Query psy1412
Match_columns 504
No_of_seqs 286 out of 1959
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 20:02:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1412.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1412hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1054|consensus 100.0 2.5E-99 5E-104 743.8 26.7 477 6-501 257-799 (897)
2 KOG4440|consensus 100.0 2.2E-61 4.8E-66 477.7 27.1 431 48-498 283-811 (993)
3 KOG1053|consensus 100.0 1.6E-60 3.6E-65 487.3 30.5 430 49-500 296-811 (1258)
4 KOG1052|consensus 100.0 3.5E-58 7.6E-63 501.9 36.8 442 27-502 83-584 (656)
5 PF00497 SBP_bac_3: Bacterial 99.9 2.4E-21 5.2E-26 182.7 14.6 220 138-493 1-225 (225)
6 PRK10797 glutamate and asparta 99.9 5.4E-21 1.2E-25 189.3 15.8 224 132-494 36-273 (302)
7 PRK09495 glnH glutamine ABC tr 99.8 2.3E-20 4.9E-25 179.8 14.5 216 134-493 23-244 (247)
8 PRK11260 cystine transporter s 99.8 2.3E-19 4.9E-24 174.9 15.1 220 131-494 36-263 (266)
9 TIGR02995 ectoine_ehuB ectoine 99.8 5.8E-19 1.3E-23 172.8 15.4 219 132-490 29-259 (275)
10 PRK15007 putative ABC transpor 99.8 4.4E-19 9.5E-24 170.3 14.1 216 134-492 19-242 (243)
11 PRK11917 bifunctional adhesin/ 99.8 6.1E-19 1.3E-23 170.9 14.5 214 132-490 34-257 (259)
12 TIGR01096 3A0103s03R lysine-ar 99.8 2.9E-18 6.2E-23 165.3 15.8 212 136-491 24-250 (250)
13 PRK10859 membrane-bound lytic 99.8 4.8E-18 1E-22 178.7 18.7 221 131-493 38-267 (482)
14 PRK15010 ABC transporter lysin 99.8 9.2E-18 2E-22 163.0 16.8 221 133-493 23-255 (260)
15 PRK15437 histidine ABC transpo 99.7 2.6E-17 5.7E-22 159.7 14.1 221 133-493 23-255 (259)
16 TIGR02285 conserved hypothetic 99.7 5.4E-16 1.2E-20 151.2 16.9 224 134-494 16-263 (268)
17 PF10613 Lig_chan-Glu_bd: Liga 99.7 3.5E-17 7.5E-22 120.1 5.6 64 147-211 1-65 (65)
18 COG0834 HisJ ABC-type amino ac 99.7 1.3E-15 2.8E-20 148.7 14.5 222 134-493 32-265 (275)
19 TIGR03870 ABC_MoxJ methanol ox 99.6 1.1E-15 2.3E-20 147.2 12.6 87 137-250 1-91 (246)
20 smart00062 PBPb Bacterial peri 99.6 3.2E-14 6.8E-19 132.0 17.0 213 137-491 1-219 (219)
21 PRK09959 hybrid sensory histid 99.6 7.5E-15 1.6E-19 172.0 14.6 215 133-493 299-521 (1197)
22 PRK09959 hybrid sensory histid 99.6 6.6E-15 1.4E-19 172.5 13.7 221 131-493 51-278 (1197)
23 cd00134 PBPb Bacterial peripla 99.6 4.9E-14 1.1E-18 130.9 16.0 210 138-491 1-218 (218)
24 TIGR03871 ABC_peri_MoxJ_2 quin 99.6 3.9E-14 8.5E-19 134.9 14.5 214 138-491 2-228 (232)
25 smart00079 PBPe Eukaryotic hom 99.6 1.8E-14 4E-19 125.0 10.9 129 363-492 1-133 (134)
26 cd06387 PBP1_iGluR_AMPA_GluR3 99.5 3.6E-14 7.8E-19 144.0 9.3 110 2-120 228-371 (372)
27 cd06390 PBP1_iGluR_AMPA_GluR1 99.4 3.9E-13 8.6E-18 136.5 8.9 107 7-120 223-363 (364)
28 cd06392 PBP1_iGluR_delta_1 N-t 99.4 6E-13 1.3E-17 135.8 8.7 112 8-121 253-399 (400)
29 cd06393 PBP1_iGluR_Kainate_Glu 99.3 2.9E-12 6.2E-17 131.6 8.1 106 7-121 244-382 (384)
30 cd06388 PBP1_iGluR_AMPA_GluR4 99.3 6.7E-12 1.5E-16 128.0 9.1 111 2-121 227-370 (371)
31 cd06389 PBP1_iGluR_AMPA_GluR2 99.2 1.8E-11 4E-16 124.9 9.4 107 8-121 229-369 (370)
32 COG4623 Predicted soluble lyti 99.2 6.4E-11 1.4E-15 114.2 11.1 227 131-493 18-248 (473)
33 cd06391 PBP1_iGluR_delta_2 N-t 99.2 3.7E-11 8.1E-16 123.5 8.2 77 44-121 293-399 (400)
34 PF00060 Lig_chan: Ligand-gate 98.9 3.5E-11 7.6E-16 106.2 -4.5 98 264-374 1-115 (148)
35 cd06380 PBP1_iGluR_AMPA N-term 98.7 2.5E-08 5.5E-13 102.4 9.0 107 8-120 236-381 (382)
36 TIGR01098 3A0109s03R phosphate 98.7 2.6E-07 5.6E-12 89.2 12.7 201 134-477 30-254 (254)
37 PRK00489 hisG ATP phosphoribos 98.6 4.2E-08 9E-13 96.4 5.0 163 200-493 51-220 (287)
38 cd06378 PBP1_iGluR_NMDA_NR2 N- 98.5 3.1E-07 6.7E-12 93.3 7.7 76 48-124 258-357 (362)
39 cd06377 PBP1_iGluR_NMDA_NR3 N- 98.5 3E-07 6.5E-12 92.8 7.2 74 49-122 269-376 (382)
40 cd06379 PBP1_iGluR_NMDA_NR1 N- 98.2 2.4E-06 5.2E-11 87.6 7.2 73 48-121 272-367 (377)
41 cd06381 PBP1_iGluR_delta_like 98.1 4.6E-06 1E-10 84.8 6.5 105 5-121 250-363 (363)
42 cd06367 PBP1_iGluR_NMDA N-term 98.0 1.1E-05 2.3E-10 82.3 7.1 69 48-116 257-351 (362)
43 cd06394 PBP1_iGluR_Kainate_KA1 97.8 5.5E-06 1.2E-10 83.0 0.7 89 7-121 238-332 (333)
44 cd06383 PBP1_iGluR_AMPA_Like N 97.8 1.7E-05 3.6E-10 80.9 3.3 105 6-117 236-361 (368)
45 TIGR03431 PhnD phosphonate ABC 97.7 0.00045 9.8E-09 68.0 11.8 81 411-491 175-265 (288)
46 cd06362 PBP1_mGluR Ligand bind 97.6 9.1E-05 2E-09 77.9 6.8 72 48-121 354-451 (452)
47 cd06374 PBP1_mGluR_groupI Liga 97.6 0.00011 2.3E-09 77.9 7.3 73 48-123 371-470 (472)
48 cd06376 PBP1_mGluR_groupIII Li 97.4 0.00027 5.8E-09 74.6 7.0 67 48-116 359-452 (463)
49 cd06382 PBP1_iGluR_Kainate N-t 96.0 0.0039 8.4E-08 62.4 2.6 85 8-120 234-326 (327)
50 cd06365 PBP1_Pheromone_recepto 96.0 0.017 3.7E-07 61.0 7.4 67 48-116 359-452 (469)
51 PF12974 Phosphonate-bd: ABC t 95.9 0.055 1.2E-06 51.6 9.7 123 359-490 92-230 (243)
52 cd06364 PBP1_CaSR Ligand-bindi 95.7 0.032 7E-07 59.6 8.1 67 49-116 397-493 (510)
53 cd06372 PBP1_GC_G_like Ligand- 95.7 0.015 3.2E-07 59.9 5.2 37 48-96 301-337 (391)
54 cd06368 PBP1_iGluR_non_NMDA_li 95.5 0.011 2.3E-07 59.1 3.2 86 7-120 232-323 (324)
55 cd06386 PBP1_NPR_C_like Ligand 95.4 0.017 3.7E-07 59.3 4.6 38 48-97 298-335 (387)
56 PF01094 ANF_receptor: Recepto 95.1 0.035 7.6E-07 55.5 5.7 79 9-98 235-319 (348)
57 cd06363 PBP1_Taste_receptor Li 95.0 0.052 1.1E-06 56.3 6.7 63 48-116 308-395 (410)
58 cd06384 PBP1_NPR_B Ligand-bind 94.0 0.094 2E-06 54.1 6.0 38 48-97 311-348 (399)
59 PF03466 LysR_substrate: LysR 94.0 1.2 2.6E-05 40.2 12.8 69 165-250 19-88 (209)
60 cd05466 PBP2_LTTR_substrate Th 93.9 2.4 5.3E-05 37.0 14.4 68 165-249 13-81 (197)
61 cd06375 PBP1_mGluR_groupII Lig 93.7 0.16 3.5E-06 53.5 7.1 67 48-116 354-454 (458)
62 cd06351 PBP1_iGluR_N_LIVBP_lik 93.5 0.029 6.2E-07 55.8 1.0 82 7-116 238-322 (328)
63 COG3221 PhnD ABC-type phosphat 93.2 1.3 2.7E-05 43.7 11.9 113 359-479 131-260 (299)
64 cd06361 PBP1_GPC6A_like Ligand 92.9 0.28 6.1E-06 50.7 7.3 68 44-119 304-396 (403)
65 cd08459 PBP2_DntR_NahR_LinR_li 92.5 1.7 3.7E-05 38.9 11.3 68 165-249 13-81 (201)
66 cd08418 PBP2_TdcA The C-termin 92.4 5 0.00011 35.6 14.3 70 165-249 13-83 (201)
67 cd08468 PBP2_Pa0477 The C-term 92.1 2.6 5.6E-05 37.9 11.9 71 165-249 13-84 (202)
68 PRK11151 DNA-binding transcrip 91.9 5 0.00011 39.4 14.6 68 165-249 104-172 (305)
69 cd08417 PBP2_Nitroaromatics_li 91.7 1.5 3.3E-05 39.1 9.9 68 165-249 13-81 (200)
70 cd08421 PBP2_LTTR_like_1 The C 91.7 2.5 5.5E-05 37.5 11.4 67 166-249 14-81 (198)
71 CHL00180 rbcR LysR transcripti 91.4 6.2 0.00013 38.8 14.6 71 165-249 108-179 (305)
72 cd08426 PBP2_LTTR_like_5 The C 91.3 10 0.00022 33.6 15.0 68 165-249 13-81 (199)
73 cd06385 PBP1_NPR_A Ligand-bind 91.1 0.35 7.5E-06 50.0 5.5 39 48-98 310-348 (405)
74 cd08415 PBP2_LysR_opines_like 90.6 6.7 0.00015 34.6 13.0 68 165-249 13-81 (196)
75 KOG1056|consensus 90.5 0.48 1E-05 52.6 6.0 74 48-123 380-478 (878)
76 PRK10341 DNA-binding transcrip 90.4 8.2 0.00018 38.1 14.5 69 166-249 111-180 (312)
77 cd08438 PBP2_CidR The C-termin 90.4 4.6 9.9E-05 35.7 11.7 68 165-249 13-81 (197)
78 PRK11553 alkanesulfonate trans 90.4 3 6.4E-05 41.4 11.3 40 169-220 44-84 (314)
79 cd08433 PBP2_Nac The C-teminal 90.1 4.6 0.0001 35.9 11.5 67 166-249 14-81 (198)
80 cd08466 PBP2_LeuO The C-termin 89.6 3.8 8.3E-05 36.5 10.6 68 165-249 13-81 (200)
81 cd08460 PBP2_DntR_like_1 The C 89.5 2.3 5.1E-05 38.1 9.1 67 165-249 13-80 (200)
82 cd08461 PBP2_DntR_like_3 The C 89.5 4.4 9.6E-05 36.0 10.9 68 165-249 13-81 (198)
83 cd08412 PBP2_PAO1_like The C-t 89.4 5.1 0.00011 35.5 11.2 68 165-249 13-81 (198)
84 cd08440 PBP2_LTTR_like_4 TThe 89.3 14 0.00031 32.3 14.6 68 165-249 13-81 (197)
85 cd08462 PBP2_NodD The C-termin 89.3 3.7 8.1E-05 36.8 10.3 67 166-250 14-81 (200)
86 cd08463 PBP2_DntR_like_4 The C 89.1 10 0.00023 34.1 13.2 70 165-250 13-83 (203)
87 cd08420 PBP2_CysL_like C-termi 88.7 13 0.00028 32.7 13.4 68 165-249 13-81 (201)
88 cd08467 PBP2_SyrM The C-termin 88.6 7.5 0.00016 34.8 11.8 68 165-249 13-81 (200)
89 cd08434 PBP2_GltC_like The sub 88.6 16 0.00035 31.9 14.0 67 166-249 14-81 (195)
90 cd08411 PBP2_OxyR The C-termin 88.5 14 0.00029 32.8 13.4 67 166-249 15-82 (200)
91 PRK12684 transcriptional regul 88.4 7.9 0.00017 38.3 12.7 76 410-489 224-302 (313)
92 cd08419 PBP2_CbbR_RubisCO_like 88.0 18 0.00038 31.8 13.9 68 165-249 12-80 (197)
93 PRK12679 cbl transcriptional r 87.8 9.1 0.0002 37.9 12.7 82 409-493 223-307 (316)
94 cd08441 PBP2_MetR The C-termin 87.7 19 0.00041 31.8 13.8 67 166-249 14-81 (198)
95 cd08435 PBP2_GbpR The C-termin 87.6 10 0.00022 33.4 12.0 69 166-249 14-83 (201)
96 cd08414 PBP2_LTTR_aromatics_li 87.5 19 0.00041 31.5 15.2 68 165-249 13-81 (197)
97 cd08413 PBP2_CysB_like The C-t 86.6 21 0.00046 31.7 13.5 68 166-249 14-82 (198)
98 PRK11242 DNA-binding transcrip 86.4 26 0.00057 33.9 15.0 68 165-249 104-172 (296)
99 cd08429 PBP2_NhaR The C-termin 86.3 25 0.00054 31.7 15.2 70 165-248 13-83 (204)
100 cd08423 PBP2_LTTR_like_6 The C 86.2 21 0.00046 31.3 13.3 70 166-249 14-86 (200)
101 cd08469 PBP2_PnbR The C-termin 85.9 8.8 0.00019 35.0 10.7 68 165-249 13-81 (221)
102 PRK12683 transcriptional regul 85.7 35 0.00076 33.6 15.5 69 410-481 224-295 (309)
103 PRK12682 transcriptional regul 85.5 14 0.0003 36.3 12.6 70 165-250 106-176 (309)
104 cd08456 PBP2_LysR The C-termin 85.4 13 0.00029 32.7 11.5 68 165-249 13-81 (196)
105 cd08425 PBP2_CynR The C-termin 85.3 12 0.00027 33.0 11.2 67 166-249 15-82 (197)
106 cd06352 PBP1_NPR_GC_like Ligan 85.1 1.8 3.9E-05 44.2 6.2 38 48-97 302-339 (389)
107 cd08442 PBP2_YofA_SoxR_like Th 84.8 13 0.00029 32.5 11.1 68 165-249 13-81 (193)
108 cd08427 PBP2_LTTR_like_2 The C 84.6 18 0.00038 31.8 11.9 70 165-249 13-83 (195)
109 TIGR02122 TRAP_TAXI TRAP trans 84.5 6.1 0.00013 39.0 9.5 42 168-221 48-90 (320)
110 cd08451 PBP2_BudR The C-termin 84.5 28 0.0006 30.6 15.0 68 166-249 15-83 (199)
111 cd08464 PBP2_DntR_like_2 The C 84.1 15 0.00032 32.5 11.2 68 165-249 13-81 (200)
112 PRK12681 cysB transcriptional 83.7 12 0.00027 37.2 11.2 84 134-249 91-175 (324)
113 TIGR01729 taurine_ABC_bnd taur 83.0 12 0.00027 36.6 10.9 38 173-222 20-57 (300)
114 PRK11233 nitrogen assimilation 82.9 31 0.00067 33.8 13.7 68 165-249 105-173 (305)
115 PRK09791 putative DNA-binding 82.5 36 0.00078 33.2 14.0 86 134-250 93-179 (302)
116 cd08416 PBP2_MdcR The C-termin 82.4 22 0.00048 31.3 11.6 70 165-249 13-83 (199)
117 cd08443 PBP2_CysB The C-termin 82.0 18 0.00039 32.2 10.9 68 166-249 14-82 (198)
118 TIGR02424 TF_pcaQ pca operon t 81.8 33 0.00072 33.3 13.5 85 134-249 91-176 (300)
119 cd08448 PBP2_LTTR_aromatics_li 81.7 35 0.00076 29.8 15.0 68 165-249 13-81 (197)
120 cd06371 PBP1_sensory_GC_DEF_li 81.1 2.2 4.9E-05 43.6 4.9 37 48-97 295-331 (382)
121 cd08453 PBP2_IlvR The C-termin 80.3 41 0.00088 29.7 15.2 71 165-249 13-84 (200)
122 cd06366 PBP1_GABAb_receptor Li 80.1 1.5 3.2E-05 44.1 3.2 24 98-121 324-347 (350)
123 TIGR01256 modA molybdenum ABC 80.1 27 0.00059 32.2 11.6 78 409-489 134-214 (216)
124 cd08437 PBP2_MleR The substrat 80.1 34 0.00074 30.1 12.0 69 166-249 14-83 (198)
125 cd06370 PBP1_Speract_GC_like L 79.4 2.9 6.3E-05 43.1 5.2 38 48-97 316-353 (404)
126 PRK15421 DNA-binding transcrip 79.3 56 0.0012 32.3 14.2 66 167-249 104-170 (317)
127 PF13531 SBP_bac_11: Bacterial 79.1 32 0.00068 32.1 11.8 76 162-250 8-89 (230)
128 PRK10837 putative DNA-binding 78.6 65 0.0014 31.0 14.5 67 166-249 103-170 (290)
129 cd08444 PBP2_Cbl The C-termina 78.6 47 0.001 29.4 14.3 69 165-249 13-82 (198)
130 cd08458 PBP2_NocR The C-termin 78.5 47 0.001 29.3 14.6 67 166-249 14-81 (196)
131 cd06373 PBP1_NPR_like Ligand b 78.0 3.5 7.6E-05 42.3 5.2 40 48-99 308-347 (396)
132 cd08436 PBP2_LTTR_like_3 The C 77.7 47 0.001 28.9 14.5 69 165-249 13-82 (194)
133 cd08457 PBP2_OccR The C-termin 77.6 44 0.00095 29.4 11.9 67 165-248 13-80 (196)
134 cd08449 PBP2_XapR The C-termin 75.8 54 0.0012 28.6 15.1 70 165-249 13-83 (197)
135 PRK10677 modA molybdate transp 75.6 44 0.00096 32.1 11.8 71 167-250 41-117 (257)
136 TIGR03339 phn_lysR aminoethylp 74.9 33 0.00071 32.8 10.9 67 166-249 98-165 (279)
137 PRK11482 putative DNA-binding 74.2 48 0.001 32.8 12.1 82 135-250 116-197 (317)
138 KOG1055|consensus 72.8 2.1 4.6E-05 46.5 2.0 21 48-68 341-361 (865)
139 KOG1419|consensus 72.2 4 8.8E-05 42.6 3.7 67 265-345 234-301 (654)
140 cd08446 PBP2_Chlorocatechol Th 71.5 70 0.0015 28.0 15.0 68 165-249 14-82 (198)
141 PRK11013 DNA-binding transcrip 71.3 60 0.0013 31.8 12.0 68 165-249 107-175 (309)
142 PRK12680 transcriptional regul 70.9 50 0.0011 32.9 11.3 84 134-249 91-175 (327)
143 PRK11074 putative DNA-binding 66.6 61 0.0013 31.6 10.8 86 134-250 90-176 (300)
144 cd06392 PBP1_iGluR_delta_1 N-t 65.4 0.32 7E-06 50.1 -5.8 46 1-46 300-348 (400)
145 COG1910 Periplasmic molybdate- 62.7 53 0.0011 30.5 8.5 68 411-486 137-206 (223)
146 cd08445 PBP2_BenM_CatM_CatR Th 62.2 1.1E+02 0.0024 26.9 15.7 68 165-249 14-82 (203)
147 PRK10094 DNA-binding transcrip 62.1 1.1E+02 0.0023 30.1 11.7 68 167-249 108-176 (308)
148 PRK13348 chromosome replicatio 59.7 1.5E+02 0.0032 28.7 12.1 67 409-478 219-286 (294)
149 cd06377 PBP1_iGluR_NMDA_NR3 N- 59.7 0.44 9.5E-06 48.6 -6.0 46 1-46 272-323 (382)
150 cd08430 PBP2_IlvY The C-termin 59.3 1.2E+02 0.0026 26.3 14.0 68 166-249 14-82 (199)
151 PRK11716 DNA-binding transcrip 58.6 1E+02 0.0022 29.0 10.6 69 165-249 80-149 (269)
152 cd08465 PBP2_ToxR The C-termin 58.3 31 0.00067 30.7 6.6 69 165-250 13-82 (200)
153 PRK09906 DNA-binding transcrip 56.6 1.9E+02 0.0041 27.8 15.4 68 165-249 103-171 (296)
154 TIGR03298 argP transcriptional 55.4 1.5E+02 0.0033 28.5 11.4 64 169-249 107-170 (292)
155 cd08432 PBP2_GcdR_TrpI_HvrB_Am 54.1 70 0.0015 27.7 8.1 61 409-471 125-188 (194)
156 PF07885 Ion_trans_2: Ion chan 53.2 23 0.0005 26.9 4.1 34 309-345 22-56 (79)
157 PF03401 TctC: Tripartite tric 52.9 74 0.0016 30.8 8.5 128 359-489 85-241 (274)
158 COG1638 DctP TRAP-type C4-dica 52.2 22 0.00047 35.7 4.7 64 168-238 47-111 (332)
159 TIGR02136 ptsS_2 phosphate bin 49.9 29 0.00064 33.8 5.2 72 165-250 48-127 (287)
160 cd08450 PBP2_HcaR The C-termin 49.4 47 0.001 29.0 6.2 69 165-250 13-82 (196)
161 PF02879 PGM_PMM_II: Phosphogl 48.3 42 0.0009 27.0 5.1 69 163-232 29-101 (104)
162 PRK03635 chromosome replicatio 48.1 2.6E+02 0.0057 26.9 11.8 66 167-249 105-170 (294)
163 cd08486 PBP2_CbnR The C-termin 44.7 58 0.0013 28.9 6.1 69 165-250 14-83 (198)
164 PRK07377 hypothetical protein; 44.3 67 0.0015 28.9 5.9 62 135-219 74-135 (184)
165 cd08452 PBP2_AlsR The C-termin 41.9 84 0.0018 27.6 6.6 68 166-250 14-82 (197)
166 PRK03601 transcriptional regul 40.1 56 0.0012 31.4 5.5 69 165-250 102-171 (275)
167 cd08428 PBP2_IciA_ArgP The C-t 39.5 2.5E+02 0.0055 24.3 12.6 62 410-474 130-192 (195)
168 cd08485 PBP2_ClcR The C-termin 39.2 75 0.0016 28.1 5.9 69 165-250 14-83 (198)
169 PRK09508 leuO leucine transcri 38.8 70 0.0015 31.4 6.1 70 165-251 125-195 (314)
170 PRK11139 DNA-binding transcrip 35.8 90 0.0019 30.3 6.2 66 410-477 220-288 (297)
171 cd08447 PBP2_LTTR_aromatics_li 35.6 99 0.0021 26.9 6.0 69 165-250 13-82 (198)
172 PF10661 EssA: WXG100 protein 33.4 54 0.0012 28.5 3.6 27 261-287 115-141 (145)
173 cd06383 PBP1_iGluR_AMPA_Like N 33.2 10 0.00022 38.6 -1.0 15 1-15 279-293 (368)
174 PF12273 RCR: Chitin synthesis 32.6 38 0.00083 28.7 2.6 23 265-287 2-24 (130)
175 cd08439 PBP2_LrhA_like The C-t 32.3 1.1E+02 0.0023 26.6 5.7 66 166-250 14-80 (185)
176 cd01324 cbb3_Oxidase_CcoQ Cyto 31.5 74 0.0016 21.9 3.3 22 265-286 11-32 (48)
177 KOG1545|consensus 30.3 15 0.00032 36.6 -0.4 84 255-352 346-436 (507)
178 cd06393 PBP1_iGluR_Kainate_Glu 29.4 4.1 8.8E-05 41.7 -4.8 43 1-46 293-335 (384)
179 TIGR01276 thiB thiamine ABC tr 27.9 5.7E+02 0.012 24.8 13.4 39 169-219 21-63 (309)
180 cd06348 PBP1_ABC_ligand_bindin 27.4 43 0.00094 33.3 2.4 20 48-67 276-295 (344)
181 cd06345 PBP1_ABC_ligand_bindin 27.1 56 0.0012 32.5 3.1 33 48-97 286-318 (344)
182 PF13379 NMT1_2: NMT1-like fam 26.9 74 0.0016 30.2 3.8 66 172-249 27-99 (252)
183 PF12916 DUF3834: Protein of u 26.7 73 0.0016 29.1 3.3 44 165-220 77-121 (201)
184 PRK10918 phosphate ABC transpo 26.6 1.3E+02 0.0029 30.3 5.6 50 199-249 61-111 (346)
185 COG3105 Uncharacterized protei 26.5 94 0.002 26.2 3.6 29 264-292 4-32 (138)
186 cd06387 PBP1_iGluR_AMPA_GluR3 25.6 2.6 5.6E-05 43.0 -6.9 45 1-46 276-326 (372)
187 cd06369 PBP1_GC_C_enterotoxin_ 25.0 2E+02 0.0043 29.4 6.4 38 47-97 285-322 (380)
188 KOG3713|consensus 25.0 45 0.00098 34.7 1.9 53 275-345 356-409 (477)
189 TIGR03863 PQQ_ABC_bind ABC tra 24.0 74 0.0016 32.0 3.3 36 48-100 252-287 (347)
190 TIGR00975 3a0107s03 phosphate 22.9 1.6E+02 0.0035 29.1 5.5 48 199-249 34-86 (314)
191 PF12273 RCR: Chitin synthesis 22.8 50 0.0011 28.0 1.5 23 268-290 2-24 (130)
192 cd08431 PBP2_HupR The C-termin 22.3 1.1E+02 0.0025 26.5 4.0 69 165-249 13-82 (195)
193 PHA02650 hypothetical protein; 22.0 2.1E+02 0.0045 21.9 4.4 28 261-288 45-72 (81)
194 cd03770 SR_TndX_transposase Se 21.8 1.8E+02 0.0039 24.8 4.9 50 168-218 24-73 (140)
195 cd06342 PBP1_ABC_LIVBP_like Ty 21.6 92 0.002 30.6 3.4 34 48-98 274-307 (334)
196 cd06391 PBP1_iGluR_delta_2 N-t 21.5 4.3 9.4E-05 41.9 -6.3 46 1-46 300-348 (400)
197 PF09084 NMT1: NMT1/THI5 like; 21.2 1.9E+02 0.0042 26.2 5.4 66 174-251 15-84 (216)
198 PF12849 PBP_like_2: PBP super 20.8 1E+02 0.0022 29.7 3.5 76 163-251 20-108 (281)
199 TIGR00787 dctP tripartite ATP- 20.8 1.9E+02 0.004 27.6 5.3 49 169-224 17-65 (257)
200 PRK11917 bifunctional adhesin/ 20.7 1.4E+02 0.0031 28.4 4.5 69 170-250 162-232 (259)
201 PRK11677 hypothetical protein; 20.6 1.2E+02 0.0025 26.1 3.3 24 267-290 2-25 (134)
202 PRK13712 conjugal transfer pro 20.1 87 0.0019 24.6 2.2 18 312-329 52-69 (115)
No 1
>KOG1054|consensus
Probab=100.00 E-value=2.5e-99 Score=743.80 Aligned_cols=477 Identities=40% Similarity=0.716 Sum_probs=435.4
Q ss_pred eeeEEEEeeecCCCccccchhhhhhhccccc-------CCCccccccccccchhhhHHHHHHHHHHHhhhcCCccc----
Q psy1412 6 HVLAAGLALLDKSSVIKTSNLSCDLEVPWRD-------GLSLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKT---- 74 (504)
Q Consensus 6 ~~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~-------g~~~~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~---- 74 (504)
.+++||||++|.+.++ ++++.++|.. |.+ ...++. .+|++||||.+.++|++.+.+.+ +..
T Consensus 257 ~aNitgFqivn~~~~~-----~~k~~~~~~~l~~~~~~g~~-~~~~k~-tsAlthDailV~~eaf~~~~~q~-~~~~rRG 328 (897)
T KOG1054|consen 257 GANITGFQIVNKNNPM-----VKKFIQRWKELDEREYPGAS-NDPIKY-TSALTHDAILVMAEAFRSLRRQR-IDISRRG 328 (897)
T ss_pred CcceeEEEEecCCChH-----HHHHHHHHhhhcccccCCCC-CCCcch-hhhhhhhHHHHHHHHHHHHHHhh-hchhccC
Confidence 4577999999999999 9999999954 322 247888 99999999999999999986422 222
Q ss_pred ccCCC--CCCCcccCchhHHHHhhh----------------------ceEEEeeccceeeeeEecCCCCceeecC---CC
Q psy1412 75 SNLSC--DLEVPWRDGLSLYNYINT----------------------LDLLKLKREELRKVGHWTPAEGINITDR---SA 127 (504)
Q Consensus 75 ~~~~c--~~~~~~~~G~~l~~~l~~----------------------~~i~~~~~~~~~~vg~W~~~~gl~~~~~---~~ 127 (504)
..-+| ++..+|.+|..+-+++++ .+|++++.++.+++|+|+...|+..... ..
T Consensus 329 ~~GD~~an~~~p~~qG~~I~ralk~v~~eGLTGniqFd~~G~R~Nyt~~i~elk~~~~rk~~~W~e~~~fv~~~t~a~~~ 408 (897)
T KOG1054|consen 329 NAGDCLANPAVPWEQGIDIERALKQVQVEGLTGNIQFDKYGRRTNYTIDIVELKSNGSRKVGYWNEGEGFVPGSTVAQSR 408 (897)
T ss_pred CCccccCCCCCchhcchhHHHHHHheeecccccceeecccCccccceEEEEEeccCCcceeeeecccCceeecccccccc
Confidence 12378 568899999999999998 7899999999999999999999886543 23
Q ss_pred ccccccCCeEEEEEeecccCeEEEecC-CCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhH
Q psy1412 128 FYETSTNNVTLIVMTREEKPYVMVKND-ANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV 206 (504)
Q Consensus 128 ~~~~~~~~~~l~V~~~~~~P~~~~~~~-~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli 206 (504)
+.....++++..|.++.+.||++.+.+ ..+.||++|+||||||+.+||+..+++|++..++|++||++++.+.-|+||+
T Consensus 409 ~d~~~~~n~tvvvttiL~spyvm~kkn~~~~egn~ryEGyCvdLa~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMv 488 (897)
T KOG1054|consen 409 NDQASKENRTVVVTTILESPYVMLKKNHEQLEGNERYEGYCVDLAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMV 488 (897)
T ss_pred ccccccccceEEEEEecCCchhHHHhhHHHhcCCcccceeHHHHHHHHHHhcCceEEEEEecCCcccccCCCcccccchh
Confidence 444556888999999999999999887 6678999999999999999999999999999999999999999444599999
Q ss_pred HHHhhccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHH
Q psy1412 207 KELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMA 286 (504)
Q Consensus 207 ~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~ 286 (504)
|+|..|+||+|++++|||.+|+++||||.|||.+|++|++++|.++.++.|+||.|+..++|+|++.+|+.|++++|+++
T Consensus 489 GeLv~grAdiavApLTIt~~REeviDFSKPfMslGISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVS 568 (897)
T KOG1054|consen 489 GELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVS 568 (897)
T ss_pred HHHhcCccceEEeeeeeehhhhhhhccccchhhcCeEEEEeCcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCCccCCCCCCCC---CCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehcc--------------ch--
Q psy1412 287 RFSPYEWSNPHPCLAE---SPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDT--------------AL-- 347 (504)
Q Consensus 287 r~~p~~~~~~~~~~~~---~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~--------------An-- 347 (504)
||||||||-.... ++ +....|.|++.|++||+++++||||+++.||++ |+||+.+ ||
T Consensus 569 rFSPYEwh~Ee~~-rg~~t~~~~~NeFgifNsLWFsLgAFMQQG~DI~PRsl---SGRIvggvWWFFTlIIiSSYTANLA 644 (897)
T KOG1054|consen 569 RFSPYEWHTEEFE-RGRFTPSDPPNEFGIFNSLWFSLGAFMQQGCDISPRSL---SGRIVGGVWWFFTLIIISSYTANLA 644 (897)
T ss_pred ccCchheeccccc-cCCCCCCCCCccchhhHHHHHHHHHHHhcCCCCCcccc---ccceeccchhhhhhhhhhhhhhHHH
Confidence 9999999976542 22 234779999999999999999999999999999 9999988 66
Q ss_pred -hhhhhhhhhhhhhcccchhhhhccCCCCceeeee----ecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhh-
Q psy1412 348 -DSKIEIYQKMWRYMESKKCILFLGGQGDETFVTI----DLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVL- 421 (504)
Q Consensus 348 -~Ltv~~~~~~~~~~~~i~s~~dL~~~~~i~~g~~----~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~- 421 (504)
|||++ ||.+||+|+|||++|++|.||+. +.+||++|+++.|++||.||++..|++|+.+++||++||+
T Consensus 645 AFLTvE------rMvsPIESaEDLAkQteIaYGt~~~GSTkeFFr~Skiavy~kMW~yM~SaepsVFv~t~aeGv~rVRk 718 (897)
T KOG1054|consen 645 AFLTVE------RMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMKSAEPSVFVRTTAEGVARVRK 718 (897)
T ss_pred HHHhHH------hhcCcchhHHHHhhcceeeeeecCCCchHHHHhhhhHHHHHHHHHHHhcCCcceeeehhhhHHHHHHh
Confidence 99999 99999999999999999999998 8899999999999999999999999999999999999996
Q ss_pred -cCCeEEEeecchhhhhhhcC-CccEEcCCccCCcceEEEecCCCCCchHHHHHHHhhhccChhHHHHHhhccCCCCCCC
Q psy1412 422 -EGDYAFLMESTMLDYEVQRN-CNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKNTGDVCN 499 (504)
Q Consensus 422 -~g~~A~i~e~~~~~y~~~~~-c~l~~vg~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~l~~kw~~~~~~~C~ 499 (504)
+|+|||+.|+++.+|..++. |+.+.||..+++.|||+|.||||.|+..+|.|+|+|.|.|++++|++|||.|+ ++|.
T Consensus 719 sKGkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGiATp~Gsslr~~vNLAvLkL~E~G~LdKLkNKWWYDk-GeC~ 797 (897)
T KOG1054|consen 719 SKGKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDK-GECG 797 (897)
T ss_pred cCCceEeehHhhhhhhhhccCCccceecccccCCcceeecCCCCcccccchhhhhhhhcccchHHHhhhhhcccc-cccC
Confidence 67799999999999998876 99999999999999999999999999999999999999999999999999997 9997
Q ss_pred CC
Q psy1412 500 RD 501 (504)
Q Consensus 500 ~~ 501 (504)
+.
