003633 6 ANGLKVPLVSFAATDPTLSALQFP-YFIRSTQSDSQQMAAMADLIDFY--GWKEVIAIYVDDD-YGRNGISALSNMLEKN 81 (806)
Q Consensus 6 ~~~~~vP~Is~~at~p~Ls~~~~p-~f~Rt~psd~~q~~ai~~ll~~~--~W~~v~ii~~d~~-~g~~~~~~l~~~l~~~ 81 (806)
+...++|+|.+....+. .....+ .+-....++...+..+++.+... |-++++++...+. ......+.+...++..
T Consensus 77 ~~~~~iPvV~~d~~~~~-~~~~~~~~~~~v~~D~~~~~~~~~~~L~~~~~G~~~i~~i~~~~~~~~~~r~~~~~~~~~a~ 155 (280)
T cd06315 77 AQKAGIPVVGWHAGPEP-GPIEEPGIFYNVTTDPLAVAEVAALYAIANSGGKAGVVIFTDSRFSIAKAKANAMKEIIEAC 155 (280)
T ss_pred HHHCCCCEEEecCCCCC-CcccCCceeEEecCCHHHHHHHHHHHHHHHcCCCceEEEEeCCCCccHHHHHHHHHHHHHhC
Confidence 44678999987543211 010011 13334555555567777776554 8999998863321 1111123444444332
Q ss_pred -CcEEEEEeccCCCCChhHHHHHHHhcCC---CCCeEEEEecCcchHHHHHHHHHHcCCccC
Q 003633 82 -MAKVSYKLPLPVQFNQHDITVLLNNSKP---LGPRVYVVHVSPDPGLRIFTTAQKLQMMTN 139 (806)
Q Consensus 82 -g~~i~~~~~~~~~~~~~~~~~~l~~ik~---~~~rvivl~~~~~~~~~i~~~a~~~gm~~~ 139 (806)
+..+............+.....++++.+ ..++ .|++++...+..+++.+++.|+..+
T Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-ai~~~~D~~A~g~~~~l~~~g~~~p 216 (280)
T cd06315 156 KGCTVLSIEDVPISRTATRMPALTARLLQRYGDKWT-HSLAINDLYFDYMAPPLASAGRKAD 216 (280)
T ss_pred CCCEEEEecccCcchhhhhhHHHHHHHHHhcCcccc-eecccchhhhHHhHHHHHHhcccCC
Confidence 3333111111111111111123333322 2245 4666677788899999999997644
No 417
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322
Probab=44.02 E-value=25 Score=25.48 Aligned_cols=25 Identities=16% Similarity=0.549 Sum_probs=20.9
Q ss_pred hhHHHHHHHHHHHHHHhhhhccccC
Q 003633 479 EMWCVTAASFVMIAVVIWILEHRVN 503 (806)
Q Consensus 479 ~~W~~~~~~~~~~~~v~~~~~~~~~ 503 (806)
++|.++..+.+++++++|.+..+..
T Consensus 12 ~~~~l~~~~~~Figiv~wa~~p~~k 36 (48)
T cd01324 12 DSWGLLYLALFFLGVVVWAFRPGRK 36 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 6789999999999999999975543
No 418
>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=43.30 E-value=1.2e+02 Score=28.67 Aligned_cols=66 Identities=9% Similarity=-0.036 Sum_probs=45.1
Q ss_pred CCeEEEEEEEcCCccc---chHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcC-CCCCeEEEEecC
Q 003633 53 GWKEVIAIYVDDDYGR---NGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSK-PLGPRVYVVHVS 120 (806)
Q Consensus 53 ~W~~v~ii~~d~~~g~---~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik-~~~~rvivl~~~ 120 (806)
..-++++|...|+-+. .....+...|++.|+++.....++ .+.+.+...+.+.. ..+.|+||..+.
T Consensus 3 ~~~rv~vit~~d~~~~~~d~n~~~l~~~L~~~G~~v~~~~iv~--Dd~~~i~~~l~~~~~~~~~DlVIttGG 72 (163)
T TIGR02667 3 IPLRIAILTVSDTRTEEDDTSGQYLVERLTEAGHRLADRAIVK--DDIYQIRAQVSAWIADPDVQVILITGG 72 (163)
T ss_pred CccEEEEEEEeCcCCccCCCcHHHHHHHHHHCCCeEEEEEEcC--CCHHHHHHHHHHHHhcCCCCEEEECCC
Confidence 3457788776554322 235577888999999988777776 34567777777764 257898888664
No 419
>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=43.26 E-value=2.2e+02 Score=24.73 Aligned_cols=45 Identities=20% Similarity=0.121 Sum_probs=23.5
Q ss_pred chHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEec
Q 003633 69 NGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHV 119 (806)
Q Consensus 69 ~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~ 119 (806)
-++..+...|++.|.++.+.... .. .....+.+++.++|+|.+.+
T Consensus 15 lGl~~la~~l~~~G~~v~~~d~~---~~---~~~l~~~~~~~~pd~V~iS~ 59 (121)
T PF02310_consen 15 LGLLYLAAYLRKAGHEVDILDAN---VP---PEELVEALRAERPDVVGISV 59 (121)
T ss_dssp HHHHHHHHHHHHTTBEEEEEESS---B----HHHHHHHHHHTTCSEEEEEE
T ss_pred HHHHHHHHHHHHCCCeEEEECCC---CC---HHHHHHHHhcCCCcEEEEEc
Confidence 34556666666667666543211 11 13334445555677766665
No 420
>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=42.91 E-value=2.4e+02 Score=28.42 Aligned_cols=69 Identities=9% Similarity=-0.069 Sum_probs=40.8
Q ss_pred CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHcCC
Q 003633 64 DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKLQM 136 (806)
Q Consensus 64 ~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~gm 136 (806)
+.|.......+.+.+++.|+.+.+...- ...+......+.+.+.+.|.+|+....... ..+..+.+.|.
T Consensus 15 ~~~~~~~~~~i~~~~~~~g~~~~~~~~~---~~~~~~~~~~~~~~~~~vdgiii~~~~~~~-~~~~~~~~~~i 83 (268)
T cd06271 15 DPFFAEFLSGLSEALAEHGYDLVLLPVD---PDEDPLEVYRRLVESGLVDGVIISRTRPDD-PRVALLLERGF 83 (268)
T ss_pred CccHHHHHHHHHHHHHHCCceEEEecCC---CcHHHHHHHHHHHHcCCCCEEEEecCCCCC-hHHHHHHhcCC
Confidence 6778888899999999999887755321 111222233333445678888876543222 23455555553
No 421
>PF13362 Toprim_3: Toprim domain
Probab=42.87 E-value=72 Score=26.82 Aligned_cols=52 Identities=23% Similarity=0.149 Sum_probs=39.5
Q ss_pred cCCeEEEEEEEcCCc--ccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHh
Q 003633 52 YGWKEVIAIYVDDDY--GRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNN 106 (806)
Q Consensus 52 ~~W~~v~ii~~d~~~--g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ 106 (806)
.++++|.+..++|.- |+..+..+.+.+.+.|..+..... .....|+...+++
T Consensus 39 ~~~~~vii~~D~D~~~~G~~~a~~~~~~~~~~g~~~~~~~p---~~~g~D~ND~l~~ 92 (96)
T PF13362_consen 39 EPGRRVIIAADNDKANEGQKAAEKAAERLEAAGIAVSIVEP---GPEGKDWNDLLQA 92 (96)
T ss_pred CCCCeEEEEECCCCchhhHHHHHHHHHHHHhCCCeEEEECC---CCCCchHHHHHHh
Confidence 478999877777777 899999999999999988775443 2223588887765
No 422
>PRK07377 hypothetical protein; Provisional
Probab=42.66 E-value=57 Score=30.97 Aligned_cols=61 Identities=18% Similarity=0.199 Sum_probs=44.9
Q ss_pred CCeEEeeeccCCccceEEeecCCceeEeeeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEe
Q 003633 356 RPLRIGVPRRASFVGFVTEEHDSHKVQGYCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVG 433 (806)
Q Consensus 356 ~~lrv~v~~~~~~~~f~~~~~~~~~~~G~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~ 433 (806)
..+|+|+... .+ ..+..-+-.++.++.+.++.+.+ .|++++. +-..+.+.+.+|++|++.+
T Consensus 75 ~~~Rlgv~~~--------~~-~~~~~~~~l~~~l~~~~~~y~~r--lElv~y~------~~~~l~~aL~~~eVh~~c~ 135 (184)
T PRK07377 75 LVMRLGVLEI--------ET-ETSSVFDQLIDQLRTILDKYHLR--LELVVYP------DLQALEQALRDKEVHAICL 135 (184)
T ss_pred cEEEEEEEec--------cc-cccccHHHHHHHHHHHHHHhCce--eeEEecC------CHHHHHHHHhcCCccEEec
Confidence 5689998753 01 12234455778888899999977 7777764 6799999999999998876
No 423
>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=42.58 E-value=1.8e+02 Score=26.23 Aligned_cols=99 Identities=13% Similarity=0.055 Sum_probs=49.6
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccC---CCCChhH--HH-HHHHhcCCCCCeEE
Q 003633 42 MAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLP---VQFNQHD--IT-VLLNNSKPLGPRVY 115 (806)
Q Consensus 42 ~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~---~~~~~~~--~~-~~l~~ik~~~~rvi 115 (806)
...+.+.+...|--....+|.+ ........+.+.|++.|+.+....... ...+..| +. ..+..+.+...+.+
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 4555555555444323444544 222346778899999999776543321 1112222 32 33344434456899
Q ss_pred EEecCcchHHHHHHHHHHcCCccCCcEEEEc
Q 003633 116 VVHVSPDPGLRIFTTAQKLQMMTNNYVWLAT 146 (806)
Q Consensus 116 vl~~~~~~~~~i~~~a~~~gm~~~~~~wi~t 146 (806)
++.+...+...+++.+++.| ..+++++
T Consensus 100 vLvSgD~Df~~~v~~l~~~g----~~V~v~~ 126 (146)
T PF01936_consen 100 VLVSGDSDFAPLVRKLRERG----KRVIVVG 126 (146)
T ss_dssp EEE---GGGHHHHHHHHHH------EEEEEE
T ss_pred EEEECcHHHHHHHHHHHHcC----CEEEEEE
Confidence 99888899999999999888 3466666
No 424
>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=42.25 E-value=3.2e+02 Score=27.47 Aligned_cols=75 Identities=3% Similarity=-0.125 Sum_probs=50.6
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++.. ++.|-......+.+++++.|.++... ....+.....+.+..+...++|.+++....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (265)
T cd06285 2 IGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVA---NTGDNPDAQRRAIEMLLDRRVDGLILGDARSDD-HFLDELTRR 77 (265)
T ss_pred EEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE---eCCCCHHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHHHc
Confidence 556665 46677888899999999999887542 222233445567777888899988887644333 346677665
Q ss_pred C
Q 003633 135 Q 135 (806)
Q Consensus 135 g 135 (806)
|
T Consensus 78 ~ 78 (265)
T cd06285 78 G 78 (265)
T ss_pred C
Confidence 5
No 425
>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=41.89 E-value=90 Score=32.59 Aligned_cols=78 Identities=8% Similarity=-0.009 Sum_probs=52.6
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a~~ 133 (806)
|+++.. ++.|-......+++++++.|..+.... +...+.......+..+...++|.||+...... ...+++++.+
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 455553 456777888999999999999876431 22233445566777777788999988754332 3566777777
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|+
T Consensus 80 ~~i 82 (298)
T cd06302 80 AGI 82 (298)
T ss_pred CCC
Confidence 664
No 426
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=41.86 E-value=1.1e+02 Score=31.04 Aligned_cols=76 Identities=9% Similarity=-0.029 Sum_probs=50.1
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++.. ++.|.......+.+++++.|.++... ....+.......++++.+.+.|.+++..... ....+..+.+.
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 456664 46677888899999999999988753 2223334455667777777889888765432 23445666665
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 78 ~i 79 (268)
T cd06273 78 GV 79 (268)
T ss_pred CC
Confidence 53
No 427
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=41.79 E-value=1e+02 Score=32.90 Aligned_cols=79 Identities=13% Similarity=-0.055 Sum_probs=56.2
Q ss_pred CeEEEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHH
Q 003633 54 WKEVIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTT 130 (806)
Q Consensus 54 W~~v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~ 130 (806)
-.+|+++.. ++.|....++.+.+++++.|..+..... ..+.......+..+.+.++|.+|+...... ....+..