T Consensus 798 sg 799 (897)
T KOG1054|consen 798 SG 799 (897)
T ss_pred CC
Confidence 64
No 2
>KOG4440|consensus
Probab=100.00 E-value=2.2e-61 Score=477.73 Aligned_cols=431 Identities=30% Similarity=0.483 Sum_probs=357.4
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCC-CCCCcccCchhHHHHhhh-----------------------ceEEEe
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSC-DLEVPWRDGLSLYNYINT-----------------------LDLLKL 103 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c-~~~~~~~~G~~l~~~l~~-----------------------~~i~~~ 103 (504)
+.+..-|+|.++|.|++.+.+.+.|...+..| +.++.|..|+.|.+.++. |||+|+
T Consensus 283 ~~~hirDsv~vlasAv~e~~~~e~I~~~P~~c~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~Fnd~gdRi~a~YdiiN~ 362 (993)
T KOG4440|consen 283 ESAHIRDSVGVLASAVHELLEKENITDPPRGCVDNTNIWKTGPLLKRVLMSSKYADGVTGRVEFNDDGDRIFANYDIINL 362 (993)
T ss_pred ccceehhhHHHHHHHHHHHHhhccCCCCCCcccCccchhcccHHHHHHHhhhcccCCcceeEEEcCCCceeeccceeEeh
Confidence 67889999999999999999888888766655 889999999999999875 999999
Q ss_pred e-ccceeeeeEecCCCCceeecC----CCc----cccccCCeEEEEEeecccCeEEEecC-CC-----------------
Q psy1412 104 K-REELRKVGHWTPAEGINITDR----SAF----YETSTNNVTLIVMTREEKPYVMVKND-AN----------------- 156 (504)
Q Consensus 104 ~-~~~~~~vg~W~~~~gl~~~~~----~~~----~~~~~~~~~l~V~~~~~~P~~~~~~~-~~----------------- 156 (504)
. ......+|..+.. .+..++. +.+ .+...-..+|||.|++++||++.+.. .+
T Consensus 363 hq~rk~Vg~~~yd~~-r~~~nd~~IiWpGg~~~KP~gi~~pthLrivTi~~~PFVYv~p~~sd~~c~eef~~~~d~~~k~ 441 (993)
T KOG4440|consen 363 HQNRKLVGVGIYDGT-RVIPNDRKIIWPGGETEKPRGIQMPTHLRIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKV 441 (993)
T ss_pred hhhhhhhhhccccce-eeccCCceeecCCCCcCCCccccccceeEEEEeccCCeEEEecCCCCcchhhhccccCCcccce
Confidence 5 3333344333221 1222222 221 22233457899999999999998742 00
Q ss_pred -CCC-------------CccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCC-------CCcchhhHHHHhhcccc
Q psy1412 157 -LTG-------------NAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHE-------TKEWNGIVKELMDKKAD 215 (504)
Q Consensus 157 -~~~-------------~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~-------~g~w~gli~~l~~g~~D 215 (504)
++| .-+..||||||+-+|++.+||+|+..+++|+++|.+... ..+|+||||+|.++.||
T Consensus 442 ~c~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~AD 521 (993)
T KOG4440|consen 442 ICTGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQAD 521 (993)
T ss_pred eecCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhCCccc
Confidence 011 134689999999999999999999999999999976432 24799999999999999
Q ss_pred ceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCCCccC
Q psy1412 216 LAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWSN 295 (504)
Q Consensus 216 ~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~~~~~ 295 (504)
|+++++||++||.++++||.||...|+.|+.+++.+. ..+-+||+||+..+|+++.++.++|++++++++|+||++...
T Consensus 522 MivaplTINpERa~yieFskPfkYqGitILeKk~~r~-Stl~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPFgRFk 600 (993)
T KOG4440|consen 522 MIVAPLTINPERAQYIEFSKPFKYQGITILEKKEIRR-STLDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPFGRFK 600 (993)
T ss_pred eEeeceeeChhhhhheeccCcccccceEEEeeCCCCC-chHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccee
Confidence 9999999999999999999999999999999988654 468899999999999999999999999999999999998544
Q ss_pred CCCCCCCCCcccCcccchhHHHHHHHHhhccCC-CCCCcccccccceehcc--------------ch---hhhhhhhhhh
Q psy1412 296 PHPCLAESPIVENQFSVSNSFWFITGTFLRQGS-GLNPKVLQQGSSRTLDT--------------AL---DSKIEIYQKM 357 (504)
Q Consensus 296 ~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~-~~~p~~~~~~s~R~v~~--------------An---~Ltv~~~~~~ 357 (504)
.... .+..+...+++.++||+||+|++.|. +..|||+ |.|++.. || ||.++
T Consensus 601 ~~ds---~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSf---SARvLGmVWaGFaMIiVASYTANLAAFLVLd----- 669 (993)
T KOG4440|consen 601 VNDS---EEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSF---SARVLGMVWAGFAMIIVASYTANLAAFLVLD----- 669 (993)
T ss_pred eccC---ccchhhhcchhhhHHHHhHhhhccccCCCCCcch---hHHHHHHHHhhhheeeehhhhhhhhhheeec-----
Confidence 3211 12234677899999999999999988 4699999 9999877 55 99999
Q ss_pred hhhcccchhhhhccC---CCCceeeee----ecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEe
Q psy1412 358 WRYMESKKCILFLGG---QGDETFVTI----DLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLM 429 (504)
Q Consensus 358 ~~~~~~i~s~~dL~~---~~~i~~g~~----~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~ 429 (504)
|.+..++.+.|-.- ..++.|||+ ...||++. .....|++.|+.++ +.+.+|+++.|++|+ .|||+
T Consensus 670 -rPe~~ltGinDpRLRNps~nf~~aTVk~SsVd~YFrRq--VELS~MyR~ME~hN----y~~A~eAiq~v~~gkL~AFIW 742 (993)
T KOG4440|consen 670 -RPEERLTGINDPRLRNPSDNFIYATVKQSSVDIYFRRQ--VELSTMYRHMEKHN----YESAAEAIQAVRDGKLHAFIW 742 (993)
T ss_pred -CccccccCCCCccccCcccceeEEEecCccHHHHHHHH--hHHHHHHHhhhhcc----hhhHHHHHHHHHcCceeEEEe
Confidence 99999999999652 346889988 34566643 35678999998866 788999999999999 89999
Q ss_pred ecchhhhhhhcCCccEEcCCccCCcceEEEecCCCCCchHHHHHHHhhhccChhHHHHHhhccCCCCCC
Q psy1412 430 ESTMLDYEVQRNCNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKNTGDVC 498 (504)
Q Consensus 430 e~~~~~y~~~~~c~l~~vg~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~l~~kw~~~~~~~C 498 (504)
|+..++|.++++|+|.+.|+.|...+|||+++|||||.+.+..|||++.|+|++++|.++|....+++|
T Consensus 743 DS~rLEfEAs~~CeLvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEkLDk~Wi~~Ggpq~ 811 (993)
T KOG4440|consen 743 DSARLEFEASQKCELVTTGELFGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEKLDKTWIRYGGPQE 811 (993)
T ss_pred ecceeeehhhcccceEeccccccccccccccccCCCCcchhhHHHHHhhhcchHHHHHHHHHhcCCcch
Confidence 999999999999999999999999999999999999999999999999999999999999998643444
No 3
>KOG1053|consensus
Probab=100.00 E-value=1.6e-60 Score=487.35 Aligned_cols=430 Identities=26% Similarity=0.490 Sum_probs=353.3
Q ss_pred cchhhhHHHHHHHHHHHhhhcC-CcccccCCCCC--CCcccCchhHHHHhhh---------------------ceEEEee
Q psy1412 49 PALMYDSVHVLAAGLALLDKSS-VIKTSNLSCDL--EVPWRDGLSLYNYINT---------------------LDLLKLK 104 (504)
Q Consensus 49 ~~~~yDav~~~a~a~~~~~~~~-~~~~~~~~c~~--~~~~~~G~~l~~~l~~---------------------~~i~~~~ 104 (504)
.+.+-|+|-++|.|...+.+.. .+.++..+|.. +.....|..+.++|.| +=|...+
T Consensus 296 ~~rVrdgvaiva~aa~s~~~~~~~lp~~~~~C~~~~~~~~~~~~~l~r~l~NvT~~g~~lsf~~~g~~v~p~lvvI~l~~ 375 (1258)
T KOG1053|consen 296 EARVRDGVAIVARAASSMLRIHGFLPEPKMDCREQEETRLTSGETLHRFLANVTWDGRDLSFNEDGYLVHPNLVVIDLNR 375 (1258)
T ss_pred HHHHhhhHHHHHHHHHHHHhhcccCCCcccccccccCccccchhhhhhhhheeeecccceeecCCceeeccceEEEecCC
Confidence 5678999999999999887543 46667789943 3456788999999988 1222233
Q ss_pred ccceeeeeEecCCCCceeecC--C---CccccccCCeEEEEEeecccCeEEEecCCCCCC--------------------
Q psy1412 105 REELRKVGHWTPAEGINITDR--S---AFYETSTNNVTLIVMTREEKPYVMVKNDANLTG-------------------- 159 (504)
Q Consensus 105 ~~~~~~vg~W~~~~gl~~~~~--~---~~~~~~~~~~~l~V~~~~~~P~~~~~~~~~~~~-------------------- 159 (504)
...|+.||.|..+ .|.+... + ..........||+|+|.+++||+++++.++.++
T Consensus 376 ~r~We~VG~We~~-~L~M~y~vWPr~~~~~q~~~d~~HL~VvTLeE~PFVive~vDP~t~~C~~ntvpc~s~~~~t~ss~ 454 (1258)
T KOG1053|consen 376 DRTWERVGSWENG-TLVMKYPVWPRYHKFLQPVPDKLHLTVVTLEERPFVIVEDVDPLTQTCVRNTVPCRSQLNSTFSSG 454 (1258)
T ss_pred CcchheeceecCC-eEEEeccccccccCccCCCCCcceeEEEEeccCCeEEEecCCCCcCcCCCCCCcchhhhhhccCCC
Confidence 4568999999876 4665553 1 112223345699999999999999877543221
Q ss_pred -------CccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeee
Q psy1412 160 -------NAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVID 232 (504)
Q Consensus 160 -------~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vd 232 (504)
..+..||||||+++||+.+||+|+++.|.+++||... ||.|+||||+|..++|||||++++|++||.++||
T Consensus 455 ~~~~~tvKkCCkGfCIDiLkKlA~~v~FtYDLYlVtnGKhGkk~--ng~WnGmIGev~~~rA~MAVgSltINeeRSevVD 532 (1258)
T KOG1053|consen 455 DEANRTVKKCCKGFCIDILKKLARDVKFTYDLYLVTNGKHGKKI--NGVWNGMIGEVVYQRADMAVGSLTINEERSEVVD 532 (1258)
T ss_pred ccCCchHHhhhhhhhHHHHHHHHhhcCcceEEEEecCCccccee--cCcchhhHHHHHhhhhheeeeeeEechhhhcccc
Confidence 1356899999999999999999999999999999887 8999999999999999999999999999999999
Q ss_pred eccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHH-HHHHHHHHHhhCCCCccCCCCCCCCCCcccCccc
Q psy1412 233 FTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLL-VSFTLFVMARFSPYEWSNPHPCLAESPIVENQFS 311 (504)
Q Consensus 233 Fs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~-v~~~~~~i~r~~p~~~~~~~~~~~~~~~~~~~~~ 311 (504)
||.||.++|++++|++.+. ..+.-+||.||++.||+++++++++ +++.+|++|++||++++.. . ..++.+....|+
T Consensus 533 FSvPFveTgIsVmV~rsng-tvspsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~-l-~~gkkpggp~Ft 609 (1258)
T KOG1053|consen 533 FSVPFVETGISVMVARSNG-TVSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRN-L-ANGKKPGGPSFT 609 (1258)
T ss_pred ccccccccceEEEEEecCC-ccCchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcCccccccc-c-cCCCCCCCccee
Confidence 9999999999999998765 4567799999999999999988776 5577889999999996432 1 234556678999
Q ss_pred chhHHHHHHHHhhccCCCC-CCcccccccceehcc--------------ch---hhhhhhhhhhhhhcccchhhhhccC-
Q psy1412 312 VSNSFWFITGTFLRQGSGL-NPKVLQQGSSRTLDT--------------AL---DSKIEIYQKMWRYMESKKCILFLGG- 372 (504)
Q Consensus 312 l~~~~w~~~~~l~~qg~~~-~p~~~~~~s~R~v~~--------------An---~Ltv~~~~~~~~~~~~i~s~~dL~~- 372 (504)
++.++|+.|+.+++....+ .|++. .+||++. || ||..+ .....+..+.|=+-
T Consensus 610 igkaiwllwaLvFnnsVpv~nPKgt---TskiMv~VWAfFavifLAsYTANLAAfMIqE------~~~d~vSGlsD~Kfq 680 (1258)
T KOG1053|consen 610 IGKAIWLLWALVFNNSVPVENPKGT---TSKIMVLVWAFFAVIFLASYTANLAAFMIQE------EYYDTVSGLSDPKFQ 680 (1258)
T ss_pred hhhHHHHHHHHHhCCCcCCCCCCch---HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh------hhhhhccccCccccc
Confidence 9999999999999887765 89999 9999877 66 77777 66666667766542
Q ss_pred ----C-CCceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcC--Ccc
Q psy1412 373 ----Q-GDETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN--CNL 444 (504)
Q Consensus 373 ----~-~~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~--c~l 444 (504)
| ..+++||+...--++.-...|.+|.+||.+.+ ....++|++.+++|+ +|||+|...++|.+.++ |+|
T Consensus 681 rP~dq~PpFRFGTVpngSTE~niR~Nyp~MHeYM~kyN----q~~v~dal~sLK~gKLDAFIyDaAVLnY~agkDegCKL 756 (1258)
T KOG1053|consen 681 RPHDQYPPFRFGTVPNGSTERNIRSNYPEMHEYMVKYN----QPGVEDALESLKNGKLDAFIYDAAVLNYMAGKDEGCKL 756 (1258)
T ss_pred CccccCCCcccccCCCCchhhhHHhccHHHHHHHHHhc----cCchHHHHHHHhcccchhHHHHHHHHHHhhccCCCceE
Confidence 1 35889999333333333358999999999855 688999999999999 99999999999999887 999
Q ss_pred EEcC--CccCCcceEEEecCCCCCchHHHHHHHhhhccChhHHHHHhhccCCCCCCCC
Q psy1412 445 TQIG--GLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKNTGDVCNR 500 (504)
Q Consensus 445 ~~vg--~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~l~~kw~~~~~~~C~~ 500 (504)
.+|| ..|.+.|||||+|||||++..||.+|++++.+|++++|++.|+. +.|.+
T Consensus 757 vTIGsgKvFAttGYGIal~k~Spwkr~IdlallQy~gdGeme~Le~~Wlt---gic~n 811 (1258)
T KOG1053|consen 757 VTIGSGKVFATTGYGIALPKNSPWKRQIDLALLQYLGDGEMEMLETLWLT---GICHN 811 (1258)
T ss_pred EEecCCceeeecceeeecCCCCcchhhHHHHHHHHhccchHHHHHHHHhh---ccccc
Confidence 9999 79999999999999999999999999999999999999999997 66764
No 4
>KOG1052|consensus
Probab=100.00 E-value=3.5e-58 Score=501.93 Aligned_cols=442 Identities=35% Similarity=0.594 Sum_probs=380.4
Q ss_pred hhhhhcccccCCCccccccccccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh---------
Q psy1412 27 SCDLEVPWRDGLSLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT--------- 97 (504)
Q Consensus 27 ~~~~~~~W~~g~~~~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~--------- 97 (504)
..++..+|... ...+.. .++++||+++++|.|++.+.. .....++|+..+.|.+|..+.+.+++
T Consensus 83 ~~~~~~~~~~~---~~~~~~-~~~~~~D~~~~~a~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (656)
T KOG1052|consen 83 LQNFVTRWQTS---NVELLV-YALWAYDAIQALARAVESLLN---IGNLSLSCGRNNSWLDALGVFNFGKKLLVVNLSGV 155 (656)
T ss_pred HHHHHHHHhhc---cccccc-hhhHHHHHHHHHHHHHHHhhc---CCCCceecCCCCcccchhHHHHHHHhhhhhccccc
Confidence 44555566543 113343 899999999999999988743 44456789888889999999888876
Q ss_pred ----------------ceEEEeeccceeeeeEecCCCCceeecC------CCccccccCCeEEEEEeecccCeEEEecCC
Q psy1412 98 ----------------LDLLKLKREELRKVGHWTPAEGINITDR------SAFYETSTNNVTLIVMTREEKPYVMVKNDA 155 (504)
Q Consensus 98 ----------------~~i~~~~~~~~~~vg~W~~~~gl~~~~~------~~~~~~~~~~~~l~V~~~~~~P~~~~~~~~ 155 (504)
|+|+|+.+.+.+.+|.|++..|..+... +..+.....+++++|++...+||++..++.
T Consensus 156 ~~~~~~~~~~~~~~~~~~i~n~~~~~~~~ig~W~~~~~~~i~~~~~~~~~~~~~~~~~~~~~l~v~~~~~~P~~~~~~~~ 235 (656)
T KOG1052|consen 156 TGQFQFFRGGLLEYFKYEILNLNGSGERRIGYWYPRGGENISWPGKDYFVPKGWFFPTNGKPLRVGVVTEPPFVDLVEDL 235 (656)
T ss_pred eeEEEecCCCccccceEEEEEecCcCceeEEEecCCCCceeeccCCcccCcCCccccCCCceEEEEEeccCCceeeeecc
Confidence 8899999999999999999876333222 122222226999999999999998877653
Q ss_pred -CCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeec
Q psy1412 156 -NLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFT 234 (504)
Q Consensus 156 -~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs 234 (504)
...++.++.|||+||++++++.|||+|+++.++++. |..++ +|+|+|++++|.+|++|++ ++++|+++|+++||||
T Consensus 236 ~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~-g~~~~-~g~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT 312 (656)
T KOG1052|consen 236 AILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGS-GSRDP-NGNWDGLVGQLVDGEADVG-ADITITPERSKYVDFT 312 (656)
T ss_pred cccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCC-CCCCC-CCChhHHHHHHhcCccccc-cceEEeecccccEEec
Confidence 444678999999999999999999999999999998 98888 5999999999999999999 9999999999999999
Q ss_pred cceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCCCccCCCCCCCCCCcccCcccchh
Q psy1412 235 KPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWSNPHPCLAESPIVENQFSVSN 314 (504)
Q Consensus 235 ~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~~~~~~~~~~~~~~~~~~~~~l~~ 314 (504)
.||++.+++++++++..... .|.|+.||+++||++++++++++++++|+++|++|++| +++ +. ....+++.+
T Consensus 313 ~p~~~~~~~i~~~~~~~~~~-~~~fl~Pf~~~vW~~i~~~~l~~~~~~~~~~~~~~~~~--~~~--~~---~~~~~~~~~ 384 (656)
T KOG1052|consen 313 IPYLQFGIVIIVRKPDSRSK-LWNFLAPFSPEVWLLILASLLLVGLLLWILERLSPYEL--PPR--QI---VTSLFSLLN 384 (656)
T ss_pred cceEeccEEEEEEecCCccc-ceEEecCCcHHHHHHHHHHHHHHHHHHHHHhccccccC--Ccc--cc---ceeEeeccc
Confidence 99999999999999988776 99999999999999999999999999999999999999 332 21 457788999
Q ss_pred HHHHHHHHhhccCCCCCCcccccccceehcc--------------ch---hhhhhhhhhhhhhcccchhhhhccCCCCce
Q psy1412 315 SFWFITGTFLRQGSGLNPKVLQQGSSRTLDT--------------AL---DSKIEIYQKMWRYMESKKCILFLGGQGDET 377 (504)
Q Consensus 315 ~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~--------------An---~Ltv~~~~~~~~~~~~i~s~~dL~~~~~i~ 377 (504)
++|++++++++||++..|++. ++|++.+ || |||++ ++.+||++++||.++..+.
T Consensus 385 ~~~~~~~~~~~q~~~~~p~~~---~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~------~~~~~i~~~~dL~~~~~~~ 455 (656)
T KOG1052|consen 385 CLWLTVGSLLQQGSDEIPRSL---STRLLLGAWWLFVLILISSYTANLTAFLTVP------RLRSPIDSLDDLADQSNIP 455 (656)
T ss_pred chhhhhHHHhccCCCccccch---hhhHHHHHHHHHHHHHHHHHHHHHHHHhccc------ccCCcccCHHHHHHhcCCe
Confidence 999999999999999999999 9999887 45 99999 9999999999999877788
Q ss_pred eeee----ecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcC---CeEEEeecchhhhhhhcC--CccEEcC
Q psy1412 378 FVTI----DLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEG---DYAFLMESTMLDYEVQRN--CNLTQIG 448 (504)
Q Consensus 378 ~g~~----~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g---~~A~i~e~~~~~y~~~~~--c~l~~vg 448 (504)
+|.. +..+++++ .+||.++.. ++.+.+.+.+|+++++++| .+|++.+...+.|...++ |++++++
T Consensus 456 ~g~~~~~~~~~~~~~~-----~~~~~~~~~-~~~~~~~~~~e~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~v~ 529 (656)
T KOG1052|consen 456 YGTQRGSFTRIYLEES-----EDMWAFKVS-QRSVPLASPEEGVERVRKGPSGGYAFASDELYLAYLFLRDEICDLTEVG 529 (656)
T ss_pred EEEEecchHHHHHHHH-----HHHHhhhcc-CCCccCCCHHHHHHHHHcCCCCceEEEeccHHHHHHHhhcCCCceEEeC
Confidence 8876 55666665 677877776 6788999999999999988 499999999999888776 9999999
Q ss_pred CccCCcceEEEecCCCCCchHHHHHHHhhhccChhHHHHHhhccCC--CCCCCCCC
Q psy1412 449 GLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKNT--GDVCNRDE 502 (504)
Q Consensus 449 ~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~l~~kw~~~~--~~~C~~~~ 502 (504)
+.+...+|| ++||||||++.+|.+|++++|.|.++++++|||..+ ...|...+
T Consensus 530 ~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g~l~~~~~kw~~~~~~~~~~~~~~ 584 (656)
T KOG1052|consen 530 EPFLYKGYG-AFPKGSPLRSLISRAILKLQETGILQKLKRKWFSKKPCLPKCSQTE 584 (656)
T ss_pred CcccCCCcc-eecCCCccHHHHHHHHHhhccccHHHHHHHHhccCCCCCCCCCCcc
Confidence 999999999 999999999999999999999999999999999975 36676544
No 5
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=99.86 E-value=2.4e-21 Score=182.73 Aligned_cols=220 Identities=22% Similarity=0.336 Sum_probs=167.4
Q ss_pred EEEEe-ecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccc
Q psy1412 138 LIVMT-REEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADL 216 (504)
Q Consensus 138 l~V~~-~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~ 216 (504)
|+|++ ...+||.+..++ +.+.|+++|+++++++++|++++++.. +|++++..|.+|++|+
T Consensus 1 l~V~~~~~~~P~~~~~~~------~~~~G~~~dl~~~i~~~~g~~~~~~~~-------------~~~~~~~~l~~g~~D~ 61 (225)
T PF00497_consen 1 LRVGVDEDYPPFSYIDED------GEPSGIDVDLLRAIAKRLGIKIEFVPM-------------PWSRLLEMLENGKADI 61 (225)
T ss_dssp EEEEEESEBTTTBEEETT------SEEESHHHHHHHHHHHHHTCEEEEEEE-------------EGGGHHHHHHTTSSSE
T ss_pred CEEEEcCCCCCeEEECCC------CCEEEEhHHHHHHHHhhcccccceeec-------------cccccccccccccccc
Confidence 68999 566899987753 789999999999999999999999853 6999999999999999
Q ss_pred eecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCCCccCC
Q psy1412 217 AVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWSNP 296 (504)
Q Consensus 217 av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~~~~~~ 296 (504)
++++++++.+|.+.++||.||+..+.++++++.+.
T Consensus 62 ~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~--------------------------------------------- 96 (225)
T PF00497_consen 62 IIGGLSITPERAKKFDFSDPYYSSPYVLVVRKGDA--------------------------------------------- 96 (225)
T ss_dssp EESSEB-BHHHHTTEEEESESEEEEEEEEEETTST---------------------------------------------
T ss_pred ccccccccccccccccccccccchhheeeeccccc---------------------------------------------
Confidence 99999999999999999999999999999986421
Q ss_pred CCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhccCCCCc
Q psy1412 297 HPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLGGQGDE 376 (504)
Q Consensus 297 ~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL~~~~~i 376 (504)
.....+++++||.+.
T Consensus 97 --------------------------------------------------------------~~~~~~~~~~dl~~~--- 111 (225)
T PF00497_consen 97 --------------------------------------------------------------PPIKTIKSLDDLKGK--- 111 (225)
T ss_dssp --------------------------------------------------------------CSTSSHSSGGGGTTS---
T ss_pred --------------------------------------------------------------cccccccchhhhcCc---
Confidence 111234566677443
Q ss_pred eeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCC--ccEEcCCccCC
Q psy1412 377 TFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNC--NLTQIGGLLDS 453 (504)
Q Consensus 377 ~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c--~l~~vg~~~~~ 453 (504)
++|........ ..+.+........+.+.+.+++++++.+|+ +|++.+...+.|++++.. ...........
T Consensus 112 ~i~~~~g~~~~-------~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 184 (225)
T PF00497_consen 112 RIGVVRGSSYA-------DYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVVIPPPISP 184 (225)
T ss_dssp EEEEETTSHHH-------HHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEE
T ss_pred ccccccchhHH-------HHhhhhccchhhhcccccHHHHHHHHhcCCeeeeeccchhhhhhhhhccccccccccccccc
Confidence 33433111111 011111111122345789999999999999 899999999999988773 33332555666
Q ss_pred cceEEEecCC-CCCchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 454 KGYGIATPKG-SPWRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 454 ~~~g~a~~k~-Spl~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
.++++++.++ +.+++.||++|.+|+++|.+++|.+||+++
T Consensus 185 ~~~~~~~~~~~~~l~~~~n~~i~~l~~~G~~~~i~~ky~g~ 225 (225)
T PF00497_consen 185 SPVYFAVRKKNPELLEIFNKAIRELKQSGEIQKILKKYLGD 225 (225)
T ss_dssp EEEEEEEETTTHHHHHHHHHHHHHHHHTTHHHHHHHHHHSS
T ss_pred ceeEEeecccccHHHHHHHHHHHHHHhCcHHHHHHHHHcCC
Confidence 7777777665 559999999999999999999999999873
No 6
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.86 E-value=5.4e-21 Score=189.26 Aligned_cols=224 Identities=21% Similarity=0.285 Sum_probs=164.6
Q ss_pred ccCCeEEEEEeecc-cCeEEEecCCCCCCCccceehhHHHHHHHHH----HcC---ceEEEEEcCCCCCccccCCCCcch
Q psy1412 132 STNNVTLIVMTREE-KPYVMVKNDANLTGNAMFEGFCIDLLKSIAA----QVG---FHFVLRLVPDHTYGVYDHETKEWN 203 (504)
Q Consensus 132 ~~~~~~l~V~~~~~-~P~~~~~~~~~~~~~~~~~G~~idll~~la~----~l~---f~~~~~~~~~~~~G~~~~~~g~w~ 203 (504)
....+.|+|++... +||.+..+ ++.++||++||++++++ ++| .+++++.. +|+
T Consensus 36 i~~~g~L~Vg~~~~~pP~~f~~~------~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~-------------~~~ 96 (302)
T PRK10797 36 IAKNGVIVVGHRESSVPFSYYDN------QQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPI-------------TSQ 96 (302)
T ss_pred HHhCCeEEEEEcCCCCCcceECC------CCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEEc-------------ChH
Confidence 34567899999865 78776532 35789999998877765 564 56666633 577
Q ss_pred hhHHHHhhccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHH
Q psy1412 204 GIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLF 283 (504)
Q Consensus 204 gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~ 283 (504)
.++..|..|++|++++++++|++|.+.++||.||+..+.++++++.+
T Consensus 97 ~~i~~L~~G~~Di~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~--------------------------------- 143 (302)
T PRK10797 97 NRIPLLQNGTFDFECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG--------------------------------- 143 (302)
T ss_pred hHHHHHHCCCccEEecCCccCcchhhcceecccEeeccEEEEEECCC---------------------------------
Confidence 89999999999999999999999999999999999999999997532
Q ss_pred HHHhhCCCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhccc
Q psy1412 284 VMARFSPYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMES 363 (504)
Q Consensus 284 ~i~r~~p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~ 363 (504)
+
T Consensus 144 -------------------------------------------------------------------------------~ 144 (302)
T PRK10797 144 -------------------------------------------------------------------------------D 144 (302)
T ss_pred -------------------------------------------------------------------------------C
Confidence 1
Q ss_pred chhhhhccCCC-CceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhc-
Q psy1412 364 KKCILFLGGQG-DETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQR- 440 (504)
Q Consensus 364 i~s~~dL~~~~-~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~- 440 (504)
|++++||.+.. .+.-|+....+++ ++.......-..+.+.+.++++++|.+|+ +|++.+...+.+...+
T Consensus 145 i~sl~dL~Gk~V~v~~gs~~~~~l~--------~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~d~~~~~~~~~~~ 216 (302)
T PRK10797 145 IKDFADLKGKAVVVTSGTTSEVLLN--------KLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKA 216 (302)
T ss_pred CCChHHcCCCEEEEeCCCcHHHHHH--------HHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEccHHHHHHHHHcC
Confidence 34566665432 1111222111111 11000000012344678899999999999 8999998776654332
Q ss_pred -C-CccEEcCCccCCcceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhccCC
Q psy1412 441 -N-CNLTQIGGLLDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWWKNT 494 (504)
Q Consensus 441 -~-c~l~~vg~~~~~~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~~~~ 494 (504)
. -.+..+++.+...+||++++|+++ +++.+|.+|.+++++|.+++|.+||+...
T Consensus 217 ~~~~~l~i~~~~~~~~~~~~a~~k~~~~L~~~in~~L~~l~~~G~l~~i~~kw~~~~ 273 (302)
T PRK10797 217 KKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFKNP 273 (302)
T ss_pred CCCcceEECCccCCcCceeEEEeCCCHHHHHHHHHHHHHHHhCchHHHHHHHHcCCC
Confidence 2 357788887788899999999987 99999999999999999999999999853
No 7
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.84 E-value=2.3e-20 Score=179.84 Aligned_cols=216 Identities=25% Similarity=0.432 Sum_probs=167.1
Q ss_pred CCeEEEEEee-cccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhc
Q psy1412 134 NNVTLIVMTR-EEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDK 212 (504)
Q Consensus 134 ~~~~l~V~~~-~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g 212 (504)
..++|+|++. ..+||.+.. ++.+.|+.+||++++++++|.+++++.. +|.+++..|.+|
T Consensus 23 ~~~~l~v~~~~~~~P~~~~~-------~g~~~G~~vdl~~~ia~~lg~~~~~~~~-------------~~~~~~~~l~~G 82 (247)
T PRK09495 23 ADKKLVVATDTAFVPFEFKQ-------GDKYVGFDIDLWAAIAKELKLDYTLKPM-------------DFSGIIPALQTK 82 (247)
T ss_pred cCCeEEEEeCCCCCCeeecC-------CCceEEEeHHHHHHHHHHhCCceEEEeC-------------CHHHHHHHHhCC
Confidence 4578999987 468887632 2678999999999999999999999743 599999999999
Q ss_pred cccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCCC
Q psy1412 213 KADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYE 292 (504)
Q Consensus 213 ~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~~ 292 (504)
++|+++++++.+++|++.++||.||+..+..+++++...
T Consensus 83 ~vDi~~~~~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~~----------------------------------------- 121 (247)
T PRK09495 83 NVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNN----------------------------------------- 121 (247)
T ss_pred CcCEEEecCccCHHHHhhccccchheecceEEEEECCCC-----------------------------------------
Confidence 999998889999999999999999999999999875321
Q ss_pred ccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhccC
Q psy1412 293 WSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLGG 372 (504)
Q Consensus 293 ~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL~~ 372 (504)
++++++||.+
T Consensus 122 ----------------------------------------------------------------------~~~~~~dL~g 131 (247)
T PRK09495 122 ----------------------------------------------------------------------DIKSVKDLDG 131 (247)
T ss_pred ----------------------------------------------------------------------CCCChHHhCC
Confidence 1345666654
Q ss_pred CCCcee--eeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcC--CccEEc
Q psy1412 373 QGDETF--VTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN--CNLTQI 447 (504)
Q Consensus 373 ~~~i~~--g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~--c~l~~v 447 (504)
.+ |.. |+....+++. .......+...+.+++++++..|+ +|++.+.....|+.++. -++..+
T Consensus 132 ~~-I~v~~g~~~~~~l~~------------~~~~~~i~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~~~~~ 198 (247)
T PRK09495 132 KV-VAVKSGTGSVDYAKA------------NIKTKDLRQFPNIDNAYLELGTGRADAVLHDTPNILYFIKTAGNGQFKAV 198 (247)
T ss_pred CE-EEEecCchHHHHHHh------------cCCCCceEEcCCHHHHHHHHHcCceeEEEeChHHHHHHHHhCCCCceEEe
Confidence 32 111 1111111110 000012233567889999999999 89999988888777654 356777
Q ss_pred CCccCCcceEEEecCCCCCchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 448 GGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 448 g~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
+......+++++++|++.+++.||++|.+++++|.++++.+||+..
T Consensus 199 ~~~~~~~~~~~a~~~~~~l~~~~n~al~~~~~~g~~~~i~~k~~~~ 244 (247)
T PRK09495 199 GDSLEAQQYGIAFPKGSELREKVNGALKTLKENGTYAEIYKKWFGT 244 (247)
T ss_pred cCcccccceEEEEcCcHHHHHHHHHHHHHHHHCCcHHHHHHHHcCC
Confidence 7767778899999999999999999999999999999999999975
No 8
>PRK11260 cystine transporter subunit; Provisional
Probab=99.81 E-value=2.3e-19 Score=174.86 Aligned_cols=220 Identities=22% Similarity=0.324 Sum_probs=168.8
Q ss_pred cccCCeEEEEEeec-ccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHH
Q psy1412 131 TSTNNVTLIVMTRE-EKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKEL 209 (504)
Q Consensus 131 ~~~~~~~l~V~~~~-~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l 209 (504)
.....++|+|++.. .+||.+... ++.+.||.+|+++++++++|.+++++.. .|.+++..|
T Consensus 36 ~i~~~~~l~v~~~~~~~P~~~~~~------~g~~~G~~~dl~~~i~~~lg~~~e~~~~-------------~~~~~~~~l 96 (266)
T PRK11260 36 KVKERGTLLVGLEGTYPPFSFQGE------DGKLTGFEVEFAEALAKHLGVKASLKPT-------------KWDGMLASL 96 (266)
T ss_pred HhhcCCeEEEEeCCCcCCceEECC------CCCEEEehHHHHHHHHHHHCCeEEEEeC-------------CHHHHHHHH
Confidence 34467889999875 588876433 3678999999999999999999999843 589999999
Q ss_pred hhccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhC
Q psy1412 210 MDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFS 289 (504)
Q Consensus 210 ~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~ 289 (504)
.+|++|+++++++++.+|.+.+.||.||+..+.++++++....
T Consensus 97 ~~G~~D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~~~------------------------------------- 139 (266)
T PRK11260 97 DSKRIDVVINQVTISDERKKKYDFSTPYTVSGIQALVKKGNEG------------------------------------- 139 (266)
T ss_pred hcCCCCEEEeccccCHHHHhccccCCceeecceEEEEEcCCcC-------------------------------------
Confidence 9999999998899999999999999999999999998754211
Q ss_pred CCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhh
Q psy1412 290 PYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILF 369 (504)
Q Consensus 290 p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~d 369 (504)
.+++++|
T Consensus 140 -------------------------------------------------------------------------~~~~~~d 146 (266)
T PRK11260 140 -------------------------------------------------------------------------TIKTAAD 146 (266)
T ss_pred -------------------------------------------------------------------------CCCCHHH
Confidence 2344556
Q ss_pred ccCCCCceeeee----ecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCc-
Q psy1412 370 LGGQGDETFVTI----DLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCN- 443 (504)
Q Consensus 370 L~~~~~i~~g~~----~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~- 443 (504)
|... .+|.. ...++++ .........+.+..++++++.+|+ ++++.+.....++.++..+
T Consensus 147 L~g~---~Igv~~G~~~~~~l~~------------~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~~~ 211 (266)
T PRK11260 147 LKGK---KVGVGLGTNYEQWLRQ------------NVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDT 211 (266)
T ss_pred cCCC---EEEEecCCcHHHHHHH------------hCCCCceEecCCHHHHHHHHHcCCCCEEEechHHHHHHHHhCCCc
Confidence 5432 22222 1111111 000011233667889999999999 8999998887877776543
Q ss_pred cEEcCCccCCcceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhccCC
Q psy1412 444 LTQIGGLLDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWWKNT 494 (504)
Q Consensus 444 l~~vg~~~~~~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~~~~ 494 (504)
+......+...+++++++|++| +++.||++|.+++++|.++++.+||+.+.
T Consensus 212 ~~~~~~~~~~~~~~~~v~~~~~~l~~~ln~~l~~~~~~g~~~~i~~k~~~~~ 263 (266)
T PRK11260 212 LAVAGEAFSRQESGVALRKGNPDLLKAVNQAIAEMQKDGTLKALSEKWFGAD 263 (266)
T ss_pred ceecCCccccCceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcCCc
Confidence 5555666778899999999987 99999999999999999999999999863
No 9
>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=99.80 E-value=5.8e-19 Score=172.83 Aligned_cols=219 Identities=16% Similarity=0.228 Sum_probs=162.6
Q ss_pred ccCCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCce-EEEEEcCCCCCccccCCCCcchhhHHHHh
Q psy1412 132 STNNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFH-FVLRLVPDHTYGVYDHETKEWNGIVKELM 210 (504)
Q Consensus 132 ~~~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~-~~~~~~~~~~~G~~~~~~g~w~gli~~l~ 210 (504)
....++|+|++...+||.+... ++.+.|+.+||++++++++|.+ ++++ ..+|+.++..|.
T Consensus 29 i~~~~~l~v~~~~~pP~~~~~~------~g~~~G~~~dl~~~i~~~lg~~~~~~~-------------~~~w~~~~~~l~ 89 (275)
T TIGR02995 29 LKEQGFARIAIANEPPFTYVGA------DGKVSGAAPDVARAIFKRLGIADVNAS-------------ITEYGALIPGLQ 89 (275)
T ss_pred HHhCCcEEEEccCCCCceeECC------CCceecchHHHHHHHHHHhCCCceeec-------------cCCHHHHHHHHH
Confidence 3466789999988899887643 3678999999999999999987 5665 346999999999
Q ss_pred hccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCC
Q psy1412 211 DKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSP 290 (504)
Q Consensus 211 ~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p 290 (504)
+|++|++++++++|++|.+.++||.||+..+.++++++.+..
T Consensus 90 ~G~~Di~~~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~~-------------------------------------- 131 (275)
T TIGR02995 90 AGRFDAIAAGLFIKPERCKQVAFTQPILCDAEALLVKKGNPK-------------------------------------- 131 (275)
T ss_pred CCCcCEEeecccCCHHHHhccccccceeecceeEEEECCCCC--------------------------------------
Confidence 999999888899999999999999999999999998865321
Q ss_pred CCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhc
Q psy1412 291 YEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFL 370 (504)
Q Consensus 291 ~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL 370 (504)
.+++++||
T Consensus 132 ------------------------------------------------------------------------~i~~~~dl 139 (275)
T TIGR02995 132 ------------------------------------------------------------------------GLKSYKDI 139 (275)
T ss_pred ------------------------------------------------------------------------CCCCHHHh
Confidence 13445555
Q ss_pred cCCCCceeeeee----cchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcC--Cc
Q psy1412 371 GGQGDETFVTID----LSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN--CN 443 (504)
Q Consensus 371 ~~~~~i~~g~~~----~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~--c~ 443 (504)
......++|.+. ..++++...+ ..+.+.+++.++++++|.+|+ +|++.+...+.+++++. .+
T Consensus 140 ~~~~g~~Igv~~g~~~~~~l~~~~~~-----------~~~i~~~~~~~~~i~~L~~grvDa~i~d~~~~~~~~~~~~~~~ 208 (275)
T TIGR02995 140 AKNPDAKIAAPGGGTEEKLAREAGVK-----------REQIIVVPDGQSGLKMVQDGRADAYSLTVLTINDLASKAGDPN 208 (275)
T ss_pred ccCCCceEEEeCCcHHHHHHHHcCCC-----------hhhEEEeCCHHHHHHHHHcCCCCEEecChHHHHHHHHhCCCCC
Confidence 433233444331 1111111000 012334678999999999999 89999999888887654 24
Q ss_pred cEEcCCcc-CC--cceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhh
Q psy1412 444 LTQIGGLL-DS--KGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490 (504)
Q Consensus 444 l~~vg~~~-~~--~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw 490 (504)
+..+.... .. ..++|+++++++ +++.||++|.++.++|.+++|.+||
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~~sG~~~~i~~ky 259 (275)
T TIGR02995 209 VEVLAPFKDAPVRYYGGAAFRPEDKELRDAFNVELAKLKESGEFAKIIAPY 259 (275)
T ss_pred ceeecCccCCccccceeEEECCCCHHHHHHHHHHHHHHHhChHHHHHHHHh
Confidence 44443321 11 223888988775 9999999999999999999999999
No 10
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.80 E-value=4.4e-19 Score=170.33 Aligned_cols=216 Identities=17% Similarity=0.318 Sum_probs=159.2
Q ss_pred CCeEEEEEee-cccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhc
Q psy1412 134 NNVTLIVMTR-EEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDK 212 (504)
Q Consensus 134 ~~~~l~V~~~-~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g 212 (504)
..++|+|++. ..+||.+... ++.++|+++|+++++++++|.+++++. .+|+.++..+.+|
T Consensus 19 ~~~~l~v~~~~~~~P~~~~~~------~g~~~G~~~dl~~~i~~~lg~~~~~~~-------------~~~~~~~~~l~~g 79 (243)
T PRK15007 19 AAETIRFATEASYPPFESIDA------NNQIVGFDVDLAQALCKEIDATCTFSN-------------QAFDSLIPSLKFR 79 (243)
T ss_pred cCCcEEEEeCCCCCCceeeCC------CCCEEeeeHHHHHHHHHHhCCcEEEEe-------------CCHHHHhHHHhCC
Confidence 3568999997 5689887643 378999999999999999999999973 3699999999999
Q ss_pred cccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCCC
Q psy1412 213 KADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYE 292 (504)
Q Consensus 213 ~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~~ 292 (504)
++|+++++++.+++|.+.++||.||+..+.+++.+...
T Consensus 80 ~~D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~v~~~~~------------------------------------------ 117 (243)
T PRK15007 80 RVEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGK------------------------------------------ 117 (243)
T ss_pred CcCEEEEcCccCHHHhcccceecCccccceEEEEeCCC------------------------------------------
Confidence 99998888999999999999999999988777754321
Q ss_pred ccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhccC
Q psy1412 293 WSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLGG 372 (504)
Q Consensus 293 ~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL~~ 372 (504)
+++++||.+
T Consensus 118 -----------------------------------------------------------------------~~~~~dL~g 126 (243)
T PRK15007 118 -----------------------------------------------------------------------YTSVDQLKG 126 (243)
T ss_pred -----------------------------------------------------------------------CCCHHHhCC
Confidence 234455543
Q ss_pred CCCceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCccEEcCCc-
Q psy1412 373 QGDETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCNLTQIGGL- 450 (504)
Q Consensus 373 ~~~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~l~~vg~~- 450 (504)
. .+|........ .+ +.+. ...-..+.+.+.++++++|..|+ +|++.+...+.++.++..++..++..
T Consensus 127 ~---~Igv~~g~~~~-----~~--l~~~-~~~~~~~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~ 195 (243)
T PRK15007 127 K---KVGVQNGTTHQ-----KF--IMDK-HPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNPKLAAVGDKV 195 (243)
T ss_pred C---eEEEecCcHHH-----HH--HHHh-CCCCeEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHhcCCCceeecCcc
Confidence 2 22322111000 00 0000 00011223567899999999999 89999988888777766656554432
Q ss_pred ----cCCcceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhcc
Q psy1412 451 ----LDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWWK 492 (504)
Q Consensus 451 ----~~~~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~~ 492 (504)
+...+++|+++++++ +++.||++|.++.++|.++++.+||+.
T Consensus 196 ~~~~~~~~~~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~i~~~w~~ 242 (243)
T PRK15007 196 TDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKWFQ 242 (243)
T ss_pred cccccCCcceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 223457999998774 999999999999999999999999985
No 11
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.80 E-value=6.1e-19 Score=170.92 Aligned_cols=214 Identities=20% Similarity=0.267 Sum_probs=157.4
Q ss_pred ccCCeEEEEEeecc-cCeEEEecCCCCCCCccceehhHHHHHHHHHHc-Cce--EEEEEcCCCCCccccCCCCcchhhHH
Q psy1412 132 STNNVTLIVMTREE-KPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQV-GFH--FVLRLVPDHTYGVYDHETKEWNGIVK 207 (504)
Q Consensus 132 ~~~~~~l~V~~~~~-~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l-~f~--~~~~~~~~~~~G~~~~~~g~w~gli~ 207 (504)
....++|+|++... |||.+.+.. ++.++||++||++++++++ |.. ++++.+ +|...+.
T Consensus 34 i~~~g~l~vg~~~~~pP~~~~~~~-----~g~~~G~~vdl~~~ia~~llg~~~~~~~~~~-------------~~~~~~~ 95 (259)
T PRK11917 34 IKSKGQLIVGVKNDVPHYALLDQA-----TGEIKGFEIDVAKLLAKSILGDDKKIKLVAV-------------NAKTRGP 95 (259)
T ss_pred HHhCCEEEEEECCCCCCceeeeCC-----CCceeEeeHHHHHHHHHHhcCCCccEEEEEc-------------ChhhHHH
Confidence 34678999999864 777765422 3689999999999999995 754 555433 4666778
Q ss_pred HHhhccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHh
Q psy1412 208 ELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMAR 287 (504)
Q Consensus 208 ~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r 287 (504)
.|.+|++|++++++++|++|.+.++||.||+.++.++++++..
T Consensus 96 ~l~~g~~D~~~~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~------------------------------------- 138 (259)
T PRK11917 96 LLDNGSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEK------------------------------------- 138 (259)
T ss_pred HHHCCCccEEEecccCChhhhheeeeccCceeeceEEEEECCC-------------------------------------
Confidence 9999999999999999999999999999999999999998542
Q ss_pred hCCCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhh
Q psy1412 288 FSPYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCI 367 (504)
Q Consensus 288 ~~p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~ 367 (504)
+++++
T Consensus 139 ---------------------------------------------------------------------------~~~s~ 143 (259)
T PRK11917 139 ---------------------------------------------------------------------------NYKSL 143 (259)
T ss_pred ---------------------------------------------------------------------------CCCCH
Confidence 13456
Q ss_pred hhccCCC-CceeeeeecchhccchhHHHHHHHHHHHhcC---CCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCC
Q psy1412 368 LFLGGQG-DETFVTIDLSQRADSKIEIYQKMWRYMESKR---PSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNC 442 (504)
Q Consensus 368 ~dL~~~~-~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~---~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c 442 (504)
+||.+.+ .+..|+.....+. +..+... ..+.+++..++++++..|+ +|++.+...+.++.++
T Consensus 144 ~dL~g~~V~v~~gs~~~~~l~-----------~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~-- 210 (259)
T PRK11917 144 ADMKGANIGVAQAATTKKAIG-----------EAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDD-- 210 (259)
T ss_pred HHhCCCeEEEecCCcHHHHHH-----------HhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEecHHHHHHhhhc--
Confidence 6665432 1111221111111 1111111 1134678899999999999 8999988876655443
Q ss_pred ccEEcCCccCCcceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhh
Q psy1412 443 NLTQIGGLLDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490 (504)
Q Consensus 443 ~l~~vg~~~~~~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw 490 (504)
+...++..+...+||++++|+++ +++.+|++|.++.. .+++|.+||
T Consensus 211 ~~~~~~~~~~~~~~~~a~~k~~~~l~~~ln~~l~~~~~--~~~~i~~kw 257 (259)
T PRK11917 211 KSEILPDSFEPQSYGIVTKKDDPAFAKYVDDFVKEHKN--EIDALAKKW 257 (259)
T ss_pred CCeecCCcCCCCceEEEEeCCCHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 34566777888899999999987 99999999999964 899999998
No 12
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.78 E-value=2.9e-18 Score=165.31 Aligned_cols=212 Identities=22% Similarity=0.368 Sum_probs=160.6
Q ss_pred eEEEEEee-cccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccc
Q psy1412 136 VTLIVMTR-EEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKA 214 (504)
Q Consensus 136 ~~l~V~~~-~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~ 214 (504)
++|+|++. ..+||.+..+ +++++||++|+++++++.+|.+++++. .+|+.++..|.+|++
T Consensus 24 ~~l~v~~~~~~~P~~~~~~------~g~~~G~~~dl~~~i~~~lg~~~~~~~-------------~~~~~~~~~l~~G~~ 84 (250)
T TIGR01096 24 GSVRIGTETGYPPFESKDA------NGKLVGFDVDLAKALCKRMKAKCKFVE-------------QNFDGLIPSLKAKKV 84 (250)
T ss_pred CeEEEEECCCCCCceEECC------CCCEEeehHHHHHHHHHHhCCeEEEEe-------------CCHHHHHHHHhCCCc
Confidence 78999986 4588887543 368899999999999999999999874 369999999999999
Q ss_pred cceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCCCcc
Q psy1412 215 DLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWS 294 (504)
Q Consensus 215 D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~~~~ 294 (504)
|+++++++.+.+|.+.+.||.||+..+..++++.....
T Consensus 85 D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~------------------------------------------ 122 (250)
T TIGR01096 85 DAIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDL------------------------------------------ 122 (250)
T ss_pred CEEEecCccCHHHhhccccccchhcCCeEEEEECCCCc------------------------------------------
Confidence 99988889999999999999999999999998764321
Q ss_pred CCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhccCCC
Q psy1412 295 NPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLGGQG 374 (504)
Q Consensus 295 ~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL~~~~ 374 (504)
+.+++||.+.
T Consensus 123 ---------------------------------------------------------------------~~~~~dl~g~- 132 (250)
T TIGR01096 123 ---------------------------------------------------------------------AKTLEDLDGK- 132 (250)
T ss_pred ---------------------------------------------------------------------CCChHHcCCC-
Confidence 1223444322
Q ss_pred Cceeeee----ecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCC---ccEE
Q psy1412 375 DETFVTI----DLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNC---NLTQ 446 (504)
Q Consensus 375 ~i~~g~~----~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c---~l~~ 446 (504)
..|.. ...+++ +.+...-..+.+.+.+++++++.+|+ ++++.+...+.+++++.. ++..
T Consensus 133 --~i~~~~g~~~~~~l~-----------~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~~~~~~l~~ 199 (250)
T TIGR01096 133 --TVGVQSGTTHEQYLK-----------DYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKF 199 (250)
T ss_pred --EEEEecCchHHHHHH-----------HhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHHhCCCCCceEE
Confidence 12211 111111 00100011233578899999999999 899999999888877653 3666
Q ss_pred cCCccCC-----cceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhc
Q psy1412 447 IGGLLDS-----KGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWW 491 (504)
Q Consensus 447 vg~~~~~-----~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~ 491 (504)
++..+.. .+++++++|+++ ++..||++|.+|+++|.+++|.+||+
T Consensus 200 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 200 VGPSVTDEKYFGDGYGIGLRKGDTELKAAFNKALAAIRADGTYQKISKKWF 250 (250)
T ss_pred eccccccccccCCceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHhhC
Confidence 6654332 248899999886 99999999999999999999999996
No 13
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.78 E-value=4.8e-18 Score=178.73 Aligned_cols=221 Identities=19% Similarity=0.220 Sum_probs=164.9
Q ss_pred cccCCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHh
Q psy1412 131 TSTNNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELM 210 (504)
Q Consensus 131 ~~~~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~ 210 (504)
...+.++|+|++.. +|+.++.+. +...||++||++++++++|.+++++.+ .+|+.++..|.
T Consensus 38 ~I~~~g~LrVg~~~-~P~~~~~~~------~~~~G~~~DLl~~ia~~LGv~~e~v~~------------~~~~~ll~aL~ 98 (482)
T PRK10859 38 QIQERGELRVGTIN-SPLTYYIGN------DGPTGFEYELAKRFADYLGVKLEIKVR------------DNISQLFDALD 98 (482)
T ss_pred HHHhCCEEEEEEec-CCCeeEecC------CCcccHHHHHHHHHHHHhCCcEEEEec------------CCHHHHHHHHh
Confidence 34467889999985 555554432 234899999999999999999999843 36999999999
Q ss_pred hccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCC
Q psy1412 211 DKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSP 290 (504)
Q Consensus 211 ~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p 290 (504)
+|++|++++++++|++|.+.++||.||+..+.++++++...
T Consensus 99 ~G~iDi~~~~lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~~--------------------------------------- 139 (482)
T PRK10859 99 KGKADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQP--------------------------------------- 139 (482)
T ss_pred CCCCCEEeccCcCChhhhccCcccCCceeeeEEEEEeCCCC---------------------------------------
Confidence 99999998999999999999999999999999999875421
Q ss_pred CCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhc
Q psy1412 291 YEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFL 370 (504)
Q Consensus 291 ~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL 370 (504)
.+++++||
T Consensus 140 ------------------------------------------------------------------------~i~~l~dL 147 (482)
T PRK10859 140 ------------------------------------------------------------------------RPRSLGDL 147 (482)
T ss_pred ------------------------------------------------------------------------CCCCHHHh
Confidence 13456666
Q ss_pred cCCC-CceeeeeecchhccchhHHHHHHHHHHHhcCC-----CcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCc
Q psy1412 371 GGQG-DETFVTIDLSQRADSKIEIYQKMWRYMESKRP-----SVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCN 443 (504)
Q Consensus 371 ~~~~-~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~-----~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~ 443 (504)
.+.. .+.-|+.....++ ++ ....+ .+...+.++++++|.+|+ ++++.+...+.+......+
T Consensus 148 ~Gk~I~V~~gS~~~~~L~--------~l----~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d~~~~~~~~~~~p~ 215 (482)
T PRK10859 148 KGGTLTVAAGSSHVETLQ--------EL----KKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPE 215 (482)
T ss_pred CCCeEEEECCCcHHHHHH--------HH----HHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEECcHHHHHHHHhCCC
Confidence 5432 1111221111111 11 00011 122458899999999999 8999988877765444567
Q ss_pred cEEcCCccCCcceEEEecCC-CC-CchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 444 LTQIGGLLDSKGYGIATPKG-SP-WRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 444 l~~vg~~~~~~~~g~a~~k~-Sp-l~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
+..........+++++++|+ ++ |++.+|++|.+++++|.+++|.+||+..
T Consensus 216 l~v~~~l~~~~~~~~av~k~~~~~L~~~ln~~L~~i~~~G~l~~L~~kyfg~ 267 (482)
T PRK10859 216 LAVAFDLTDEQPVAWALPPSGDDSLYAALLDFFNQIKEDGTLARLEEKYFGH 267 (482)
T ss_pred ceeeeecCCCceeEEEEeCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHhhh
Confidence 77665555667899999994 44 9999999999999999999999999985
No 14
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.77 E-value=9.2e-18 Score=162.97 Aligned_cols=221 Identities=17% Similarity=0.195 Sum_probs=158.0
Q ss_pred cCCeEEEEEee-cccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhh
Q psy1412 133 TNNVTLIVMTR-EEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMD 211 (504)
Q Consensus 133 ~~~~~l~V~~~-~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~ 211 (504)
...++|+|++. ..+||.+..+ ++.+.|+++||++++++++|.+++++.. +|+.++..+..
T Consensus 23 ~~~~~l~v~~~~~~pPf~~~~~------~g~~~G~~vdl~~~ia~~lg~~~~~~~~-------------~~~~~~~~l~~ 83 (260)
T PRK15010 23 ALPETVRIGTDTTYAPFSSKDA------KGDFVGFDIDLGNEMCKRMQVKCTWVAS-------------DFDALIPSLKA 83 (260)
T ss_pred ccCCeEEEEecCCcCCceeECC------CCCEEeeeHHHHHHHHHHhCCceEEEeC-------------CHHHHHHHHHC
Confidence 34578999998 4688887543 3678999999999999999999998843 59999999999
Q ss_pred ccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCC
Q psy1412 212 KKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPY 291 (504)
Q Consensus 212 g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~ 291 (504)
|++|+++++++.|++|++.++||.||+..+.++++++.....
T Consensus 84 g~~Di~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~-------------------------------------- 125 (260)
T PRK15010 84 KKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQ-------------------------------------- 125 (260)
T ss_pred CCCCEEEecCcCCHHHHhhcccccceEeccEEEEEECCCCCC--------------------------------------
Confidence 999999999999999999999999999999999987653210
Q ss_pred CccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhcc
Q psy1412 292 EWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLG 371 (504)
Q Consensus 292 ~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL~ 371 (504)
.+++||.
T Consensus 126 -------------------------------------------------------------------------~~~~dl~ 132 (260)
T PRK15010 126 -------------------------------------------------------------------------PTLDSLK 132 (260)
T ss_pred -------------------------------------------------------------------------CChhHcC
Confidence 1234443
Q ss_pred CCCCceeeeeecchhccchhHHHHHHHHHHHh-cCCCcccCChHHHHHhhhcCC-eEEEeecchhhh-hhhcC-C-ccEE
Q psy1412 372 GQGDETFVTIDLSQRADSKIEIYQKMWRYMES-KRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDY-EVQRN-C-NLTQ 446 (504)
Q Consensus 372 ~~~~i~~g~~~~~~~~~s~~~~~~~~~~~~~~-~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y-~~~~~-c-~l~~ 446 (504)
++ ++|...... ...|- ...... .-..+.+.+.++++++|.+|+ +|++.+.....+ +.++. . ++..
T Consensus 133 g~---~Igv~~gs~-----~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d~~~~~~~~~~~~~~~~~~~ 202 (260)
T PRK15010 133 GK---HVGVLQGST-----QEAYA--NETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQDEVAASEGFLKQPAGKDFAF 202 (260)
T ss_pred CC---EEEEecCch-----HHHHH--HHhcccCCceEEecCCHHHHHHHHHcCCccEEEeCcHHHHHHHHhCCCCCceEE
Confidence 32 122220000 00000 000000 011223567889999999999 899988877654 33332 2 3444
Q ss_pred cCCc-----cCCcceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 447 IGGL-----LDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 447 vg~~-----~~~~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
.+.. +...+++++++++.+ +++.+|++|.+++++|.+++|.+||+..
T Consensus 203 ~~~~~~~~~~~~~~~~~a~~~~~~~L~~~ln~~l~~l~~~G~~~~i~~ky~~~ 255 (260)
T PRK15010 203 AGPSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELRQDGTYDKMAKKYFDF 255 (260)
T ss_pred ecCccccccccCCceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcCC
Confidence 4432 222346899998875 9999999999999999999999999873
No 15
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.74 E-value=2.6e-17 Score=159.66 Aligned_cols=221 Identities=17% Similarity=0.219 Sum_probs=157.7
Q ss_pred cCCeEEEEEeec-ccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhh
Q psy1412 133 TNNVTLIVMTRE-EKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMD 211 (504)
Q Consensus 133 ~~~~~l~V~~~~-~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~ 211 (504)
....+|+|++.. .+||.+.++ ++.+.|+++|+++++++++|.+++++.. +|+.++..+.+
T Consensus 23 a~~~~l~v~~~~~~~P~~~~~~------~g~~~G~~vdi~~~ia~~lg~~i~~~~~-------------pw~~~~~~l~~ 83 (259)
T PRK15437 23 AIPQNIRIGTDPTYAPFESKNS------QGELVGFDIDLAKELCKRINTQCTFVEN-------------PLDALIPSLKA 83 (259)
T ss_pred ccCCeEEEEeCCCCCCcceeCC------CCCEEeeeHHHHHHHHHHcCCceEEEeC-------------CHHHHHHHHHC
Confidence 345789999985 689887644 3688999999999999999999999853 59999999999
Q ss_pred ccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCC
Q psy1412 212 KKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPY 291 (504)
Q Consensus 212 g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~ 291 (504)
|++|+++++++.|++|.+.++||.||...+.++++++..+.
T Consensus 84 g~~D~~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~--------------------------------------- 124 (259)
T PRK15437 84 KKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDI--------------------------------------- 124 (259)
T ss_pred CCCCEEEecCCCCHHHhhhccccchhhcCceEEEEECCCCC---------------------------------------
Confidence 99999999999999999999999999999999998764310
Q ss_pred CccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhcc
Q psy1412 292 EWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLG 371 (504)
Q Consensus 292 ~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL~ 371 (504)
..+++||.
T Consensus 125 ------------------------------------------------------------------------~~~~~dl~ 132 (259)
T PRK15437 125 ------------------------------------------------------------------------QPTVESLK 132 (259)
T ss_pred ------------------------------------------------------------------------CCChHHhC
Confidence 01344553
Q ss_pred CCCCceeeeeecchhccchhHHH-HHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhh-hhhcC--CccEE
Q psy1412 372 GQGDETFVTIDLSQRADSKIEIY-QKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDY-EVQRN--CNLTQ 446 (504)
Q Consensus 372 ~~~~i~~g~~~~~~~~~s~~~~~-~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y-~~~~~--c~l~~ 446 (504)
+. ..|....... ..| +..+. ......+.+.+.++++++|..|+ ++++.+.....+ +.++. -++..
T Consensus 133 g~---~Igv~~g~~~-----~~~~~~~~~--~~~~~~~~~~~~~~~i~~L~~grvD~~v~~~~~~~~~~~~~~~~~~~~~ 202 (259)
T PRK15437 133 GK---RVGVLQGTTQ-----ETFGNEHWA--PKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKF 202 (259)
T ss_pred CC---EEEEecCcHH-----HHHHHhhcc--ccCceEEecCCHHHHHHHHHcCCccEEEechHHHHHHHHhCCCCCceEE
Confidence 32 2222211000 001 00000 00011234567789999999999 898888876643 22322 23433
Q ss_pred cCC-----ccCCcceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 447 IGG-----LLDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 447 vg~-----~~~~~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
.+. .+...+++++++++.+ +++.+|.+|.+++++|.+++|.+||+.-
T Consensus 203 ~~~~i~~~~~~~~~~~ia~~~~~~~l~~~~n~~l~~~~~~G~~~~i~~k~~~~ 255 (259)
T PRK15437 203 GGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDF 255 (259)
T ss_pred ecCccccccccCcceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHHhcCC
Confidence 322 2233457899987765 9999999999999999999999999873
No 16
>TIGR02285 conserved hypothetical protein. Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown.
Probab=99.69 E-value=5.4e-16 Score=151.23 Aligned_cols=224 Identities=16% Similarity=0.154 Sum_probs=156.4
Q ss_pred CCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhc
Q psy1412 134 NNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDK 212 (504)
Q Consensus 134 ~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g 212 (504)
..++|++++...|||.+... ++...|+.+++++++++++ ++++++... +|++++..| .|
T Consensus 16 ~~~~l~~~~~~~pPf~~~~~------~~~~~G~~~~i~~~i~~~~~~~~~~~~~~-------------pw~r~l~~l-~~ 75 (268)
T TIGR02285 16 AKEAITWIVNDFPPFFIFSG------PSKGRGVFDVILQEIRRALPQYEHRFVRV-------------SFARSLKEL-QG 75 (268)
T ss_pred ccceeEEEecccCCeeEeCC------CCCCCChHHHHHHHHHHHcCCCceeEEEC-------------CHHHHHHHH-hc
Confidence 35789999998899987532 3567899999999999998 888888843 699999999 78
Q ss_pred cccceecceeeecccceeeeeccceee-ccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCC
Q psy1412 213 KADLAVASMTINYARESVIDFTKPFMN-LGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPY 291 (504)
Q Consensus 213 ~~D~av~~~tit~~R~~~vdFs~p~~~-~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~ 291 (504)
+.|.++.++++|+||++.++||.||+. ...++++++.+.....
T Consensus 76 ~~d~~~~~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~~~------------------------------------ 119 (268)
T TIGR02285 76 KGGVCTVNLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAGVR------------------------------------ 119 (268)
T ss_pred CCCeEEeeccCCcchhhceeecCCccccCCceEEEccchhhhcc------------------------------------
Confidence 888888889999999999999999975 5788888764321100
Q ss_pred CccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhc---ccchhhh
Q psy1412 292 EWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYM---ESKKCIL 368 (504)
Q Consensus 292 ~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~---~~i~s~~ 368 (504)
... ..+.++.
T Consensus 120 -------------------------------------------------------------------~~~d~~~~~~~l~ 132 (268)
T TIGR02285 120 -------------------------------------------------------------------DEQDGDVDLKKLL 132 (268)
T ss_pred -------------------------------------------------------------------ccCCCCccHHHHh
Confidence 000 0122233
Q ss_pred hccCCCCceeeee----ecchhccchhHHHHHHHHHHHhcC-----CCcccCChHHHHHhhhcCC-eEEEeecchhhhhh
Q psy1412 369 FLGGQGDETFVTI----DLSQRADSKIEIYQKMWRYMESKR-----PSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEV 438 (504)
Q Consensus 369 dL~~~~~i~~g~~----~~~~~~~s~~~~~~~~~~~~~~~~-----~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~ 438 (504)
||.+ .+.|.. ....++ +..+... ......+.++++++|..|+ +|++.+...+.|+.
T Consensus 133 ~l~g---~~vgv~~g~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~L~~GrvD~~v~d~~~~~~~~ 198 (268)
T TIGR02285 133 ASKK---KRLGVIASRSYGQQID-----------DILSDSGYQHNTRIIGNAAMGNLFKMLEKGRVNYTLAYPPEKTYYE 198 (268)
T ss_pred cCCC---eEEEEecceeccHHHH-----------HHHHhCCcccceeeeccchHHHHHHHHHcCCccEEEeCcHHHHHHH
Confidence 3332 223332 111111 1111100 1122456778899999999 89999999888887
Q ss_pred hcC----CccEEcCCc--cCCcceEEEecCCC---CCchHHHHHHHhhhccChhHHHHHhhccCC
Q psy1412 439 QRN----CNLTQIGGL--LDSKGYGIATPKGS---PWRDRISLAILELQEKGTIQMLYDKWWKNT 494 (504)
Q Consensus 439 ~~~----c~l~~vg~~--~~~~~~g~a~~k~S---pl~~~in~ail~l~e~G~l~~l~~kw~~~~ 494 (504)
++. ..+..+... ....+++|+++|++ .+++.||++|.+|.++|.+++|.+||+..+
T Consensus 199 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~i~~k~~~~~ 263 (268)
T TIGR02285 199 ELNNGALPPLKFLPVAGMPAHISVWVACPKTEWGRKVIADIDQALSELNVDPKYYKYFDRWLSPE 263 (268)
T ss_pred HhccCCcCCeeEeecCCCccceEEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhCCHh
Confidence 642 244444322 12346899999974 499999999999999999999999999753
No 17
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=99.69 E-value=3.5e-17 Score=120.14 Aligned_cols=64 Identities=47% Similarity=0.984 Sum_probs=54.8
Q ss_pred CeEEEecC-CCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhh
Q psy1412 147 PYVMVKND-ANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMD 211 (504)
Q Consensus 147 P~~~~~~~-~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~ 211 (504)
||++.+++ ...+++.+++||||||+++||+.|||+|+++.++|++||+.++ +|+|+|||++|++
T Consensus 1 Pfvm~~~~~~~~~g~~~~eGyciDll~~la~~l~F~y~i~~~~Dg~yG~~~~-~g~W~GmiGeli~ 65 (65)
T PF10613_consen 1 PFVMLKEDGENLTGNDRYEGYCIDLLEELAEELNFTYEIYLVPDGKYGSKNP-NGSWNGMIGELIR 65 (65)
T ss_dssp TTBEE-TTSSGSBGGGGEESHHHHHHHHHHHHHT-EEEEEE-TTS--EEBET-TSEBEHHHHHHHT
T ss_pred CeEEEecCCcccCCCccEEEEHHHHHHHHHHHcCCeEEEEECCCCCCcCcCC-CCcCcCHHHHhcC
Confidence 88888776 5677899999999999999999999999999999999999999 9999999999974
No 18
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.66 E-value=1.3e-15 Score=148.67 Aligned_cols=222 Identities=24% Similarity=0.321 Sum_probs=161.7
Q ss_pred CCeEEEEEeecc-c-CeEEEecCCCCCCCccceehhHHHHHHHHHHcCce--EEEEEcCCCCCccccCCCCcchhhHHHH
Q psy1412 134 NNVTLIVMTREE-K-PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFH--FVLRLVPDHTYGVYDHETKEWNGIVKEL 209 (504)
Q Consensus 134 ~~~~l~V~~~~~-~-P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~--~~~~~~~~~~~G~~~~~~g~w~gli~~l 209 (504)
..+.++|++... + |+.+.... .+.+.||++|+++++++.++.. .+++ ...|++++..|
T Consensus 32 ~~~~~~v~~~~~~~~p~~~~~~~-----~~~~~G~dvdl~~~ia~~l~~~~~~~~~-------------~~~~~~~~~~l 93 (275)
T COG0834 32 ARGKLRVGTEATYAPPFEFLDAK-----GGKLVGFDVDLAKAIAKRLGGDKKVEFV-------------PVAWDGLIPAL 93 (275)
T ss_pred hcCeEEEEecCCCCCCcccccCC-----CCeEEeeeHHHHHHHHHHhCCcceeEEe-------------ccchhhhhHHH
Confidence 456788888744 4 66664432 1589999999999999999886 4555 34799999999
Q ss_pred hhccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhC
Q psy1412 210 MDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFS 289 (504)
Q Consensus 210 ~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~ 289 (504)
..|++|++++.+++|.+|.+.++||.||+..+..+++++....
T Consensus 94 ~~g~~D~~~~~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~~------------------------------------- 136 (275)
T COG0834 94 KAGKVDIIIAGMTITPERKKKVDFSDPYYYSGQVLLVKKDSDI------------------------------------- 136 (275)
T ss_pred hcCCcCEEEeccccCHHHhccccccccccccCeEEEEECCCCc-------------------------------------
Confidence 9999999999999999999999999999999999999865421
Q ss_pred CCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhh
Q psy1412 290 PYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILF 369 (504)
Q Consensus 290 p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~d 369 (504)
.+.+.+|
T Consensus 137 -------------------------------------------------------------------------~~~~~~D 143 (275)
T COG0834 137 -------------------------------------------------------------------------GIKSLED 143 (275)
T ss_pred -------------------------------------------------------------------------CcCCHHH
Confidence 1345666
Q ss_pred ccCCC-CceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhh--hhcCCc-c
Q psy1412 370 LGGQG-DETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYE--VQRNCN-L 444 (504)
Q Consensus 370 L~~~~-~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~--~~~~c~-l 444 (504)
|.... .+..|+. ................+.+++..++++.+++|+ +|++.+.+.+.+. ....-. .
T Consensus 144 L~gk~v~v~~gt~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~~~~~~~~~~~~ 213 (275)
T COG0834 144 LKGKKVGVQLGTT----------DEAEEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLY 213 (275)
T ss_pred hCCCEEEEEcCcc----------hhHHHHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcchHhhhhhhhhhcCCCCc
Confidence 66521 2222322 000000000000112344667788999999999 8999999999883 333322 2
Q ss_pred EEcCCccCC-cceEEEecCC--CCCchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 445 TQIGGLLDS-KGYGIATPKG--SPWRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 445 ~~vg~~~~~-~~~g~a~~k~--Spl~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
......... ..+|++++|+ ..+++.+|.+|.++.++|.++++.+||+..
T Consensus 214 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~in~~l~~l~~~G~~~~i~~kw~~~ 265 (275)
T COG0834 214 VLLVFPGLSVEYLGIALRKGDDPELLEAVNKALKELKADGTLQKISDKWFGP 265 (275)
T ss_pred eeeeccCCCcceeEEEeccCCcHHHHHHHHHHHHHHHhCccHHHHHHHhcCc
Confidence 233333333 7899999999 479999999999999999999999999984
No 19
>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=99.65 E-value=1.1e-15 Score=147.20 Aligned_cols=87 Identities=24% Similarity=0.312 Sum_probs=72.7
Q ss_pred EEEEEeecc-cCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhH---HHHhhc
Q psy1412 137 TLIVMTREE-KPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV---KELMDK 212 (504)
Q Consensus 137 ~l~V~~~~~-~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli---~~l~~g 212 (504)
+|+||+... |||.+. + + .||++||++++++++|++++++.. +|++++ ..|.+|
T Consensus 1 ~l~vg~~~~~pPf~~~--~------~--~Gfdvdl~~~ia~~lg~~~~~~~~-------------~~~~~~~~~~~L~~g 57 (246)
T TIGR03870 1 TLRVCAATKEAPYSTK--D------G--SGFENKIAAALAAAMGRKVVFVWL-------------AKPAIYLVRDGLDKK 57 (246)
T ss_pred CeEEEeCCCCCCCccC--C------C--CcchHHHHHHHHHHhCCCeEEEEe-------------ccchhhHHHHHHhcC
Confidence 478998765 777763 1 1 599999999999999999999843 577776 699999
Q ss_pred cccceecceeeecccceeeeeccceeeccEEEEEEccC
Q psy1412 213 KADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPT 250 (504)
Q Consensus 213 ~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~ 250 (504)
++|+++ +++++++| ++||.||+.++.++++++.+
T Consensus 58 ~~Dii~-~~~~t~~r---~~fS~PY~~~~~~~v~~k~~ 91 (246)
T TIGR03870 58 LCDVVL-GLDTGDPR---VLTTKPYYRSSYVFLTRKDR 91 (246)
T ss_pred CccEEE-eCCCChHH---HhcccCcEEeeeEEEEeCCC
Confidence 999988 58888887 68999999999999998754
No 20
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.60 E-value=3.2e-14 Score=132.01 Aligned_cols=213 Identities=27% Similarity=0.455 Sum_probs=159.8
Q ss_pred EEEEEe-ecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhcccc
Q psy1412 137 TLIVMT-REEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKAD 215 (504)
Q Consensus 137 ~l~V~~-~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D 215 (504)
+|+|++ ...+|+.+... ++.+.|+++|+++.+.+++|++++++.. .|..++..|.+|++|
T Consensus 1 ~l~v~~~~~~~p~~~~~~------~g~~~G~~~~~~~~~~~~~g~~~~~~~~-------------~~~~~~~~l~~g~~D 61 (219)
T smart00062 1 TLRVGTNGDYPPFSFADE------DGELTGFDVDLAKAIAKELGLKVEFVEV-------------SFDNLLTALKSGKID 61 (219)
T ss_pred CEEEEecCCCCCcEEECC------CCCcccchHHHHHHHHHHhCCeEEEEec-------------cHHHHHHHHHCCccc
Confidence 478888 44578777543 3669999999999999999999888742 688999999999999
Q ss_pred ceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCCCccC
Q psy1412 216 LAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWSN 295 (504)
Q Consensus 216 ~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~~~~~ 295 (504)
++++....+.+|...+.|+.|+...+.++++++..