T Consensus 25 ~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~~---~~~~~~~~~~i~~l~~~~vDGiIi~~~~~~~~~~~l~~ 101 (330)
T PRK10355 25 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSA---NGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVIKE 101 (330)
T ss_pred CceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHHHH
Confidence 456777663 5778899999999999999999875422 233455667788888889999998765432 2345666
Q ss_pred HHHcC
Q 003633 131 AQKLQ 135 (806)
Q Consensus 131 a~~~g 135 (806)
+.+.|
T Consensus 102 ~~~~~ 106 (330)
T PRK10355 102 AKQEG 106 (330)
T ss_pred HHHCC
Confidence 66655
No 428
>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=41.54 E-value=1.1e+02 Score=31.05 Aligned_cols=76 Identities=5% Similarity=-0.049 Sum_probs=50.4
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++.. ++.|-......+.+.+++.|..+..... ..+.+.....+..+.+.+.+.+|+.........+++.+++.
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 456664 4567777888999999999988765432 12334455667777778889888865433334566666665
Q ss_pred C
Q 003633 135 Q 135 (806)
Q Consensus 135 g 135 (806)
|
T Consensus 79 ~ 79 (269)
T cd06281 79 D 79 (269)
T ss_pred C
Confidence 5
No 429
>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=41.35 E-value=1.6e+02 Score=26.14 Aligned_cols=62 Identities=10% Similarity=0.004 Sum_probs=39.6
Q ss_pred chHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc----hHHHHHHHHHHcCC
Q 003633 69 NGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD----PGLRIFTTAQKLQM 136 (806)
Q Consensus 69 ~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~----~~~~i~~~a~~~gm 136 (806)
-+..-+...|+..|.++.+--... .....+..+.+.++++|.+++... .+..++++.++.|.
T Consensus 14 lG~~~~~~~l~~~G~~vi~lG~~v------p~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~ 79 (122)
T cd02071 14 RGAKVIARALRDAGFEVIYTGLRQ------TPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELGA 79 (122)
T ss_pred HHHHHHHHHHHHCCCEEEECCCCC------CHHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcCC
Confidence 345666677889999988654332 223455666677899999887644 33445566666654
No 430
>COG1810 Uncharacterized protein conserved in archaea [Function unknown]
Probab=41.10 E-value=3e+02 Score=27.24 Aligned_cols=75 Identities=16% Similarity=0.170 Sum_probs=45.0
Q ss_pred EEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCC--ChhHHHHHHHhcCCCCCeEEEEec-CcchHHHHHHHHH
Q 003633 56 EVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQF--NQHDITVLLNNSKPLGPRVYVVHV-SPDPGLRIFTTAQ 132 (806)
Q Consensus 56 ~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~--~~~~~~~~l~~ik~~~~rvivl~~-~~~~~~~i~~~a~ 132 (806)
+++++| +..||....+.+.-. .....+.....+|... .-++-.+.|.++ ..+|++|.++ +++....+..+|.
T Consensus 3 ki~vlt-~g~yG~R~~~nl~~~--~f~~~~v~v~~~Pe~~~~fie~P~~~Lp~~--~e~Di~va~~lHPDl~~~L~e~~~ 77 (224)
T COG1810 3 KILVLT-DGEYGKRAVNNLACK--GFKNQFVAVKEYPEELPDFIEEPEDLLPKL--PEADIVVAYGLHPDLLLALPEKAA 77 (224)
T ss_pred EEEEEe-eccchHHHHHhHhhh--ccccceEEEEeccccccchhhCHHHhcCCC--CCCCEEEEeccCccHHHHHHHHHH
Confidence 678888 688998877776621 1123444444444211 112234556665 8999999985 5677677777775
Q ss_pred HcC
Q 003633 133 KLQ 135 (806)
Q Consensus 133 ~~g 135 (806)
+.|
T Consensus 78 ~~~ 80 (224)
T COG1810 78 EGG 80 (224)
T ss_pred hCC
Confidence 433
No 431
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=41.05 E-value=1.1e+02 Score=30.61 Aligned_cols=106 Identities=17% Similarity=0.173 Sum_probs=60.8
Q ss_pred CCCCChhHhhhCCCceeEEeCchh-HHHhh--hhcccccccceeCC-CHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhh
Q 003633 571 TSVKGIESLITNDWPIGYQVGSFA-YSYLS--DSLRIQKSRLISLG-SPEDYERALRQGPRNGGVAAIVDELPYVQLFLS 646 (806)
Q Consensus 571 ~~i~s~~dL~~~~~~ig~~~gs~~-~~~l~--~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~ 646 (806)
..|...+|| -|++|++..=|.. +..|. ++.+++...+..++ .+.+...+.++ |.+|+.....|.+.-+..
T Consensus 120 sgI~kpeDL--~GK~iavPFvSTtHysLLaaLkhw~idp~~V~IlNl~Pp~IaAAwqR----GDIDgAyVW~PAl~el~k 193 (334)
T COG4521 120 SGIEKPEDL--IGKRIAVPFVSTTHYSLLAALKHWGIDPGQVEILNLQPPAIAAAWQR----GDIDGAYVWAPALSELKK 193 (334)
T ss_pred CCcCChHHh--ccCeeccceeehhHHHHHHHHHHcCCCccceeEeccCCHHHHHHHHc----CCCCceeeccHhHHHHhh
Confidence 489999999 5888988765433 33221 34555544433332 45678888899 899987777777665443
Q ss_pred CCCCe----EEeCCccccCCceeeecCCC----C-chHHHHHHHHh
Q 003633 647 NQTDF----GIIGQPFTRSGWGFAFQRDS----P-LAVGMSTAILK 683 (806)
Q Consensus 647 ~~~~l----~~~~~~~~~~~~~~~~~k~s----p-l~~~~n~~il~ 683 (806)
. .+. .-+++.-....-+++.+|+. | ....|-+..+.
T Consensus 194 s-GkVltDs~qvgqwgaPTfdvwVvrkdfAekhPe~v~aFakv~~d 238 (334)
T COG4521 194 S-GKVLTDSEQVGQWGAPTFDVWVVRKDFAEKHPEVVAAFAKVALD 238 (334)
T ss_pred c-CcEeccHHHhhccCCCceeeEEeehHhhHhChHHHHHHHHHHHH
Confidence 3 221 12222222233356666653 4 55555555443
No 432
>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=41.02 E-value=1e+02 Score=33.10 Aligned_cols=95 Identities=8% Similarity=0.093 Sum_probs=61.5
Q ss_pred HHHHHHH-HcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 44 AMADLID-FYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 44 ai~~ll~-~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
-+.++++ ..+.+++.++. |........+.+.+.|++.| .+... +.+..+.+.+...+..+++.++|+||..+...
T Consensus 14 ~l~~~l~~~~~~~~~liv~-d~~~~~~~~~~v~~~l~~~~-~~~~~--~~~~~~~~~v~~~~~~~~~~~~d~iIaiGGGs 89 (339)
T cd08173 14 KIPNVLRDLLLGGRVLVVT-GPTTKSIAGKKVEALLEDEG-EVDVV--IVEDATYEEVEKVESSARDIGADFVIGVGGGR 89 (339)
T ss_pred HHHHHHHHhCCCCeEEEEE-CCchHHHHHHHHHHHHHhcC-CeEEE--EeCCCCHHHHHHHHHHhhhcCCCEEEEeCCch
Confidence 4556676 46789998888 44333456778888898888 44322 33345677888888889888999999777543
Q ss_pred --hHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 123 --PGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 123 --~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
+..+++. ...| -.++-|-|.
T Consensus 90 ~~D~aK~~a--~~~~---~p~i~iPTT 111 (339)
T cd08173 90 VIDVAKVAA--YKLG---IPFISVPTA 111 (339)
T ss_pred HHHHHHHHH--HhcC---CCEEEecCc
Confidence 4555544 2223 245555544
No 433
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=40.81 E-value=1e+02 Score=33.01 Aligned_cols=81 Identities=11% Similarity=0.036 Sum_probs=54.4
Q ss_pred CeEEEEEEEc--CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchH-HHHHHH
Q 003633 54 WKEVIAIYVD--DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPG-LRIFTT 130 (806)
Q Consensus 54 W~~v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~-~~i~~~ 130 (806)
=+.|+++..+ +.|.....+.+.+++++.|.++.+...-. ..+.+.....++.+.+.++|.||+....... ...+ +
T Consensus 46 t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~-~~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l-~ 123 (343)
T PRK10936 46 AWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGG-YYNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDL-E 123 (343)
T ss_pred CeEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCC-CCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHH-H
Confidence 4678888854 56777788899999999999887653221 1223344566777778889999887654333 2444 6
Q ss_pred HHHcCC
Q 003633 131 AQKLQM 136 (806)
Q Consensus 131 a~~~gm 136 (806)
+.+.|.
T Consensus 124 ~~~~gi 129 (343)
T PRK10936 124 LQAANI 129 (343)
T ss_pred HHHCCC
Confidence 666664
No 434
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=40.50 E-value=1.9e+02 Score=26.98 Aligned_cols=65 Identities=8% Similarity=0.028 Sum_probs=34.9
Q ss_pred eeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeC--CccccCCceeeecCCCCchHHHHHH
Q 003633 610 ISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIG--QPFTRSGWGFAFQRDSPLAVGMSTA 680 (806)
Q Consensus 610 ~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~k~spl~~~~n~~ 680 (806)
..+++.+...+.+.. |..-+++-+.. +..... ...+.... +......++++.+++.+....+...
T Consensus 124 ~~~~~~~~~~~~v~~----g~Gi~~~p~~~-~~~~~~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 190 (194)
T cd08481 124 MRFEQFSMLAQAAVA----GLGVALLPRFL-IEEELA-RGRLVVPFNLPLTSDKAYYLVYPEDKAESPPVQAF 190 (194)
T ss_pred eEeccHHHHHHHHHh----CCCeEEecHHH-HHHHHH-CCCEEeecCccccCCCeEEEEeCcccccCHHHHHH
Confidence 345677788888888 55555554433 332222 22333221 2223456788888877655544443
No 435
>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=40.24 E-value=88 Score=32.49 Aligned_cols=79 Identities=8% Similarity=0.099 Sum_probs=51.1
Q ss_pred EEEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHHH
Q 003633 56 EVIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTAQ 132 (806)
Q Consensus 56 ~v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a~ 132 (806)
||++|.. ++.|-......+.+++++.|..+.+.. +...+.......+..+...++|.||+...... ...++.++.
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 3566664 345666778889999999999876431 22223344456677776778998888654332 356678887
Q ss_pred HcCC
Q 003633 133 KLQM 136 (806)
Q Consensus 133 ~~gm 136 (806)
+.|.
T Consensus 79 ~~~i 82 (294)
T cd06316 79 EAGI 82 (294)
T ss_pred HcCC
Confidence 7764
No 436
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=40.09 E-value=1.4e+02 Score=31.75 Aligned_cols=79 Identities=11% Similarity=-0.008 Sum_probs=54.3
Q ss_pred eEEEEEEEc--CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHH
Q 003633 55 KEVIAIYVD--DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQ 132 (806)
Q Consensus 55 ~~v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~ 132 (806)
+.++++..+ +.|.......+.+++++.|..+.... ...+.+.....+..+.+.+.|.||+..........+..+.
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 467888753 56778888999999999998765432 1223345566777787888999998765433345666666
Q ss_pred HcCC
Q 003633 133 KLQM 136 (806)
Q Consensus 133 ~~gm 136 (806)
+.|.
T Consensus 142 ~~~i 145 (342)
T PRK10014 142 EKGI 145 (342)
T ss_pred hcCC
Confidence 6653
No 437
>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=39.92 E-value=1.3e+02 Score=28.02 Aligned_cols=64 Identities=19% Similarity=0.151 Sum_probs=43.1
Q ss_pred EEEEEEEcCCc--cc---chHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCC-CCCeEEEEecCc
Q 003633 56 EVIAIYVDDDY--GR---NGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKP-LGPRVYVVHVSP 121 (806)
Q Consensus 56 ~v~ii~~d~~~--g~---~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~-~~~rvivl~~~~ 121 (806)
++++|...|+- |+ .....+...|++.|.++.....++ .+.+++.+.+++..+ .++|+||..+..