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------- 96 (219)
T smart00062 62 VVAAGMTITPERAKQVDFSDPYYKSGQVILVRKDS--------------------------------------------- 96 (219)
T ss_pred EEeccccCCHHHHhheeeccceeeceeEEEEecCC---------------------------------------------
Confidence 99988877889999999999999999888887532
Q ss_pred CCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhccCCCC
Q psy1412 296 PHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLGGQGD 375 (504)
Q Consensus 296 ~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL~~~~~ 375 (504)
++.+++||.+.
T Consensus 97 -------------------------------------------------------------------~~~~~~dL~g~-- 107 (219)
T smart00062 97 -------------------------------------------------------------------PIKSLEDLKGK-- 107 (219)
T ss_pred -------------------------------------------------------------------CCCChHHhCCC--
Confidence 13456666432
Q ss_pred ceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcC--CccEEcCCccC
Q psy1412 376 ETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN--CNLTQIGGLLD 452 (504)
Q Consensus 376 i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~--c~l~~vg~~~~ 452 (504)
.+|... . ..+..+............+.+..+++.++.+|+ +|++...+...+..++. +++..+.....
T Consensus 108 -~i~~~~-----g---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 178 (219)
T smart00062 108 -KVAVVA-----G---TTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELKIVGDPLD 178 (219)
T ss_pred -EEEEec-----C---ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCCceeeccCCCC
Confidence 122110 0 011111111111112344567889999999999 88888888877776654 67777766555
Q ss_pred C-cceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhc
Q psy1412 453 S-KGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWW 491 (504)
Q Consensus 453 ~-~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~ 491 (504)
. ..++++++|+++ +.+.++++|.+++++|.++++.+||+
T Consensus 179 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~ 219 (219)
T smart00062 179 TPEGYAFAVRKGDPELLDKINKALKELKADGTLKKIYEKWF 219 (219)
T ss_pred CCcceEEEEECCCHHHHHHHHHHHHHHHhCchHHHHHhccC
Confidence 5 788999999986 89999999999999999999999995
No 21
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.59 E-value=7.5e-15 Score=171.98 Aligned_cols=215 Identities=20% Similarity=0.232 Sum_probs=157.8
Q ss_pred cCCeEEEEEeecc-cCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhh
Q psy1412 133 TNNVTLIVMTREE-KPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMD 211 (504)
Q Consensus 133 ~~~~~l~V~~~~~-~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~ 211 (504)
.+.++++|++... +||.+..+ ++.+.||.+|+++++++++|.+++++.. ..|..++..|.+
T Consensus 299 ~~~~~l~v~~~~~~pP~~~~d~------~g~~~G~~~Dll~~i~~~~g~~~~~v~~------------~~~~~~~~~l~~ 360 (1197)
T PRK09959 299 KQHPDLKVLENPYSPPYSMTDE------NGSVRGVMGDILNIITLQTGLNFSPITV------------SHNIHAGTQLNP 360 (1197)
T ss_pred HHCCceEEEcCCCCCCeeEECC------CCcEeeehHHHHHHHHHHHCCeEEEEec------------CCHHHHHHHHHC
Confidence 3567899998875 78887643 3789999999999999999999988854 257778889999
Q ss_pred ccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCC
Q psy1412 212 KKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPY 291 (504)
Q Consensus 212 g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~ 291 (504)
|++|++. +++.|++|.+.++||.||+....++++++.....
T Consensus 361 g~~D~i~-~~~~t~~r~~~~~fs~py~~~~~~~v~~~~~~~~-------------------------------------- 401 (1197)
T PRK09959 361 GGWDIIP-GAIYSEDRENNVLFAEAFITTPYVFVMQKAPDSE-------------------------------------- 401 (1197)
T ss_pred CCceEee-cccCCccccccceeccccccCCEEEEEecCCCCc--------------------------------------
Confidence 9999854 6668999999999999999999999987542100
Q ss_pred CccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhcc
Q psy1412 292 EWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLG 371 (504)
Q Consensus 292 ~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL~ 371 (504)
.++.
T Consensus 402 ----------------------------------------------------------------------------~~~~ 405 (1197)
T PRK09959 402 ----------------------------------------------------------------------------QTLK 405 (1197)
T ss_pred ----------------------------------------------------------------------------cccc
Confidence 0000
Q ss_pred CCCCce--eeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcC--Ccc-E
Q psy1412 372 GQGDET--FVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN--CNL-T 445 (504)
Q Consensus 372 ~~~~i~--~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~--c~l-~ 445 (504)
+...|. .|+....+++ ..|+ .-..+.+++.++++++|.+|+ +|++.+...+.|++++. -++ .
T Consensus 406 ~g~~vav~~g~~~~~~~~----~~~p--------~~~~~~~~~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~~l~~ 473 (1197)
T PRK09959 406 KGMKVAIPYYYELHSQLK----EMYP--------EVEWIKVDNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNELYH 473 (1197)
T ss_pred cCCEEEEeCCcchHHHHH----HHCC--------CcEEEEcCCHHHHHHHHHcCCCCEEehhhHHHHHHHHhccccccee
Confidence 000011 0111011111 0010 012345788999999999999 89999999999998764 233 2
Q ss_pred EcCCccCCcceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 446 QIGGLLDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 446 ~vg~~~~~~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
.....+...+++|+++|+.| |++.+|++|..+.++ .+++|.+||+..
T Consensus 474 ~~~~~~~~~~~~~av~k~~~~L~~~lnk~l~~i~~~-~~~~i~~kW~~~ 521 (1197)
T PRK09959 474 FLIPGVPNASLSFAFPRGEPELKDIINKALNAIPPS-EVLRLTEKWIKM 521 (1197)
T ss_pred eecCCCCchheEEeeCCCCHHHHHHHHHHHHhCCHH-HHHHHHhhcccC
Confidence 33334556789999999987 999999999999999 899999999874
No 22
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.59 E-value=6.6e-15 Score=172.46 Aligned_cols=221 Identities=11% Similarity=0.104 Sum_probs=162.8
Q ss_pred cccCCeEEEEEeecc-cCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHH
Q psy1412 131 TSTNNVTLIVMTREE-KPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKEL 209 (504)
Q Consensus 131 ~~~~~~~l~V~~~~~-~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l 209 (504)
...+.++|+||+... +||.++.+. ++++.||.+|+++++++++|.+++++.. .+|++++..|
T Consensus 51 ~l~~~~~l~vgv~~~~~p~~~~~~~-----~g~~~G~~~D~l~~ia~~lG~~~e~v~~------------~~~~~~l~~l 113 (1197)
T PRK09959 51 WLASKKNLVIAVHKSQTATLLHTDS-----QQRVRGINADYLNLLKRALNIKLTLREY------------ADHQKAMDAL 113 (1197)
T ss_pred HHhhCCeEEEEecCCCCCCceeecC-----CCccceecHHHHHHHHHhcCCceEEEeC------------CCHHHHHHHH
Confidence 334678899999864 565554322 4789999999999999999999999853 3799999999
Q ss_pred hhccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhC
Q psy1412 210 MDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFS 289 (504)
Q Consensus 210 ~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~ 289 (504)
.+|++|++.+.++++++|.+.++||.||+....++++++....
T Consensus 114 ~~g~iDl~~~~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~~~------------------------------------- 156 (1197)
T PRK09959 114 EEGEVDIVLSHLVASPPLNDDIAATKPLIITFPALVTTLHDSM------------------------------------- 156 (1197)
T ss_pred HcCCCcEecCccccccccccchhcCCCccCCCceEEEeCCCCC-------------------------------------
Confidence 9999999988999999999999999999999999999865321
Q ss_pred CCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhh
Q psy1412 290 PYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILF 369 (504)
Q Consensus 290 p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~d 369 (504)
++++|
T Consensus 157 ---------------------------------------------------------------------------~~~~~ 161 (1197)
T PRK09959 157 ---------------------------------------------------------------------------RPLTS 161 (1197)
T ss_pred ---------------------------------------------------------------------------CCccc
Confidence 11112
Q ss_pred ccCCC-CceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcC--CccE
Q psy1412 370 LGGQG-DETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN--CNLT 445 (504)
Q Consensus 370 L~~~~-~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~--c~l~ 445 (504)
|.... .+.-|+....+++. .|++ -..+.+++..+++++|.+|+ +|++.+...+.|+++++ -++.
T Consensus 162 l~~~~i~~~~g~~~~~~~~~----~~p~--------~~i~~~~s~~~al~av~~G~~Da~i~~~~~~~~~i~~~~~~~l~ 229 (1197)
T PRK09959 162 SKPVNIARVANYPPDEVIHQ----SFPK--------ATIISFTNLYQALASVSAGQNDYFIGSNIITSSMISRYFTHSLN 229 (1197)
T ss_pred ccCeEEEEeCCCCCHHHHHH----hCCC--------CEEEeCCCHHHHHHHHHcCCCCEEEccHHHHHHHHhcccccceE
Confidence 21100 00001111111110 1110 12356789999999999999 99999999999988765 3555
Q ss_pred EcCCc-cCCcceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 446 QIGGL-LDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 446 ~vg~~-~~~~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
.++.. .....++++++|+.| +.+.+|++|..+.++|.. +|.+||+..
T Consensus 230 ~~~~~~~~~~~~~~~~~~~~~~L~~~lnkal~~i~~~~~~-~i~~kW~~~ 278 (1197)
T PRK09959 230 VVKYYNSPRQYNFFLTRKESVILNEVLNRFVDALTNEVRY-EVSQNWLDT 278 (1197)
T ss_pred EEeeccCCCCceeEEEcCCcHHHHHHHHHHHHhCCHHHHH-HHHHhccCC
Confidence 55432 233446788999988 889999999999999988 899999974
No 23
>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=99.58 E-value=4.9e-14 Score=130.94 Aligned_cols=210 Identities=26% Similarity=0.422 Sum_probs=155.4
Q ss_pred EEEEeecc-cCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccc
Q psy1412 138 LIVMTREE-KPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADL 216 (504)
Q Consensus 138 l~V~~~~~-~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~ 216 (504)
|+|++... +||.+... ++.+.|++.|+++.+++++|.+++++.. .|..++..|.+|++|+
T Consensus 1 l~i~~~~~~~p~~~~~~------~g~~~G~~~~~~~~~~~~~g~~~~~~~~-------------~~~~~~~~l~~g~~D~ 61 (218)
T cd00134 1 LTVGTAGTYPPFSFRDA------NGELTGFDVDLAKAIAKELGVKVKFVEV-------------DWDGLITALKSGKVDL 61 (218)
T ss_pred CEEecCCCCCCeeEECC------CCCEEeeeHHHHHHHHHHhCCeEEEEeC-------------CHHHHHHHHhcCCcCE
Confidence 46676665 66665432 4789999999999999999988888843 4889999999999999
Q ss_pred eecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCCCccCC
Q psy1412 217 AVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWSNP 296 (504)
Q Consensus 217 av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~~~~~~ 296 (504)
+++....+.+|.+.+.|+.|+.....++++++..+
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------- 96 (218)
T cd00134 62 IAAGMTITPERAKQVDFSDPYYKSGQVILVKKGSP--------------------------------------------- 96 (218)
T ss_pred EeecCcCCHHHHhhccCcccceeccEEEEEECCCC---------------------------------------------
Confidence 99888889999999999999999999999986532
Q ss_pred CCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhccCCCCc
Q psy1412 297 HPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLGGQGDE 376 (504)
Q Consensus 297 ~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL~~~~~i 376 (504)
+.+++||.... +
T Consensus 97 -------------------------------------------------------------------~~~~~dl~g~~-i 108 (218)
T cd00134 97 -------------------------------------------------------------------IKSVKDLKGKK-V 108 (218)
T ss_pred -------------------------------------------------------------------CCChHHhCCCE-E
Confidence 12344454321 1
Q ss_pred ee--eeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcC-CccEEcCCc--
Q psy1412 377 TF--VTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN-CNLTQIGGL-- 450 (504)
Q Consensus 377 ~~--g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~-c~l~~vg~~-- 450 (504)
.. |.....++. + .........+.+.++++++|.+|+ +|++.+.....+..++. +++..+...
T Consensus 109 ~~~~~~~~~~~~~-----------~-~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~ 176 (218)
T cd00134 109 AVQKGSTAEKYLK-----------K-ALPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPELKIVGPSID 176 (218)
T ss_pred EEEcCchHHHHHH-----------H-hCCcccEEEeCCHHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCcEEeccccC
Confidence 11 110001111 0 000122345677899999999999 89998888888877665 788877753
Q ss_pred cCCcceEEEecCCC-CCchHHHHHHHhhhccChhHHHHHhhc
Q psy1412 451 LDSKGYGIATPKGS-PWRDRISLAILELQEKGTIQMLYDKWW 491 (504)
Q Consensus 451 ~~~~~~g~a~~k~S-pl~~~in~ail~l~e~G~l~~l~~kw~ 491 (504)
.....++++..+++ .+.+.|+++|.+++++|.++++.+||+
T Consensus 177 ~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~g~~~~i~~~~~ 218 (218)
T cd00134 177 LEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF 218 (218)
T ss_pred CCccceEEEEcCCCHHHHHHHHHHHHHHHhCccHHHHHHhhC
Confidence 44445677777776 489999999999999999999999996
No 24
>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=99.57 E-value=3.9e-14 Score=134.91 Aligned_cols=214 Identities=14% Similarity=0.109 Sum_probs=139.5
Q ss_pred EEEEeecc-cCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccc
Q psy1412 138 LIVMTREE-KPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADL 216 (504)
Q Consensus 138 l~V~~~~~-~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~ 216 (504)
|+|++... +||.+. ...||++||++++++++|.+++++..+. .|.-++..|.+|++|+
T Consensus 2 l~v~~~~~~~P~~~~----------~~~G~~~el~~~i~~~~g~~i~~~~~~~-----------~~~~~~~~l~~g~~Di 60 (232)
T TIGR03871 2 LRVCADPNNLPFSNE----------KGEGFENKIAQLLADDLGLPLEYTWFPQ-----------RRGFVRNTLNAGRCDV 60 (232)
T ss_pred eEEEeCCCCCCccCC----------CCCchHHHHHHHHHHHcCCceEEEecCc-----------chhhHHHHHhcCCccE
Confidence 78888775 777642 2369999999999999999999986542 2333567899999999
Q ss_pred eecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCCCCccCC
Q psy1412 217 AVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWSNP 296 (504)
Q Consensus 217 av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p~~~~~~ 296 (504)
+++ +.+|.+.++||.||+..+.++++++....
T Consensus 61 ~~~----~~~r~~~~~fs~py~~~~~~lv~~~~~~~-------------------------------------------- 92 (232)
T TIGR03871 61 VIG----VPAGYEMVLTTRPYYRSTYVFVTRKDSLL-------------------------------------------- 92 (232)
T ss_pred EEe----ccCccccccccCCcEeeeEEEEEeCCCcc--------------------------------------------
Confidence 865 57799999999999999999999865311
Q ss_pred CCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhh--ccCCC
Q psy1412 297 HPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILF--LGGQG 374 (504)
Q Consensus 297 ~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~d--L~~~~ 374 (504)
++++++| |.+..
T Consensus 93 ------------------------------------------------------------------~~~~~~d~~l~g~~ 106 (232)
T TIGR03871 93 ------------------------------------------------------------------DVKSLDDPRLKKLR 106 (232)
T ss_pred ------------------------------------------------------------------cccchhhhhhcCCe
Confidence 1233343 32211
Q ss_pred -CceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcC-CccEEcCCc-
Q psy1412 375 -DETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN-CNLTQIGGL- 450 (504)
Q Consensus 375 -~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~-c~l~~vg~~- 450 (504)
.+.-|+....++...... ..+..+. .........+..+++++|.+|+ +|++.+...+.|+.++. -++......
T Consensus 107 V~v~~g~~~~~~l~~~~~~--~~~~~~~-~~~~~~~~~~~~~~~~~l~~G~~Da~i~~~~~~~~~~~~~~~~~~~~~~~~ 183 (232)
T TIGR03871 107 IGVFAGTPPAHWLARHGLV--ENVVGYS-LFGDYRPESPPGRMVEDLAAGEIDVAIVWGPIAGYFAKQAGPPLVVVPLLP 183 (232)
T ss_pred EEEEcCChHHHHHHhcCcc--ccccccc-ccccccccCCHHHHHHHHHcCCcCEEEeccHHHHHHHHhCCCCceeecccc
Confidence 111122212222111000 0000000 0000011246789999999999 89999988888877654 234443321
Q ss_pred -----cCCcceEEEecCCCC-CchHHHHHHHhhhccChhHHHHHhhc
Q psy1412 451 -----LDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWW 491 (504)
Q Consensus 451 -----~~~~~~g~a~~k~Sp-l~~~in~ail~l~e~G~l~~l~~kw~ 491 (504)
....+++|+++|+++ +++.||++|.++. |.+++|.+||-
T Consensus 184 ~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~--~~~~~i~~kyg 228 (232)
T TIGR03871 184 EDGGIPFDYRIAMGVRKGDKAWKDELNAVLDRRQ--AEIDAILREYG 228 (232)
T ss_pred CCCCCCccceEEEEEecCCHHHHHHHHHHHHHHH--HHHHHHHHHcC
Confidence 123356888998876 9999999999986 48999999984
No 25
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.57 E-value=1.8e-14 Score=124.99 Aligned_cols=129 Identities=48% Similarity=0.796 Sum_probs=104.1
Q ss_pred cchhhhhccCCCCcee----eeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCCeEEEeecchhhhhh
Q psy1412 363 SKKCILFLGGQGDETF----VTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGDYAFLMESTMLDYEV 438 (504)
Q Consensus 363 ~i~s~~dL~~~~~i~~----g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~~A~i~e~~~~~y~~ 438 (504)
||++++||.+++...+ |+....+++......+.+++..+. ..+.+.+.+..+++.+|.+|++|++.+.+.+.|+.
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~g~da~v~d~~~~~~~~ 79 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGNPEYSRMWNYMS-ASPSVFVKSYAEGVQRVRVSNYAFLMESTYLDYEL 79 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHhCCChHHHHHHHHHH-hCCCCCCCCHHHHHHHHHcCCCEEEeehHhHHHHH
Confidence 5789999987532233 555666676655544455544331 01345678899999999988899999999999988
Q ss_pred hcCCccEEcCCccCCcceEEEecCCCCCchHHHHHHHhhhccChhHHHHHhhcc
Q psy1412 439 QRNCNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWK 492 (504)
Q Consensus 439 ~~~c~l~~vg~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~l~~kw~~ 492 (504)
++.|++.+++..+...+|||+++||++|++.||.+|.+|.++|.++++.+||+.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~~l~~kw~~ 133 (134)
T smart00079 80 SQNCDLMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQKLENKWWK 133 (134)
T ss_pred hCCCCeEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHHHHHHhhcc
Confidence 878999999988888999999999999999999999999999999999999986
No 26
>cd06387 PBP1_iGluR_AMPA_GluR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=99.51 E-value=3.6e-14 Score=144.00 Aligned_cols=110 Identities=19% Similarity=0.373 Sum_probs=87.8
Q ss_pred CccceeeEEEEeeecCCCccccchhhhhhhcccccC-----CCc-cccccccccchhhhHHHHHHHHHHHhhhcCCcccc
Q psy1412 2 YDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDG-----LSL-YNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTS 75 (504)
Q Consensus 2 ~d~v~~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g-----~~~-~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~ 75 (504)
|.+|+ +||||++|+..+. ++++..+|... ++. .+.++. +++|+|||||++|+|++++. ...+.++
T Consensus 228 ~g~~N--Itg~rl~~~~~~~-----~~~f~~~w~~~~~~~~~~~~~~~l~~-~~al~yDaV~~~A~A~~~l~-~~~~~~~ 298 (372)
T cd06387 228 HGGAN--ITGFQIVNNENPM-----VQQFLQRWVRLDEREFPEAKNSPLKY-TSALTHDAILVIAEAFRYLR-RQRVDVS 298 (372)
T ss_pred cCCcc--eeEEEEecCCCch-----HHHHHHHHHhCCcccCCCCCCCCcch-HHHHHHHHHHHHHHHHHHHH-hcCCCcc
Confidence 44455 4999999999888 89999999541 111 125666 99999999999999999984 3333333
Q ss_pred ----cCCCCC--CCcccCchhHHHHhhh----------------------ceEEEeeccceeeeeEecCCCCc
Q psy1412 76 ----NLSCDL--EVPWRDGLSLYNYINT----------------------LDLLKLKREELRKVGHWTPAEGI 120 (504)
Q Consensus 76 ----~~~c~~--~~~~~~G~~l~~~l~~----------------------~~i~~~~~~~~~~vg~W~~~~gl 120 (504)
..+|.. ..+|++|+.|+++|++ |+|+|+.++|+++||+|++..|+
T Consensus 299 ~~~~~~~C~~~~~~~W~~G~~l~~~ik~v~~~GLTG~i~F~~~G~R~~~~ldIinl~~~g~~kIG~W~~~~g~ 371 (372)
T cd06387 299 RRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDVYEMKPSGSRKAGYWNEYERF 371 (372)
T ss_pred cCCCCCCcCCCCCCCccchHHHHHHHHhcccCCCccceeeCCCCCcccceEEEEEecCCCceeEEEECCCCCc
Confidence 338944 6789999999999997 99999999999999999999887
No 27
>cd06390 PBP1_iGluR_AMPA_GluR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=99.42 E-value=3.9e-13 Score=136.47 Aligned_cols=107 Identities=24% Similarity=0.500 Sum_probs=85.6
Q ss_pred eeEEEEeeecCCCccccchhhhhhhcccccCC-----Cc-cccccccccchhhhHHHHHHHHHHHhhhcCCcccc----c
Q psy1412 7 VLAAGLALLDKSSVIKTSNLSCDLEVPWRDGL-----SL-YNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTS----N 76 (504)
Q Consensus 7 ~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g~-----~~-~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~----~ 76 (504)
+++||||++|+..+. ++++..+|.... .. ...++. +++++|||||++|+|++++.+ ....++ .
T Consensus 223 ~nitg~r~~~~~~~~-----~~~~~~~w~~~~~~~~~~~~~~~~~~-~~~l~yDaV~~~A~A~~~l~~-~~~~~~~~~~~ 295 (364)
T cd06390 223 ANVTGFQLVNYTDTT-----VSRIMQQWKNFDARDLPRVDWKRPKY-TSALTYDGVRVMAEAFQNLRK-QRIDISRRGNA 295 (364)
T ss_pred cCceEEEEecCCCHH-----HHHHHHHHHhhccccCCCCCcCCcch-HHHHHHHHHHHHHHHHHHHHH-cCCCcccCCCC
Confidence 345999999998888 899999996411 11 114665 899999999999999999853 333333 2
Q ss_pred CCCCC--CCcccCchhHHHHhhh----------------------ceEEEeeccceeeeeEecCCCCc
Q psy1412 77 LSCDL--EVPWRDGLSLYNYINT----------------------LDLLKLKREELRKVGHWTPAEGI 120 (504)
Q Consensus 77 ~~c~~--~~~~~~G~~l~~~l~~----------------------~~i~~~~~~~~~~vg~W~~~~gl 120 (504)
.+|.. ..+|++|+.|+++|++ |+|+|+++.|+++||+|++..|+
T Consensus 296 ~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~i~F~~~G~r~~~~~~I~~~~~~g~~~vG~W~~~~g~ 363 (364)
T cd06390 296 GDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDEKL 363 (364)
T ss_pred CCCCCCCCCCCccHHHHHHHHHhhcccccccceeeCCCCCcccceEEEEEecCCcceEEEEECCCCCc
Confidence 38844 5689999999999997 99999999999999999999887
No 28
>cd06392 PBP1_iGluR_delta_1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdel
Probab=99.40 E-value=6e-13 Score=135.79 Aligned_cols=112 Identities=17% Similarity=0.282 Sum_probs=83.2
Q ss_pred eEEEEeeecCCCccccchhhhhhhccccc---CC--CccccccccccchhhhHHHHHHHHHHHhh-hcCCcccccCCC--
Q psy1412 8 LAAGLALLDKSSVIKTSNLSCDLEVPWRD---GL--SLYNYINTAEPALMYDSVHVLAAGLALLD-KSSVIKTSNLSC-- 79 (504)
Q Consensus 8 ~~tg~r~~d~~~~~~~~~~~~~~~~~W~~---g~--~~~~~i~~~~~~~~yDav~~~a~a~~~~~-~~~~~~~~~~~c-- 79 (504)
++||||++++..+... ++..+...+|.. ++ .....++. ++|+||||||++|+|++++. ....+.+..++|
T Consensus 253 niT~~r~~~~~~~~~~-~~~~~~~~r~~~~~~~~~~~~~~~l~~-~aalayDaV~~~A~Al~~ll~~~~~~~~~~l~C~~ 330 (400)
T cd06392 253 RMTVIRQIFPLSKDNN-QRCIRNNHRISSLLCDPQEGYLQMLQV-SNLYLYDSVLMLANAFHRKLEDRKWHSMASLNCIR 330 (400)
T ss_pred ceeeEEEecCCcHHHH-HHHHHHHHHHHhhhcccccccccccch-hHHHHHHHHHHHHHHHHHHhhccccCCCCCCccCC
Confidence 4599999876554311 111223467741 11 11114776 99999999999999999864 345566777899
Q ss_pred CCCCcccCchhHHHHhhh----------------------ceEEEe-----eccceeeeeEecCCCCce
Q psy1412 80 DLEVPWRDGLSLYNYINT----------------------LDLLKL-----KREELRKVGHWTPAEGIN 121 (504)
Q Consensus 80 ~~~~~~~~G~~l~~~l~~----------------------~~i~~~-----~~~~~~~vg~W~~~~gl~ 121 (504)
+...+|.+|..|+++|++ |||+|+ .+.|+++||+|++..||.
T Consensus 331 ~~~~~w~~G~~ll~~ik~v~f~GLTG~I~F~~~G~r~~~~ldIi~l~~~~~~g~g~~~iG~W~~~~gl~ 399 (400)
T cd06392 331 KSTKPWNGGRSMLETIKKGHITGLTGVMEFKEDGANPHVQFEILGTSYSETFGKDVRRLATWDSEKGLN 399 (400)
T ss_pred CCCCCCCChHHHHHHHHhCCCccCccceeECCCCCCcCCceEEEeccccccCCCCceEeEEecCCCCCC
Confidence 567899999999999998 999995 467799999999998875
No 29
>cd06393 PBP1_iGluR_Kainate_GluR5_7 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated
Probab=99.32 E-value=2.9e-12 Score=131.64 Aligned_cols=106 Identities=29% Similarity=0.571 Sum_probs=86.5
Q ss_pred eeEEEEeeecCCCccccchhhhhhhcccccC-CCc--------c-ccccccccchhhhHHHHHHHHHHHhhhcCCccccc
Q psy1412 7 VLAAGLALLDKSSVIKTSNLSCDLEVPWRDG-LSL--------Y-NYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSN 76 (504)
Q Consensus 7 ~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g-~~~--------~-~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~~ 76 (504)
+++||||+.|++.+. ++++.++|... .+. . +.++. .++++||||+++++|+++.. .+...+
T Consensus 244 ~~it~~~~~~~~~~~-----~~~f~~~~~~~~~~~~p~~~~~~~~~~~~~-~aal~yDav~~~a~A~~~~~---~~~~~~ 314 (384)
T cd06393 244 VNLTGFRILNVDNPH-----VSSIVEKWSMERLQAAPKPETGLLDGVMMT-DAALLYDAVHMVSVCYQRAP---QMTVNS 314 (384)
T ss_pred ceEEEEEecCCCcHH-----HHHHHHHHHhhhhccccccccccccccccc-hhHHhhhhHHHHHHHHhhhh---hcCCCC
Confidence 446999999998777 88888888531 111 0 12344 89999999999999999653 334566
Q ss_pred CCCCCCCcccCchhHHHHhhh-----------------------ceEEEeeccceeeeeEecCCCCce
Q psy1412 77 LSCDLEVPWRDGLSLYNYINT-----------------------LDLLKLKREELRKVGHWTPAEGIN 121 (504)
Q Consensus 77 ~~c~~~~~~~~G~~l~~~l~~-----------------------~~i~~~~~~~~~~vg~W~~~~gl~ 121 (504)
++|+...+|++|..+.++|++ |+|+|++++|+++||+|++..||.
T Consensus 315 ~~c~~~~~w~~G~~i~~~l~~~~~~GltG~i~Fd~~~g~r~~~~~~i~~~~~~g~~~vg~W~~~~g~~ 382 (384)
T cd06393 315 LQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEKVGVWNPNTGLN 382 (384)
T ss_pred CCCCCCCCCcccHHHHHHHhheeecccccceEecCCCCeeeeeEEEEEEecCCcceeeEEEcCCCCcC
Confidence 799999999999999999997 999999999999999999999986
No 30
>cd06388 PBP1_iGluR_AMPA_GluR4 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=99.29 E-value=6.7e-12 Score=127.96 Aligned_cols=111 Identities=23% Similarity=0.418 Sum_probs=85.8
Q ss_pred CccceeeEEEEeeecCCCccccchhhhhhhcccccC-----CCccccccccccchhhhHHHHHHHHHHHhhhcCCccc--
Q psy1412 2 YDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDG-----LSLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKT-- 74 (504)
Q Consensus 2 ~d~v~~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g-----~~~~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~-- 74 (504)
|.+++ +||+|++|+..+. ++++.++|... ++....++. ++|++||||+++|.|++++.+ .....
T Consensus 227 ~g~~n--itg~~~~~~~~~~-----v~~~~~~~~~~~~~~~~~~~~~~~~-~aAl~YDaV~l~a~A~~~l~~-~~~~~~~ 297 (371)
T cd06388 227 HGGAN--VTGFQLVDFNTPM-----VTKLMQRWKKLDQREYPGSESPPKY-TSALTYDGVLVMAEAFRNLRR-QKIDISR 297 (371)
T ss_pred ccCCc--eEEEEeecCCChh-----HHHHHHHHHhcCccccCCCCCCccc-hHHHHHHHHHHHHHHHHHHHh-cCCCccc
Confidence 44555 4999999887777 78888888531 111014555 899999999999999999853 22332
Q ss_pred --ccCCCC--CCCcccCchhHHHHhhh----------------------ceEEEeeccceeeeeEecCCCCce
Q psy1412 75 --SNLSCD--LEVPWRDGLSLYNYINT----------------------LDLLKLKREELRKVGHWTPAEGIN 121 (504)
Q Consensus 75 --~~~~c~--~~~~~~~G~~l~~~l~~----------------------~~i~~~~~~~~~~vg~W~~~~gl~ 121 (504)
.+.+|. +..+|++|.+|.++|++ ++|++++++|+++||+|++..||.
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 234894 46799999999999997 899999999999999999999885
No 31
>cd06389 PBP1_iGluR_AMPA_GluR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=99.25 E-value=1.8e-11 Score=124.85 Aligned_cols=107 Identities=22% Similarity=0.468 Sum_probs=85.6
Q ss_pred eEEEEeeecCCCccccchhhhhhhccccc----CC-Cc-cccccccccchhhhHHHHHHHHHHHhhhcCCccc----ccC
Q psy1412 8 LAAGLALLDKSSVIKTSNLSCDLEVPWRD----GL-SL-YNYINTAEPALMYDSVHVLAAGLALLDKSSVIKT----SNL 77 (504)
Q Consensus 8 ~~tg~r~~d~~~~~~~~~~~~~~~~~W~~----g~-~~-~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~----~~~ 77 (504)
+++|||++|+..+. ++++.++|+. .. +. ...+.. ++|++||||++++.|++++.+ ..... +..
T Consensus 229 nitg~~~~~~~~~~-----v~~f~~~~~~~~~~~~~~~~~~~~~~-~aAl~yDAV~v~a~A~~~l~~-~~~~~~~~~~~~ 301 (370)
T cd06389 229 NVSGFQIVDYDDPL-----VSKFIQRWSTLEEKEYPGAHTKTIKY-TSALTYDAVQVMTEAFRNLRK-QRIEISRRGNAG 301 (370)
T ss_pred ceEEEEEecCCCch-----HHHHHHHHHhcCccccCCCCCcCcch-HHHHHHHHHHHHHHHHHHHHH-cCCCcccCCCCC
Confidence 46999999998777 8899999964 11 10 124666 899999999999999999853 22222 345
Q ss_pred CCC--CCCcccCchhHHHHhhh----------------------ceEEEeeccceeeeeEecCCCCce
Q psy1412 78 SCD--LEVPWRDGLSLYNYINT----------------------LDLLKLKREELRKVGHWTPAEGIN 121 (504)
Q Consensus 78 ~c~--~~~~~~~G~~l~~~l~~----------------------~~i~~~~~~~~~~vg~W~~~~gl~ 121 (504)
+|. +..+|.+|..|.++|++ ++|++++++|+++||+|++..|+.
T Consensus 302 ~C~~~~~~~w~~G~~i~~~l~~~~~~GlTG~i~Fd~~G~r~~~~~~ii~l~~~g~~kvG~W~~~~~~~ 369 (370)
T cd06389 302 DCLANPAVPWGQGVEIERALKQVQVEGLTGNIKFDQNGKRINYTINVMELKSNGPRKIGYWSEVDKMV 369 (370)
T ss_pred CcCCCCCCCCCCcHHHHHHHHhcccCccccceEeCCCCccccceEEEEEecCCcceEEEEEcCCCCcc
Confidence 894 46799999999999997 899999999999999999998875
No 32
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.22 E-value=6.4e-11 Score=114.16 Aligned_cols=227 Identities=16% Similarity=0.146 Sum_probs=163.7
Q ss_pred cccCCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHh
Q psy1412 131 TSTNNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELM 210 (504)
Q Consensus 131 ~~~~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~ 210 (504)
.....+.|+|+|.. .|..++.. ++..+|++.++.+++++.||.+.++...+ .-+.+..+|.
T Consensus 18 ~Iq~rGvLrV~tin-sp~sy~~~------~~~p~G~eYelak~Fa~yLgV~Lki~~~~------------n~dqLf~aL~ 78 (473)
T COG4623 18 AIQARGVLRVSTIN-SPLSYFED------KGGPTGLEYELAKAFADYLGVKLKIIPAD------------NIDQLFDALD 78 (473)
T ss_pred HHHhcCeEEEEeec-Cccceecc------CCCccchhHHHHHHHHHHhCCeEEEEecC------------CHHHHHHHHh
Confidence 34467899999985 55555544 35667999999999999999999988643 3578999999
Q ss_pred hccccceecceeeecccceeeeeccceeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHHHHhhCC
Q psy1412 211 DKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSP 290 (504)
Q Consensus 211 ~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~i~r~~p 290 (504)
+|++|++.+++...++|.+.+....-|......++.++....+.+
T Consensus 79 ng~~DL~Aagl~~~~~~l~~~~~gP~y~svs~qlVyRkG~~Rp~~----------------------------------- 123 (473)
T COG4623 79 NGNADLAAAGLLYNSERLKNFQPGPTYYSVSQQLVYRKGQYRPRS----------------------------------- 123 (473)
T ss_pred CCCcceecccccCChhHhcccCCCCceecccHHHHhhcCCCCCCC-----------------------------------
Confidence 999999999999999999988888888888888888776543221
Q ss_pred CCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccchhhhhc
Q psy1412 291 YEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFL 370 (504)
Q Consensus 291 ~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i~s~~dL 370 (504)
+++|
T Consensus 124 ----------------------------------------------------------------------------l~~L 127 (473)
T COG4623 124 ----------------------------------------------------------------------------LGQL 127 (473)
T ss_pred ----------------------------------------------------------------------------HHHc
Confidence 2222
Q ss_pred cC-CCCceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCccEEcC
Q psy1412 371 GG-QGDETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCNLTQIG 448 (504)
Q Consensus 371 ~~-~~~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~l~~vg 448 (504)
.. +-.+.-|+...+.++..+...|+.+.-... -..+.+|-+++|..|+ +..+.|++.+....+-+.++.+.-
T Consensus 128 ~g~~i~v~~gs~~~~~l~~lk~~kyP~l~~k~d------~~~~~~dLle~v~~Gkldytiads~~is~~q~i~P~laVaf 201 (473)
T COG4623 128 KGRQITVAKGSAHVEDLKLLKETKYPELIWKVD------DKLGVEDLLEMVAEGKLDYTIADSVEISLFQRVHPELAVAF 201 (473)
T ss_pred cCceeeccCCcHHHHHHHHHHHhhcchhhhhhc------ccccHHHHHHHHhcCCcceeeeccHHHHHHHHhCccceeee
Confidence 21 111111211111111111122332221111 1346789999999999 778889998888766667877776
Q ss_pred CccCCcceEEEecCCC--CCchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 449 GLLDSKGYGIATPKGS--PWRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 449 ~~~~~~~~g~a~~k~S--pl~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
..-...+..+.+|.+. .|...+...+-.+.|.|.++++++|+++.
T Consensus 202 d~tde~~v~Wy~~~~dd~tL~a~ll~F~~~~~e~g~larleeky~gH 248 (473)
T COG4623 202 DLTDEQPVAWYLPRDDDSTLSAALLDFLNEAKEDGLLARLEEKYLGH 248 (473)
T ss_pred ecccccCceeeccCCchHHHHHHHHHHHHHhhcchHHHHHHHHHhcc
Confidence 6666688899999865 49999999999999999999999999975
No 33
>cd06391 PBP1_iGluR_delta_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related to non-NMDA receptors. GluRdelta2 was shown to function as a
Probab=99.19 E-value=3.7e-11 Score=123.47 Aligned_cols=77 Identities=27% Similarity=0.538 Sum_probs=66.2
Q ss_pred ccccccchhhhHHHHHHHHHHHhh-hcCCcccccCCCCC--CCcccCchhHHHHhhh----------------------c
Q psy1412 44 INTAEPALMYDSVHVLAAGLALLD-KSSVIKTSNLSCDL--EVPWRDGLSLYNYINT----------------------L 98 (504)
Q Consensus 44 i~~~~~~~~yDav~~~a~a~~~~~-~~~~~~~~~~~c~~--~~~~~~G~~l~~~l~~----------------------~ 98 (504)
++. ++++||||||++|+|++++. ....+.+..++|.. ..+|.+|+.|+++|++ |
T Consensus 293 ~~~-~~alayDaV~~~A~A~~~l~~~~~~~~~~~~~c~~~~~~~w~~G~~ll~~i~~~~f~GlTG~i~f~~~g~r~~~~~ 371 (400)
T cd06391 293 MEI-SNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFNENGGNPNVHF 371 (400)
T ss_pred ccc-hhhHHHHHHHHHHHHHHHHHhhccccCCCCcccccCCCCCCCChHHHHHHHHhcCcccceeceEECCCCCccCCce
Confidence 454 89999999999999999985 23456667789954 5699999999999996 9
Q ss_pred eEEEee-----ccceeeeeEecCCCCce
Q psy1412 99 DLLKLK-----REELRKVGHWTPAEGIN 121 (504)
Q Consensus 99 ~i~~~~-----~~~~~~vg~W~~~~gl~ 121 (504)
||+|++ ++|+++||+|++..|+.
T Consensus 372 dIin~~~~~~~~~g~rkiG~Ws~~~gl~ 399 (400)
T cd06391 372 EILGTNYGEDLGRGVRKLGCWNPITGLN 399 (400)
T ss_pred EEEEeeccccCCCcceEEEEEcCCcCCC
Confidence 999996 89999999999998874
No 34
>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=98.92 E-value=3.5e-11 Score=106.19 Aligned_cols=98 Identities=38% Similarity=0.693 Sum_probs=66.0
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHhhCCCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceeh
Q psy1412 264 AVEIWLYVLAAYLLVSFTLFVMARFSPYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTL 343 (504)
Q Consensus 264 ~~~vWl~i~~~~~~v~~~~~~i~r~~p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v 343 (504)
+++||++++++++++++++|+++|+++++|+..+. +......+++.+++|++++++++|+....|++. ++|++
T Consensus 1 s~~vW~~il~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~s~---s~Ril 73 (148)
T PF00060_consen 1 SWSVWLLILLSILLVSLVLWLFERFSPYEWRKNQS----SPPRRWRFSLSNSFWYTFGTLLQQGSSIRPRSW---SGRIL 73 (148)
T ss_dssp -HHHHHHHHHHHHHHHTTGGGT----------------------HHHHHHHHHHHCCCCCHHHHH------H---HHHHH
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHhhhhhccccc----cccccCcccHHHHHHHHHHhhccccccccccch---HHHHH
Confidence 57899999999999999999999999988766211 122335678999999999999999999999999 99999
Q ss_pred cc-----------------chhhhhhhhhhhhhhcccchhhhhccCCC
Q psy1412 344 DT-----------------ALDSKIEIYQKMWRYMESKKCILFLGGQG 374 (504)
Q Consensus 344 ~~-----------------An~Ltv~~~~~~~~~~~~i~s~~dL~~~~ 374 (504)
.+ +++||++ +.+++|++++||.+++
T Consensus 74 ~~~w~l~~lil~~~Yta~L~s~Lt~~------~~~~~i~sl~dL~~~~ 115 (148)
T PF00060_consen 74 LAFWWLFSLILIASYTANLTSFLTVP------KYEPPIDSLEDLANSG 115 (148)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCH------HHTSS-SSHHHHHTHS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccc------CcCCCCCCHHHHHHCC
Confidence 88 3388888 9999999999999865
No 35
>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=98.75 E-value=2.5e-08 Score=102.36 Aligned_cols=107 Identities=26% Similarity=0.461 Sum_probs=80.8
Q ss_pred eEEEEeeecCCCccccchhhhhhhcccccCCCc------cccccccccchhhhHHHHHHHHHHHhhhcC---------Cc
Q psy1412 8 LAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSL------YNYINTAEPALMYDSVHVLAAGLALLDKSS---------VI 72 (504)
Q Consensus 8 ~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g~~~------~~~i~~~~~~~~yDav~~~a~a~~~~~~~~---------~~ 72 (504)
.++|+++.+++.+. ..++.++|...... ...+.. +++++||||+++|.|++++.+.. ..
T Consensus 236 ~~~~~~~~~~~~~~-----~~~f~~~~~~~~~~~~~~~~~~~~~~-~aa~aYDav~~~a~Al~~~~~~~~~~~~~~~~~~ 309 (382)
T cd06380 236 NITGFQLVDNTNPT-----VQKFLQRWKKLDPREWPGAGTSPIKY-TAALAHDAVLVMAEAFRSLRRQRGSGRHRIDISR 309 (382)
T ss_pred eeEEEeccCCCCHH-----HHHHHHHHHhcCccccCcCCcCCcch-HHHHHHHHHHHHHHHHHHHHHhcccccccccccc
Confidence 46999988876555 67777777542110 012444 78999999999999999985322 12
Q ss_pred ccccCCCCC--CCcccCchhHHHHhhh----------------------ceEEEeeccceeeeeEecCCCCc
Q psy1412 73 KTSNLSCDL--EVPWRDGLSLYNYINT----------------------LDLLKLKREELRKVGHWTPAEGI 120 (504)
Q Consensus 73 ~~~~~~c~~--~~~~~~G~~l~~~l~~----------------------~~i~~~~~~~~~~vg~W~~~~gl 120 (504)
..+..+|.. ..+|.+|..+.++|++ ++|+++++.++++||+|++..|+
T Consensus 310 ~~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG~i~Fd~~G~~~~~~~~i~~~~~~~~~~vg~w~~~~g~ 381 (382)
T cd06380 310 RGNGGDCLANPAVPWEHGIDIERALKKVQFEGLTGNVQFDEFGQRTNYTLDVVELKTRGLRKVGYWNEDDGL 381 (382)
T ss_pred CCCCCcCCCCCCCCccchHHHHHHHHhcccCCcccceEECCCCCcccccEEEEEecCCCceEEEEECCCcCc
Confidence 234568954 5689999999999997 88999999999999999998886
No 36
>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=98.66 E-value=2.6e-07 Score=89.16 Aligned_cols=201 Identities=15% Similarity=0.079 Sum_probs=128.7
Q ss_pred CCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhcc
Q psy1412 134 NNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKK 213 (504)
Q Consensus 134 ~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~ 213 (504)
..++|+|++....| ...+.+...++.+.+++++|.+++++.. ++|+.++..+.+|+
T Consensus 30 ~~~~l~vg~~~~~~------------~~~~~~~~~~l~~~l~~~~g~~v~~~~~------------~~~~~~~~~l~~g~ 85 (254)
T TIGR01098 30 VPKELNFGILPGEN------------ASNLTRRWEPLADYLEKKLGIKVQLFVA------------TDYSAVIEAMRFGR 85 (254)
T ss_pred CCCceEEEECCCCC------------HHHHHHHHHHHHHHHHHHhCCcEEEEeC------------CCHHHHHHHHHcCC
Confidence 34578999864422 1234456779999999999999988742 46999999999999
Q ss_pred ccceecceeeec---ccceeeeeccceeec------cEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHHHHHHHHH
Q psy1412 214 ADLAVASMTINY---ARESVIDFTKPFMNL------GIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFV 284 (504)
Q Consensus 214 ~D~av~~~tit~---~R~~~vdFs~p~~~~------g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~v~~~~~~ 284 (504)
+|+++.+..... +|....+|+.||... ..++++++.
T Consensus 86 ~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d----------------------------------- 130 (254)
T TIGR01098 86 VDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKAD----------------------------------- 130 (254)
T ss_pred ccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECC-----------------------------------
Confidence 999986654433 577778888876543 235555432
Q ss_pred HHhhCCCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhhhhhcccc
Q psy1412 285 MARFSPYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESK 364 (504)
Q Consensus 285 i~r~~p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~~~~~~~i 364 (504)
.+|
T Consensus 131 -----------------------------------------------------------------------------~~i 133 (254)
T TIGR01098 131 -----------------------------------------------------------------------------SPI 133 (254)
T ss_pred -----------------------------------------------------------------------------CCC
Confidence 234
Q ss_pred hhhhhccCCCCceeee---eecc-----hhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhh
Q psy1412 365 KCILFLGGQGDETFVT---IDLS-----QRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLD 435 (504)
Q Consensus 365 ~s~~dL~~~~~i~~g~---~~~~-----~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~ 435 (504)
++++||... .|.++. .... .+.+......++ .. .......+..++++.|.+|+ +|.+.+.+...
T Consensus 134 ~~~~dL~gk-~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~---~~---~~i~~~~~~~~~~~al~~G~~Da~~~~~~~~~ 206 (254)
T TIGR01098 134 KSLKDLKGK-TFAFGDPASTSGYLVPRYQLKKEGGLDADG---FF---SEVVFSGSHDASALAVANGKVDAATNNSSAIG 206 (254)
T ss_pred CChHHhcCC-EEEeeCCCCccchHhHHHHHHHhcCCChHH---hh---hheeecCchHHHHHHHHcCCCCeEEecHHHHH
Confidence 556666432 222211 0000 111000000000 00 01223455788999999999 88888888776
Q ss_pred hhhhcC----CccEEcCCccCCcceEEEecCC-CC-CchHHHHHHHhh
Q psy1412 436 YEVQRN----CNLTQIGGLLDSKGYGIATPKG-SP-WRDRISLAILEL 477 (504)
Q Consensus 436 y~~~~~----c~l~~vg~~~~~~~~g~a~~k~-Sp-l~~~in~ail~l 477 (504)
.+.++. -++.+++......+++++++|+ .+ +++.||++|+.|
T Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 207 RLKKRGPSDMKKVRVIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred HHHHhCccchhheEEEEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 665543 2678888766667789999999 54 999999999865
No 37
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.60 E-value=4.2e-08 Score=96.40 Aligned_cols=163 Identities=13% Similarity=0.056 Sum_probs=112.8
Q ss_pred CcchhhHHHHhhccccceecceeeecccceeeeeccc--eeeccEEEEEEccCCCCCCcccccccCchhHHHHHHHHHHH
Q psy1412 200 KEWNGIVKELMDKKADLAVASMTINYARESVIDFTKP--FMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLL 277 (504)
Q Consensus 200 g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p--~~~~g~~ilv~~~~~~~~~~~~fl~Pf~~~vWl~i~~~~~~ 277 (504)
.+|++++..|.+|++|+++++.+++.+|.+.++|+.| |....++++++...
T Consensus 51 ~~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~--------------------------- 103 (287)
T PRK00489 51 LRPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDS--------------------------- 103 (287)
T ss_pred ECcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCC---------------------------
Confidence 4689999999999999999999999999999999988 77777888876432
Q ss_pred HHHHHHHHHhhCCCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCCCCCCcccccccceehccchhhhhhhhhhh
Q psy1412 278 VSFTLFVMARFSPYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKM 357 (504)
Q Consensus 278 v~~~~~~i~r~~p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~~~~p~~~~~~s~R~v~~An~Ltv~~~~~~ 357 (504)
T Consensus 104 -------------------------------------------------------------------------------- 103 (287)
T PRK00489 104 -------------------------------------------------------------------------------- 103 (287)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhhcccchhhhhccCCC-CceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEeecchhh
Q psy1412 358 WRYMESKKCILFLGGQG-DETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLMESTMLD 435 (504)
Q Consensus 358 ~~~~~~i~s~~dL~~~~-~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e~~~~~ 435 (504)
+|++++||.+.. ...++.....+|.+..+. -..+...+..|+ .+..|. +|++.......
T Consensus 104 -----~i~sl~DL~Gk~ia~~~~~~~~~~l~~~gi~------------~~iv~~~gs~ea--a~~~G~aDaivd~~~~~~ 164 (287)
T PRK00489 104 -----DWQGVEDLAGKRIATSYPNLTRRYLAEKGID------------AEVVELSGAVEV--APRLGLADAIVDVVSTGT 164 (287)
T ss_pred -----CCCChHHhCCCEEEEcCcHHHHHHHHHcCCc------------eEEEECCCchhh--hhcCCcccEEEeeHHHHH
Confidence 245577776541 111222222222221110 011233444444 455587 78887676666
Q ss_pred hhhhcCCccEEcCCccCCcceEEEecC--CCC-CchHHHHHHHhhhccChhHHHHHhhccC
Q psy1412 436 YEVQRNCNLTQIGGLLDSKGYGIATPK--GSP-WRDRISLAILELQEKGTIQMLYDKWWKN 493 (504)
Q Consensus 436 y~~~~~c~l~~vg~~~~~~~~g~a~~k--~Sp-l~~~in~ail~l~e~G~l~~l~~kw~~~ 493 (504)
.+.+. ++..+ +.......+++.+| ++| .++.++..+.+| +|.+.++.+||+..
T Consensus 165 ~l~~~--~L~~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g~l~a~~~k~~~~ 220 (287)
T PRK00489 165 TLRAN--GLKIV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QGVLRARESKYLMM 220 (287)
T ss_pred HHHHC--CCEEE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HHHHHhhceEEEEE
Confidence 66553 67777 45556678999999 666 788999999999 59999999999974
No 38
>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=98.47 E-value=3.1e-07 Score=93.32 Aligned_cols=76 Identities=20% Similarity=0.279 Sum_probs=62.5
Q ss_pred ccchhhhHHHHHHHHHHHhhh-cCCcccccCCCCC-CC-cccCchhHHHHhhh--------------------ceEEEee
Q psy1412 48 EPALMYDSVHVLAAGLALLDK-SSVIKTSNLSCDL-EV-PWRDGLSLYNYINT--------------------LDLLKLK 104 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~-~~~~~~~~~~c~~-~~-~~~~G~~l~~~l~~--------------------~~i~~~~ 104 (504)
..+++||||+++|+|++.+.+ ...+.....+|.. .. +|.+|+.|+++|++ |+|+|++
T Consensus 258 ~~a~~~DaV~vva~Al~~l~~~~~~~~~~~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~~i~F~~~G~r~~~~ldIinl~ 337 (362)
T cd06378 258 LRARVRDGVAIIATGASAMLRQHGFIPEAKGSCYGQAEKRDLPPNTLHRYMMNVTWEGRDLSFTEDGYLVNPKLVVISLN 337 (362)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCCCCCCCcCCCCCCCCCchHHHHHHhhcceECCCceeECCCCeEccceEEEEEec
Confidence 367899999999999998863 3456667789954 33 49999999999998 9999999
Q ss_pred c-cceeeeeEecCCCCceeec
Q psy1412 105 R-EELRKVGHWTPAEGINITD 124 (504)
Q Consensus 105 ~-~~~~~vg~W~~~~gl~~~~ 124 (504)
+ .++++||+|++ .+|.+..
T Consensus 338 ~~~g~~kVG~W~~-~~L~~~~ 357 (362)
T cd06378 338 KERVWEEVGKWEN-GSLRLKY 357 (362)
T ss_pred CCCCceEEEEEcC-CeEEEec
Confidence 7 59999999995 4787654
No 39
>cd06377 PBP1_iGluR_NMDA_NR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=98.47 E-value=3e-07 Score=92.82 Aligned_cols=74 Identities=15% Similarity=0.260 Sum_probs=62.6
Q ss_pred cchhhhHHHHHHHHHHHhh---hcCCcccccCCCCCC--C-cccCchhHHHHhhh-----------------------ce
Q psy1412 49 PALMYDSVHVLAAGLALLD---KSSVIKTSNLSCDLE--V-PWRDGLSLYNYINT-----------------------LD 99 (504)
Q Consensus 49 ~~~~yDav~~~a~a~~~~~---~~~~~~~~~~~c~~~--~-~~~~G~~l~~~l~~-----------------------~~ 99 (504)
.+++||||+++|+|++.+. ....+.++.++|... . +|.+|..|+++|++ ++
T Consensus 269 ~ali~DAV~lvA~a~~~l~~~~~~~~l~~~~~~C~~~~~~~~W~~G~~l~~~Lknv~~eGlTG~I~F~~g~R~~~~~~l~ 348 (382)
T cd06377 269 EAYVQDALELVARAVGSATLVQPELALIPATVNCMDLPTKGNESSGQYLARFLANTSFDGRTGPVWVTGSSQVHSSRHFK 348 (382)
T ss_pred HHHHHHHHHHHHHHHHHhhhcccccccCCCCCCcccCCCCCCCCchHHHHHHHHhCcccccceeEEEccCeeecccceEE
Confidence 7899999999999999874 346788888999654 6 99999999999998 88
Q ss_pred EEEee--ccce---eeeeEecCCCCcee
Q psy1412 100 LLKLK--REEL---RKVGHWTPAEGINI 122 (504)
Q Consensus 100 i~~~~--~~~~---~~vg~W~~~~gl~~ 122 (504)
|++++ ..|. ++||+|+++..+.+
T Consensus 349 I~~L~~~~~G~~~W~kVG~W~~~~~~~~ 376 (382)
T cd06377 349 VWSLRRDPVGQPTWTTVGSWQGGRKIVM 376 (382)
T ss_pred EEEeccccCCCccceEEEEecCCCceec
Confidence 99999 6666 99999998744443
No 40
>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=98.21 E-value=2.4e-06 Score=87.58 Aligned_cols=73 Identities=22% Similarity=0.352 Sum_probs=60.7
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCC-CcccCchhHHHHhhh----------------------ceEEEee
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLE-VPWRDGLSLYNYINT----------------------LDLLKLK 104 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~-~~~~~G~~l~~~l~~----------------------~~i~~~~ 104 (504)
+++++||||+++|+|++++.+..........|... .+|..|..++++|++ |+|+|++
T Consensus 272 ~~~~~yDAV~~~A~Al~~~~~~~~~~~~~~~c~~~~~~~~~g~~l~~~l~~v~f~G~tg~i~Fd~~Gd~~~~~~~I~~~~ 351 (377)
T cd06379 272 ESSHIRDAVAVLASAIQELFEKENITEPPRECVGNTVIWETGPLFKRALMSSKYPGETGRVEFNDDGDRKFANYDIMNIQ 351 (377)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCCCCccccCCCCCCcchHHHHHHHHhCCcCCccCceEECCCCCccCccEEEEEec
Confidence 67899999999999999986544445555689654 379999999999997 8999999
Q ss_pred ccceeeeeEecCCCCce
Q psy1412 105 REELRKVGHWTPAEGIN 121 (504)
Q Consensus 105 ~~~~~~vg~W~~~~gl~ 121 (504)
+.++++||+|+++ .+.
T Consensus 352 ~~~~~~VG~w~~~-~l~ 367 (377)
T cd06379 352 NRKLVQVGLYNGD-ILR 367 (377)
T ss_pred CCCceEeeEEcCc-EEE
Confidence 9999999999874 444
No 41
>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=98.11 E-value=4.6e-06 Score=84.83 Aligned_cols=105 Identities=15% Similarity=0.135 Sum_probs=63.8
Q ss_pred ceeeEEEEeeecCCCccccchhhhhhhccccc----CCCccccccccccchhhhHHHHHHHHHHHhhhcCCcccccCCCC
Q psy1412 5 VHVLAAGLALLDKSSVIKTSNLSCDLEVPWRD----GLSLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCD 80 (504)
Q Consensus 5 v~~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~----g~~~~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~ 80 (504)
+..++||||++|+.+.. ..++++++...|.. .+...+.++. ++||+||||+++-+++++.. -+.+ ...+..+
T Consensus 250 ~~~nitgfrl~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~al~yDaV~~~~~~~~~~~-~~GL-TG~i~F~ 325 (363)
T cd06381 250 AHGRMTVIRQTFSKEKT-NQRCLRNNHRISSLLCDPKDGYLQMLEI-SNLYIYDSVLLLLETIKKGP-ITGL-TGKLEFN 325 (363)
T ss_pred cCccEEEEEEecCCcCc-hHHHHHHHHHHHHhhcCCCCCCCCChhH-HHHHHHHHHHHHHHHHHhcC-ccCc-ceeEEeC
Confidence 44566999999876655 23334566666632 2222236776 99999999999955554431 1111 1111222
Q ss_pred CCCcccCchhHHHHhhhceEEEeeccc-----eeeeeEecCCCCce
Q psy1412 81 LEVPWRDGLSLYNYINTLDLLKLKREE-----LRKVGHWTPAEGIN 121 (504)
Q Consensus 81 ~~~~~~~G~~l~~~l~~~~i~~~~~~~-----~~~vg~W~~~~gl~ 121 (504)
.. |.+- .. +++|+++..++ .+++|+|++..|+.
T Consensus 326 ~~-----g~r~--~~-~l~i~~~~~~~~~~~~~~~~~~w~~~~~~~ 363 (363)
T cd06381 326 EG-----GDNS--NV-QFEILGTGYSETLGKDGRWLATWNPSKGLN 363 (363)
T ss_pred CC-----CCcc--cc-EEEEEEeccCCccccceEEeeeccCCCCCC
Confidence 11 1110 01 19999999776 89999999988863
No 42
>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=98.01 E-value=1.1e-05 Score=82.28 Aligned_cols=69 Identities=19% Similarity=0.336 Sum_probs=57.8
Q ss_pred ccchhhhHHHHHHHHHHHhhh-cCCcccccCCCCCCC--cccCchhHHHHhhh----------------------ceEEE
Q psy1412 48 EPALMYDSVHVLAAGLALLDK-SSVIKTSNLSCDLEV--PWRDGLSLYNYINT----------------------LDLLK 102 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~-~~~~~~~~~~c~~~~--~~~~G~~l~~~l~~----------------------~~i~~ 102 (504)
.++++||||+++|+|++++.+ ......+..+|.... +|.+|..++++|++ |+|+|
T Consensus 257 ~~~~~~Dav~~~a~Al~~~~~~~~~~~~~~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg~v~F~~~G~~~~~~~~I~~ 336 (362)
T cd06367 257 LEARVRDAVAIVARAAESLLRDKGALPEPPVNCYDTANKRESSGQYLARFLMNVTFDGETGDVSFNEDGYLSNPKLVIIN 336 (362)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcCCCCCCCCCchHHHHHHHhcccccCCCCceeECCCcccccceEEEEE
Confidence 678999999999999999865 233445567896643 39999999999997 99999
Q ss_pred ee-ccceeeeeEecC
Q psy1412 103 LK-REELRKVGHWTP 116 (504)
Q Consensus 103 ~~-~~~~~~vg~W~~ 116 (504)
++ +.++++||.|++
T Consensus 337 l~~~~~~~~VG~W~~ 351 (362)
T cd06367 337 LRRNRKWERVGSWEN 351 (362)
T ss_pred ecCCCcceEEEEEcC
Confidence 99 889999999985
No 43
>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=97.80 E-value=5.5e-06 Score=83.04 Aligned_cols=89 Identities=21% Similarity=0.401 Sum_probs=58.3
Q ss_pred eeEEEEeeecCCCccccchhhhhhhccccc------CCCccccccccccchhhhHHHHHHHHHHHhhhcCCcccccCCCC
Q psy1412 7 VLAAGLALLDKSSVIKTSNLSCDLEVPWRD------GLSLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCD 80 (504)
Q Consensus 7 ~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~------g~~~~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~ 80 (504)
+++||||++|++++. ++++.+.|.. .........+ ++||+||||+++ + + +. ++..+
T Consensus 238 ~niTgF~l~d~~~~~-----v~~f~~~~~~~~~~~~~~~~~~~~~~-~~al~~D~v~~~--g---l--Tg-----~i~f~ 299 (333)
T cd06394 238 SNILGFSMFNQSHAF-----YQEFIRSLNQSWRENCDHSPYTGPAL-SSALLFDAVYAV--G---L--TG-----RIEFN 299 (333)
T ss_pred cceEEEEeecCCcHH-----HHHHHHHHHHhhhhhcccccCCCccc-ceeeecceEEEE--e---e--ec-----ceecC
Confidence 456999999999877 7777775543 1111111223 899999999999 1 1 11 11121
Q ss_pred CCCcccCchhHHHHhhhceEEEeeccceeeeeEecCCCCce
Q psy1412 81 LEVPWRDGLSLYNYINTLDLLKLKREELRKVGHWTPAEGIN 121 (504)
Q Consensus 81 ~~~~~~~G~~l~~~l~~~~i~~~~~~~~~~vg~W~~~~gl~ 121 (504)
. .|.+- .. +++|++++.+|+++||+|++..||.
T Consensus 300 ~-----~g~R~--~~-~l~v~~l~~~g~~kig~W~~~~gl~ 332 (333)
T cd06394 300 S-----KGQRS--NY-TLKILQKTRSGFRQIGQWHSNETLS 332 (333)
T ss_pred C-----CCcCc--cc-EEEEEEecCCcceEEEEEeCCCCcC
Confidence 1 11110 00 1899999999999999999999886
No 44
>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=97.75 E-value=1.7e-05 Score=80.95 Aligned_cols=105 Identities=12% Similarity=0.075 Sum_probs=65.1
Q ss_pred eeeEEEEeeecCCCccccchhhhhhhcccccCC---CccccccccccchhhhHHHHHHHHHHHhhhcCCccc-----ccC
Q psy1412 6 HVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGL---SLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKT-----SNL 77 (504)
Q Consensus 6 ~~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g~---~~~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~-----~~~ 77 (504)
.++|||||+++..... ++.+.++|.+.. .....++. ++||+||||+++++|++++. .+.... ...
T Consensus 236 ~~Nitgfrl~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~-~~aL~~Dav~~~~~a~~~l~-~~~~~~~~~~~~~~ 308 (368)
T cd06383 236 NASIFVTRPMMDYQSS-----VRGALLRTDEPTLRPVFYFEWAF-RLFLAYDAVLAVGEWPRRMR-KKRVEDGSTGTSVL 308 (368)
T ss_pred cCcEEEeeccccchhh-----hccceeeccCCccCchhHHHHHH-HHHHHHHHHHHhccccchhh-eeeccCCCcCcccc
Confidence 4556999997555555 566666674421 11115776 89999999999999999873 221111 122
Q ss_pred CCCC---CCcc-cCchhHHHHhhhceE------EEeeccc---eeeeeEecCC
Q psy1412 78 SCDL---EVPW-RDGLSLYNYINTLDL------LKLKREE---LRKVGHWTPA 117 (504)
Q Consensus 78 ~c~~---~~~~-~~G~~l~~~l~~~~i------~~~~~~~---~~~vg~W~~~ 117 (504)
.|.. ..+| .+|..+.++|++.++ |.+...| --.+|.|+..
T Consensus 309 ~~~g~~~~~~w~~~g~~~~~~~k~~~~~gltG~i~f~~~g~R~~~~l~~~~~~ 361 (368)
T cd06383 309 PGFGISPESPLMTLQSSPFNGSSEIKFEMLAGRVAIDEGSSVSTKTIGSWSAS 361 (368)
T ss_pred CCCCCCcccchhhcccccccCccceeEeeecCeEEEecCceeeeeeeeeEecC
Confidence 4533 2367 777799999998333 3333333 2467778763
No 45
>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=97.66 E-value=0.00045 Score=67.95 Aligned_cols=81 Identities=16% Similarity=0.068 Sum_probs=55.4
Q ss_pred CChHHHHHhhhcCC-eEEEeecchhhhhhhcC-----CccEEcCCccCCcceEEEecCCC-C-CchHHHHHHHhhhccCh
Q psy1412 411 SDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN-----CNLTQIGGLLDSKGYGIATPKGS-P-WRDRISLAILELQEKGT 482 (504)
Q Consensus 411 ~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~-----c~l~~vg~~~~~~~~g~a~~k~S-p-l~~~in~ail~l~e~G~ 482 (504)
.+..+.+..|.+|+ +|.+.+.+.+..+.++. -++..+...-...+.+++++++- + +++.++++|.++.+++.
T Consensus 175 ~~~~~~~~al~~G~vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~ 254 (288)
T TIGR03431 175 GSHEAAILAVANGTVDAATTNDENLDRMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDK 254 (288)
T ss_pred CchHHHHHHHHcCCCCeEeccHHHHHHHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcH
Confidence 36788999999999 88888777666555422 12444432212234678899994 3 99999999999999966
Q ss_pred hHH--HHHhhc
Q psy1412 483 IQM--LYDKWW 491 (504)
Q Consensus 483 l~~--l~~kw~ 491 (504)
.++ ...+|.
T Consensus 255 ~~~~~~~~~~~ 265 (288)
T TIGR03431 255 ACFEKIAGGDL 265 (288)
T ss_pred HHHHhhhcccc
Confidence 554 334553
No 46
>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=97.64 E-value=9.1e-05 Score=77.88 Aligned_cols=72 Identities=24% Similarity=0.373 Sum_probs=55.0
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh----------------------ceEEEeec
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT----------------------LDLLKLKR 105 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~----------------------~~i~~~~~ 105 (504)
.++++||||+++|+||+++.+..-. .....|.... |.+|..|+++|++ |+|+|++.
T Consensus 354 ~~~~vyDAV~a~A~AL~~~l~~~~~-~~~~~c~~~~-~~~~~~l~~~l~~v~f~g~tg~~v~Fd~~G~~~~~y~I~~~~~ 431 (452)
T cd06362 354 KVQFVIDAVYAMAHALHNMHRDLCP-GTTGLCDAMK-PIDGRKLLFYLRNVSFSGLAGGPVRFDANGDGPGRYDIFNYQR 431 (452)
T ss_pred chhHHHHHHHHHHHHHHHHHHhhCC-CCCCCCcCcc-CCCHHHHHHHHHhCCcCCCCCceEEECCCCCCCCceEEEEEEE
Confidence 6789999999999999998632211 1123576533 7889999999998 89999984
Q ss_pred ----cceeeeeEecCCCCce
Q psy1412 106 ----EELRKVGHWTPAEGIN 121 (504)
Q Consensus 106 ----~~~~~vg~W~~~~gl~ 121 (504)
.++++||+|+++.|+.
T Consensus 432 ~~~~~~~~~VG~w~~~~~~~ 451 (452)
T cd06362 432 TNGKYDYVKVGSWKGELSLN 451 (452)
T ss_pred cCCceEEEEEEEEecccccC
Confidence 2479999999887764
No 47
>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=97.63 E-value=0.00011 Score=77.85 Aligned_cols=73 Identities=21% Similarity=0.356 Sum_probs=54.5
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh----------------------ceEEEeec
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT----------------------LDLLKLKR 105 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~----------------------~~i~~~~~ 105 (504)
.++++||||+++|+||+++....- ......|+... +..|..|+++|++ |+|+|++.
T Consensus 371 ~~~~vyDAVyaiA~ALh~~~~~~~-~~~~~~c~~~~-~~~~~~l~~~l~~v~F~g~tG~~v~Fd~~G~~~~~ydI~n~~~ 448 (472)
T cd06374 371 KMGFVINAIYAMAHGLHNMHQDLC-PGHVGLCDAMK-PIDGRKLLEYLLKTSFSGVSGEEVYFDENGDSPGRYDIMNLQY 448 (472)
T ss_pred eeHHHHHHHHHHHHHHHHHHHhhC-CCCCCCCcCCC-CCCHHHHHHHHHhCcccCCCCCeEEEcCCCCCCCceEEEEEEE
Confidence 567999999999999999853221 11223686543 4789999999998 99999995
Q ss_pred -----cceeeeeEecCCCCceee
Q psy1412 106 -----EELRKVGHWTPAEGINIT 123 (504)
Q Consensus 106 -----~~~~~vg~W~~~~gl~~~ 123 (504)
.++++||.|++ .+|.++
T Consensus 449 ~~~~~~~~~~VG~w~~-~~l~~~ 470 (472)
T cd06374 449 TEDLRFDYINVGSWHE-GDLGID 470 (472)
T ss_pred CCCCCEEEEEEEEEeC-Cccccc
Confidence 24799999985 467653
No 48
>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=97.43 E-value=0.00027 Score=74.58 Aligned_cols=67 Identities=24% Similarity=0.382 Sum_probs=51.1
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh----------------------ceEEEeec
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT----------------------LDLLKLKR 105 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~----------------------~~i~~~~~ 105 (504)
.++++||||+++|+||+++.+.+- ......|... .|.+|..|+++|++ |+|+|++.
T Consensus 359 ~~~~v~dAVyaiA~ALh~l~~~~c-~~~~~~C~~~-~~~~~~~l~~~L~~v~F~g~tg~~v~Fd~~G~~~~~Ydi~n~q~ 436 (463)
T cd06376 359 KVQFVIDAVYAMAHALHSMHKDLC-PGYTGVCPEM-EPADGKKLLKYIRAVNFNGSAGTPVMFNENGDAPGRYDIFQYQI 436 (463)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhhC-CCCCCCCccC-CCCCHHHHHHHHHhCCccCCCCCeEEeCCCCCCCCceEEEEEEe
Confidence 578999999999999999853221 1122468554 37889999999997 88988883
Q ss_pred -----cceeeeeEecC
Q psy1412 106 -----EELRKVGHWTP 116 (504)
Q Consensus 106 -----~~~~~vg~W~~ 116 (504)
.++++||.|++
T Consensus 437 ~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 437 TNTSSPGYRLIGQWTD 452 (463)
T ss_pred cCCCceeEEEEEEECC
Confidence 35789999975
No 49
>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=96.03 E-value=0.0039 Score=62.43 Aligned_cols=85 Identities=32% Similarity=0.501 Sum_probs=56.6
Q ss_pred eEEEEeeecCCCccccchhhhhhhcccccCCCc------cccccccccchhhhHHHHHHHHHHHhhhcCCcccccCCCCC
Q psy1412 8 LAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSL------YNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDL 81 (504)
Q Consensus 8 ~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g~~~------~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~ 81 (504)
.++++++.+++.+. ..++.++|...... ...... .++++||||+++ ++ +.. +..++
T Consensus 234 ~~~~~~~~~~~~~~-----~~~f~~~~~~~~~~~~~~~~~~~p~~-~~a~~yDav~~~--g~-----tG~-----v~f~~ 295 (327)
T cd06382 234 NITGFRLVDPDSPE-----VKEVIRSLELSWDEGCRILPSTGVTT-ESALMYDAVYLF--GL-----TGR-----IEFDS 295 (327)
T ss_pred eEEEEEEecCCchh-----HHHHHHHHHhhcccccccCCCCCcch-hhhhhhceEEEe--ec-----ccc-----eeeCC
Confidence 56999998877665 67777777542211 012444 789999999999 11 111 11111
Q ss_pred CCcccCchhHHHHhhh--ceEEEeeccceeeeeEecCCCCc
Q psy1412 82 EVPWRDGLSLYNYINT--LDLLKLKREELRKVGHWTPAEGI 120 (504)
Q Consensus 82 ~~~~~~G~~l~~~l~~--~~i~~~~~~~~~~vg~W~~~~gl 120 (504)
+|.+ .+ |+|+|+.++++++||+|++..||
T Consensus 296 -----~g~r-----~~~~~~~~~~~~~~~~~vg~w~~~~~~ 326 (327)
T cd06382 296 -----SGQR-----SNFTLDVIELTESGLRKVGTWNSSEGL 326 (327)
T ss_pred -----CCCE-----eeeEEEEEeccccCceEEEEECCCCCc
Confidence 2322 22 89999999999999999998876
No 50
>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=95.99 E-value=0.017 Score=61.01 Aligned_cols=67 Identities=21% Similarity=0.236 Sum_probs=45.9
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh----------------------ceEEEeec
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT----------------------LDLLKLKR 105 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~----------------------~~i~~~~~ 105 (504)
.+..+||||.++|+||+++.+-..-.-+..+|.. . -..+..++++|++ |+|+|++.