T Consensus 2 ~~~ii~~~~e~~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~--Dd~~~i~~~l~~~~~~~~~DlVittGG~ 71 (152)
T cd00886 2 RAAVLTVSDTRSAGEAEDRSGPALVELLEEAGHEVVAYEIVP--DDKDEIREALIEWADEDGVDLILTTGGT 71 (152)
T ss_pred EEEEEEEcCcccCCCCccchHHHHHHHHHHcCCeeeeEEEcC--CCHHHHHHHHHHHHhcCCCCEEEECCCc
Confidence 56777766642 22 234568888999999988776666 345677777776543 378988886643
No 438
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=39.60 E-value=3.4e+02 Score=26.96 Aligned_cols=92 Identities=18% Similarity=0.144 Sum_probs=54.3
Q ss_pred CCCceeEEeCchhHHHhhhhcccccccceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeCCccccC
Q 003633 582 NDWPIGYQVGSFAYSYLSDSLRIQKSRLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIGQPFTRS 661 (806)
Q Consensus 582 ~~~~ig~~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~~~~~~~ 661 (806)
.+.+|+..-....+.|+.+ .+.+ ..++...-.-|.. +.-|-.|++++-.....-+..+ +|.++.+.+. .
T Consensus 114 ~~~rIATkYp~it~~yf~~-~gv~-~~iv~l~GsvE~a------P~~GlAD~IvDivsTG~TLr~N--gL~~ie~Il~-s 182 (215)
T PRK01686 114 PRLRVATKYPNIARRYFAE-KGEQ-VEIIKLYGSVELA------PLVGLADAIVDIVETGNTLRAN--GLVEVEEIMD-I 182 (215)
T ss_pred CCCEEEeCCHHHHHHHHHH-cCCe-EEEEECcCceeec------cccCCccEEEEeecChHHHHHC--cCEEeeEEEe-e
Confidence 5677888777788888854 3553 4555544333332 2227788998877666665555 4666655544 3
Q ss_pred CceeeecCCCC--chHHHHHHHHhh
Q 003633 662 GWGFAFQRDSP--LAVGMSTAILKL 684 (806)
Q Consensus 662 ~~~~~~~k~sp--l~~~~n~~il~l 684 (806)
.-.+...+.|. -.+.++..+.++
T Consensus 183 ~A~LI~n~~s~~~k~~~i~~l~~~l 207 (215)
T PRK01686 183 SARLIVNRASLKLKREEIRPLIEKL 207 (215)
T ss_pred EEEEEEecccchhhHHHHHHHHHHH
Confidence 44455566664 224555555555
No 439
>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=39.31 E-value=1.2e+02 Score=30.91 Aligned_cols=75 Identities=3% Similarity=-0.052 Sum_probs=49.9
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
++++.. +++|.......+.+.+++.|.++..... ..+.......+..+.+.+.|.+++....... ..+..+.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (270)
T cd06296 2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSES---GRRTSPERQWVERLSARRTDGVILVTPELTS-AQRAALRRT 77 (270)
T ss_pred eEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecC---CCchHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHhcC
Confidence 455553 4678888899999999999998765432 1223345566777777889988876543332 346666665
Q ss_pred C
Q 003633 135 Q 135 (806)
Q Consensus 135 g 135 (806)
|
T Consensus 78 ~ 78 (270)
T cd06296 78 G 78 (270)
T ss_pred C
Confidence 5
No 440
>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=39.24 E-value=1.1e+02 Score=31.89 Aligned_cols=78 Identities=10% Similarity=0.167 Sum_probs=51.8
Q ss_pred EEEEEEE--cCCcccchHHHHHHHHHh--CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc-chHHHHHHH
Q 003633 56 EVIAIYV--DDDYGRNGISALSNMLEK--NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP-DPGLRIFTT 130 (806)
Q Consensus 56 ~v~ii~~--d~~~g~~~~~~l~~~l~~--~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~-~~~~~i~~~ 130 (806)
+|++|.. ++.|-......+.+++++ .|.++... +...+.+.....+..+.+.+++.||+.... ......+++
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~---~~~~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~ 77 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFY---DAKNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINK 77 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEe---cCCCCHHHHHHHHHHHHHcCCCEEEEecCchhhHHHHHHH
Confidence 3566664 355667778899999999 78877643 222334445567777888899988876533 333567777
Q ss_pred HHHcCC
Q 003633 131 AQKLQM 136 (806)
Q Consensus 131 a~~~gm 136 (806)
+.+.|+
T Consensus 78 ~~~~gi 83 (303)
T cd01539 78 AKQKNI 83 (303)
T ss_pred HHHCCC
Confidence 777664
No 441
>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=38.84 E-value=2.6e+02 Score=29.24 Aligned_cols=41 Identities=15% Similarity=0.079 Sum_probs=30.2
Q ss_pred eHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEee
Q 003633 385 CIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGD 434 (806)
Q Consensus 385 ~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~ 434 (806)
.-.|++.+.+.+|+++++ .. .+-.-+...|.+|.+|+.+..
T Consensus 23 ~~~i~~~iLE~~Gy~Ve~--~~-------~~~~~~~~al~~GdiD~~~e~ 63 (290)
T TIGR03414 23 TTALASVLLEGLGYQPKV--TL-------LSVPVTYAGLKDGDLDVFLGN 63 (290)
T ss_pred HHHHHHHHHHHcCCccee--EE-------ccHHHHHHHHHcCCceEeccc
Confidence 346777788888998655 33 244677888999999998864
No 442
>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=38.61 E-value=1.1e+02 Score=31.20 Aligned_cols=77 Identities=6% Similarity=-0.065 Sum_probs=51.5
Q ss_pred EEEEEE---cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc-hHHHHHHHHH
Q 003633 57 VIAIYV---DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD-PGLRIFTTAQ 132 (806)
Q Consensus 57 v~ii~~---d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~-~~~~i~~~a~ 132 (806)
|++|.. ++.|.....+.+.+++++.|..+.... ...+.+.-...++.+...++|.+++..... .....+..+.
T Consensus 2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~---~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~l~~~~ 78 (275)
T cd06317 2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVLD---ANGDVARQAAQVEDLIAQKVDGIILWPTDGQAYIPGLRKAK 78 (275)
T ss_pred eEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEEc---CCcCHHHHHHHHHHHHHcCCCEEEEecCCccccHHHHHHHH
Confidence 455553 456888889999999999998877542 122334445566777777899988876433 2345667777
Q ss_pred HcCC
Q 003633 133 KLQM 136 (806)
Q Consensus 133 ~~gm 136 (806)
+.|.
T Consensus 79 ~~~i 82 (275)
T cd06317 79 QAGI 82 (275)
T ss_pred HCCC
Confidence 7664
No 443
>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=38.58 E-value=1.1e+02 Score=31.03 Aligned_cols=77 Identities=4% Similarity=-0.063 Sum_probs=50.8
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a~~ 133 (806)
+++|.. ++.|.......+.+++++.|..+... +...+.++....+.++.+.+++.+++...... ....+.++.+
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~---~~~~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~~~l~~l~~ 78 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKELGYELTVL---DAQNDAAKQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAANE 78 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHcCceEEec---CCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHH
Confidence 344553 46677888899999999999888643 22234445567777777788998887643322 2346666666
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|.
T Consensus 79 ~~i 81 (268)
T cd06323 79 AGI 81 (268)
T ss_pred CCC
Confidence 553
No 444
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=38.47 E-value=1.7e+02 Score=30.96 Aligned_cols=80 Identities=8% Similarity=-0.052 Sum_probs=51.7
Q ss_pred CeEEEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHH
Q 003633 54 WKEVIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTA 131 (806)
Q Consensus 54 W~~v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a 131 (806)
-+.|+++.. ++.|.......+.+++++.|..+..... ..+.+.-...+..+.+.+.|.+|+..........+.++
T Consensus 61 ~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 137 (328)
T PRK11303 61 TRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACS---DDQPDNEMRCAEHLLQRQVDALIVSTSLPPEHPFYQRL 137 (328)
T ss_pred CceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEcCCCCCChHHHHHH
Confidence 346788775 3567777888999999999998875432 12223334566667777899988865432223455666
Q ss_pred HHcCC
Q 003633 132 QKLQM 136 (806)
Q Consensus 132 ~~~gm 136 (806)
.+.|.
T Consensus 138 ~~~~i 142 (328)
T PRK11303 138 QNDGL 142 (328)
T ss_pred HhcCC
Confidence 66553
No 445
>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=38.41 E-value=1.2e+02 Score=30.81 Aligned_cols=76 Identities=11% Similarity=0.048 Sum_probs=49.3
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|++|.. ++.|-......+.+++++.|.++..... ..+.......+.++.+.++|.+++...... ...+..+.+.
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 455554 3556677788899999999988765321 223345567777887888998888765433 3445555555
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 78 ~i 79 (268)
T cd01575 78 GI 79 (268)
T ss_pred CC
Confidence 53
No 446
>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=38.26 E-value=1.4e+02 Score=30.76 Aligned_cols=79 Identities=14% Similarity=-0.029 Sum_probs=53.0
Q ss_pred eEEEEEEEc--CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHH
Q 003633 55 KEVIAIYVD--DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTA 131 (806)
Q Consensus 55 ~~v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a 131 (806)
|+|+++..+ +.|-...+..+.+++++.|.++..... ..+.+.....+..+.+.+.|.||+...... ....+..+
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 467777753 556677889999999999988765421 223444557778888889999988754322 23445666
Q ss_pred HHcCC
Q 003633 132 QKLQM 136 (806)
Q Consensus 132 ~~~gm 136 (806)
.+.|.
T Consensus 78 ~~~~i 82 (280)
T cd06315 78 QKAGI 82 (280)
T ss_pred HHCCC
Confidence 66554
No 447
>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=37.86 E-value=1.1e+02 Score=31.16 Aligned_cols=79 Identities=14% Similarity=0.074 Sum_probs=49.7
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc-hHHHHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD-PGLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~-~~~~i~~~a~~ 133 (806)
+++|.. ++.|.....+.+.+++++.|..+..... +...+...-...+.++...+.+.+|+..... .....+..+.+
T Consensus 2 igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~ 80 (275)
T cd06320 2 YGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAA-PSEGDQQGQLSIAENMINKGYKGLLFSPISDVNLVPAVERAKK 80 (275)
T ss_pred eeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEcc-CCCCCHHHHHHHHHHHHHhCCCEEEECCCChHHhHHHHHHHHH
Confidence 556654 4567778888999999999988765422 1112333344566777777889887765432 22345666666
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|.
T Consensus 81 ~~i 83 (275)
T cd06320 81 KGI 83 (275)
T ss_pred CCC
Confidence 664
No 448
>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=37.52 E-value=1e+02 Score=31.54 Aligned_cols=77 Identities=5% Similarity=-0.050 Sum_probs=50.4
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTAQK 133 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a~~ 133 (806)
+++|.. ++.|.......+.+.+++.|.++... ....+.+.-...++++.+.++|.+|+...... ....+..+.+
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 455553 46677788899999999999887643 21223333456677777788999887654332 3456677777
Q ss_pred cCC
Q 003633 134 LQM 136 (806)
Q Consensus 134 ~gm 136 (806)
.|.
T Consensus 79 ~~i 81 (277)
T cd06319 79 AKI 81 (277)
T ss_pred CCC
Confidence 663
No 449
>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=37.49 E-value=1.2e+02 Score=31.01 Aligned_cols=80 Identities=4% Similarity=-0.022 Sum_probs=50.7
Q ss_pred EEEEEEE--cCCcccchHHHHHHHHHhC---CcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHH
Q 003633 56 EVIAIYV--DDDYGRNGISALSNMLEKN---MAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFT 129 (806)
Q Consensus 56 ~v~ii~~--d~~~g~~~~~~l~~~l~~~---g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~ 129 (806)
||+++.. ++.|-......+.+++++. |.++.... .....+.+.....++++...++|.||+...... ....+.
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 3555553 4456677788888999888 87432221 222234455667788877789999998765433 344667
Q ss_pred HHHHcCC
Q 003633 130 TAQKLQM 136 (806)
Q Consensus 130 ~a~~~gm 136 (806)
.+.+.|.
T Consensus 80 ~~~~~~i 86 (272)
T cd06300 80 EACEAGI 86 (272)
T ss_pred HHHHCCC
Confidence 7777664
No 450
>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=37.32 E-value=3.5e+02 Score=27.20 Aligned_cols=62 Identities=5% Similarity=-0.081 Sum_probs=43.1
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
|+++.. ++.|.......+.+++++.|.++.... ...+.+.....+..+.+.++|.|++....
T Consensus 2 igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 65 (269)
T cd06275 2 IGMLVTTSTNPFFAEVVRGVEQYCYRQGYNLILCN---TEGDPERQRSYLRMLAQKRVDGLLVMCSE 65 (269)
T ss_pred EEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEEe---CCCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 455554 356778888999999999998876432 22234445566777878889988887644
No 451
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=37.25 E-value=2.2e+02 Score=26.53 Aligned_cols=81 Identities=11% Similarity=0.139 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC
Q 003633 41 QMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS 120 (806)
Q Consensus 41 q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~ 120 (806)
.+..+..++++++-+++.++- |..-.....+.+.+...-.|+++.... .++....+.+-+..+.++++++-+
T Consensus 13 HGQV~~~W~~~~~~~~IiVvd-D~~A~D~~~k~~lkma~P~gvk~~i~s-------ve~a~~~l~~~~~~~~~v~vl~k~ 84 (151)
T TIGR00854 13 HGQVGTTWTKVAGANRIIVVN-DDVANDEVRQTLMGIVAPTGFKVRFVS-------LEKTINVIHKPAYHDQTIFLLFRN 84 (151)
T ss_pred hhHhhhhhhcccCCCEEEEEc-ccccCCHHHHHHHHhhCCCCCEEEEEE-------HHHHHHHHhCcCCCCceEEEEECC
Confidence 356677789999999987665 333344455666666666788876432 345666676666677899999999
Q ss_pred cchHHHHHH
Q 003633 121 PDPGLRIFT 129 (806)
Q Consensus 121 ~~~~~~i~~ 129 (806)
+.++..+++
T Consensus 85 ~~da~~l~~ 93 (151)
T TIGR00854 85 PQDVLTLVE 93 (151)
T ss_pred HHHHHHHHH
Confidence 999988866
No 452
>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=37.11 E-value=1.1e+02 Score=32.03 Aligned_cols=77 Identities=5% Similarity=0.012 Sum_probs=49.4
Q ss_pred EEEEEE---cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCC--CCeEEEEecCcchHHHHHHHH
Q 003633 57 VIAIYV---DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPL--GPRVYVVHVSPDPGLRIFTTA 131 (806)
Q Consensus 57 v~ii~~---d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~--~~rvivl~~~~~~~~~i~~~a 131 (806)
|+++.. ++.|.......+++++++.|.++..... ..+.+.....+..+.+. ++|.||+.........+++.+
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~~---~~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~ 78 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLYA---ERDRFLMLQQARTILQRPDKPDALIFTNEKSVAPELLRLA 78 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHHHhccCCCEEEEcCCccchHHHHHHH
Confidence 455553 3557777788899999999988765421 22333344566677777 899988865433344566777
Q ss_pred HHcCC
Q 003633 132 QKLQM 136 (806)
Q Consensus 132 ~~~gm 136 (806)
.+.|+
T Consensus 79 ~~~gi 83 (305)
T cd06324 79 EGAGV 83 (305)
T ss_pred HhCCC
Confidence 76664
No 453
>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=36.78 E-value=4.2e+02 Score=26.70 Aligned_cols=62 Identities=3% Similarity=-0.143 Sum_probs=44.7
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
|+++.. ++.|.....+.+.+++++.|..+...... .+...-...+..+.+.++|.+|+....
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~gy~v~~~~~~---~~~~~~~~~i~~~~~~~~dgiii~~~~ 65 (269)
T cd06293 2 IGLVVPDIANPFFAELADAVEEEADARGLSLVLCATR---NRPERELTYLRWLDTNHVDGLIFVTNR 65 (269)
T ss_pred EEEEeCCCCCCcHHHHHHHHHHHHHHCCCEEEEEeCC---CCHHHHHHHHHHHHHCCCCEEEEeCCC
Confidence 566664 35677888999999999999988654322 233445566777888899999987643
No 454
>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=36.61 E-value=1.4e+02 Score=26.94 Aligned_cols=61 Identities=21% Similarity=0.231 Sum_probs=40.5
Q ss_pred EEEEEEcCCc--c---cchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC
Q 003633 57 VIAIYVDDDY--G---RNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS 120 (806)
Q Consensus 57 v~ii~~d~~~--g---~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~ 120 (806)
+++|...|+- | ......+.+.+++.|.++.+...++ .+.+.+.+.+.+..+. +|+|+..+.
T Consensus 2 v~ii~~G~El~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~--Dd~~~i~~~i~~~~~~-~DlvittGG 67 (133)
T cd00758 2 VAIVTVSDELSQGQIEDTNGPALEALLEDLGCEVIYAGVVP--DDADSIRAALIEASRE-ADLVLTTGG 67 (133)
T ss_pred EEEEEeCccccCCceEEchHHHHHHHHHHCCCEEEEeeecC--CCHHHHHHHHHHHHhc-CCEEEECCC
Confidence 4555544432 2 2335677888999999988766665 3456777877776544 899888764
No 455
>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=36.55 E-value=1.6e+02 Score=29.89 Aligned_cols=76 Identities=5% Similarity=-0.061 Sum_probs=50.6
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
+++|.. ++.|.......+.+++++.|.++..... ..+.+.-...+..+.+.++|.||+....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~~~ 77 (268)
T cd06270 2 IGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITAG---HHSAEKEREAIEFLLERRCDALILHSKALSD-DELIELAAQ 77 (268)
T ss_pred EEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEeC---CCchHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhC
Confidence 344442 5678888899999999999998775322 1233344567777778899999887653332 236777766
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 78 ~i 79 (268)
T cd06270 78 VP 79 (268)
T ss_pred CC
Confidence 63
No 456
>PRK00843 egsA NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed
Probab=36.53 E-value=1.4e+02 Score=32.15 Aligned_cols=96 Identities=7% Similarity=0.023 Sum_probs=62.0
Q ss_pred HHHHHHHHHcCC-eEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 43 AAMADLIDFYGW-KEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 43 ~ai~~ll~~~~W-~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
..+.++++.++. +++.+|.....+. ...+.+.+.|++.| .+... +.+..+.+.+...+..+++.++|+||..+..
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 456677787876 7888887544432 34567888888877 44322 3445667788888899988889999877764
Q ss_pred c--hHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 122 D--PGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 122 ~--~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
. +...++. ...| -.++-|-|.
T Consensus 98 sv~D~ak~vA--~~rg---ip~I~IPTT 120 (350)
T PRK00843 98 KVIDVAKLAA--YRLG---IPFISVPTA 120 (350)
T ss_pred hHHHHHHHHH--HhcC---CCEEEeCCC
Confidence 3 4455543 2233 345555554
No 457
>cd00001 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate.
Probab=36.46 E-value=2.2e+02 Score=26.46 Aligned_cols=82 Identities=13% Similarity=0.108 Sum_probs=57.5
Q ss_pred HHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC
Q 003633 41 QMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS 120 (806)
Q Consensus 41 q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~ 120 (806)
.+..+..++++++-+++.++- |..-.....+.+.+...-.|+++... +.++....+.+-+..+-++++++-+
T Consensus 12 HGQV~~~W~~~~~~~~IvVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~-------sve~a~~~l~~~~~~~~~v~il~k~ 83 (151)
T cd00001 12 HGQVATTWTKELNANRIIVVN-DEVANDELRKTLLKLAAPPGVKLRIF-------TVEKAIEAINSPKYDKQRVFLLFKN 83 (151)
T ss_pred hhHhhhhhhcccCCCEEEEEc-ccccCCHHHHHHHHhhCCCCCeEEEE-------EHHHHHHHHhCcCCCCceEEEEECC
Confidence 466777889999999987664 33334445555665555678877643 2345666677666677899999999
Q ss_pred cchHHHHHHH
Q 003633 121 PDPGLRIFTT 130 (806)
Q Consensus 121 ~~~~~~i~~~ 130 (806)
+.++..+++.
T Consensus 84 ~~~~~~l~~~ 93 (151)
T cd00001 84 PQDVLRLVEG 93 (151)
T ss_pred HHHHHHHHHc
Confidence 9999888663
No 458
>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=36.15 E-value=3.1e+02 Score=24.37 Aligned_cols=25 Identities=24% Similarity=0.215 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003633 39 SQQMAAMADLIDFYGWKEVIAIYVDD 64 (806)
Q Consensus 39 ~~q~~ai~~ll~~~~W~~v~ii~~d~ 64 (806)
..|-+.+-++....||.-+. +|.|.
T Consensus 17 ~~Q~~~~~~~a~~~g~~i~~-~~~d~ 41 (137)
T cd00338 17 ERQREALREYAARNGLEVVG-EYEDA 41 (137)
T ss_pred HHHHHHHHHHHHHCCCEEEE-EEEeC
Confidence 46677777777777887554 44444
No 459
>PRK09756 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=35.85 E-value=2.1e+02 Score=26.80 Aligned_cols=81 Identities=5% Similarity=0.041 Sum_probs=55.5
Q ss_pred HHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHH-hCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEec
Q 003633 41 QMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLE-KNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHV 119 (806)
Q Consensus 41 q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~-~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~ 119 (806)
.+..+..++++++-+++.++- |..-.....+.+.+... -.|+++... +.++....+.+ +..+-++++++-
T Consensus 17 HGQV~~~W~~~~~~~~IiVvd-D~vA~D~~~k~~lkma~~P~gvk~~i~-------sv~~a~~~l~~-~~~~~~vlvl~~ 87 (158)
T PRK09756 17 HGQVGVTWTSTIGANLLVVVD-DVVANDDIQQKLMGITAETYGFGIRFF-------TIEKTINVIGK-AAPHQKIFLICR 87 (158)
T ss_pred hHHHHHhhhcccCCCEEEEEc-chhcCCHHHHHHHHhcCCCCCCEEEEE-------EHHHHHHHHHh-ccCCceEEEEEC
Confidence 467777889999999987664 33333344555555444 467777643 23456666777 666779999999
Q ss_pred CcchHHHHHHH
Q 003633 120 SPDPGLRIFTT 130 (806)
Q Consensus 120 ~~~~~~~i~~~ 130 (806)
++.++..++++
T Consensus 88 ~~~da~~l~~~ 98 (158)
T PRK09756 88 TPQTVRKLVEG 98 (158)
T ss_pred CHHHHHHHHHc
Confidence 99999888763
No 460
>PRK09701 D-allose transporter subunit; Provisional
Probab=35.59 E-value=1.5e+02 Score=31.16 Aligned_cols=85 Identities=7% Similarity=-0.048 Sum_probs=56.9
Q ss_pred HcCCeEEEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHH
Q 003633 51 FYGWKEVIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRI 127 (806)
Q Consensus 51 ~~~W~~v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i 127 (806)
.+--.+|+++.. ++.|.......+.+++++.|.++..... +...+.+.-...+..+.+.++|.||+...... ....
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 355668999985 4668888899999999999998865321 21122334456677777788999988765432 2344
Q ss_pred HHHHHHcCC
Q 003633 128 FTTAQKLQM 136 (806)
Q Consensus 128 ~~~a~~~gm 136 (806)
+.++.+.|+
T Consensus 100 l~~~~~~gi 108 (311)
T PRK09701 100 VARAWKKGI 108 (311)
T ss_pred HHHHHHCCC
Confidence 566666664
No 461
>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=35.45 E-value=2.4e+02 Score=30.31 Aligned_cols=101 Identities=7% Similarity=-0.100 Sum_probs=60.1
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHh-CCcEEEEEeccCCCCChhHHHHHHHhcCC---CCCeEEEEe
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEK-NMAKVSYKLPLPVQFNQHDITVLLNNSKP---LGPRVYVVH 118 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~-~g~~i~~~~~~~~~~~~~~~~~~l~~ik~---~~~rvivl~ 118 (806)
+.+.++++.++-+++.++.+..- .....+.+.+.|++ .++.+.......+..+.+.+...+..+++ .+.|+||..
T Consensus 12 ~~l~~~~~~~~~~k~livtd~~v-~~~~~~~v~~~L~~~~~~~~~~~~~~e~~k~~~~v~~~~~~~~~~~~~r~d~IIai 90 (344)
T cd08169 12 ESVESYTTRDLFDQYFFISDSGV-ADLIAHYIAEYLSKILPVHILVIEGGEEYKTFETVTRILERAIALGANRRTAIVAV 90 (344)
T ss_pred HHHHHHHHhcCCCeEEEEECccH-HHHHHHHHHHHHHhhcCceEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEEE
Confidence 34556777778889888874333 33566778888877 67665432233333455667776666664 458888877
Q ss_pred cCcc--hHHHHHHHHHHcCCccCCcEEEEcC
Q 003633 119 VSPD--PGLRIFTTAQKLQMMTNNYVWLATD 147 (806)
Q Consensus 119 ~~~~--~~~~i~~~a~~~gm~~~~~~wi~t~ 147 (806)
+... +...++......| ..++-|-|.