T Consensus 359 ~~~~v~dAVya~AhALh~~l~c~~~~~~~~~~~~-~-~~~~~~l~~~l~~v~F~~~~g~~v~Fd~nGd~~~~YdI~n~q~ 436 (469)
T cd06365 359 ESYNVYNAVYAVAHALHEMLLQQVETQSENNGKR-L-IFLPWQLHSFLKNIQFKNPAGDEVNLNQKRKLDTEYDILNYWN 436 (469)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhccCCCcCCCCC-C-CccHHHHHHHHHhccccCCCCCEEEecCCCCcCceeeEEEEEE
Confidence 3567999999999999999642211111233432 1 2355678899987 99999973
Q ss_pred --cc---eeeeeEecC
Q psy1412 106 --EE---LRKVGHWTP 116 (504)
Q Consensus 106 --~~---~~~vg~W~~ 116 (504)
.+ +++||.|++
T Consensus 437 ~~~~~~~~~~VG~~~~ 452 (469)
T cd06365 437 FPQGLGLKVKVGEFSP 452 (469)
T ss_pred CCCCCEEEEEEEEEeC
Confidence 22 689999975
No 51
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=95.86 E-value=0.055 Score=51.65 Aligned_cols=123 Identities=15% Similarity=0.163 Sum_probs=69.6
Q ss_pred hhcccchhhhhccCCCCceeeee--------ecchh-ccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEE
Q psy1412 359 RYMESKKCILFLGGQGDETFVTI--------DLSQR-ADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFL 428 (504)
Q Consensus 359 ~~~~~i~s~~dL~~~~~i~~g~~--------~~~~~-~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i 428 (504)
+..++|++++||.+.. +.++.. ....+ ++..+.. .+. -..+++.+.+..++.|.+|+ +|.+
T Consensus 92 ~~ds~i~~l~dL~Gk~-v~~~~~~s~sg~l~~~~~L~~~~Gl~~-~~~-------~~~~~~~~~~~~~~~l~~G~~Da~~ 162 (243)
T PF12974_consen 92 RADSPITSLADLKGKR-VAFPDPSSTSGYLIPRYELLREAGLDP-GDD-------FKQVFVGSHDAVLEALLNGKADAAA 162 (243)
T ss_dssp ETTSS--SHHHHGGSE-EEEE-TT-TTTTHHHHHHTCCCCT--H-HHH-------SSEEEEE-HHHHHHHHHTTSSSEEE
T ss_pred ECCCCCCChhhcCCCE-EEEecCCccHHHHHHHHHHHHHcCCCh-hHc-------eeEEEeCCHHHHHHHHHcCCccEEE
Confidence 6667889999996542 333211 12223 2222221 110 12346778899999999999 7766
Q ss_pred eecchhhhhhhcC----CccEEcCCccCCcceEEEecCCCC--CchHHHHHHHhhhccChhHHHHHhh
Q psy1412 429 MESTMLDYEVQRN----CNLTQIGGLLDSKGYGIATPKGSP--WRDRISLAILELQEKGTIQMLYDKW 490 (504)
Q Consensus 429 ~e~~~~~y~~~~~----c~l~~vg~~~~~~~~g~a~~k~Sp--l~~~in~ail~l~e~G~l~~l~~kw 490 (504)
......+-+.... -++.++...-...++.++..++-| .++.|-.+++.+..+-.-.++.+.+
T Consensus 163 ~~~~~~~~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~~~~~l~~~ 230 (243)
T PF12974_consen 163 IPSDAFERLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPEGKAILDAF 230 (243)
T ss_dssp EEHHHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHHHHHHHHHT
T ss_pred EechhHHHHHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChhhHHHHHhc
Confidence 6665555444432 367777653333445777777755 8999999999999864445554443
No 52
>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=95.70 E-value=0.032 Score=59.57 Aligned_cols=67 Identities=13% Similarity=0.151 Sum_probs=46.6
Q ss_pred cchhhhHHHHHHHHHHHhhhcC--CcccccCCCCCCCcccCchhHHHHhhh----------------------ceEEEee
Q psy1412 49 PALMYDSVHVLAAGLALLDKSS--VIKTSNLSCDLEVPWRDGLSLYNYINT----------------------LDLLKLK 104 (504)
Q Consensus 49 ~~~~yDav~~~a~a~~~~~~~~--~~~~~~~~c~~~~~~~~G~~l~~~l~~----------------------~~i~~~~ 104 (504)
+..+||||.++|+||+++..-. ........|..... -++..++++|++ |||+|++
T Consensus 397 ~~~v~~AVyAvAhaLh~~~~c~~~~~~~~~~~c~~~~~-~~~~~l~~~L~~v~F~~~~g~~v~Fd~~Gd~~~~YdI~n~q 475 (510)
T cd06364 397 SYNVYLAVYSIAHALQDIYTCTPGKGLFTNGSCADIKK-VEAWQVLKHLRHLNFTDNMGEQVRFDEGGDLVGNYSIINWH 475 (510)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCCccCCCCCCCCC-CCHHHHHHHHHhcEEecCCCCEEEEecCCCCccceeEEEee
Confidence 4569999999999999996311 11111236855322 356688899997 9999998
Q ss_pred c---cc---eeeeeEecC
Q psy1412 105 R---EE---LRKVGHWTP 116 (504)
Q Consensus 105 ~---~~---~~~vg~W~~ 116 (504)
. .+ +.+||.|++
T Consensus 476 ~~~~~~~~~~v~VG~~~~ 493 (510)
T cd06364 476 LSPEDGSVVFKEVGYYNV 493 (510)
T ss_pred ecCCCCcEEEEEEEEEcC
Confidence 4 22 579999975
No 53
>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=95.66 E-value=0.015 Score=59.86 Aligned_cols=37 Identities=22% Similarity=0.275 Sum_probs=30.3
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhh
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYIN 96 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~ 96 (504)
+++++||||+++|+|++++.+ |. ..|.+|..+.+.|+
T Consensus 301 ~a~~~yDav~~~A~Al~~~~~----------~g--~~~~~g~~l~~~l~ 337 (391)
T cd06372 301 YSAYLHDAVLLYALAVKEMLK----------AG--KDFRNGRQLVSTLR 337 (391)
T ss_pred HHHHHHHHHHHHHHHHHHHHh----------cC--CCCCCHHHHHHHHh
Confidence 789999999999999998752 21 23678899999988
No 54
>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=95.47 E-value=0.011 Score=59.07 Aligned_cols=86 Identities=34% Similarity=0.529 Sum_probs=55.9
Q ss_pred eeEEEEeeecCCCccccchhhhhhhcccccCCCc------cccccccccchhhhHHHHHHHHHHHhhhcCCcccccCCCC
Q psy1412 7 VLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSL------YNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCD 80 (504)
Q Consensus 7 ~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g~~~------~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~ 80 (504)
..++|+++.++..+. ...+.++|+..... ...... .++++||||+++ +. .+..+
T Consensus 232 ~~~~~~~~~~~~~~~-----~~~f~~~~~~~~~~~~~~~~~~~p~~-~aa~~yDav~~~---------tg-----~~~f~ 291 (324)
T cd06368 232 VNITGFRLVDPDNPE-----VQKFIQRWERSDHRICPGSGLKPIKT-ESALTYDAVLLF---------TG-----RIQFD 291 (324)
T ss_pred ceEEEEEEecCCChH-----HHHHHHHHHhccccccCCCCCCCcch-hhHhhhcEEEEe---------ee-----eeEeC
Confidence 346999988776665 77788888642111 012333 899999999998 11 11111
Q ss_pred CCCcccCchhHHHHhhhceEEEeeccceeeeeEecCCCCc
Q psy1412 81 LEVPWRDGLSLYNYINTLDLLKLKREELRKVGHWTPAEGI 120 (504)
Q Consensus 81 ~~~~~~~G~~l~~~l~~~~i~~~~~~~~~~vg~W~~~~gl 120 (504)
+. |.+ . --.|+|+|+...+.+++|+|++..|+
T Consensus 292 ~~-----g~~-~--~~~~~i~~~~~~~~~~~g~W~~~~~~ 323 (324)
T cd06368 292 EN-----GQR-S--NFTLDILELKEGGLRKVGTWNPEDGL 323 (324)
T ss_pred CC-----CcC-c--ceEEEEEEEcCCCceEEEEECCCCCC
Confidence 11 111 0 01299999999999999999998776
No 55
>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=95.39 E-value=0.017 Score=59.34 Aligned_cols=38 Identities=16% Similarity=0.093 Sum_probs=30.6
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT 97 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~ 97 (504)
.++++||||+++|+|++++.... ..|.+|+.|.+.|++
T Consensus 298 ~aa~~yDav~l~A~Al~~~~~~g------------~~~~~g~~l~~~l~~ 335 (387)
T cd06386 298 FVEGFHDAILLYALALHEVLKNG------------YSKKDGTKITQRMWN 335 (387)
T ss_pred HHHHHHHHHHHHHHHHHHHhhCC------------CCCCCHHHHHHHHhC
Confidence 78999999999999999874211 136789999999887
No 56
>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=95.11 E-value=0.035 Score=55.54 Aligned_cols=79 Identities=22% Similarity=0.273 Sum_probs=51.7
Q ss_pred EEEEeeecCCCccccchhhhhhhcccccCC------CccccccccccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCC
Q psy1412 9 AAGLALLDKSSVIKTSNLSCDLEVPWRDGL------SLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLE 82 (504)
Q Consensus 9 ~tg~r~~d~~~~~~~~~~~~~~~~~W~~g~------~~~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~ 82 (504)
++++++..+..+. ..++.++|.... ........ +++++||||+++|+|++++.+...-. +...
T Consensus 235 ~~~~~~~~~~~~~-----~~~f~~~~~~~~~~~~~~~~~~~~~~-~~~~~yDAv~~~a~al~~~~~~~~~~-----~~~~ 303 (348)
T PF01094_consen 235 VLGFTPPPPSSPE-----FEDFMKKWKESNNQSSTSGSDQEPSP-YAAYAYDAVYLLAHALNRALQDGGPV-----TNGR 303 (348)
T ss_dssp EEEEEESTTTSHH-----HHHHHHHHHTTTHTTTTTTTTSSGCH-HHHHHHHHHHHHHHHHHHHHHHHSTT-----TSSS
T ss_pred eeeeeeecccccc-----hhhhhcccChhhccCcccccccccce-eeeeehhhhHHHHHHHHHHHHhccCC-----CCCc
Confidence 4666665554444 677777776421 11113333 78999999999999999986432111 1111
Q ss_pred CcccCchhHHHHhhhc
Q psy1412 83 VPWRDGLSLYNYINTL 98 (504)
Q Consensus 83 ~~~~~G~~l~~~l~~~ 98 (504)
.+|.+|..+.++|++.
T Consensus 304 ~~~~~g~~l~~~l~~~ 319 (348)
T PF01094_consen 304 NPWQNGSQLLKYLRNV 319 (348)
T ss_dssp GTSTTHHHHHHHHHTE
T ss_pred cccccHHHHHHHHhhe
Confidence 7899999999999973
No 57
>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=94.99 E-value=0.052 Score=56.28 Aligned_cols=63 Identities=14% Similarity=0.135 Sum_probs=42.0
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh---------------------ceEEEeecc
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT---------------------LDLLKLKRE 106 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~---------------------~~i~~~~~~ 106 (504)
.++.+||||+++|+|++++.... ...|... .+..+..+.++|++ ++|+++..+
T Consensus 308 ~~~~~YDaV~~~a~Al~~a~~~~-----~~~~~~~-~~~~~~~l~~~L~~~~~~g~~g~i~fd~~G~~~~~~~i~~~~~~ 381 (410)
T cd06363 308 FAFSVYAAVYAVAHALHNVLQCG-----SGGCPKR-VPVYPWQLLEELKKVNFTLLGQTVRFDENGDPNFGYDIVVWWWD 381 (410)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCC-----CCCCCCC-CCCCHHHHHHHHhccEEecCCcEEEeCCCCCCccceEEEEEEEc
Confidence 56789999999999999874221 1235422 12455668888776 667776443
Q ss_pred ----ceeeeeEecC
Q psy1412 107 ----ELRKVGHWTP 116 (504)
Q Consensus 107 ----~~~~vg~W~~ 116 (504)
+.++||+|.+
T Consensus 382 ~~~~~~~~vG~~~~ 395 (410)
T cd06363 382 NSSGTFEEVGSYSF 395 (410)
T ss_pred CCceeEEEEEEEEC
Confidence 3677888876
No 58
>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=94.03 E-value=0.094 Score=54.11 Aligned_cols=38 Identities=21% Similarity=0.242 Sum_probs=31.2
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT 97 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~ 97 (504)
.++++||||+++|.|+++..+. .++|.+|..+.++|++
T Consensus 311 ~aa~~YDav~l~a~Al~~~~~~------------~~~~~~g~~i~~~l~~ 348 (399)
T cd06384 311 IAGCFYDGVMLYAMALNETLAE------------GGSQKDGLNITRKMQD 348 (399)
T ss_pred hhhhhHHHHHHHHHHHHHHHhc------------CCCCCCcHhHHHHHhC
Confidence 6899999999999999987421 2357789999999997
No 59
>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=93.98 E-value=1.2 Score=40.17 Aligned_cols=69 Identities=12% Similarity=0.177 Sum_probs=48.6
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.++++. .+..+.++..|.+|++|++++.... ....+. ..|+.+..++
T Consensus 19 ~~l~~~l~~~~~~~P~i~i~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~ 81 (209)
T PF03466_consen 19 SLLPPLLAEFRERHPNIRIEIR-------------EGDSDELIEALRSGELDLAITFGPP---PPPGLE-SEPLGEEPLV 81 (209)
T ss_dssp HTHHHHHHHHHHHSTTEEEEEE-------------EESHHHHHHHHHTTSSSEEEESSSS---SSTTEE-EEEEEEEEEE
T ss_pred HHHHHHHHHHHHHCCCcEEEEE-------------eccchhhhHHHhcccccEEEEEeec---cccccc-cccccceeee
Confidence 34457788887766 4566666 3456789999999999999876655 233333 3688889999
Q ss_pred EEEEccC
Q psy1412 244 ILFKVPT 250 (504)
Q Consensus 244 ilv~~~~ 250 (504)
+++++..
T Consensus 82 ~~~~~~~ 88 (209)
T PF03466_consen 82 LVVSPDH 88 (209)
T ss_dssp EEEETTS
T ss_pred eeeeccc
Confidence 9988653
No 60
>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=93.88 E-value=2.4 Score=37.01 Aligned_cols=68 Identities=13% Similarity=0.280 Sum_probs=44.9
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++..+.++. +.++++.. ..+..++..|.+|++|++++.... ....++ ..+.....++
T Consensus 13 ~~l~~~i~~~~~~~p~i~i~~~~-------------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~ 75 (197)
T cd05466 13 YLLPPLLAAFRQRYPGVELSLVE-------------GGSSELLEALLEGELDLAIVALPV---DDPGLE-SEPLFEEPLV 75 (197)
T ss_pred HHhHHHHHHHHHHCCCCEEEEEE-------------CChHHHHHHHHcCCceEEEEcCCC---CCCcce-EeeeeccceE
Confidence 44557777777665 35566652 345679999999999999866543 223344 3466777777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 76 ~~~~~~ 81 (197)
T cd05466 76 LVVPPD 81 (197)
T ss_pred EEecCC
Confidence 777654
No 61
>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=93.74 E-value=0.16 Score=53.49 Aligned_cols=67 Identities=22% Similarity=0.466 Sum_probs=43.1
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHH-HHhhh---------------------------ce
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLY-NYINT---------------------------LD 99 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~-~~l~~---------------------------~~ 99 (504)
.+..+||||.++|+||++|.+.. -...+..|..... -++..++ ++|++ ||
T Consensus 354 ~~~~v~~AVyA~AhaLh~~l~~~-c~~~~~~c~~~~~-~~~~~l~~~~L~~v~F~~~~~~~~~g~~v~Fd~nGd~~~~Yd 431 (458)
T cd06375 354 KIMFVVNAVYAMAHALHNMQRDL-CPNTTKLCDAMKP-LDGKKLYKEYLLNVSFTAPFRPDLADSEVKFDSQGDGLGRYN 431 (458)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhc-CCCCCCCCCCCCC-CCHHHHHHHHHHhccccccccCCCCCCeeEECCCCCCCcceE
Confidence 46779999999999999996321 1111135754322 2455666 36665 88
Q ss_pred EEEeec--cc----eeeeeEecC
Q psy1412 100 LLKLKR--EE----LRKVGHWTP 116 (504)
Q Consensus 100 i~~~~~--~~----~~~vg~W~~ 116 (504)
|+|.+. ++ +.+||.|+.
T Consensus 432 I~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 432 IFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred EEEEEEcCCCCcEEEEEEEEEec
Confidence 888883 22 468888854
No 62
>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=93.52 E-value=0.029 Score=55.80 Aligned_cols=82 Identities=28% Similarity=0.413 Sum_probs=54.2
Q ss_pred eeEEEEeeecCCCccccchhhhhhhcccccC--CCccccccccccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCc
Q psy1412 7 VLAAGLALLDKSSVIKTSNLSCDLEVPWRDG--LSLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVP 84 (504)
Q Consensus 7 ~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g--~~~~~~i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~ 84 (504)
..++|+|++++.... +.++..+|... ......+.. +++++||+++++ +..+. .+.
T Consensus 238 ~~i~g~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~-~~~~~~d~~~~~---------tg~i~-----f~~--- 294 (328)
T cd06351 238 ANITGFRLVDPDSPD-----VSQFLQRWLEESPGVNLRAPIY-DAALLYDAVLLL---------TGTVS-----FDE--- 294 (328)
T ss_pred cceEEEEEeCCCchH-----HHHHHHhhhhccCCCCcCccch-hhHhhhcEEEEE---------EeeEE-----ECC---
Confidence 456999999988877 77787887331 111124555 899999999888 11111 111
Q ss_pred ccCchhHHHHhhhceEEEee-ccceeeeeEecC
Q psy1412 85 WRDGLSLYNYINTLDLLKLK-REELRKVGHWTP 116 (504)
Q Consensus 85 ~~~G~~l~~~l~~~~i~~~~-~~~~~~vg~W~~ 116 (504)
+|.+. --+++|+++. ..+++++|.|+.
T Consensus 295 --~g~r~---~~~l~i~~l~~~~~~~~vg~W~~ 322 (328)
T cd06351 295 --DGVRS---NFTLDIIELNRSRGWRKVGTWNG 322 (328)
T ss_pred --CCccc---ceEEEEEEecCCCCceEEEEecC
Confidence 12222 1128999999 899999999993
No 63
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=93.22 E-value=1.3 Score=43.68 Aligned_cols=113 Identities=19% Similarity=0.084 Sum_probs=67.6
Q ss_pred hhcccchhhhhccCCCCceeeee--------ecchhc-cchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEE-
Q psy1412 359 RYMESKKCILFLGGQGDETFVTI--------DLSQRA-DSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAF- 427 (504)
Q Consensus 359 ~~~~~i~s~~dL~~~~~i~~g~~--------~~~~~~-~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~- 427 (504)
+..++|++++||...+ +.++.. ...++. ...+.. . +......+..+.+.++..|.+|+ ++.
T Consensus 131 ~~ds~i~sl~dlkgk~-~af~d~~StSG~l~P~~~L~~~g~~d~-~------~~f~~v~~~G~H~~a~~aV~nG~vDva~ 202 (299)
T COG3221 131 RADSPIKSLEDLKGKR-FAFGDPDSTSGYLFPLYYLAKEGGIDP-D------KFFGEVIFSGGHDAAVLAVANGQVDVAA 202 (299)
T ss_pred eCCCCcchHHHhcCCe-EeccCCCcchhhHhHHHHHHHhcCCCh-h------hhhceeeccChHHHHHHHHHcCCceEEe
Confidence 7788999999998652 344332 111111 111111 0 00112334455899999999999 654
Q ss_pred EeecchhhhhhhcC----CccEEcCCccCCcceEEEecCCCC--CchHHHHHHHhhhc
Q psy1412 428 LMESTMLDYEVQRN----CNLTQIGGLLDSKGYGIATPKGSP--WRDRISLAILELQE 479 (504)
Q Consensus 428 i~e~~~~~y~~~~~----c~l~~vg~~~~~~~~g~a~~k~Sp--l~~~in~ail~l~e 479 (504)
.............. -++.++...--..+..|++++.-| +++++..+++.|.+
T Consensus 203 ~~~~~~~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 203 VNSSARGLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred ccHHHHhhhhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 44444333332221 267777765555566788888765 99999999999986
No 64
>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=92.89 E-value=0.28 Score=50.72 Aligned_cols=68 Identities=13% Similarity=0.166 Sum_probs=46.2
Q ss_pred ccccccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh---------------------ceEEE
Q psy1412 44 INTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT---------------------LDLLK 102 (504)
Q Consensus 44 i~~~~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~---------------------~~i~~ 102 (504)
++.+....+||||+++|+||+++... ..|.... ..++..++++|++ |+|+|
T Consensus 304 ~~~~~~~~v~~AVyaiA~Al~~~~~~-------~~c~~~~-~~~~~~l~~~L~~~~f~g~~~~v~Fd~~gd~~~~y~I~~ 375 (403)
T cd06361 304 LKNLLIHSIQLAVFALAHAIRDLCQE-------RQCQNPN-AFQPWELLGQLKNVTFEDGGNMYHFDANGDLNLGYDVVL 375 (403)
T ss_pred HHHhhHHHHHHHHHHHHHHHHHhccC-------CCCCCCC-CcCHHHHHHHHheeEEecCCceEEECCCCCCCcceEEEE
Confidence 33334456899999999999987421 2474432 2357788888886 77777
Q ss_pred eeccc----eeeeeEecCCCC
Q psy1412 103 LKREE----LRKVGHWTPAEG 119 (504)
Q Consensus 103 ~~~~~----~~~vg~W~~~~g 119 (504)
++..+ +.+||.|++...
T Consensus 376 ~~~~~~~~~~~~vg~~~~~~~ 396 (403)
T cd06361 376 WKEDNGHMTVTIMAEYDPQND 396 (403)
T ss_pred eEecCCcEEEEEEEEEeCCCC
Confidence 77532 477888877654
No 65
>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=92.53 E-value=1.7 Score=38.94 Aligned_cols=68 Identities=13% Similarity=0.068 Sum_probs=46.0
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.+++++ .+..+.+...|.+|++|+++...... ...+. +.|..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~v~i~-------------~~~~~~~~~~l~~g~~D~~i~~~~~~---~~~l~-~~~l~~~~~~ 75 (201)
T cd08459 13 YFLPRLLAALREVAPGVRIETV-------------RLPVDELEEALESGEIDLAIGYLPDL---GAGFF-QQRLFRERYV 75 (201)
T ss_pred HHHHHHHHHHHHHCCCCeEEEE-------------ecCccCHHHHhhCCCceEEEEcCCCC---cccce-EEEeecCceE
Confidence 34457788887776 4566665 34556789999999999998543221 22344 3688888888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 ~v~~~~ 81 (201)
T cd08459 76 CLVRKD 81 (201)
T ss_pred EEEcCC
Confidence 887654
No 66
>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=92.44 E-value=5 Score=35.62 Aligned_cols=70 Identities=10% Similarity=0.190 Sum_probs=44.3
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .+....+...|.+|++|++++..... .....+.+ .|.....++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~~~-~~l~~~~~~ 77 (201)
T cd08418 13 TLMPAVINRFKEQFPDVQISIY-------------EGQLSSLLPELRDGRLDFAIGTLPDE-MYLKELIS-EPLFESDFV 77 (201)
T ss_pred hhhHHHHHHHHHHCCCceEEEE-------------eCcHHHHHHHHHcCCCcEEEEecCCC-CCCcceeE-EeecCCceE
Confidence 34456777777765 4566665 34567899999999999998643211 11223443 566677777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 78 ~v~~~~ 83 (201)
T cd08418 78 VVARKD 83 (201)
T ss_pred EEeCCC
Confidence 777543
No 67
>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=92.05 E-value=2.6 Score=37.93 Aligned_cols=71 Identities=11% Similarity=0.076 Sum_probs=47.3
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++.++.++. +.+++++ .+..+.+++.|.+|++|++++.......-...+.+ .|..+...+
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~-~~l~~~~~~ 78 (202)
T cd08468 13 AVMPRLMARLEELAPSVRLNLV-------------HAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEE-RDWWEDTYV 78 (202)
T ss_pred HHhHHHHHHHHhhCCCCEEEEE-------------ECChHhHHHHHHCCCccEEEecccccccCCCCEEE-EEEecCcEE
Confidence 44567888888876 4667766 34567899999999999998643221000123443 577777888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 79 ~~~~~~ 84 (202)
T cd08468 79 VIASRD 84 (202)
T ss_pred EEEeCC
Confidence 887654
No 68
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=91.92 E-value=5 Score=39.43 Aligned_cols=68 Identities=9% Similarity=0.125 Sum_probs=44.8
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
++-..++..+.+.. +.++++. .++-+.++..|.+|++|+++.......+ -+ .+.|+....++
T Consensus 104 ~~~~~~l~~~~~~~P~v~i~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~l-~~~~l~~~~~~ 166 (305)
T PRK11151 104 YLLPHIIPMLHQTFPKLEMYLH-------------EAQTHQLLAQLDSGKLDCAILALVKESE---AF-IEVPLFDEPML 166 (305)
T ss_pred HHHHHHHHHHHHHCCCcEEEEE-------------eCCHHHHHHHHHcCCccEEEEecCCCCC---Ce-EEEEeccCcEE
Confidence 34446777776654 4555555 3345789999999999999864332222 12 34788888888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 167 ~~~~~~ 172 (305)
T PRK11151 167 LAVYED 172 (305)
T ss_pred EEecCC
Confidence 888654
No 69
>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=91.69 E-value=1.5 Score=39.07 Aligned_cols=68 Identities=12% Similarity=0.176 Sum_probs=45.0
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.+++++ .+..+.+...|.+|++|+++.... .....+. ..|+.+..++
T Consensus 13 ~~~~~~i~~~~~~~P~i~l~~~-------------~~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~ 75 (200)
T cd08417 13 LLLPPLLARLRQEAPGVRLRFV-------------PLDRDDLEEALESGEIDLAIGVFP---ELPPGLR-SQPLFEDRFV 75 (200)
T ss_pred HHHHHHHHHHHhhCCCeEEEec-------------cCCHHHHHHHHHcCCCCEEEeecc---cCCCccc-hhhhhcCceE
Confidence 44456777777665 3556655 445678999999999999985432 2222233 3577788888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 ~v~~~~ 81 (200)
T cd08417 76 CVARKD 81 (200)
T ss_pred EEecCC
Confidence 887644
No 70
>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=91.68 E-value=2.5 Score=37.55 Aligned_cols=67 Identities=16% Similarity=0.249 Sum_probs=45.5
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.+.. +.++++. .++...++..|.+|++|+++..... ....+.+ .|.....+++
T Consensus 14 ~l~~~l~~~~~~~P~i~i~~~-------------~~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~~-~~l~~~~~~~ 76 (198)
T cd08421 14 FLPEDLASFLAAHPDVRIDLE-------------ERLSADIVRAVAEGRADLGIVAGNV---DAAGLET-RPYRTDRLVV 76 (198)
T ss_pred hhHHHHHHHHHHCCCceEEEE-------------ecCcHHHHHHHhcCCceEEEEecCC---CCCCcEE-EEeecCcEEE
Confidence 4457888887765 4566665 3356779999999999998854322 2333443 5777888888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
++++.
T Consensus 77 v~~~~ 81 (198)
T cd08421 77 VVPRD 81 (198)
T ss_pred EeCCC
Confidence 87654
No 71
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=91.39 E-value=6.2 Score=38.79 Aligned_cols=71 Identities=8% Similarity=0.192 Sum_probs=45.7
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.++++. .+....++..|.+|++|+++..-....+....+. ..|+....++
T Consensus 108 ~~~~~~l~~~~~~~P~v~i~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~-~~~l~~~~~~ 173 (305)
T CHL00180 108 YLMPRLIGLFRQRYPQINVQLQ-------------VHSTRRIAWNVANGQIDIAIVGGEVPTELKKILE-ITPYVEDELA 173 (305)
T ss_pred hHHHHHHHHHHHHCCCceEEEE-------------eCCHHHHHHHHHcCCccEEEEcCccCccccccee-EEEeccCcEE
Confidence 34456777777765 3566665 3356789999999999999864322221112233 4677888888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 174 ~v~~~~ 179 (305)
T CHL00180 174 LIIPKS 179 (305)
T ss_pred EEECCC
Confidence 887654
No 72
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=91.30 E-value=10 Score=33.62 Aligned_cols=68 Identities=15% Similarity=0.194 Sum_probs=44.8
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .+....++..|.+|++|+++...... ...+. +.+..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~~~~D~~i~~~~~~---~~~~~-~~~l~~~~~~ 75 (199)
T cd08426 13 ELLPSLIARFRQRYPGVFFTVD-------------VASTADVLEAVLSGEADIGLAFSPPP---EPGIR-VHSRQPAPIG 75 (199)
T ss_pred HHHHHHHHHHHHhCCCeEEEEE-------------eCCcHHHHHHHHCCCccEEEecCCCC---CCCeE-EEeeccCcEE
Confidence 34457777777765 4556665 33557799999999999998543222 22243 3677788888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 76 ~v~~~~ 81 (199)
T cd08426 76 AVVPPG 81 (199)
T ss_pred EEecCC
Confidence 887654
No 73
>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=91.14 E-value=0.35 Score=49.97 Aligned_cols=39 Identities=15% Similarity=0.060 Sum_probs=30.6
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhhc
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTL 98 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~~ 98 (504)
.++++||||+++|.|+++..+. .+.|.+|..+.++|++.
T Consensus 310 ~aa~~YDav~l~a~Al~~~~~~------------~~~~~~g~~i~~~l~~~ 348 (405)
T cd06385 310 IAGGFYDGVMLYAHALNETMAK------------GGTRPPGTAITQRMWNR 348 (405)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc------------CCCCCCHHHHHHHhhCc
Confidence 7889999999999999987421 11356789999998873
No 74
>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=90.57 E-value=6.7 Score=34.59 Aligned_cols=68 Identities=15% Similarity=0.235 Sum_probs=46.1
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++.++.+.. +.++++. .+..+.+...|.+|++|+++...... ...++ +.|+....++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~ 75 (196)
T cd08415 13 SLLPRAIARFRARHPDVRISLH-------------TLSSSTVVEAVLSGQADLGLASLPLD---HPGLE-SEPLASGRAV 75 (196)
T ss_pred cccHHHHHHHHHHCCCcEEEEE-------------ecchHHHHHHHHcCCccEEEEeCCCC---CCcce-eeeecccceE
Confidence 44567888887765 5566665 34567799999999999998643222 22233 4677778888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 76 ~v~~~~ 81 (196)
T cd08415 76 CVLPPG 81 (196)
T ss_pred EEEcCC
Confidence 877643
No 75
>KOG1056|consensus
Probab=90.48 E-value=0.48 Score=52.59 Aligned_cols=74 Identities=22% Similarity=0.377 Sum_probs=55.4
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh---------------------ceEEEeecc
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT---------------------LDLLKLKRE 106 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~---------------------~~i~~~~~~ 106 (504)
..-.++|||.++|+||+.|.+.- -......|....+ -+|..|++++++ |+|++.+..
T Consensus 380 k~~~Vi~aVya~A~aLh~m~~~l-c~~~~~~C~~m~~-~dg~~L~~~l~~vnF~~~~~~v~Fd~~gD~~~~y~I~~~~~~ 457 (878)
T KOG1056|consen 380 KVQFVIDAVYAMAHALHNMHQDL-CPGTSGLCSAMKA-IDGSLLLKYLLNVNFTGPAGSVRFDENGDGPGRYDILNYQLT 457 (878)
T ss_pred ccccHHHHHHHHHHHHHHHHHhh-cCCccccCcCccc-cCHHHHHhhhheeEEecCCCceeecCCCCCccceeEEEeecc
Confidence 45679999999999999986321 1112346766555 789999999987 999999865
Q ss_pred c----eeeeeEecCCCCceee
Q psy1412 107 E----LRKVGHWTPAEGINIT 123 (504)
Q Consensus 107 ~----~~~vg~W~~~~gl~~~ 123 (504)
+ +.++|.|++...+.+.
T Consensus 458 ~~~~~y~~vg~w~~~~~l~i~ 478 (878)
T KOG1056|consen 458 NGSYTYKEVGYWSEGLSLNIE 478 (878)
T ss_pred CCCccceeeeeecccccccce
Confidence 4 7999999987655543
No 76
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=90.44 E-value=8.2 Score=38.11 Aligned_cols=69 Identities=9% Similarity=0.237 Sum_probs=45.8
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.+.. +.++++. .+..+.++..|.+|++|+++....... ....+. ..|+.+..+++
T Consensus 111 ~l~~~l~~~~~~~p~v~i~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~~~l~-~~~l~~~~~~l 175 (312)
T PRK10341 111 FMSDMINKFKEVFPKAQVSMY-------------EAQLSSFLPAIRDGRLDFAIGTLSNEM-KLQDLH-VEPLFESEFVL 175 (312)
T ss_pred hHHHHHHHHHHhCCCCEEEEE-------------eCCHHHHHHHHHcCCCcEEEecCCccc-ccCCee-EEEEecccEEE
Confidence 4447778877765 4556665 345678999999999999985432211 112243 36888888888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
++++.