T Consensus 91 GGGsv~D~ak~vA~~~~rg---ip~i~VPTT 118 (344)
T cd08169 91 GGGATGDVAGFVASTLFRG---IAFIRVPTT 118 (344)
T ss_pred CCcHHHHHHHHHHHHhccC---CcEEEecCC
Confidence 7543 5555554443333 245555554
No 462
>PF13155 Toprim_2: Toprim-like
Probab=35.19 E-value=52 Score=27.56 Aligned_cols=41 Identities=15% Similarity=0.288 Sum_probs=34.7
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCC
Q 003633 42 MAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNM 82 (806)
Q Consensus 42 ~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g 82 (806)
...+.++++..+-++|.+..++|.-|+...+.+.+.+.+.+
T Consensus 35 ~~~~~~~l~~~~~~~i~l~~DnD~aG~~~~~~~~~~l~~~~ 75 (96)
T PF13155_consen 35 EKQQIKFLKENPYKKIVLAFDNDEAGRKAAEKLQKELKEEG 75 (96)
T ss_pred HHHHHHHHHhCCCCcEEEEeCCCHHHHHHHHHHHHHHHhhC
Confidence 45778888766668888888888899999999999999877
No 463
>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=35.09 E-value=1.3e+02 Score=30.22 Aligned_cols=75 Identities=11% Similarity=-0.045 Sum_probs=49.8
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++.. ++.|.....+.+.+++++.|.++..... ..+.+.....++++.+.++|.+|+...... ..++..+.+.
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 455554 3456677889999999999998865422 223445556777787889999998765432 3455666555
Q ss_pred C
Q 003633 135 Q 135 (806)
Q Consensus 135 g 135 (806)
|
T Consensus 78 ~ 78 (259)
T cd01542 78 N 78 (259)
T ss_pred C
Confidence 5
No 464
>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=34.92 E-value=5.2e+02 Score=26.57 Aligned_cols=64 Identities=16% Similarity=0.050 Sum_probs=40.5
Q ss_pred HHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEecc
Q 003633 387 DILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPIN 463 (806)
Q Consensus 387 dl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~~ 463 (806)
.++..+.+.. .+++.+.. ++-..+++.|.+|++|+++..... ....+. +.|+.+..+++++++.
T Consensus 107 ~~l~~~~~~~--~i~i~l~~-------~~~~~~~~~l~~g~~d~~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~~ 170 (292)
T TIGR03298 107 PALAPVLAQE--GVLLDLVV-------EDQDHTAELLRSGEVLGAVTTQAK---PVQGCR-VVPLGAMRYLAVASPA 170 (292)
T ss_pred HHHHHHHhCC--CceEEEEe-------CcchhHHHHHhCCCceEEEecCCC---CCCCce-EEecCCceEEEEECch
Confidence 4555666653 44566654 244678899999999999864221 122333 4677788888887654
No 465
>PF08659 KR: KR domain; InterPro: IPR013968 This domain is found in bacterial polyketide synthases that catalyse the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group. ; PDB: 3QP9_D 2FR0_A 2FR1_A 2Z5L_A 3SLK_B 3MJE_B 3MJC_A 3MJT_B 3MJV_A 3MJS_B ....
Probab=34.80 E-value=3.3e+02 Score=25.96 Aligned_cols=79 Identities=15% Similarity=0.064 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeE-EEE
Q 003633 39 SQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRV-YVV 117 (806)
Q Consensus 39 ~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rv-ivl 117 (806)
.-.+..+++.+..-+.++++++... .-.......+.+.+++.|.+|.+...-. .+.++....+.++++..+++ -|+
T Consensus 10 gglg~~la~~La~~~~~~~il~~r~-~~~~~~~~~~i~~l~~~g~~v~~~~~Dv--~d~~~v~~~~~~~~~~~~~i~gVi 86 (181)
T PF08659_consen 10 GGLGQSLARWLAERGARRLILLGRS-GAPSAEAEAAIRELESAGARVEYVQCDV--TDPEAVAAALAQLRQRFGPIDGVI 86 (181)
T ss_dssp SHHHHHHHHHHHHTT-SEEEEEESS-GGGSTTHHHHHHHHHHTT-EEEEEE--T--TSHHHHHHHHHTSHTTSS-EEEEE
T ss_pred cHHHHHHHHHHHHcCCCEEEEeccC-CCccHHHHHHHHHHHhCCCceeeeccCc--cCHHHHHHHHHHHHhccCCcceee
Confidence 3457788888877778888877754 2334455677888888899888765433 45677888888887765555 355
Q ss_pred ecC
Q 003633 118 HVS 120 (806)
Q Consensus 118 ~~~ 120 (806)
|+.
T Consensus 87 h~a 89 (181)
T PF08659_consen 87 HAA 89 (181)
T ss_dssp E--
T ss_pred eee
Confidence 554
No 466
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=34.56 E-value=1.9e+02 Score=30.02 Aligned_cols=80 Identities=6% Similarity=-0.019 Sum_probs=53.4
Q ss_pred CeEEEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHH
Q 003633 54 WKEVIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTT 130 (806)
Q Consensus 54 W~~v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~ 130 (806)
-+.++++.. ++.|-...+..+.+++++.|+++..... ..+.+.....++++...+++.+++...... ....+..
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 567888875 3557778889999999999998765321 223344456677777778898877654332 2356677
Q ss_pred HHHcCC
Q 003633 131 AQKLQM 136 (806)
Q Consensus 131 a~~~gm 136 (806)
+++.|.
T Consensus 103 ~~~~~i 108 (295)
T PRK10653 103 ANQANI 108 (295)
T ss_pred HHHCCC
Confidence 776664
No 467
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=34.43 E-value=40 Score=30.47 Aligned_cols=29 Identities=14% Similarity=0.196 Sum_probs=18.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 003633 722 WGLYLLCGTITFTAFLVFLLRMVCQYVRY 750 (806)
Q Consensus 722 ~g~F~il~~g~~lal~vf~~E~~~~~~~~ 750 (806)
|.+|.|+.+++++.|+++++.--+++++-
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~rRR~r~G 30 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNRRRRRRG 30 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 44566666666666666666667777663
No 468
>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=34.20 E-value=61 Score=28.84 Aligned_cols=28 Identities=11% Similarity=0.179 Sum_probs=14.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 003633 723 GLYLLCGTITFTAFLVFLLRMVCQYVRY 750 (806)
Q Consensus 723 g~F~il~~g~~lal~vf~~E~~~~~~~~ 750 (806)
-..+|+|+.+++.++++++-++.+|+|+
T Consensus 66 i~~Ii~gv~aGvIg~Illi~y~irR~~K 93 (122)
T PF01102_consen 66 IIGIIFGVMAGVIGIILLISYCIRRLRK 93 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHS-
T ss_pred eeehhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3455666666655555555544444443
No 469
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=34.04 E-value=1.5e+02 Score=29.89 Aligned_cols=75 Identities=11% Similarity=0.055 Sum_probs=49.5
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++.. ++.|-....+.+.+.+++.|.++.+... ..+. +....+.++.+.++|.+++...... ...++.+.+.
T Consensus 2 I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~-~~~~~i~~~~~~~vdgiii~~~~~~-~~~~~~~~~~ 76 (266)
T cd06278 2 IGVVVADLDNPFYSELLEALSRALQARGYQPLLINT---DDDE-DLDAALRQLLQYRVDGVIVTSGTLS-SELAEECRRN 76 (266)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcC---CCCH-HHHHHHHHHHHcCCCEEEEecCCCC-HHHHHHHhhc
Confidence 345553 4567788888999999999998765432 1222 5566677777788998887654332 2446777766
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 77 ~i 78 (266)
T cd06278 77 GI 78 (266)
T ss_pred CC
Confidence 64
No 470
>PLN02727 NAD kinase
Probab=34.00 E-value=4.5e+02 Score=32.14 Aligned_cols=108 Identities=8% Similarity=0.020 Sum_probs=68.7
Q ss_pred CCcccCCCCceEEecCCcHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEec-cCCCCChhH
Q 003633 21 PTLSALQFPYFIRSTQSDSQQMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLP-LPVQFNQHD 99 (806)
Q Consensus 21 p~Ls~~~~p~f~Rt~psd~~q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~-~~~~~~~~~ 99 (806)
+.+++..---|+|..+.+..+.+.+++ .|.|.|+-+-.|++-+.......+++.++.|++..+.-. .....+.++
T Consensus 253 ~~~~~~~~~~~~rsgQpspe~la~LA~----~GfKTIINLRpd~E~~q~~~~ee~eAae~~GL~yVhIPVs~~~apt~Eq 328 (986)
T PLN02727 253 DIDSKESEAAFWRGGQVTEEGLKWLLE----KGFKTIVDLRAEIVKDNFYQAAVDDAISSGKIEVVKIPVEVRTAPSAEQ 328 (986)
T ss_pred ccccccceeeEEEeCCCCHHHHHHHHH----CCCeEEEECCCCCcCCCchhHHHHHHHHHcCCeEEEeecCCCCCCCHHH
Confidence 455543223567777777765544333 699999988877764455567788999999999876532 222245677
Q ss_pred HHHHHHhcCCCCCeEEEEecCcch-HHHHHHHHH
Q 003633 100 ITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTAQ 132 (806)
Q Consensus 100 ~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a~ 132 (806)
+......+++.-++-|++||-... ...++-+.+
T Consensus 329 Ve~fa~~l~~slpkPVLvHCKSGarRAGamvA~y 362 (986)
T PLN02727 329 VEKFASLVSDSSKKPIYLHSKEGVWRTSAMVSRW 362 (986)
T ss_pred HHHHHHHHHhhcCCCEEEECCCCCchHHHHHHHH
Confidence 777777775555677888886543 444444333
No 471
>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=33.87 E-value=1.7e+02 Score=29.49 Aligned_cols=76 Identities=9% Similarity=-0.036 Sum_probs=49.8
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|+++.. ++.|-......+.+.+++.|.++..... ..+.+.....+..+...+.|.+++......... ++++.+.
T Consensus 2 igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~-~~~~~~~ 77 (264)
T cd06274 2 IGLIIPDLENRSFARIAKRLEALARERGYQLLIACS---DDDPETERETVETLIARQVDALIVAGSLPPDDP-YYLCQKA 77 (264)
T ss_pred EEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEcCCCCchHH-HHHHHhc
Confidence 345553 4567777888999999999998775432 123344456777788889999888765433322 5566665
Q ss_pred CC
Q 003633 135 QM 136 (806)
Q Consensus 135 gm 136 (806)
|.
T Consensus 78 ~i 79 (264)
T cd06274 78 GL 79 (264)
T ss_pred CC
Confidence 63
No 472
>PLN02428 lipoic acid synthase
Probab=33.73 E-value=3e+02 Score=29.61 Aligned_cols=100 Identities=17% Similarity=0.218 Sum_probs=58.1
Q ss_pred CCcHHHHHHHHHHHHHcCCeEEEEEEEc----CCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCC
Q 003633 36 QSDSQQMAAMADLIDFYGWKEVIAIYVD----DDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLG 111 (806)
Q Consensus 36 psd~~q~~ai~~ll~~~~W~~v~ii~~d----~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~ 111 (806)
+.|......+++.+...|.++|+++..| .|.|......+.+.+++....+......|.... + ...|..|++++
T Consensus 129 ~~d~~Ep~~vA~~v~~~Glk~vvltSg~rddl~D~ga~~~~elir~Ir~~~P~i~Ie~L~pdf~~--d-~elL~~L~eAG 205 (349)
T PLN02428 129 PPDPDEPENVAEAIASWGVDYVVLTSVDRDDLPDGGSGHFAETVRRLKQLKPEILVEALVPDFRG--D-LGAVETVATSG 205 (349)
T ss_pred CCChhhHHHHHHHHHHcCCCEEEEEEcCCCCCCcccHHHHHHHHHHHHHhCCCcEEEEeCccccC--C-HHHHHHHHHcC
Confidence 4444445567777888999998887764 255665666666777765432322222221111 1 45788888888
Q ss_pred CeEEEEecC---------------cchHHHHHHHHHHc--CCcc
Q 003633 112 PRVYVVHVS---------------PDPGLRIFTTAQKL--QMMT 138 (806)
Q Consensus 112 ~rvivl~~~---------------~~~~~~i~~~a~~~--gm~~ 138 (806)
++++-.... .+....+++.|++. |+..