T Consensus 176 v~~~~ 180 (312)
T PRK10341 176 VASKS 180 (312)
T ss_pred EEcCC
Confidence 88654
No 77
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=90.43 E-value=4.6 Score=35.68 Aligned_cols=68 Identities=12% Similarity=0.199 Sum_probs=44.3
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++..+.+.. +..+++. .++...++..|.+|++|+++...... ...+.+ .|+.+..++
T Consensus 13 ~~l~~~l~~~~~~~p~v~i~i~-------------~~~~~~~~~~L~~~~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~ 75 (197)
T cd08438 13 LLFAPLLAAFRQRYPNIELELV-------------EYGGKKVEQAVLNGELDVGITVLPVD---EEEFDS-QPLCNEPLV 75 (197)
T ss_pred hhcHHHHHHHHHHCcCeEEEEE-------------EcCcHHHHHHHHcCCCCEEEEecccc---cCCcee-EEeccccEE
Confidence 34557888888775 3555554 23557789999999999998643322 222333 466777777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 76 ~v~~~~ 81 (197)
T cd08438 76 AVLPRG 81 (197)
T ss_pred EEecCC
Confidence 777644
No 78
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=90.41 E-value=3 Score=41.35 Aligned_cols=40 Identities=10% Similarity=0.047 Sum_probs=27.8
Q ss_pred HHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecc
Q psy1412 169 DLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVAS 220 (504)
Q Consensus 169 dll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~ 220 (504)
+....+.++. +.+++++..+ +...++..|.+|++|+++.+
T Consensus 44 ~~~~~~~~~~p~v~ie~~~~~------------~~~~~~~aL~~G~iDia~~~ 84 (314)
T PRK11553 44 KSHQLLEKRFPQTKISWVEFP------------AGPQMLEALNVGSIDLGSTG 84 (314)
T ss_pred HhhCHHHHhCCCCeeEEEECC------------CcHHHHHHHHcCCCCEEccC
Confidence 4444555554 6777776532 23579999999999998865
No 79
>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=90.09 E-value=4.6 Score=35.89 Aligned_cols=67 Identities=13% Similarity=0.208 Sum_probs=43.0
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.+.. +.++++.. +.-..+...|.+|++|+++.... .....+. +.|..+..+++
T Consensus 14 ~l~~~l~~~~~~~P~i~i~~~~-------------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~ 76 (198)
T cd08433 14 LAVPLLRAVRRRYPGIRLRIVE-------------GLSGHLLEWLLNGRLDLALLYGP---PPIPGLS-TEPLLEEDLFL 76 (198)
T ss_pred cchHHHHHHHHHCCCcEEEEEe-------------cCcHHHHHHHhCCCCcEEEEeCC---CCCCCee-EEEeccccEEE
Confidence 3456788887776 45666652 23467889999999999885322 2222232 35777778877
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 77 ~~~~~ 81 (198)
T cd08433 77 VGPAD 81 (198)
T ss_pred EecCC
Confidence 77643
No 80
>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=89.63 E-value=3.8 Score=36.48 Aligned_cols=68 Identities=9% Similarity=0.101 Sum_probs=45.9
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .++...+...|.+|++|+++.... .....+. +.|+....++
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~ 75 (200)
T cd08466 13 LLLPRLLARLKQLAPNISLRES-------------PSSEEDLFEDLRLQEVDLVIDYVP---FRDPSFK-SELLFEDELV 75 (200)
T ss_pred HHHHHHHHHHHHHCCCCEEEEe-------------cCchHhHHHHHHcCCccEEEeccc---CCCCCce-eeeecccceE
Confidence 44557777777776 4566665 445677999999999999985321 1222233 3577788888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 lv~~~~ 81 (200)
T cd08466 76 CVARKD 81 (200)
T ss_pred EEEeCC
Confidence 888754
No 81
>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=89.54 E-value=2.3 Score=38.10 Aligned_cols=67 Identities=16% Similarity=0.191 Sum_probs=44.5
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .++. .++..|.+|++|++++.... ....+.+ .|..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~v~l~-------------~~~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~~-~~l~~~~~~ 74 (200)
T cd08460 13 AFGPALLAAVAAEAPGVRLRFV-------------PESD-KDVDALREGRIDLEIGVLGP---TGPEIRV-QTLFRDRFV 74 (200)
T ss_pred HHHHHHHHHHHHHCCCCEEEEe-------------cCch-hHHHHHHCCCccEEEecCCC---CCcchhe-eeeeccceE
Confidence 45567788887776 3456654 3344 68899999999999863322 1223443 677888888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 75 ~v~~~~ 80 (200)
T cd08460 75 GVVRAG 80 (200)
T ss_pred EEEeCC
Confidence 887654
No 82
>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=89.51 E-value=4.4 Score=35.99 Aligned_cols=68 Identities=15% Similarity=0.225 Sum_probs=45.0
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++.++.++. +.++++. .+..+.+...|.+|++|+++..... ....+. +.++....++
T Consensus 13 ~~l~~~l~~f~~~~P~v~i~i~-------------~~~~~~~~~~l~~~~~Di~i~~~~~---~~~~~~-~~~l~~~~~~ 75 (198)
T cd08461 13 AILPPLLAALRQEAPGVRVAIR-------------DLESDNLEAQLERGEVDLALTTPEY---APDGLR-SRPLFEERYV 75 (198)
T ss_pred HHhHHHHHHHHHHCCCcEEEEe-------------eCCcccHHHHHhcCCCcEEEecCcc---CCccce-eeeeecCcEE
Confidence 44567778877766 4667775 2344568999999999999853222 122233 4577778888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 lv~~~~ 81 (198)
T cd08461 76 CVTRRG 81 (198)
T ss_pred EEEcCC
Confidence 887654
No 83
>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=89.44 E-value=5.1 Score=35.50 Aligned_cols=68 Identities=15% Similarity=0.104 Sum_probs=46.2
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .++...++..|.+|++|+++..... ....+. +.|+.+..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~ 75 (198)
T cd08412 13 YYLPGLLRRFREAYPGVEVRVV-------------EGNQEELEEGLRSGELDLALTYDLD---LPEDIA-FEPLARLPPY 75 (198)
T ss_pred hhhHHHHHHHHHHCCCcEEEEE-------------ECCHHHHHHHHHcCCCcEEEEcCCC---CCcccc-eeeeeccceE
Confidence 45568888888776 4677776 3455678999999999998853221 222333 3677788887
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 ~~~~~~ 81 (198)
T cd08412 76 VWLPAD 81 (198)
T ss_pred EEecCC
Confidence 777644
No 84
>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=89.35 E-value=14 Score=32.30 Aligned_cols=68 Identities=12% Similarity=0.233 Sum_probs=45.8
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .+....+...|.+|++|+++..... ....+.+ .++.+..++
T Consensus 13 ~~l~~~l~~~~~~~p~v~i~i~-------------~~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~~-~~l~~~~~~ 75 (197)
T cd08440 13 TLLPPVLAAFRRRHPGIRVRLR-------------DVSAEQVIEAVRSGEVDFGIGSEPE---ADPDLEF-EPLLRDPFV 75 (197)
T ss_pred hHHHHHHHHHHHhCCCcEEEEE-------------eCChHHHHHHHHcCCccEEEEeCCC---CCCCeeE-EEeecccEE
Confidence 45567888887776 4666665 3456789999999999999864322 2222332 577777888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 76 ~~~~~~ 81 (197)
T cd08440 76 LVCPKD 81 (197)
T ss_pred EEecCC
Confidence 877644
No 85
>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=89.32 E-value=3.7 Score=36.80 Aligned_cols=67 Identities=13% Similarity=0.132 Sum_probs=43.0
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-..++..+.++. +.+++++ .++. .++..|.+|++|++++.-... ...+. ..|+....+++
T Consensus 14 ~l~~~i~~~~~~~P~i~l~i~-------------~~~~-~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~ 75 (200)
T cd08462 14 LLPPVIERVAREAPGVRFELL-------------PPDD-QPHELLERGEVDLLIAPERFM---SDGHP-SEPLFEEEFVC 75 (200)
T ss_pred HHHHHHHHHHHHCCCCEEEEe-------------cCCh-hHHHHHhcCCeeEEEecCCCC---CCCce-eeeeeccceEE
Confidence 3456777777665 3566665 2333 799999999999998643221 12233 34777788888
Q ss_pred EEEccC
Q psy1412 245 LFKVPT 250 (504)
Q Consensus 245 lv~~~~ 250 (504)
+++...
T Consensus 76 v~~~~h 81 (200)
T cd08462 76 VVWADN 81 (200)
T ss_pred EEcCCC
Confidence 876543
No 86
>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=89.13 E-value=10 Score=34.15 Aligned_cols=70 Identities=11% Similarity=0.115 Sum_probs=47.7
Q ss_pred ehhHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++.++.++.+ ..+++.. .++.+.++..|.+|++|++++..... ...+++ .|+.+...+
T Consensus 13 ~~~~~~l~~~~~~~P~~~v~~~~------------~~~~~~l~~~L~~g~lDl~i~~~~~~---~~~l~~-~~l~~~~~~ 76 (203)
T cd08463 13 LFLPELVARFRREAPGARLEIHP------------LGPDFDYERALASGELDLVIGNWPEP---PEHLHL-SPLFSDEIV 76 (203)
T ss_pred HHhHHHHHHHHHHCCCCEEEEEe------------CCcchhHHHHHhcCCeeEEEeccccC---CCCcEE-eEeecCceE
Confidence 455688888887763 5677652 12457899999999999998642221 122443 578888888
Q ss_pred EEEEccC
Q psy1412 244 ILFKVPT 250 (504)
Q Consensus 244 ilv~~~~ 250 (504)
+++++..
T Consensus 77 lv~~~~h 83 (203)
T cd08463 77 CLMRADH 83 (203)
T ss_pred EEEeCCC
Confidence 8887553
No 87
>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=88.72 E-value=13 Score=32.67 Aligned_cols=68 Identities=13% Similarity=0.198 Sum_probs=44.4
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.+++++. +.-..++..|.+|++|+++...... ...+. +.|..+..+.
T Consensus 13 ~~l~~~l~~~~~~~P~~~l~~~~-------------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~ 75 (201)
T cd08420 13 YLLPRLLARFRKRYPEVRVSLTI-------------GNTEEIAERVLDGEIDLGLVEGPVD---HPDLI-VEPFAEDELV 75 (201)
T ss_pred hhhHHHHHHHHHHCCCceEEEEe-------------CCcHHHHHHHHCCCccEEEecCCCC---CcceE-EEeecCccEE
Confidence 44457888887775 45666652 3446688999999999998643322 22233 2577777777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 ~v~~~~ 81 (201)
T cd08420 76 LVVPPD 81 (201)
T ss_pred EEecCC
Confidence 777643
No 88
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=88.62 E-value=7.5 Score=34.81 Aligned_cols=68 Identities=15% Similarity=0.168 Sum_probs=45.5
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .+....++..|.+|++|+++..... . ...+. ..+.....++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~-------------~~~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~~-~~~l~~~~~~ 75 (200)
T cd08467 13 ALLPRLAPRLRERAPGLDLRLC-------------PIGDDLAERGLEQGTIDLAVGRFAV--P-PDGLV-VRRLYDDGFA 75 (200)
T ss_pred HHHHHHHHHHHhhCCCCEEEEe-------------cCCcccHHHHhhCCCcCEEEecCCC--C-Cccce-eEEeeeccEE
Confidence 45567888887765 4567666 3456679999999999999853221 1 22243 3577788888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 76 ~v~~~~ 81 (200)
T cd08467 76 CLVRHG 81 (200)
T ss_pred EEEcCC
Confidence 887643
No 89
>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=88.55 E-value=16 Score=31.92 Aligned_cols=67 Identities=18% Similarity=0.313 Sum_probs=44.3
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-..++.++.++. +.++++. .+....++.+|.+|++|+++..... ....+++ .|+.+..+++
T Consensus 14 ~l~~~l~~~~~~~P~i~i~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~l~~-~~l~~~~~~~ 76 (195)
T cd08434 14 LVPDLIRAFRKEYPNVTFELH-------------QGSTDELLDDLKNGELDLALCSPVP---DEPDIEW-IPLFTEELVL 76 (195)
T ss_pred hhHHHHHHHHHhCCCeEEEEe-------------cCcHHHHHHHHHcCCccEEEEccCC---CCCCeeE-EEeecceEEE
Confidence 4446777777765 5556665 3345678999999999998854322 2333443 5777788888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
++++.
T Consensus 77 v~~~~ 81 (195)
T cd08434 77 VVPKD 81 (195)
T ss_pred EecCC
Confidence 87654
No 90
>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre
Probab=88.47 E-value=14 Score=32.82 Aligned_cols=67 Identities=13% Similarity=0.232 Sum_probs=43.6
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.++. +.++++. .++...++..|.+|++|+++..... ....+.+ .++.+..+++
T Consensus 15 ~l~~~l~~~~~~~P~i~i~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~~-~~l~~~~~~~ 77 (200)
T cd08411 15 LLPRLLPALRQAYPKLRLYLR-------------EDQTERLLEKLRSGELDAALLALPV---DEPGLEE-EPLFDEPFLL 77 (200)
T ss_pred hhHHHHHHHHHHCCCcEEEEE-------------eCcHHHHHHHHHcCCccEEEEeccC---CCCCceE-EEeeccceEE
Confidence 4457777777765 3566665 3456789999999999999853221 1222332 4667777777
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 78 v~~~~ 82 (200)
T cd08411 78 AVPKD 82 (200)
T ss_pred EecCC
Confidence 77643
No 91
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=88.40 E-value=7.9 Score=38.26 Aligned_cols=76 Identities=18% Similarity=0.121 Sum_probs=45.9
Q ss_pred cCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCccEEcC--CccCCcceEEEecCCCCCchHHHHHHHhhhccChhHHH
Q psy1412 410 VSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCNLTQIG--GLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQML 486 (504)
Q Consensus 410 ~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~l~~vg--~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~l 486 (504)
+++.+..+..|.+|. .+++.+.. .+.... -++..+. .......++++.+|+.++...+...+..+++. +..++
T Consensus 224 ~~~~~~~~~~v~~g~Gv~~lp~~~-~~~~~~--~~l~~~~i~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~-~~~~~ 299 (313)
T PRK12684 224 AIDADVIKTYVELGLGVGIVADMA-FDPERD--RNLRAIDAGHLFGSSTTRLGLRRGAYLRGYVYTFIELFAPT-LNRKL 299 (313)
T ss_pred eCCHHHHHHHHHhCCceEEeehhh-cccccc--CCeEEEECCCCCcceeEEEEEECCCcCCHHHHHHHHHHHHH-hCHHH
Confidence 457778888888887 67776533 332222 2344333 23344578999999988777766666655543 44444
Q ss_pred HHh
Q psy1412 487 YDK 489 (504)
Q Consensus 487 ~~k 489 (504)
-++
T Consensus 300 ~~~ 302 (313)
T PRK12684 300 VEQ 302 (313)
T ss_pred HHH
Confidence 433
No 92
>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=87.98 E-value=18 Score=31.75 Aligned_cols=68 Identities=19% Similarity=0.311 Sum_probs=44.6
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++..+.++. +.++++. .+....+...|.+|++|+++...... ...+. +.+.....++
T Consensus 12 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~ 74 (197)
T cd08419 12 YFAPRLLGAFCRRHPGVEVSLR-------------VGNREQVLERLADNEDDLAIMGRPPE---DLDLV-AEPFLDNPLV 74 (197)
T ss_pred hHhhHHHHHHHHHCCCceEEEE-------------ECCHHHHHHHHhcCCccEEEecCCCC---CCCeE-EEEeccCCEE
Confidence 34557788887775 5667776 33566789999999999998543221 11222 3577777787
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 75 ~~~~~~ 80 (197)
T cd08419 75 VIAPPD 80 (197)
T ss_pred EEecCC
Confidence 777643
No 93
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=87.81 E-value=9.1 Score=37.88 Aligned_cols=82 Identities=13% Similarity=0.092 Sum_probs=57.1
Q ss_pred ccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCccEEcC--CccCCcceEEEecCCCCCchHHHHHHHhhhccChhHH
Q psy1412 409 FVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCNLTQIG--GLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQM 485 (504)
Q Consensus 409 ~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~l~~vg--~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~ 485 (504)
.+.+.+..++.|.+|. .+++-... .... +...+..+. .......++++.+|+.+....+...+.-+.+.--.+.
T Consensus 223 ~~~s~~~~~~~v~~g~Gi~~lp~~~-~~~~--~~~~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~ 299 (316)
T PRK12679 223 SAQDSDVIKTYVALGLGIGLVAEQS-SGEQ--EESNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVED 299 (316)
T ss_pred EeccHHHHHHHHHcCCcEEEecccc-cccc--cCCcEEEEECcccCCCceEEEEEeCCchhhHHHHHHHHHHhcccCHHH
Confidence 3567788888888887 66665443 3322 234455443 2334567899999999988888888888888777888
Q ss_pred HHHhhccC
Q psy1412 486 LYDKWWKN 493 (504)
Q Consensus 486 l~~kw~~~ 493 (504)
++++-..+
T Consensus 300 ~~~~~~~~ 307 (316)
T PRK12679 300 IKRQVMEN 307 (316)
T ss_pred HHHHHhhc
Confidence 88886553
No 94
>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=87.69 E-value=19 Score=31.82 Aligned_cols=67 Identities=12% Similarity=0.177 Sum_probs=43.4
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-..++..+.++. +.++++. .+....+...|.+|++|+++..-.. ....+. ..+.....+++
T Consensus 14 ~~~~~l~~~~~~~P~i~i~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~ 76 (198)
T cd08441 14 WLMPVLDQFRERWPDVELDLS-------------SGFHFDPLPALLRGELDLVITSDPL---PLPGIA-YEPLFDYEVVL 76 (198)
T ss_pred hhHHHHHHHHHhCCCeEEEEE-------------eCCchhHHHHHHcCCceEEEecCCc---CCCCcE-EEEccCCcEEE
Confidence 3456777777776 3566665 3456679999999999999853222 122233 24667777777
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 77 ~~~~~ 81 (198)
T cd08441 77 VVAPD 81 (198)
T ss_pred EEcCC
Confidence 77643
No 95
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=87.62 E-value=10 Score=33.44 Aligned_cols=69 Identities=7% Similarity=0.068 Sum_probs=43.4
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.+.. +..+++. .++-..++..|.+|++|++++.... ..+...+.+ .|.....+++
T Consensus 14 ~l~~~l~~~~~~~P~v~i~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~~~~-~~l~~~~~~~ 78 (201)
T cd08435 14 LLPPAIARLLARHPRLTVRVV-------------EGTSDELLEGLRAGELDLAIGRLAD-DEQPPDLAS-EELADEPLVV 78 (201)
T ss_pred HHHHHHHHHHHHCCCeEEEEE-------------eCCHHHHHHHHHcCCccEEEEecCc-ccCCCCcEE-EEcccCcEEE
Confidence 3456777777765 3455554 3345678899999999998853221 111223433 5777888888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
++++.
T Consensus 79 ~~~~~ 83 (201)
T cd08435 79 VARPG 83 (201)
T ss_pred EEeCC
Confidence 87654
No 96
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=87.47 E-value=19 Score=31.55 Aligned_cols=68 Identities=13% Similarity=0.190 Sum_probs=44.7
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++..+.+.. +.++++. .+....++..|.+|++|+++...... ...+.+ .|..+..++
T Consensus 13 ~~l~~~l~~~~~~~p~i~i~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~ 75 (197)
T cd08414 13 GLLPRLLRRFRARYPDVELELR-------------EMTTAEQLEALRAGRLDVGFVRPPPD---PPGLAS-RPLLREPLV 75 (197)
T ss_pred HHHHHHHHHHHHHCCCcEEEEe-------------cCChHHHHHHHHcCCccEEEEcCCCC---CCCeeE-EEEeeccEE
Confidence 34557777777765 3556655 34557799999999999998643222 222333 577778888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 76 ~v~~~~ 81 (197)
T cd08414 76 VALPAD 81 (197)
T ss_pred EEecCC
Confidence 887654
No 97
>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=86.56 E-value=21 Score=31.73 Aligned_cols=68 Identities=12% Similarity=0.164 Sum_probs=44.9
Q ss_pred hhHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.++.+ .++++. .+....+...|.+|++|+++...... ....+. +.|..+..+++
T Consensus 14 ~l~~~l~~~~~~~P~i~v~~~-------------~~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~~-~~~l~~~~~~~ 77 (198)
T cd08413 14 VLPPVIAAFRKRYPKVKLSLH-------------QGTPSQIAEMVLKGEADIAIATEALD--DHPDLV-TLPCYRWNHCV 77 (198)
T ss_pred hccHHHHHHHHhCCceEEEEE-------------eCCHHHHHHHHHcCCCCEEEEccCCC--CCCCcE-EEEeeeeeEEE
Confidence 34578888877763 456665 34567799999999999998532221 122244 36777888888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 78 v~~~~ 82 (198)
T cd08413 78 IVPPG 82 (198)
T ss_pred EecCC
Confidence 87654
No 98
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=86.43 E-value=26 Score=33.93 Aligned_cols=68 Identities=16% Similarity=0.257 Sum_probs=45.3
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +..+++. .+....++..|.+|++|+++.... .+...+. +.++.+..++
T Consensus 104 ~~l~~~l~~~~~~~p~~~i~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~l~-~~~l~~~~~~ 166 (296)
T PRK11242 104 YLIGPLIDAFHARYPGITLTIR-------------EMSQERIEALLADDELDVGIAFAP---VHSPEIE-AQPLFTETLA 166 (296)
T ss_pred hhhHHHHHHHHHHCCCCEEEEE-------------eCCHHHHHHHHHCCCCcEEEEecC---CCCccee-EEEeeeccEE
Confidence 34457888888775 3445554 335577899999999999985432 2233343 3677888888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 167 ~~~~~~ 172 (296)
T PRK11242 167 LVVGRH 172 (296)
T ss_pred EEEcCC
Confidence 887754
No 99
>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=86.35 E-value=25 Score=31.75 Aligned_cols=70 Identities=11% Similarity=0.149 Sum_probs=43.4
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.++++. .+..+.++..|.+|++|+++........-...+. ..|..+..++
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~i~-------------~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~~-~~~l~~~~~~ 78 (204)
T cd08429 13 SIAYRLLEPAMDLHEPIRLVCR-------------EGKLEQLLADLALHRLDMVLADRPMPSSLDVKGY-SHRLGECGVS 78 (204)
T ss_pred HHHHHHHHHHHHhCCCcEEEEE-------------eCCHHHHHHHHHcCCccEEEecCCCccccchhee-eccccccceE
Confidence 44567777777765 4566665 4567889999999999998853322111001122 3477777776
Q ss_pred EEEEc
Q psy1412 244 ILFKV 248 (504)
Q Consensus 244 ilv~~ 248 (504)
++++.
T Consensus 79 ~~~~~ 83 (204)
T cd08429 79 FFAAP 83 (204)
T ss_pred EEecC
Confidence 66543
No 100
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=86.24 E-value=21 Score=31.35 Aligned_cols=70 Identities=17% Similarity=0.171 Sum_probs=44.3
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeee--cccceeeeeccceeeccE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTIN--YARESVIDFTKPFMNLGI 242 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit--~~R~~~vdFs~p~~~~g~ 242 (504)
+-.+++..+.+.. +.++++. .++...+...|.+|++|+++..-... ......+. +.+..+..+
T Consensus 14 ~l~~~l~~~~~~~P~i~i~~~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~-~~~l~~~~~ 79 (200)
T cd08423 14 LLPPALAALRARHPGLEVRLR-------------EAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGLT-RVPLLDDPL 79 (200)
T ss_pred hhhHHHHHHHHhCCCCeEEEE-------------eCCHHHHHHHHhcCCccEEEEeccccccCCCCCCcE-EEEeccCcE
Confidence 4457777777775 4666665 23456789999999999988532110 11222333 457777788
Q ss_pred EEEEEcc
Q psy1412 243 GILFKVP 249 (504)
Q Consensus 243 ~ilv~~~ 249 (504)
+++++..
T Consensus 80 ~~~~~~~ 86 (200)
T cd08423 80 DLVLPAD 86 (200)
T ss_pred EEEecCC
Confidence 8777644
No 101
>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=85.88 E-value=8.8 Score=34.96 Aligned_cols=68 Identities=7% Similarity=0.096 Sum_probs=45.5
Q ss_pred ehhHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++..+.++.+ .++++. .++...+.+.|.+|++|++++... .....+.+ .|.....++
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~i~-------------~~~~~~~~~~l~~g~~Di~i~~~~---~~~~~l~~-~~l~~~~~~ 75 (221)
T cd08469 13 VLLPALVRRLETEAPGIDLRIR-------------PVTRLDLAEQLDLGRIDLVIGIFE---QIPPRFRR-RTLFDEDEV 75 (221)
T ss_pred HHHHHHHHHHHHHCCCcEEEEe-------------eCChhhHHHHHHCCCccEEEecCC---CCCcccee-eeeeccceE
Confidence 445677777777653 456655 335667999999999999986432 22233443 577888888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 ~v~~~~ 81 (221)
T cd08469 76 WVMRKD 81 (221)
T ss_pred EEEeCC
Confidence 887754
No 102
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=85.72 E-value=35 Score=33.56 Aligned_cols=69 Identities=14% Similarity=0.079 Sum_probs=43.6
Q ss_pred cCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCccEEcC--CccCCcceEEEecCCCCCchHHHHHHHhhhccC
Q psy1412 410 VSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCNLTQIG--GLLDSKGYGIATPKGSPWRDRISLAILELQEKG 481 (504)
Q Consensus 410 ~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~l~~vg--~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G 481 (504)
+.+.+..++.|..|. .+++-+. ..... ...++..+. +......++++.+|+.++.......+..+.+..
T Consensus 224 ~~~~~~~~~~v~~g~Gi~~lp~~-~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~l~~~~ 295 (309)
T PRK12683 224 ALDADVIKTYVELGMGVGIVAAM-AYDPQ--RDTGLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFAPHL 295 (309)
T ss_pred eccHHHHHHHHHhCCCeEEeehh-hcccc--CCCceEEEeCCCCcccceEEEEEECCCcCCHHHHHHHHHHHhhh
Confidence 567777788888888 5666443 33322 123455554 223356789999999888777766666665543
No 103
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=85.51 E-value=14 Score=36.32 Aligned_cols=70 Identities=9% Similarity=0.159 Sum_probs=46.4
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.++++. .+.-+.++..|.+|++|++++.-... ....++. .|+.....+
T Consensus 106 ~~l~~~l~~~~~~~P~i~i~i~-------------~~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~l~~-~~l~~~~~~ 169 (309)
T PRK12682 106 YVLPRVVAAFRKRYPKVNLSLH-------------QGSPDEIARMVISGEADIGIATESLA--DDPDLAT-LPCYDWQHA 169 (309)
T ss_pred HHHHHHHHHHHHhCCCeEEEEe-------------cCCHHHHHHHHHcCCccEEEecCccc--CCCcceE-EEeeeeeEE
Confidence 45567888887765 4566665 33456799999999999998643221 1223443 578888888
Q ss_pred EEEEccC
Q psy1412 244 ILFKVPT 250 (504)
Q Consensus 244 ilv~~~~ 250 (504)
++++...
T Consensus 170 ~~~~~~~ 176 (309)
T PRK12682 170 VIVPPDH 176 (309)
T ss_pred EEecCCC
Confidence 8887543
No 104
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=85.44 E-value=13 Score=32.70 Aligned_cols=68 Identities=12% Similarity=0.152 Sum_probs=44.2
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.++++. .+....++..|.+|++|+++...... ...+. +.+.....++
T Consensus 13 ~~l~~~l~~~~~~~P~i~~~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~ 75 (196)
T cd08456 13 SFLPRAIKAFLQRHPDVTISIH-------------TRDSPTVEQWLSAQQCDLGLVSTLHE---PPGIE-RERLLRIDGV 75 (196)
T ss_pred hhHHHHHHHHHHHCCCcEEEEE-------------eCCHHHHHHHHHcCCccEEEEecCCC---CCCee-EEEeeccCeE
Confidence 45567888888876 4566665 34556788999999999998532221 22233 3566677777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 ~~~~~~ 81 (196)
T cd08456 76 CVLPPG 81 (196)
T ss_pred EEecCC
Confidence 776543
No 105
>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=85.31 E-value=12 Score=32.99 Aligned_cols=67 Identities=22% Similarity=0.353 Sum_probs=43.4
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.++. +.++++. .+....+...|.+|++|+++..... ....+++ .++.+..+++
T Consensus 15 ~l~~~l~~~~~~~P~v~i~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~~-~~l~~~~~~~ 77 (197)
T cd08425 15 LIGPLIDRFHARYPGIALSLR-------------EMPQERIEAALADDRLDLGIAFAPV---RSPDIDA-QPLFDERLAL 77 (197)
T ss_pred hhHHHHHHHHHHCCCcEEEEE-------------ECcHHHHHHHHHcCCccEEEEecCC---CCCCcEE-EEeccccEEE
Confidence 3457778877765 3556665 2345678899999999999854322 2223333 5777778888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
++++.
T Consensus 78 v~~~~ 82 (197)
T cd08425 78 VVGAT 82 (197)
T ss_pred EecCC
Confidence 77654
No 106
>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=85.12 E-value=1.8 Score=44.20 Aligned_cols=38 Identities=18% Similarity=0.170 Sum_probs=29.2
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT 97 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~ 97 (504)
.++.+||||+++++|++++.. |.. .|.++..+.+.|++
T Consensus 302 ~a~~~YDav~~~a~Al~~~~~----------~~~--~~~~~~~v~~~l~~ 339 (389)
T cd06352 302 YAGYLYDAVLLYAHALNETLA----------EGG--DYNGGLIITRRMWN 339 (389)
T ss_pred hhhhHHHHHHHHHHHHHHHHH----------hCC--CCCchHHHHHHhcC
Confidence 789999999999999999852 111 15677788888776
No 107
>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=84.77 E-value=13 Score=32.53 Aligned_cols=68 Identities=12% Similarity=0.119 Sum_probs=45.4
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .+....++..|.+|++|+++... ......+. ..+..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~ 75 (193)
T cd08442 13 VRLPPLLAAYHARYPKVDLSLS-------------TGTTGALIQAVLEGRLDGAFVAG---PVEHPRLE-QEPVFQEELV 75 (193)
T ss_pred hhhHHHHHHHHHHCCCceEEEE-------------eCCcHHHHHHHHCCCccEEEEeC---CCCCCCcE-EEEeecCcEE
Confidence 44567888887766 5667776 34567899999999999988532 22222333 3567777777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 ~v~~~~ 81 (193)
T cd08442 76 LVSPKG 81 (193)
T ss_pred EEecCC
Confidence 777643
No 108
>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=84.57 E-value=18 Score=31.75 Aligned_cols=70 Identities=7% Similarity=0.019 Sum_probs=45.4
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.++++. .+..+.++..|.+|++|+++..-... .....+. +.+..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~~-~~~l~~~~~~ 77 (195)
T cd08427 13 GLLPRALARLRRRHPDLEVHIV-------------PGLSAELLARVDAGELDAAIVVEPPF-PLPKDLV-WTPLVREPLV 77 (195)
T ss_pred HHhHHHHHHHHHHCCCceEEEE-------------eCCcHHHHHHHHCCCCCEEEEcCCCC-ccccCce-EEEcccCcEE
Confidence 34457788887766 5566665 34567899999999999998542211 1012233 3567778888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 78 ~v~~~~ 83 (195)
T cd08427 78 LIAPAE 83 (195)
T ss_pred EEECCC
Confidence 887654
No 109
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=84.48 E-value=6.1 Score=38.99 Aligned_cols=42 Identities=21% Similarity=0.150 Sum_probs=31.1
Q ss_pred HHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecce
Q psy1412 168 IDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASM 221 (504)
Q Consensus 168 idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~ 221 (504)
.++.+.+.+.++ .+++++. .+.....+..|.+|++|+++...
T Consensus 48 ~~la~~~~~~~~~i~v~~~~------------~~~~~~~~~~l~~G~~D~~~~~~ 90 (320)
T TIGR02122 48 GAIAQLINKKSGKLRVRVQS------------TGGSVENVNLLEAGEADLAIVQS 90 (320)
T ss_pred HHHHHHHhccCCCeeEEEEe------------CcchHHHHHHHhCCCCcEEEEcc
Confidence 467777878877 7777663 23456788999999999988653
No 110
>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=84.47 E-value=28 Score=30.60 Aligned_cols=68 Identities=9% Similarity=0.145 Sum_probs=45.3
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.++++++.++. +.++++. .+..+.++..|.+|++|+++...... ....+. +.|..+..+++
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~~-~~~l~~~~~~~ 78 (199)
T cd08451 15 LVPGLIRRFREAYPDVELTLE-------------EANTAELLEALREGRLDAAFVRPPVA--RSDGLV-LELLLEEPMLV 78 (199)
T ss_pred ccHHHHHHHHHHCCCcEEEEe-------------cCChHHHHHHHHCCCccEEEEecCCC--CCCcee-EEEeecccEEE
Confidence 4456788888776 4567766 34567899999999999998543221 112233 35777788888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 79 v~~~~ 83 (199)
T cd08451 79 ALPAG 83 (199)
T ss_pred EecCC
Confidence 87644
No 111
>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=84.12 E-value=15 Score=32.51 Aligned_cols=68 Identities=19% Similarity=0.229 Sum_probs=44.0
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
++-..++..+.++. +.++++. .+....++..|.+|++|+++..... . ...+. +.|..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~l~i~-------------~~~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~~-~~~l~~~~~~ 75 (200)
T cd08464 13 WLAPPLLAALRAEAPGVRLVFR-------------QVDPFNVGDMLDRGEIDLAIGVFGE--L-PAWLK-REVLYTEGYA 75 (200)
T ss_pred HHHHHHHHHHHHHCCCcEEEEe-------------cCCcccHHHHHhcCcccEEEecCCC--C-cccce-eeeecccceE
Confidence 44557777777765 4666665 3345678899999999999853221 1 22333 3577777777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 ~v~~~~ 81 (200)
T cd08464 76 CLFDPQ 81 (200)
T ss_pred EEEeCC
Confidence 777543
No 112
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=83.66 E-value=12 Score=37.20 Aligned_cols=84 Identities=11% Similarity=0.108 Sum_probs=51.6
Q ss_pred CCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhc
Q psy1412 134 NNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDK 212 (504)
Q Consensus 134 ~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g 212 (504)
..++|+|++..... ..+-.+++..+.+.. +.++++. .+..+.++..|.+|
T Consensus 91 ~~g~l~Ig~~~~~~----------------~~~l~~~l~~f~~~~P~i~i~i~-------------~~~~~~~~~~L~~g 141 (324)
T PRK12681 91 DKGSLYIATTHTQA----------------RYALPPVIKGFIERYPRVSLHMH-------------QGSPTQIAEAAAKG 141 (324)
T ss_pred CCCeEEEEechhHH----------------HHhhHHHHHHHHHHCCCcEEEEE-------------eCCHHHHHHHHHcC
Confidence 35679998853211 133446777777665 3455555 45678899999999
Q ss_pred cccceecceeeecccceeeeeccceeeccEEEEEEcc
Q psy1412 213 KADLAVASMTINYARESVIDFTKPFMNLGIGILFKVP 249 (504)
Q Consensus 213 ~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~ 249 (504)
++|++++.-.. .+...+.+ .|......+++++..
T Consensus 142 ~iDl~i~~~~~--~~~~~l~~-~~l~~~~~~~v~~~~ 175 (324)
T PRK12681 142 NADFAIATEAL--HLYDDLIM-LPCYHWNRSVVVPPD 175 (324)
T ss_pred CCCEEEecCcc--cCCCCeEE-EEeccceeEEEeCCC
Confidence 99999863211 11222333 466667777777543
No 113
>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=83.00 E-value=12 Score=36.56 Aligned_cols=38 Identities=16% Similarity=0.142 Sum_probs=29.3
Q ss_pred HHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceeccee
Q psy1412 173 SIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222 (504)
Q Consensus 173 ~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~t 222 (504)
.+++++|.+++++..+ ++..++..|..|++|+++.+.+
T Consensus 20 ~~~k~~Gl~Ve~~~~~------------~~~~~~~al~~G~iD~~~~~~~ 57 (300)
T TIGR01729 20 AAAKEAGATIDWRKFD------------SGADISTALASGNVPIGVIGSS 57 (300)
T ss_pred chHHhcCCeeEEEecC------------cHHHHHHHHHcCCCCEeccCCC
Confidence 3556689999988643 4678999999999999975543
No 114
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=82.93 E-value=31 Score=33.83 Aligned_cols=68 Identities=16% Similarity=0.264 Sum_probs=44.3
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++..+.++. +..+++. .+....+...|.+|++|+++..-... ...++ ..|+.+..+.
T Consensus 105 ~~~~~~l~~~~~~~p~i~l~~~-------------~~~~~~~~~~l~~g~~Di~i~~~~~~---~~~~~-~~~l~~~~~~ 167 (305)
T PRK11233 105 SLTMPLLQAVRAEFPGIVLYLH-------------ENSGATLNEKLMNGQLDMAVIYEHSP---VAGLS-SQPLLKEDLF 167 (305)
T ss_pred HHHHHHHHHHHHHCCCcEEEEE-------------ECCcHHHHHHHHCCCCCEEEEcCCcC---CCCcE-EEEEeeeeEE
Confidence 44556888887775 5566665 23456788999999999998532211 12233 3577788887
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 168 lv~~~~ 173 (305)
T PRK11233 168 LVGTQD 173 (305)
T ss_pred EEEcCc
Confidence 777643
No 115
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=82.46 E-value=36 Score=33.18 Aligned_cols=86 Identities=6% Similarity=0.101 Sum_probs=54.6
Q ss_pred CCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhc
Q psy1412 134 NNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDK 212 (504)
Q Consensus 134 ~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g 212 (504)
..++|+|++....+ ..+-.+++..+.+..+ .++++. .++..+++..|.+|
T Consensus 93 ~~g~l~I~~~~~~~----------------~~~l~~~l~~~~~~~p~i~~~~~-------------~~~~~~~~~~l~~g 143 (302)
T PRK09791 93 LAGQINIGMGASIA----------------RSLMPAVISRFHQQHPQVKVRIM-------------EGQLVSMINELRQG 143 (302)
T ss_pred cceEEEEEechHHH----------------HhhhHHHHHHHHHHCCCeEEEEE-------------eCChHHHHHHHHCC
Confidence 45789999854322 1344567777777664 445554 23567899999999
Q ss_pred cccceecceeeecccceeeeeccceeeccEEEEEEccC
Q psy1412 213 KADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPT 250 (504)
Q Consensus 213 ~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~ 250 (504)
++|+++....-. .....+.+ .|+.+..+++++++..
T Consensus 144 ~~Di~i~~~~~~-~~~~~~~~-~~l~~~~~~l~~~~~~ 179 (302)
T PRK09791 144 ELDFTINTYYQG-PYDHEFTF-EKLLEKQFAVFCRPGH 179 (302)
T ss_pred CccEEEEecCCc-ccccceeE-EEeccceEEEEEcCCC
Confidence 999988532111 11223444 6888888888877543
No 116
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=82.44 E-value=22 Score=31.29 Aligned_cols=70 Identities=10% Similarity=0.135 Sum_probs=44.7
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
++-.+++.++.++. +.++++. .+....+...|.+|++|+++...... .....+. +.+.....+.