T Consensus 206 ~d~i~hnlETv~rL~~~Ir~~~~sye~~Le~L~~ak~~~pGi~t 249 (349)
T PLN02428 206 LDVFAHNIETVERLQRIVRDPRAGYKQSLDVLKHAKESKPGLLT 249 (349)
T ss_pred CCEEccCccCcHHHHHHhcCCCCCHHHHHHHHHHHHHhCCCCeE
Confidence 887543222 23345566777777 6543
No 473
>PRK10481 hypothetical protein; Provisional
Probab=33.50 E-value=2.8e+02 Score=27.75 Aligned_cols=75 Identities=12% Similarity=0.065 Sum_probs=48.5
Q ss_pred HHHHHHc-CCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchH
Q 003633 46 ADLIDFY-GWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPG 124 (806)
Q Consensus 46 ~~ll~~~-~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~ 124 (806)
..++..+ +-++++++....+ ..+.-.+.+.+.|..+.+...-|...+.........+++..++|+||+.|..-..
T Consensus 120 ~~lv~Al~~g~riGVitP~~~----qi~~~~~kw~~~G~~v~~~~aspy~~~~~~l~~aa~~L~~~gaD~Ivl~C~G~~~ 195 (224)
T PRK10481 120 PPLVAAIVGGHQVGVIVPVEE----QLAQQAQKWQVLQKPPVFALASPYHGSEEELIDAGKELLDQGADVIVLDCLGYHQ 195 (224)
T ss_pred HHHHHHhcCCCeEEEEEeCHH----HHHHHHHHHHhcCCceeEeecCCCCCCHHHHHHHHHHhhcCCCCEEEEeCCCcCH
Confidence 3444332 3489999997544 3334445555558887765544433444567777888888999999998875543
No 474
>PRK11425 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=33.13 E-value=2.6e+02 Score=26.19 Aligned_cols=80 Identities=13% Similarity=0.094 Sum_probs=55.4
Q ss_pred HHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC
Q 003633 41 QMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS 120 (806)
Q Consensus 41 q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~ 120 (806)
.+..+..++++++-+++.++- |..-.....+.+.....-.|+++.... .++....+.+ ...+-++++++-+
T Consensus 15 HGQV~~~W~~~~~~~~IvVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~s-------v~~a~~~l~~-~~~~~~v~il~k~ 85 (157)
T PRK11425 15 HGQVGVQWVGFAGANLVLVAN-DEVAEDPVQQNLMEMVLAEGIAVRFWT-------LQKVIDNIHR-AADRQKILLVCKT 85 (157)
T ss_pred hHHhhhhhhcccCCCEEEEEc-chhcCCHHHHHHHHhhCCCCCeEEEEE-------HHHHHHHHhc-cCCCceEEEEECC
Confidence 466777889999999876554 333334455555555555788776432 3466677777 6667789999999
Q ss_pred cchHHHHHH
Q 003633 121 PDPGLRIFT 129 (806)
Q Consensus 121 ~~~~~~i~~ 129 (806)
+.++..+++
T Consensus 86 ~~d~~~l~~ 94 (157)
T PRK11425 86 PADFLTLVK 94 (157)
T ss_pred HHHHHHHHH
Confidence 999888866
No 475
>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=32.84 E-value=2.7e+02 Score=23.42 Aligned_cols=76 Identities=20% Similarity=0.233 Sum_probs=0.0
Q ss_pred EEEEEcCCcccchHHHHHHHHHhCCc-EEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEe--cCcchHHHHHHHHHHc
Q 003633 58 IAIYVDDDYGRNGISALSNMLEKNMA-KVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVH--VSPDPGLRIFTTAQKL 134 (806)
Q Consensus 58 ~ii~~d~~~g~~~~~~l~~~l~~~g~-~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~--~~~~~~~~i~~~a~~~ 134 (806)
++|.+|+. .....+.+.++..|. .+.... +....+..++...++++++. .....+..++++.++.
T Consensus 1 Ilivd~~~---~~~~~l~~~l~~~~~~~v~~~~---------~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~ 68 (112)
T PF00072_consen 1 ILIVDDDP---EIRELLEKLLERAGYEEVTTAS---------SGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIRQI 68 (112)
T ss_dssp EEEEESSH---HHHHHHHHHHHHTTEEEEEEES---------SHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHHHH
T ss_pred cEEEECCH---HHHHHHHHHHHhCCCCEEEEEC---------CHHHHHHHhcccCceEEEEEeeeccccccccccccccc
Q ss_pred CCccCCcEEEEcC
Q 003633 135 QMMTNNYVWLATD 147 (806)
Q Consensus 135 gm~~~~~~wi~t~ 147 (806)
+ ...-+.+.++
T Consensus 69 ~--~~~~ii~~t~ 79 (112)
T PF00072_consen 69 N--PSIPIIVVTD 79 (112)
T ss_dssp T--TTSEEEEEES
T ss_pred c--ccccEEEecC
No 476
>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=32.83 E-value=94 Score=31.74 Aligned_cols=71 Identities=10% Similarity=0.104 Sum_probs=50.1
Q ss_pred cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHHHHcCC
Q 003633 63 DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTAQKLQM 136 (806)
Q Consensus 63 d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a~~~gm 136 (806)
++.|-....+.+.+++++.|.++.+... ..+.+.....++.+...++|.+|+...... ....++++.+.|.
T Consensus 10 ~~~~~~~~~~~~~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~i~~~~~~~i 81 (273)
T cd06309 10 ESPWRTAETKSIKDAAEKRGFDLKFADA---QQKQENQISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAAGI 81 (273)
T ss_pred CCHHHHHHHHHHHHHHHhcCCEEEEeCC---CCCHHHHHHHHHHHHHcCCCEEEEcCCccccchHHHHHHHHCCC
Confidence 5677788899999999999999886421 223444556777787788999888654333 2456777777664
No 477
>PF00218 IGPS: Indole-3-glycerol phosphate synthase; InterPro: IPR013798 Indole-3-glycerol phosphate synthase (4.1.1.48 from EC) (IGPS) catalyses the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyses N-(5'-phosphoribosyl)anthranilate isomerase (5.3.1.24 from EC) (PRAI) activity (see IPR001240 from INTERPRO), the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (2.4.2 from EC) (GATase) N-terminal domain (see IPR000991 from INTERPRO). A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium E. coli (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand []. ; GO: 0004425 indole-3-glycerol-phosphate synthase activity; PDB: 1VC4_A 1PII_A 1JCM_P 1I4N_B 1J5T_A 3TSM_B 4FB7_A 3QJA_A 1JUL_A 2C3Z_A ....
Probab=32.69 E-value=1.6e+02 Score=30.10 Aligned_cols=89 Identities=11% Similarity=0.083 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC
Q 003633 41 QMAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS 120 (806)
Q Consensus 41 q~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~ 120 (806)
....++.-....|-.-+.++. |..|..+..+.|...-+..++.|-.+..+- + .-++.+.+..++|+|++...
T Consensus 69 d~~~~a~~y~~~GA~aiSVlT-e~~~F~Gs~~dL~~v~~~~~~PvL~KDFIi---d----~~QI~eA~~~GADaVLLI~~ 140 (254)
T PF00218_consen 69 DPAEIAKAYEEAGAAAISVLT-EPKFFGGSLEDLRAVRKAVDLPVLRKDFII---D----PYQIYEARAAGADAVLLIAA 140 (254)
T ss_dssp SHHHHHHHHHHTT-SEEEEE---SCCCHHHHHHHHHHHHHSSS-EEEES------S----HHHHHHHHHTT-SEEEEEGG
T ss_pred CHHHHHHHHHhcCCCEEEEEC-CCCCCCCCHHHHHHHHHHhCCCcccccCCC---C----HHHHHHHHHcCCCEeehhHH
Confidence 346677777788989888888 667777888888887777777766544332 1 12455566789999988775
Q ss_pred c---chHHHHHHHHHHcCCc
Q 003633 121 P---DPGLRIFTTAQKLQMM 137 (806)
Q Consensus 121 ~---~~~~~i~~~a~~~gm~ 137 (806)
. .....++..|.++||.
T Consensus 141 ~L~~~~l~~l~~~a~~lGle 160 (254)
T PF00218_consen 141 ILSDDQLEELLELAHSLGLE 160 (254)
T ss_dssp GSGHHHHHHHHHHHHHTT-E
T ss_pred hCCHHHHHHHHHHHHHcCCC
Confidence 2 3446789999999985
No 478
>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=32.66 E-value=1.8e+02 Score=26.60 Aligned_cols=48 Identities=19% Similarity=0.135 Sum_probs=35.7
Q ss_pred HHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 71 ISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 71 ~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
...+...|++.|+++.....++ .+.+++.+.+.+..+ +.|+||..+..
T Consensus 29 ~~~l~~~l~~~G~~v~~~~~v~--Dd~~~i~~~l~~~~~-~~DliIttGG~ 76 (144)
T TIGR00177 29 GPLLAALLEEAGFNVSRLGIVP--DDPEEIREILRKAVD-EADVVLTTGGT 76 (144)
T ss_pred HHHHHHHHHHCCCeEEEEeecC--CCHHHHHHHHHHHHh-CCCEEEECCCC
Confidence 5678888999999988776665 345677777777643 78999987643
No 479
>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=32.45 E-value=1.3e+02 Score=31.43 Aligned_cols=72 Identities=14% Similarity=-0.017 Sum_probs=51.2
Q ss_pred EcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc-hHHHHHHHHHHcCC
Q 003633 62 VDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD-PGLRIFTTAQKLQM 136 (806)
Q Consensus 62 ~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~-~~~~i~~~a~~~gm 136 (806)
.+++|.....+.+.+++++.|.++.... ...+.......+..+.+.++|.|++..... .....++.+.+.|+
T Consensus 8 ~~~~~~~~~~~~i~~~a~~~g~~v~~~~---~~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~~~i 80 (302)
T TIGR02634 8 LRLERWQKDRDIFVAAAESLGAKVFVQS---ANGNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKDEGI 80 (302)
T ss_pred cchhhHHHHHHHHHHHHHhcCCEEEEEe---CCCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHHCCC
Confidence 3677888889999999999999886542 223344455677788888999988876433 34567777777664
No 480
>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....
Probab=32.42 E-value=4e+02 Score=24.78 Aligned_cols=71 Identities=10% Similarity=0.015 Sum_probs=44.4
Q ss_pred EEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHH
Q 003633 56 EVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIF 128 (806)
Q Consensus 56 ~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~ 128 (806)
+|+||.- +.--....+...+.|++.|+....+ ......+.+.+...++++...+.+|||..+..+.+..=+
T Consensus 2 ~V~Ii~g-s~SD~~~~~~a~~~L~~~gi~~~~~-V~saHR~p~~l~~~~~~~~~~~~~viIa~AG~~a~Lpgv 72 (150)
T PF00731_consen 2 KVAIIMG-STSDLPIAEEAAKTLEEFGIPYEVR-VASAHRTPERLLEFVKEYEARGADVIIAVAGMSAALPGV 72 (150)
T ss_dssp EEEEEES-SGGGHHHHHHHHHHHHHTT-EEEEE-E--TTTSHHHHHHHHHHTTTTTESEEEEEEESS--HHHH
T ss_pred eEEEEeC-CHHHHHHHHHHHHHHHHcCCCEEEE-EEeccCCHHHHHHHHHHhccCCCEEEEEECCCcccchhh
Confidence 4666662 2223456788888899988665543 234345667788888888888888888877665444333
No 481
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=32.39 E-value=1.1e+02 Score=31.13 Aligned_cols=89 Identities=17% Similarity=0.082 Sum_probs=45.4
Q ss_pred CCcHHHHHHHHHH--HHHc---CCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCC
Q 003633 36 QSDSQQMAAMADL--IDFY---GWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPL 110 (806)
Q Consensus 36 psd~~q~~ai~~l--l~~~---~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~ 110 (806)
|++...++.++++ ++.. .-++|.++- |..+-+.|.+.|++.|.+|.....|.......+.......+...
T Consensus 107 ~p~~~~se~Ll~~~~l~~~~~~~~~~vLi~r-----g~~~r~~L~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~~~~~ 181 (255)
T PRK05752 107 PEQGDDSEALLALPALRQALAVPDPRVLIMR-----GEGGRELLAERLREQGASVDYLELYRRCLPDYPAGTLLQRVEAE 181 (255)
T ss_pred CCCCCCcHHHHhChhhhccccCCCCEEEEEc-----cCccHHHHHHHHHHCCCEEeEEEEEeecCCCCCHHHHHHHHHhC
Confidence 3344446666665 2221 223443333 33456678889999998876555443211111223334444555
Q ss_pred CCeEEEEecCcchHHHHHHH
Q 003633 111 GPRVYVVHVSPDPGLRIFTT 130 (806)
Q Consensus 111 ~~rvivl~~~~~~~~~i~~~ 130 (806)
..++|++. ++..+..+++.
T Consensus 182 ~~d~v~ft-S~~~~~~~~~~ 200 (255)
T PRK05752 182 RLNGLVVS-SGQGFEHLQQL 200 (255)
T ss_pred CCCEEEEC-CHHHHHHHHHH
Confidence 66666555 44555555443
No 482
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=32.33 E-value=3.9e+02 Score=24.27 Aligned_cols=26 Identities=4% Similarity=0.065 Sum_probs=15.5
Q ss_pred hhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 97 QHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 97 ~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
.+.+..+|..++..+.|+|++.--..
T Consensus 54 Rp~l~~ll~~~~~g~vd~vvv~~ldR 79 (140)
T cd03770 54 RPGFNRMIEDIEAGKIDIVIVKDMSR 79 (140)
T ss_pred CHHHHHHHHHHHcCCCCEEEEeccch
Confidence 34566666666666666666654433
No 483
>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=32.30 E-value=1.7e+02 Score=29.72 Aligned_cols=77 Identities=8% Similarity=-0.018 Sum_probs=50.1
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHh--CCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcch-HHHHHHHH
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEK--NMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDP-GLRIFTTA 131 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~--~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~-~~~i~~~a 131 (806)
|+++.. ++.|-......+.+++++ .|.++... +...+.+.....+..+.+.++|.+|++..... ....++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~ 78 (271)
T cd06321 2 IGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVV---SADYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRA 78 (271)
T ss_pred eEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEc---cCCCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHH
Confidence 556664 466778889999999999 77776533 21223344556677777788999888764332 34566777
Q ss_pred HHcCC
Q 003633 132 QKLQM 136 (806)
Q Consensus 132 ~~~gm 136 (806)
.+.|.
T Consensus 79 ~~~~i 83 (271)
T cd06321 79 QAAGI 83 (271)
T ss_pred HHCCC
Confidence 66553
No 484
>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=32.28 E-value=2.9e+02 Score=24.15 Aligned_cols=62 Identities=6% Similarity=-0.094 Sum_probs=36.7
Q ss_pred cchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc----chHHHHHHHHHHcC
Q 003633 68 RNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP----DPGLRIFTTAQKLQ 135 (806)
Q Consensus 68 ~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~----~~~~~i~~~a~~~g 135 (806)
.-++..+...|+..|.++.+-.. ... ....+..+.+.++++|.+.+.. ..+..+.++.++.+
T Consensus 13 ~lG~~~~~~~l~~~G~~V~~lg~---~~~---~~~l~~~~~~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~ 78 (119)
T cd02067 13 DIGKNIVARALRDAGFEVIDLGV---DVP---PEEIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELKEAG 78 (119)
T ss_pred hHHHHHHHHHHHHCCCEEEECCC---CCC---HHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHHcC
Confidence 34456677778888888765321 112 2344555566788888887652 23445556666654
No 485
>PRK15138 aldehyde reductase; Provisional
Probab=31.92 E-value=2.1e+02 Score=31.40 Aligned_cols=84 Identities=8% Similarity=0.017 Sum_probs=55.0
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCc-ccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDY-GRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~-g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
+.+.++++. + +++.+++.+... ..+..+.+.+.|+ |+.+.....+.++.+.+++.......++.++|+||-.+..
T Consensus 20 ~~l~~~l~~-~-~~~livt~~~~~~~~g~~~~v~~~L~--~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 95 (387)
T PRK15138 20 AGLREQIPA-D-ARVLITYGGGSVKKTGVLDQVLDALK--GMDVLEFGGIEPNPTYETLMKAVKLVREEKITFLLAVGGG 95 (387)
T ss_pred HHHHHHHhc-C-CeEEEECCCchHHhcCcHHHHHHHhc--CCeEEEECCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCh
Confidence 444455665 4 888887743322 2345677788885 6666544456666677888888889999999999976653
Q ss_pred c--hHHHHHHH
Q 003633 122 D--PGLRIFTT 130 (806)
Q Consensus 122 ~--~~~~i~~~ 130 (806)
. ++.+.+..
T Consensus 96 S~iD~AK~ia~ 106 (387)
T PRK15138 96 SVLDGTKFIAA 106 (387)
T ss_pred HHHHHHHHHHH
Confidence 3 55555443
No 486
>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=31.91 E-value=1.6e+02 Score=30.08 Aligned_cols=80 Identities=8% Similarity=-0.039 Sum_probs=50.3
Q ss_pred EEEEEEEc--CCcccchHHHHHHHHHhCCcEEEEEec-cCCCCChhHHHHHHHhcCCCCCeEEEEecCcchH-HHHHHHH
Q 003633 56 EVIAIYVD--DDYGRNGISALSNMLEKNMAKVSYKLP-LPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPG-LRIFTTA 131 (806)
Q Consensus 56 ~v~ii~~d--~~~g~~~~~~l~~~l~~~g~~i~~~~~-~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~-~~i~~~a 131 (806)
+|+++..+ +.|.....+.+.+++++.|.++..... .+...+.......+..+.. ++|.+++....... ..+++++
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 36667653 457777889999999998765332221 1112233445566777777 89998887654333 4667887
Q ss_pred HHcCC
Q 003633 132 QKLQM 136 (806)
Q Consensus 132 ~~~gm 136 (806)
.+.|.
T Consensus 80 ~~~~i 84 (275)
T cd06307 80 AAAGV 84 (275)
T ss_pred HHCCC
Confidence 77664
No 487
>cd03522 MoeA_like MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is unknown.
Probab=31.87 E-value=2.3e+02 Score=29.92 Aligned_cols=69 Identities=12% Similarity=0.102 Sum_probs=50.1
Q ss_pred HcCCeEEEEEEEcCCc--c---cchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 51 FYGWKEVIAIYVDDDY--G---RNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 51 ~~~W~~v~ii~~d~~~--g---~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
-|.-.+|++|...++- | ......+...+++.|+++......+ .+.+.+...+.++.+.++|+||..+..
T Consensus 156 v~r~~rv~II~TG~Ev~~G~i~D~~~~~l~~~L~~~G~~v~~~~iv~--Dd~~~I~~ai~~~~~~g~DlIItTGGt 229 (312)
T cd03522 156 PFRPLRVGLIVTGSEVYGGRIEDKFGPVLRARLAALGVELVEQVIVP--HDEAAIAAAIAEALEAGAELLILTGGA 229 (312)
T ss_pred ecCCCEEEEEEcCCcCCCCcEEEhHHHHHHHHHHHCCCEEEEEEEcC--CCHHHHHHHHHHHhcCCCCEEEEeCCc
Confidence 3566788888876532 2 2335678888999999988777676 346678888888766668999887754
No 488
>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=31.72 E-value=4.2e+02 Score=24.54 Aligned_cols=68 Identities=13% Similarity=-0.007 Sum_probs=37.9
Q ss_pred cceeCCCHhHHHHHHhcCCCCCCeEEEEeCchhHHHHhhCCCCeEEeC--CccccCCceeeecCCCCchHHHHHHH
Q 003633 608 RLISLGSPEDYERALRQGPRNGGVAAIVDELPYVQLFLSNQTDFGIIG--QPFTRSGWGFAFQRDSPLAVGMSTAI 681 (806)
Q Consensus 608 ~~~~~~~~~~~~~~l~~~~~~g~~~a~i~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~k~spl~~~~n~~i 681 (806)
.....++.+..++.+.. |..-+++.+ ..++.... ...+..+. .......+.++.+++......+...+
T Consensus 127 ~~~~~~~~~~~~~~v~~----g~gi~~~p~-~~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (199)
T cd08475 127 PRLQFDDGEAIADAALA----GLGIAQLPT-WLVADHLQ-RGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAV 196 (199)
T ss_pred CcEEECCHHHHHHHHHh----CCCEEeeeH-HHHHhHhh-cCcEEEecCCCcCCCccEEEEeCCcccCCHHHHHHH
Confidence 34556788888899888 544444443 33333322 22344332 22334567888888776555554443
No 489
>PF03830 PTSIIB_sorb: PTS system sorbose subfamily IIB component; InterPro: IPR004720 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This entry is specific for the IIB components of this family of PTS transporters [].; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 3LFJ_B 1BLE_A 3P3V_B 1NRZ_C 3EYE_A 1VSQ_C 2JZH_A 2JZN_C 2JZO_D.
Probab=31.62 E-value=1e+02 Score=28.69 Aligned_cols=82 Identities=15% Similarity=0.129 Sum_probs=59.7
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCc
Q 003633 42 MAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSP 121 (806)
Q Consensus 42 ~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~ 121 (806)
+..+..++++++-+++.++- |..-.....+.+.+...-.|+++... +.++....+.+-...+.++++++-++
T Consensus 14 GQV~~~W~~~~~~~~IiVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~-------sv~~a~~~l~~~~~~~~~v~ii~k~~ 85 (151)
T PF03830_consen 14 GQVATAWVKKLNANRIIVVD-DEVANDPFQKMILKMAAPAGVKLSIF-------SVEEAIEKLKKPEYSKKRVLIIVKSP 85 (151)
T ss_dssp TTHHHHHHHHHTTSEEEEE--HHHHHSHHHHHHHHHTSHTTSEEEEE--------HHHHHHHHCGGGGTTEEEEEEESSH
T ss_pred eeeeEEEhhhcccCEEEEEC-HHHhcCHHHHHHHHHhhcCCCceEEE-------EHHHHHHHHHhcccCCceEEEEECCH
Confidence 45677889999999988665 44444455666666666778887643 24566677777777789999999999
Q ss_pred chHHHHHHHH
Q 003633 122 DPGLRIFTTA 131 (806)
Q Consensus 122 ~~~~~i~~~a 131 (806)
.++..++++-
T Consensus 86 ~d~~~l~~~g 95 (151)
T PF03830_consen 86 EDALRLVEAG 95 (151)
T ss_dssp HHHHHHHHTT
T ss_pred HHHHHHHhcC
Confidence 9988887653
No 490
>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=31.43 E-value=2.2e+02 Score=28.71 Aligned_cols=76 Identities=7% Similarity=-0.015 Sum_probs=47.8
Q ss_pred EEEEEE--cCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcchHHHHHHHHHHc
Q 003633 57 VIAIYV--DDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPDPGLRIFTTAQKL 134 (806)
Q Consensus 57 v~ii~~--d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~~~~~i~~~a~~~ 134 (806)
|++|.. ++.|.......+.+++++.|..+.....- ..+.......+..+.+.+.|.+++........ .+.++.+.
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 455553 45677778899999999999887654321 11224455667777777899988766543333 23444454
Q ss_pred C
Q 003633 135 Q 135 (806)
Q Consensus 135 g 135 (806)
|
T Consensus 79 ~ 79 (264)
T cd01574 79 D 79 (264)
T ss_pred C
Confidence 4
No 491
>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=31.19 E-value=1.5e+02 Score=30.95 Aligned_cols=72 Identities=7% Similarity=0.008 Sum_probs=45.8
Q ss_pred cCCcccchHHHHHHHHHhCC-cEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc-hHHHHHHHHHHcCC
Q 003633 63 DDDYGRNGISALSNMLEKNM-AKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD-PGLRIFTTAQKLQM 136 (806)
Q Consensus 63 d~~~g~~~~~~l~~~l~~~g-~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~-~~~~i~~~a~~~gm 136 (806)
++.|.....+.+.+++++.| ..+.+.. +...+.......+..+.+.++|.||+..... .....++++.+.|.
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 35677777888999999998 4443321 1122334455677777778899888866432 33456777777664
No 492
>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=30.92 E-value=1.6e+02 Score=25.73 Aligned_cols=71 Identities=17% Similarity=0.078 Sum_probs=45.3
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEec-cCCCCChhHHHHHHHhcCCCCCeEEEEecC
Q 003633 42 MAAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLP-LPVQFNQHDITVLLNNSKPLGPRVYVVHVS 120 (806)
Q Consensus 42 ~~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~-~~~~~~~~~~~~~l~~ik~~~~rvivl~~~ 120 (806)
...++.+++..|| +|.++-.+. ..+.+.+.+.+.+..+..-.. .. .+.......++.+|+..+++.++.+.
T Consensus 17 l~~la~~l~~~G~-~v~~~d~~~-----~~~~l~~~~~~~~pd~V~iS~~~~--~~~~~~~~l~~~~k~~~p~~~iv~GG 88 (121)
T PF02310_consen 17 LLYLAAYLRKAGH-EVDILDANV-----PPEELVEALRAERPDVVGISVSMT--PNLPEAKRLARAIKERNPNIPIVVGG 88 (121)
T ss_dssp HHHHHHHHHHTTB-EEEEEESSB------HHHHHHHHHHTTCSEEEEEESSS--THHHHHHHHHHHHHTTCTTSEEEEEE
T ss_pred HHHHHHHHHHCCC-eEEEECCCC-----CHHHHHHHHhcCCCcEEEEEccCc--CcHHHHHHHHHHHHhcCCCCEEEEEC
Confidence 4677788999999 444442221 227788888887777665544 33 33456677778888887776555444
No 493
>COG0134 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]
Probab=30.84 E-value=81 Score=32.01 Aligned_cols=87 Identities=14% Similarity=0.111 Sum_probs=64.7
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC--
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS-- 120 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~-- 120 (806)
..++...+.+|-.-+.++. |..|..+..+.|...-+...+.|--+..+. + .-++...+..++|+|++...
T Consensus 69 ~~ia~~Ye~~GAa~iSVLT-d~~~F~Gs~e~L~~v~~~v~~PvL~KDFii---D----~yQI~~Ar~~GADavLLI~~~L 140 (254)
T COG0134 69 VEIAKAYEEGGAAAISVLT-DPKYFQGSFEDLRAVRAAVDLPVLRKDFII---D----PYQIYEARAAGADAVLLIVAAL 140 (254)
T ss_pred HHHHHHHHHhCCeEEEEec-CccccCCCHHHHHHHHHhcCCCeeeccCCC---C----HHHHHHHHHcCcccHHHHHHhc
Confidence 4577888899999999888 778889999999887777777665444332 1 13455666789999876553
Q ss_pred -cchHHHHHHHHHHcCCc
Q 003633 121 -PDPGLRIFTTAQKLQMM 137 (806)
Q Consensus 121 -~~~~~~i~~~a~~~gm~ 137 (806)
......++..|.++||.
T Consensus 141 ~~~~l~el~~~A~~LGm~ 158 (254)
T COG0134 141 DDEQLEELVDRAHELGME 158 (254)
T ss_pred CHHHHHHHHHHHHHcCCe
Confidence 44578899999999985
No 494
>PF09651 Cas_APE2256: CRISPR-associated protein (Cas_APE2256); InterPro: IPR013442 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 150 amino acids found in a family of Cas proteins in at least five archaeal and three bacterial species. In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus.; PDB: 3QYF_A.
Probab=30.76 E-value=1.9e+02 Score=26.25 Aligned_cols=50 Identities=20% Similarity=0.186 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHcCCe---EEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEe
Q 003633 40 QQMAAMADLIDFYGWK---EVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKL 89 (806)
Q Consensus 40 ~q~~ai~~ll~~~~W~---~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~ 89 (806)
..-..+..+.+..... .+.++++|+.-|+-.++.+++.+.+.|+.+....
T Consensus 5 AElnsl~~~~~~~~~~~~~~~~Ll~SDT~~G~~~a~il~~~l~~~g~~v~~~~ 57 (136)
T PF09651_consen 5 AELNSLVRLLEKGKDDDKDEVVLLHSDTPDGRLCAEILKEYLEEKGINVEVVE 57 (136)
T ss_dssp HHHHHHHHHHHHHT--GGGEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEE
T ss_pred HhHHHHHHHHHhCccccCcEEEEEeCCCHHHHHHHHHHHHHHHHcCCeEEEEE
Confidence 3445666666554442 8999999999999999999999999998865443
No 495
>PF01054 MMTV_SAg: Mouse mammary tumour virus superantigen; InterPro: IPR001213 The Mouse mammary tumor virus (MMTV) is a milk-transmitted type B retrovirus. The superantigen (SAg) is encoded in the long terminal repeat [].
Probab=30.49 E-value=48 Score=32.03 Aligned_cols=60 Identities=23% Similarity=0.266 Sum_probs=39.5
Q ss_pred HHHHHhhcCCCCCCCcCcC-----------CCCccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 003633 691 QKLHEKWFCKEGCPEERRQ-----------HSEPHQLRLISFWGLYLLCGTITFTAFLVFLLRMVCQYVRY 750 (806)
Q Consensus 691 ~~i~~kw~~~~~c~~~~~~-----------~~~~~~L~l~~~~g~F~il~~g~~lal~vf~~E~~~~~~~~ 750 (806)
-++.+||+++..|+....+ .+....++-.+---+.+.|-+|+.+.++-++.|+..+-+|.
T Consensus 2 prlqqkwlnsrecptlr~eaakglfptkddpsa~~~mspsdkdi~i~ccklgiallclgllgevavra~ra 72 (313)
T PF01054_consen 2 PRLQQKWLNSRECPTLRREAAKGLFPTKDDPSACTRMSPSDKDILILCCKLGIALLCLGLLGEVAVRARRA 72 (313)
T ss_pred chhhhhhcccccCCCchhhhhcCCCCCCCCchhhccCCCCcCceEEeehhhhHHHHHHHHHHHHHHHHHhh
Confidence 4678999998899854211 10223444444444556677788888888899987776665
No 496
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=30.27 E-value=1.8e+02 Score=27.57 Aligned_cols=46 Identities=11% Similarity=0.014 Sum_probs=28.0
Q ss_pred HHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEec
Q 003633 71 ISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHV 119 (806)
Q Consensus 71 ~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~ 119 (806)
...+...|++.|+++.....++ .+.+.+...+.++.+ ..|+||..+
T Consensus 21 ~~~l~~~L~~~G~~v~~~~~v~--Dd~~~I~~~l~~~~~-~~dlVIttG 66 (170)
T cd00885 21 AAFLAKELAELGIEVYRVTVVG--DDEDRIAEALRRASE-RADLVITTG 66 (170)
T ss_pred HHHHHHHHHHCCCEEEEEEEeC--CCHHHHHHHHHHHHh-CCCEEEECC
Confidence 4567777777888777665554 334556666655543 456666544
No 497
>cd08483 PBP2_HvrB The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold. The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transp
Probab=30.27 E-value=4.4e+02 Score=24.27 Aligned_cols=64 Identities=16% Similarity=0.115 Sum_probs=36.9
Q ss_pred eeHHHHHHHHHhCCCCcceEEEEcCCCCCCCCHHHHHHHHHcCcccEEEeeEEEecCccceeEecccccccceEEEEec
Q 003633 384 YCIDILLEALKLVPYDVPYKFELFGDGLSNPSYDGLVKMVANDVFDAAVGDIAIVTNRTKIVDFSQPYISTGLVIVAPI 462 (806)
Q Consensus 384 ~~idl~~~i~~~l~~~~~~~~~~~~~~~~n~s~~~l~~~l~~g~~D~~~~~~~it~~r~~~vdft~p~~~~~~~~~v~~ 462 (806)
+-..++..+.+..+ .+++++.. ...+.++.+|++|+++.... .....+. ..++.+..++++++.
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~~~~----------~~~~~~l~~g~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~ 77 (190)
T cd08483 14 WLMPRLGSFWAKHP-EIELSLLP----------SADLVDLRPDGIDVAIRYGN---GDWPGLE-SEPLTAAPFVVVAAP 77 (190)
T ss_pred hHHhhHHHHHHHCC-CceEEEEe----------cCCcCCCCCCCcCEEEEecC---CCCCCcE-EEeecccceEeeeCH
Confidence 33456667776665 34455542 12245688999999986321 1122233 356677777777754
No 498
>PF15179 Myc_target_1: Myc target protein 1
Probab=30.10 E-value=68 Score=30.27 Aligned_cols=38 Identities=8% Similarity=-0.050 Sum_probs=29.6
Q ss_pred ccccccccchhHHHH-HHHHHHHHHHHHHHHHHHHHhhc
Q 003633 713 PHQLRLISFWGLYLL-CGTITFTAFLVFLLRMVCQYVRY 750 (806)
Q Consensus 713 ~~~L~l~~~~g~F~i-l~~g~~lal~vf~~E~~~~~~~~ 750 (806)
.+.++++++..+|.+ +++|++++.+|+++-.+..+||.
T Consensus 13 ~~~f~~~~lIlaF~vSm~iGLviG~li~~LltwlSRRRA 51 (197)
T PF15179_consen 13 LENFDWEDLILAFCVSMAIGLVIGALIWALLTWLSRRRA 51 (197)
T ss_pred hhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 456778888888866 67889999999988777776665
No 499
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=30.04 E-value=3.3e+02 Score=25.59 Aligned_cols=81 Identities=14% Similarity=0.155 Sum_probs=0.0
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHHhCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecCcc
Q 003633 43 AAMADLIDFYGWKEVIAIYVDDDYGRNGISALSNMLEKNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVSPD 122 (806)
Q Consensus 43 ~ai~~ll~~~~W~~v~ii~~d~~~g~~~~~~l~~~l~~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~~~ 122 (806)
..+.+.+..+|.+ .++..++.-...+=...+.+-+..+....-. .++.||.+++.++++.+.+|+++.....
T Consensus 69 ~~l~~~l~~~Gf~---pv~~kG~~Dv~laIDame~~~~~~iD~~vLv-----SgD~DF~~Lv~~lre~G~~V~v~g~~~~ 140 (160)
T TIGR00288 69 DKLIEAVVNQGFE---PIIVAGDVDVRMAVEAMELIYNPNIDAVALV-----TRDADFLPVINKAKENGKETIVIGAEPG 140 (160)
T ss_pred HHHHHHHHHCCce---EEEecCcccHHHHHHHHHHhccCCCCEEEEE-----eccHhHHHHHHHHHHCCCEEEEEeCCCC
Q ss_pred hHHHHHHHH
Q 003633 123 PGLRIFTTA 131 (806)
Q Consensus 123 ~~~~i~~~a 131 (806)
.+..+..++
T Consensus 141 ts~~L~~ac 149 (160)
T TIGR00288 141 FSTALQNSA 149 (160)
T ss_pred ChHHHHHhc
No 500
>PRK13805 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional
Probab=29.98 E-value=2.8e+02 Score=34.20 Aligned_cols=92 Identities=9% Similarity=0.009 Sum_probs=0.0
Q ss_pred HHHHHHHHc-CCeEEEEEEEcCCcccchHHHHHHHHH--hCCcEEEEEeccCCCCChhHHHHHHHhcCCCCCeEEEEecC
Q 003633 44 AMADLIDFY-GWKEVIAIYVDDDYGRNGISALSNMLE--KNMAKVSYKLPLPVQFNQHDITVLLNNSKPLGPRVYVVHVS 120 (806)
Q Consensus 44 ai~~ll~~~-~W~~v~ii~~d~~~g~~~~~~l~~~l~--~~g~~i~~~~~~~~~~~~~~~~~~l~~ik~~~~rvivl~~~ 120 (806)
++.++-... +-+++.+++...-+..+..+.+.+.|+ +.|+.+.....+.++.+.+.+...+..++..++|.||-.+.
T Consensus 469 ~l~~l~~~l~~~~~~lvVtd~~~~~~g~~~~v~~~L~~~~~~i~~~~~~~v~~np~~~~v~~~~~~~~~~~~D~IIaiGG 548 (862)
T PRK13805 469 SLPYLLDELDGKKRAFIVTDRFMVELGYVDKVTDVLKKRENGVEYEVFSEVEPDPTLSTVRKGAELMRSFKPDTIIALGG 548 (862)
T ss_pred HHHHHHHHhcCCCEEEEEECcchhhcchHHHHHHHHhcccCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCC
Q ss_pred cc--hHHHHHHHHHHcC
Q 003633 121 PD--PGLRIFTTAQKLQ 135 (806)
Q Consensus 121 ~~--~~~~i~~~a~~~g 135 (806)
.. +..+++......+
T Consensus 549 GSviD~AK~ia~~~~~~ 565 (862)
T PRK13805 549 GSPMDAAKIMWLFYEHP 565 (862)
T ss_pred chHHHHHHHHHHHHhCC
Done!