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~~-~~~~~l~-~~~l~~~~~~ 77 (199)
T cd08416 13 NTVPRIIMGLKLRRPELDIELT-------------LGSNKDLLKKLKDGELDAILVATPEG-LNDPDFE-VVPLFEDDIF 77 (199)
T ss_pred hhhHHHHHHHHHhCCCeEEEEE-------------EcCcHHHHHHHhCCCCCEEEEecCCc-CCCCCeE-EEEeecceEE
Confidence 44567777777766 4667765 33456788999999999998643210 0122233 3567777777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 78 ~v~~~~ 83 (199)
T cd08416 78 LAVPAT 83 (199)
T ss_pred EEECCC
Confidence 777643
No 117
>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=82.01 E-value=18 Score=32.23 Aligned_cols=68 Identities=12% Similarity=0.105 Sum_probs=44.1
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.+.. +.++++. .+..+.+...|.+|++|+++..-.. .....+. +.++.+..+++
T Consensus 14 ~l~~~l~~f~~~~P~~~i~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~ 77 (198)
T cd08443 14 VLPPVIKGFIERYPRVSLQMH-------------QGSPTQIAEMVSKGLVDFAIATEAL--HDYDDLI-TLPCYHWNRCV 77 (198)
T ss_pred ECcHHHHHHHHHCCCeEEEEE-------------eCCHHHHHHHHHCCCccEEEEeccc--cccCCce-EeeeeeceEEE
Confidence 3446788877765 4556665 3455679999999999999853221 1122343 35777888888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 78 v~~~~ 82 (198)
T cd08443 78 VVKRD 82 (198)
T ss_pred EEcCC
Confidence 87654
No 118
>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=81.82 E-value=33 Score=33.34 Aligned_cols=85 Identities=12% Similarity=0.110 Sum_probs=52.8
Q ss_pred CCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhc
Q psy1412 134 NNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDK 212 (504)
Q Consensus 134 ~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g 212 (504)
..++|+|++....+ ..+-.+++..+.++.+ .++.+. .+..+.++.+|.+|
T Consensus 91 ~~~~l~I~~~~~~~----------------~~~~~~~l~~~~~~~P~~~i~~~-------------~~~~~~~~~~l~~g 141 (300)
T TIGR02424 91 EGPTVRIGALPTVA----------------ARLMPEVVKRFLARAPRLRVRIM-------------TGPNAYLLDQLRVG 141 (300)
T ss_pred CCceEEEecccHHH----------------HhhhHHHHHHHHHhCCCcEEEEE-------------eCchHHHHHHHHCC
Confidence 35678998753211 1233467777776653 455555 33557799999999
Q ss_pred cccceecceeeecccceeeeeccceeeccEEEEEEcc
Q psy1412 213 KADLAVASMTINYARESVIDFTKPFMNLGIGILFKVP 249 (504)
Q Consensus 213 ~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~ 249 (504)
++|++++..... .....+.+ .|..+...++++++.
T Consensus 142 ~~D~~i~~~~~~-~~~~~~~~-~~l~~~~~~~~~~~~ 176 (300)
T TIGR02424 142 ALDLVVGRLGAP-ETMQGLSF-EHLYNEPVVFVVRAG 176 (300)
T ss_pred CCCEEEEecCCc-ccccceee-eeecCCceEEEEcCC
Confidence 999998644321 22233443 477778888887643
No 119
>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=81.70 E-value=35 Score=29.78 Aligned_cols=68 Identities=10% Similarity=0.068 Sum_probs=46.4
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.+++++ .+...++...|.+|++|+++.... .....+++ .+..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~i~-------------~~~~~~~~~~l~~~~~Di~i~~~~---~~~~~~~~-~~l~~~~~~ 75 (197)
T cd08448 13 RGLPRILRAFRAEYPGIEVALH-------------EMSSAEQIEALLRGELDLGFVHSR---RLPAGLSA-RLLHREPFV 75 (197)
T ss_pred HHHHHHHHHHHHHCCCCeEEEE-------------eCCHHHHHHHHHcCCcceEEEeCC---CCCcCceE-EEEecCcEE
Confidence 45567888887776 5667766 345678999999999999875322 22233443 577778888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 76 ~~~~~~ 81 (197)
T cd08448 76 CCLPAG 81 (197)
T ss_pred EEeeCC
Confidence 776643
No 120
>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=81.15 E-value=2.2 Score=43.63 Aligned_cols=37 Identities=16% Similarity=0.115 Sum_probs=26.3
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT 97 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~ 97 (504)
.++++||||+++|.|+++...... ..+|..+.+.|.+
T Consensus 295 ~~~~~YDav~~~a~Al~~a~~~g~-------------~~d~~~l~~~l~~ 331 (382)
T cd06371 295 LFGTIYNSIYLLAHAVENARAAGG-------------GVSGANLAQHTRN 331 (382)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCC-------------CccHHHHHHHHhC
Confidence 456899999999999998753110 1356677777765
No 121
>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=80.31 E-value=41 Score=29.66 Aligned_cols=71 Identities=8% Similarity=0.146 Sum_probs=45.2
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .+..+.+...|.+|++|+++............++ +.|..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~-~~~l~~~~~~ 78 (200)
T cd08453 13 SVLPELVRRFREAYPDVELQLR-------------EATSDVQLEALLAGEIDAGIVIPPPGASAPPALA-YRPLLSEPLV 78 (200)
T ss_pred HHHHHHHHHHHHhCCCceEEEE-------------eCCHHHHHHHHHcCCCCEEEEecCcccCCCccee-EEEeeeCceE
Confidence 34456777777665 4566665 3456678999999999998853221111122233 3677788888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 79 ~v~~~~ 84 (200)
T cd08453 79 LAVPAA 84 (200)
T ss_pred EEEECC
Confidence 887754
No 122
>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=80.12 E-value=1.5 Score=44.11 Aligned_cols=24 Identities=21% Similarity=0.768 Sum_probs=22.2
Q ss_pred ceEEEeeccceeeeeEecCCCCce
Q psy1412 98 LDLLKLKREELRKVGHWTPAEGIN 121 (504)
Q Consensus 98 ~~i~~~~~~~~~~vg~W~~~~gl~ 121 (504)
|+++++.+.+++.||+|+++.|+.
T Consensus 324 ~~~~~~~~~~~~~vg~~~~~~~~~ 347 (350)
T cd06366 324 FEIINIIGKGYRKIGFWSSESGLS 347 (350)
T ss_pred eEEEEecCCceEEEEEEeCCCCcc
Confidence 899999999999999999988876
No 123
>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=80.10 E-value=27 Score=32.16 Aligned_cols=78 Identities=15% Similarity=0.129 Sum_probs=41.5
Q ss_pred ccCChHHHHHhhhcCC-eEEE-eecchhhhhhhcCCccEEcCC-ccCCcceEEEecCCCCCchHHHHHHHhhhccChhHH
Q psy1412 409 FVSDYEEGVKRVLEGD-YAFL-MESTMLDYEVQRNCNLTQIGG-LLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQM 485 (504)
Q Consensus 409 ~~~~~~egi~~v~~g~-~A~i-~e~~~~~y~~~~~c~l~~vg~-~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~ 485 (504)
...+..+..+.+.+|+ ++.+ ..+..... ...+....++. ......+++++.|+++-.+.-.+.|.-|... .-++
T Consensus 134 ~~~~~~~~~~~~~~Ge~~~~~~~~~~~~~~--~~~~~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl~s~-e~q~ 210 (216)
T TIGR01256 134 YGEDVRQALQFVETGNAPAGIVALSDVIPS--KKVGSVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYLKSP-EAKE 210 (216)
T ss_pred ecCcHHHHHHHHHcCCCCEEeeehhhhccc--CCccEEEEeCccccCCccccEEEEECCCChHHHHHHHHHHcCH-HHHH
Confidence 3456678888888898 4433 33332221 22233333333 2334567999999998655544444444332 3344
Q ss_pred HHHh
Q psy1412 486 LYDK 489 (504)
Q Consensus 486 l~~k 489 (504)
+..+
T Consensus 211 ~~~~ 214 (216)
T TIGR01256 211 ILRK 214 (216)
T ss_pred HHHH
Confidence 4444
No 124
>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=80.09 E-value=34 Score=30.10 Aligned_cols=69 Identities=12% Similarity=0.075 Sum_probs=44.9
Q ss_pred hhHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++.++.++.+ .++++. .+..+.++..|.+|++|+++.... .......+++ .+..+..+++
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~l~~-~~l~~~~~~~ 78 (198)
T cd08437 14 YFPKLAKDLIKTGLMIQIDTY-------------EGGSAELLEQLLQGDLDIALLGSL-TPLENSALHS-KIIKTQHFMI 78 (198)
T ss_pred HhHHHHHHHHHhCCceEEEEE-------------EcCHHHHHHHHHcCCCCEEEecCC-CCCCcccceE-EEeecceEEE
Confidence 44577788877763 456665 335677999999999999985321 1112233443 5777788888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 79 ~~~~~ 83 (198)
T cd08437 79 IVSKD 83 (198)
T ss_pred EecCC
Confidence 87654
No 125
>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=79.42 E-value=2.9 Score=43.10 Aligned_cols=38 Identities=24% Similarity=0.220 Sum_probs=29.3
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT 97 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~ 97 (504)
+++++||||+++|+|++++.+ |... ..+|..|.++|++
T Consensus 316 ~aa~~yDAv~~~a~Al~~~~~----------~~~~--~~~g~~i~~~l~~ 353 (404)
T cd06370 316 EAAYLYDAVMLYAKALDETLL----------EGGD--IYNGTAIVSHILN 353 (404)
T ss_pred eeehhHHHHHHHHHHHHHHHH----------hcCC--CCCHHHHHHHHhC
Confidence 789999999999999998742 1110 1578889999887
No 126
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=79.28 E-value=56 Score=32.27 Aligned_cols=66 Identities=11% Similarity=0.136 Sum_probs=43.3
Q ss_pred hHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEEE
Q psy1412 167 CIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGIL 245 (504)
Q Consensus 167 ~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~il 245 (504)
-.+++..+.+.. +..+++.. +.-..+...|.+|++|+++..-.. ....+.+ .|+....++++
T Consensus 104 l~~~l~~~~~~~P~i~l~~~~-------------~~~~~~~~~L~~g~~Dl~i~~~~~---~~~~~~~-~~l~~~~~~lv 166 (317)
T PRK15421 104 LTPALENFHKNWPQVEMDFKS-------------GVTFDPQPALQQGELDLVMTSDIL---PRSGLHY-SPMFDYEVRLV 166 (317)
T ss_pred HHHHHHHHHHHCCCceEEEEe-------------CccHHHHHHHHCCCcCEEEecCcc---cCCCceE-EEeccceEEEE
Confidence 346777777665 45666652 234568899999999999854322 2223443 67778888888
Q ss_pred EEcc
Q psy1412 246 FKVP 249 (504)
Q Consensus 246 v~~~ 249 (504)
++..
T Consensus 167 ~~~~ 170 (317)
T PRK15421 167 LAPD 170 (317)
T ss_pred EcCC
Confidence 7654
No 127
>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A ....
Probab=79.12 E-value=32 Score=32.06 Aligned_cols=76 Identities=13% Similarity=0.134 Sum_probs=50.9
Q ss_pred cceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhc-cccceecceeeecccc---eeee--ecc
Q psy1412 162 MFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDK-KADLAVASMTINYARE---SVID--FTK 235 (504)
Q Consensus 162 ~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g-~~D~av~~~tit~~R~---~~vd--Fs~ 235 (504)
...+..-++.+...+.-|++++++..+ -..++..|..| ++|+.+.+-....++. ..++ -..
T Consensus 8 ~~~~~~~~l~~~f~~~~g~~v~v~~~~-------------s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~ 74 (230)
T PF13531_consen 8 GLAPALEELAEAFEKQPGIKVEVSFGG-------------SGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPA 74 (230)
T ss_dssp GGHHHHHHHHHHHHHHHCEEEEEEEEC-------------HHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEE
T ss_pred cHHHHHHHHHHHHHhccCCeEEEEECC-------------hHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCccc
Confidence 345566788888888889999888542 24577777766 7888876543222221 2233 457
Q ss_pred ceeeccEEEEEEccC
Q psy1412 236 PFMNLGIGILFKVPT 250 (504)
Q Consensus 236 p~~~~g~~ilv~~~~ 250 (504)
|+..+.+++++++..
T Consensus 75 ~~~~~~~vl~~~~~~ 89 (230)
T PF13531_consen 75 PLARSPLVLAVPKGN 89 (230)
T ss_dssp EEEEEEEEEEEETTS
T ss_pred ccccCceEEEeccCc
Confidence 899999999998765
No 128
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=78.63 E-value=65 Score=31.00 Aligned_cols=67 Identities=6% Similarity=0.141 Sum_probs=42.8
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.+.. +.++++. .+....++..|.+|++|+++...... ...+.. .|.....+++
T Consensus 103 ~~~~~l~~~~~~~P~i~i~v~-------------~~~~~~~~~~l~~g~~Di~i~~~~~~---~~~~~~-~~l~~~~~~l 165 (290)
T PRK10837 103 ILPAMIARYRRDYPQLPLELS-------------VGNSQDVINAVLDFRVDIGLIEGPCH---SPELIS-EPWLEDELVV 165 (290)
T ss_pred hhHHHHHHHHHHCCCceEEEE-------------ECCHHHHHHHHHhCCceEEEecCCCC---CCceeE-EEeecceEEE
Confidence 3346777777765 5566665 33456799999999999998532211 122332 4666777777
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
++++.
T Consensus 166 v~~~~ 170 (290)
T PRK10837 166 FAAPD 170 (290)
T ss_pred EEcCC
Confidence 77644
No 129
>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=78.56 E-value=47 Score=29.38 Aligned_cols=69 Identities=17% Similarity=0.224 Sum_probs=45.8
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
++-.+++.++.++. +..+++. .+..+.++..|.+|++|+++..-.. .....+. +.|..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~l~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~ 76 (198)
T cd08444 13 YALPWVVQAFKEQFPNVHLVLH-------------QGSPEEIASMLANGQADIGIATEAL--ENHPELV-SFPYYDWHHH 76 (198)
T ss_pred hhhhHHHHHHHHHCCCeEEEEE-------------eCCHHHHHHHHHCCCccEEEecccc--CCCcCcE-Eeecccccee
Confidence 45567888888876 4667766 3456678999999999999853221 1122233 3577777888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 77 ~~~~~~ 82 (198)
T cd08444 77 IIVPVG 82 (198)
T ss_pred EEecCC
Confidence 877654
No 130
>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=78.49 E-value=47 Score=29.30 Aligned_cols=67 Identities=13% Similarity=0.151 Sum_probs=41.9
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.++. +..+++. .+.-.++...|.+|++|+++...... ...+. +.++.+..+++
T Consensus 14 ~l~~~l~~f~~~~P~v~i~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~ 76 (196)
T cd08458 14 FMSGVIQTFIADRPDVSVYLD-------------TVPSQTVLELVSLQHYDLGISILAGD---YPGLT-TEPVPSFRAVC 76 (196)
T ss_pred hhHHHHHHHHHHCCCcEEEEe-------------ccChHHHHHHHHcCCCCEEEEeccCC---CCCce-EEEeccCceEE
Confidence 3356777777766 3455554 33456688999999999998643221 12233 25677777777
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 77 v~~~~ 81 (196)
T cd08458 77 LLPPG 81 (196)
T ss_pred EecCC
Confidence 77643
No 131
>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=78.04 E-value=3.5 Score=42.29 Aligned_cols=40 Identities=20% Similarity=0.126 Sum_probs=29.9
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhhce
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTLD 99 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~~~ 99 (504)
.++.+||||+++++|++++.+.. +.+.+|..+.++|++.+
T Consensus 308 ~a~~~YDav~~~a~Al~~~~~~~------------~~~~~~~~i~~~l~~~~ 347 (396)
T cd06373 308 FAGAFYDAVLLYALALNETLAEG------------GDPRDGTNITRRMWNRT 347 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc------------CCCCChHHHHHHhcCCc
Confidence 68899999999999999874211 11357888888888633
No 132
>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=77.66 E-value=47 Score=28.85 Aligned_cols=69 Identities=13% Similarity=0.131 Sum_probs=44.5
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++.++.+.. +..+++. .++...+...|.+|++|+++..... +....+.+ .+..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~~~-~~l~~~~~~ 76 (194)
T cd08436 13 VDLPELLARFHRRHPGVDIRLR-------------QAGSDDLLAAVREGRLDLAFVGLPE--RRPPGLAS-RELAREPLV 76 (194)
T ss_pred HHHHHHHHHHHHHCCCcEEEEe-------------cCCHHHHHHHHHcCCccEEEEecCC--CCCCCcEE-EEeecceEE
Confidence 44567777777765 4556665 3345678999999999999864332 12233333 566777777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 77 ~~~~~~ 82 (194)
T cd08436 77 AVVAPD 82 (194)
T ss_pred EEecCC
Confidence 777644
No 133
>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=77.64 E-value=44 Score=29.38 Aligned_cols=67 Identities=16% Similarity=0.141 Sum_probs=41.7
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++.++.++. +.++++.. +.-.++...|.+|++|+++...... ...+. ..++.+..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~~-------------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~ 75 (196)
T cd08457 13 GFLPRFLAAFLRLRPNLHLSLMG-------------LSSSQVLEAVASGRADLGIADGPLE---ERQGF-LIETRSLPAV 75 (196)
T ss_pred cccHHHHHHHHHHCCCeEEEEEe-------------cCcHHHHHHHHcCCccEEEeccCCC---CCCcE-EEEeccCCeE
Confidence 34457888888776 35566652 2345788899999999998543221 22233 2456666777
Q ss_pred EEEEc
Q psy1412 244 ILFKV 248 (504)
Q Consensus 244 ilv~~ 248 (504)
++++.
T Consensus 76 ~~~~~ 80 (196)
T cd08457 76 VAVPM 80 (196)
T ss_pred EEeeC
Confidence 66654
No 134
>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=75.75 E-value=54 Score=28.59 Aligned_cols=70 Identities=10% Similarity=0.053 Sum_probs=44.4
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-..++..+.++. +.++++. .+..+.++..|.+|++|++++...... +...+.+ .|..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~~-~~l~~~~~~ 77 (197)
T cd08449 13 GGLGPALRRFKRQYPNVTVRFH-------------ELSPEAQKAALLSKRIDLGFVRFADTL-NDPPLAS-ELLWREPMV 77 (197)
T ss_pred hhHHHHHHHHHHHCCCeEEEEE-------------ECCHHHHHHHHhCCCccEEEecccccC-CCCCceE-EEEEEeeEE
Confidence 34457777777765 4556655 345678899999999999985432210 1222332 567777777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 78 ~v~~~~ 83 (197)
T cd08449 78 VALPEE 83 (197)
T ss_pred EEecCC
Confidence 777643
No 135
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=75.57 E-value=44 Score=32.05 Aligned_cols=71 Identities=13% Similarity=0.149 Sum_probs=41.5
Q ss_pred hHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhcc-ccceecceeeeccc---ceeee-ec-cceeec
Q psy1412 167 CIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKK-ADLAVASMTINYAR---ESVID-FT-KPFMNL 240 (504)
Q Consensus 167 ~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~-~D~av~~~tit~~R---~~~vd-Fs-~p~~~~ 240 (504)
.-++.+++.++.|.++++..- .-..+..++.+|. +|+.+++-.-..++ ...++ .+ .+|...
T Consensus 41 ~~~l~~~Fe~~~g~~v~~~~~-------------~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~n 107 (257)
T PRK10677 41 LQDIAAQYKKEKGVDVVSSFA-------------SSSTLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLGN 107 (257)
T ss_pred HHHHHHHHHhhhCCeEEEEec-------------ccHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeecC
Confidence 335666666666777777632 1124677777776 88887654221111 22222 21 367888
Q ss_pred cEEEEEEccC
Q psy1412 241 GIGILFKVPT 250 (504)
Q Consensus 241 g~~ilv~~~~ 250 (504)
.+++++++..
T Consensus 108 ~lvl~~~~~~ 117 (257)
T PRK10677 108 SLVVVAPKAS 117 (257)
T ss_pred EEEEEEECCC
Confidence 8898887653
No 136
>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=74.89 E-value=33 Score=32.76 Aligned_cols=67 Identities=15% Similarity=0.207 Sum_probs=43.8
Q ss_pred hhHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.+..+ .+++++ .+..+.++..|.+|++|+++..-.... ..+.+ .|+....+++
T Consensus 98 ~~~~~l~~~~~~~p~v~l~i~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~~~-~~l~~~~~~l 160 (279)
T TIGR03339 98 YVLDLVARFRQRYPGIEVSVR-------------IGNSQEVLQALQSYRVDVAVSSEVVDD---PRLDR-VVLGNDPLVA 160 (279)
T ss_pred HHHHHHHHHHHHCCCcEEEEE-------------ECCHHHHHHHHHcCCCcEEEEecccCC---CceEE-EEcCCceEEE
Confidence 44567777777654 566665 335567899999999999985333222 22332 5677778888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
++++.
T Consensus 161 v~s~~ 165 (279)
T TIGR03339 161 VVHRQ 165 (279)
T ss_pred EECCC
Confidence 87654
No 137
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=74.19 E-value=48 Score=32.77 Aligned_cols=82 Identities=11% Similarity=0.124 Sum_probs=51.5
Q ss_pred CeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccc
Q psy1412 135 NVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKA 214 (504)
Q Consensus 135 ~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~ 214 (504)
.++++|++....+ ..+-..++..+.+..+ ++++.. +.+++++..|.+|++
T Consensus 116 ~~~l~Ig~~~~~~----------------~~~l~~~l~~f~~~~P-~i~i~~-------------~~~~~~~~~l~~g~~ 165 (317)
T PRK11482 116 QRTITIATTPSVG----------------ALVMPVIYQAIKTHYP-QLLLRN-------------IPISDAENQLSQFQT 165 (317)
T ss_pred CceEEEEecHHHH----------------HHHHHHHHHHHHHHCC-CCEEEE-------------ecchhHHHHHHCCCc
Confidence 4678888753321 1344567777777664 333432 134578999999999
Q ss_pred cceecceeeecccceeeeeccceeeccEEEEEEccC
Q psy1412 215 DLAVASMTINYARESVIDFTKPFMNLGIGILFKVPT 250 (504)
Q Consensus 215 D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~ 250 (504)
|++++.... ....+.+ .|..+..++++++...
T Consensus 166 Dl~i~~~~~---~~~~~~~-~~l~~~~~~lv~~~~h 197 (317)
T PRK11482 166 DLIIDTHSC---SNRTIQH-HVLFTDNVVLVCRQGH 197 (317)
T ss_pred CEEEeccCC---CCCceEE-EEEecCcEEEEEeCCC
Confidence 999865432 2233443 5788888888877543
No 138
>KOG1055|consensus
Probab=72.84 E-value=2.1 Score=46.54 Aligned_cols=21 Identities=33% Similarity=0.441 Sum_probs=18.6
Q ss_pred ccchhhhHHHHHHHHHHHhhh
Q psy1412 48 EPALMYDSVHVLAAGLALLDK 68 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~ 68 (504)
++.+||||||++|.|+.+...
T Consensus 341 ~~~~ayd~Iwa~ala~n~t~e 361 (865)
T KOG1055|consen 341 EAPLAYDAIWALALALNKTME 361 (865)
T ss_pred cCchHHHHHHHHHHHHHHHHh
Confidence 688999999999999988753
No 139
>KOG1419|consensus
Probab=72.24 E-value=4 Score=42.65 Aligned_cols=67 Identities=15% Similarity=0.283 Sum_probs=53.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCC-CCCCcccccccceeh
Q psy1412 265 VEIWLYVLAAYLLVSFTLFVMARFSPYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGS-GLNPKVLQQGSSRTL 343 (504)
Q Consensus 265 ~~vWl~i~~~~~~v~~~~~~i~r~~p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~-~~~p~~~~~~s~R~v 343 (504)
...|+.-++.+++.++++|+.|+--+.|= .....-+..+++|+..-+++..|+ ++.|..+ .+|++
T Consensus 234 iTt~YIGFL~LIfsSflVYLaEKd~~~e~-----------~n~~F~TyADALWWG~ITltTIGYGDk~P~TW---lGr~l 299 (654)
T KOG1419|consen 234 ITTWYIGFLVLIFSSFLVYLAEKDAQGEG-----------TNDEFPTYADALWWGVITLTTIGYGDKTPQTW---LGRLL 299 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccccccc-----------ccccchhHHHHHHhhheeEEeeccCCcCcccc---hhHHH
Confidence 45788888999999999999988644331 111223688999999999999998 6799999 99999
Q ss_pred cc
Q psy1412 344 DT 345 (504)
Q Consensus 344 ~~ 345 (504)
+.
T Consensus 300 aa 301 (654)
T KOG1419|consen 300 AA 301 (654)
T ss_pred HH
Confidence 87
No 140
>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=71.46 E-value=70 Score=27.97 Aligned_cols=68 Identities=9% Similarity=0.051 Sum_probs=44.8
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++.++.++. +.++++. .+.+..+...|.+|++|++++.... ....+. +.+.....+.
T Consensus 14 ~~l~~~i~~~~~~~P~v~l~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~ 76 (198)
T cd08446 14 DTVPRLLRAFLTARPDVTVSLH-------------NMTKDEQIEALRAGRIHIGFGRFYP---VEPDIA-VENVAQERLY 76 (198)
T ss_pred HHHHHHHHHHHHHCCCeEEEEe-------------eCCHHHHHHHHHCCCccEEEEecCC---CCCCce-eEEeeeccEE
Confidence 34457778877765 4556665 4567789999999999999853322 122232 3567777888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 77 ~v~~~~ 82 (198)
T cd08446 77 LAVPKS 82 (198)
T ss_pred EEEeCC
Confidence 777654
No 141
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=71.29 E-value=60 Score=31.81 Aligned_cols=68 Identities=10% Similarity=0.074 Sum_probs=41.5
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.++++.. +.-..+...|.+|++|+++...... ...+. ..+.......
T Consensus 107 ~~l~~~l~~~~~~~P~v~i~i~~-------------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~ 169 (309)
T PRK11013 107 SLLPGLCQPFLARYPDVSLNIVP-------------QESPLLEEWLSAQRHDLGLTETLHT---PAGTE-RTELLTLDEV 169 (309)
T ss_pred hhHHHHHHHHHHHCCCCeEEEEe-------------CCHHHHHHHHHcCCCCEEEEcCCCC---CCCce-eeeecceeEE
Confidence 34457778887766 56677763 2335688999999999998543211 11222 2355555666
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 170 ~~~~~~ 175 (309)
T PRK11013 170 CVLPAG 175 (309)
T ss_pred EEEcCC
Confidence 666543
No 142
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=70.92 E-value=50 Score=32.86 Aligned_cols=84 Identities=13% Similarity=0.017 Sum_probs=54.2
Q ss_pred CCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhc
Q psy1412 134 NNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDK 212 (504)
Q Consensus 134 ~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g 212 (504)
..++++|++..... ..+-.+++..+.++.+ .++++. .+..+.++..|.+|
T Consensus 91 ~~g~lrIg~~~~~~----------------~~~l~~~l~~f~~~~P~v~i~l~-------------~~~~~~~~~~l~~g 141 (327)
T PRK12680 91 SQGQLTLTTTHTQA----------------RFVLPPAVAQIKQAYPQVSVHLQ-------------QAAESAALDLLGQG 141 (327)
T ss_pred CceEEEEEecchhH----------------HHhhHHHHHHHHHHCCCcEEEEE-------------eCChHHHHHHHHCC
Confidence 34678988753211 1344578888877774 566665 34567899999999
Q ss_pred cccceecceeeecccceeeeeccceeeccEEEEEEcc
Q psy1412 213 KADLAVASMTINYARESVIDFTKPFMNLGIGILFKVP 249 (504)
Q Consensus 213 ~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~ 249 (504)
++|+++....... ..... ..|+....+.++++..
T Consensus 142 ~~Dl~i~~~~~~~--~~~~~-~~~l~~~~~~l~~~~~ 175 (327)
T PRK12680 142 DADIAIVSTAGGE--PSAGI-AVPLYRWRRLVVVPRG 175 (327)
T ss_pred CCcEEEEecCCCC--CCcce-EEEeeccceEEEEeCC
Confidence 9999985422111 11122 3688888888887754
No 143
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=66.60 E-value=61 Score=31.59 Aligned_cols=86 Identities=13% Similarity=0.171 Sum_probs=52.1
Q ss_pred CCeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhc
Q psy1412 134 NNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDK 212 (504)
Q Consensus 134 ~~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g 212 (504)
..++++|++..... ..+..+++..+.++.. .++.+. .+..+.++..|.+|
T Consensus 90 ~~g~l~Ig~~~~~~----------------~~~l~~~l~~~~~~~p~i~i~i~-------------~~~~~~~~~~l~~g 140 (300)
T PRK11074 90 WRGQLSIAVDNIVR----------------PDRTRQLIVDFYRHFDDVELIIR-------------QEVFNGVWDALADG 140 (300)
T ss_pred CCceEEEEEcCccc----------------hhHHHHHHHHHHHhCCCceEEEE-------------ehhhhHHHHHHHCC
Confidence 35789999742221 1334467777776654 456555 34556799999999
Q ss_pred cccceecceeeecccceeeeeccceeeccEEEEEEccC
Q psy1412 213 KADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPT 250 (504)
Q Consensus 213 ~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~~~ 250 (504)
++|++++..... .....+.+ .+.....+++++++..
T Consensus 141 ~~Dl~i~~~~~~-~~~~~l~~-~~l~~~~~~~v~~~~h 176 (300)
T PRK11074 141 RVDIAIGATRAI-PVGGRFAF-RDMGMLSWACVVSSDH 176 (300)
T ss_pred CCCEEEecCccC-Ccccccce-eecccceEEEEEcCCC
Confidence 999999643211 11122333 4677777778776543
No 144
>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=65.39 E-value=0.32 Score=50.06 Aligned_cols=46 Identities=30% Similarity=0.569 Sum_probs=34.1
Q ss_pred CCccceeeEEEEee-ecCCCccccchhhh--hhhcccccCCCccccccc
Q psy1412 1 MYDSVHVLAAGLAL-LDKSSVIKTSNLSC--DLEVPWRDGLSLYNYINT 46 (504)
Q Consensus 1 ~~d~v~~~~tg~r~-~d~~~~~~~~~~~~--~~~~~W~~g~~~~~~i~~ 46 (504)
+||||.++|.|++- ++.++.....++.| +...+|..|..++++|++
T Consensus 300 ayDaV~~~A~Al~~ll~~~~~~~~~~l~C~~~~~~~w~~G~~ll~~ik~ 348 (400)
T cd06392 300 LYDSVLMLANAFHRKLEDRKWHSMASLNCIRKSTKPWNGGRSMLETIKK 348 (400)
T ss_pred HHHHHHHHHHHHHHHhhccccCCCCCCccCCCCCCCCCChHHHHHHHHh
Confidence 69999999999995 33334444555678 568899998888777665
No 145
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=62.65 E-value=53 Score=30.51 Aligned_cols=68 Identities=15% Similarity=0.090 Sum_probs=43.4
Q ss_pred CChHHHHHhhhcCC-eEEEeecchhhhhhhcC-CccEEcCCccCCcceEEEecCCCCCchHHHHHHHhhhccChhHHH
Q psy1412 411 SDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN-CNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQML 486 (504)
Q Consensus 411 ~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~-c~l~~vg~~~~~~~~g~a~~k~Spl~~~in~ail~l~e~G~l~~l 486 (504)
.+....-++|..|+ +|=+...+.+ .++ -++. ++....|-|+.+|+.-=.+.+...+..|+..+.-.++
T Consensus 137 ~th~avA~aVa~G~AD~GvGlr~~A----~~~gL~Fi----pl~~E~YD~virke~~~~~~vr~fi~~L~s~~~~~~l 206 (223)
T COG1910 137 TTHDAVASAVASGRADAGVGLRHAA----EKYGLDFI----PLGDEEYDFVIRKERLDKPVVRAFIKALKSEGFAANL 206 (223)
T ss_pred cccHHHHHHHHcCCCCccccHHHHH----HHcCCceE----EcccceEEEEEehhHccCHHHHHHHHHhccccccccC
Confidence 44555567778898 8877744433 333 3454 3566789999999876666666666666665544443
No 146
>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=62.18 E-value=1.1e+02 Score=26.90 Aligned_cols=68 Identities=10% Similarity=0.168 Sum_probs=45.3
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++.++.++. +.++++. .+....++..|.+|++|++++..... ...+. +.|+....++
T Consensus 14 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~ 76 (203)
T cd08445 14 GLLPELIRRFRQAAPDVEIELI-------------EMTTVQQIEALKEGRIDVGFGRLRIE---DPAIR-RIVLREEPLV 76 (203)
T ss_pred hHHHHHHHHHHHHCCCeEEEEE-------------eCChHHHHHHHHcCCCcEEEecCCCC---CCCce-eEEEEeccEE
Confidence 45567888887765 4556665 33467899999999999998533221 12233 3467777888
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 77 ~v~~~~ 82 (203)
T cd08445 77 VALPAG 82 (203)
T ss_pred EEeeCC
Confidence 887654
No 147
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=62.07 E-value=1.1e+02 Score=30.06 Aligned_cols=68 Identities=13% Similarity=0.205 Sum_probs=42.9
Q ss_pred hHHHHHHHHHHcC-ceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEEE
Q psy1412 167 CIDLLKSIAAQVG-FHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGIL 245 (504)
Q Consensus 167 ~idll~~la~~l~-f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~il 245 (504)
-.+++..+.++.+ ..+++. .+.-..+...|.+|++|++++-.. ...-..-+.+ .|.....++++
T Consensus 108 l~~~l~~~~~~~P~i~l~l~-------------~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~~-~~l~~~~~~~v 172 (308)
T PRK10094 108 VAQLLAWLNERYPFTQFHIS-------------RQIYMGVWDSLLYEGFSLAIGVTG-TEALANTFSL-DPLGSVQWRFV 172 (308)
T ss_pred HHHHHHHHHHhCCCcEEEEE-------------eehhhhHHHHHhCCCccEEEeccc-CccccCCeeE-EEecceeEEEE
Confidence 3478888887664 456655 234567889999999999885211 1111223443 47777788887
Q ss_pred EEcc
Q psy1412 246 FKVP 249 (504)
Q Consensus 246 v~~~ 249 (504)
+++.
T Consensus 173 ~~~~ 176 (308)
T PRK10094 173 MAAD 176 (308)
T ss_pred ECCC
Confidence 7644
No 148
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=59.73 E-value=1.5e+02 Score=28.66 Aligned_cols=67 Identities=7% Similarity=-0.023 Sum_probs=39.4
Q ss_pred ccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCccEEcCCccCCcceEEEecCCCCCchHHHHHHHhhh
Q psy1412 409 FVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQ 478 (504)
Q Consensus 409 ~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~l~~vg~~~~~~~~g~a~~k~Spl~~~in~ail~l~ 478 (504)
.+.+.....+.|.+|. .+++-+.....+. . .+.+..+.... ...++++.+|+.+....+...+..+.
T Consensus 219 ~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~-~-~~~l~~l~~~~-~~~~~l~~~~~~~~~~~~~~~~~~i~ 286 (294)
T PRK13348 219 YVPSTHAHLAAIRHGLGYGMVPELLIGPLL-A-AGRLVDLAPGH-PVDVALYWHHWEVESPTMEALSQRVV 286 (294)
T ss_pred EeCcHHHHHHHHHcCCeeEeCCHHHHHHHH-h-cCeeeecCCCC-CCCceeEEeeccccChHHHHHHHHHH
Confidence 3566777788888888 4555444333222 2 24455554432 45678899999876555555444443
No 149
>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=59.68 E-value=0.44 Score=48.57 Aligned_cols=46 Identities=11% Similarity=0.175 Sum_probs=36.2
Q ss_pred CCccceeeEEEEeeec---CCCccccchhhhhhh--c-ccccCCCccccccc
Q psy1412 1 MYDSVHVLAAGLALLD---KSSVIKTSNLSCDLE--V-PWRDGLSLYNYINT 46 (504)
Q Consensus 1 ~~d~v~~~~tg~r~~d---~~~~~~~~~~~~~~~--~-~W~~g~~~~~~i~~ 46 (504)
|||||++++.|++.++ +.+.+...++.|... . +|..|..+.++|+.
T Consensus 272 i~DAV~lvA~a~~~l~~~~~~~~l~~~~~~C~~~~~~~~W~~G~~l~~~Lkn 323 (382)
T cd06377 272 VQDALELVARAVGSATLVQPELALIPATVNCMDLPTKGNESSGQYLARFLAN 323 (382)
T ss_pred HHHHHHHHHHHHHHhhhcccccccCCCCCCcccCCCCCCCCchHHHHHHHHh
Confidence 6899999999999643 666666666788765 6 89999888877765
No 150
>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=59.26 E-value=1.2e+02 Score=26.32 Aligned_cols=68 Identities=16% Similarity=0.183 Sum_probs=44.4
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.++. +.++++. .+++..++..|.+|++|+++...... ....+. ..++.+..+.+
T Consensus 14 ~l~~~l~~~~~~~P~v~l~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~l~-~~~l~~~~~~~ 77 (199)
T cd08430 14 FLPPILERFRAQHPQVEIKLH-------------TGDPADAIDKVLNGEADIAIAARPDK--LPARLA-FLPLATSPLVF 77 (199)
T ss_pred eccHHHHHHHHHCCCceEEEE-------------eCCHHHHHHHHHCCCCCEEEEecCCC--CCcccE-EEeeccceEEE
Confidence 3346888888887 5677776 34677899999999999998532211 112233 25666677777
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 78 ~~~~~ 82 (199)
T cd08430 78 IAPNI 82 (199)
T ss_pred EEeCC
Confidence 76643
No 151
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=58.61 E-value=1e+02 Score=29.04 Aligned_cols=69 Identities=16% Similarity=0.163 Sum_probs=44.1
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++..+.+.. +.+++++ .+.-++++..|.+|++|+++...... ....+. ..+.....++
T Consensus 80 ~~~~~~l~~~~~~~p~i~l~i~-------------~~~~~~~~~~l~~~~~D~~i~~~~~~--~~~~~~-~~~l~~~~~~ 143 (269)
T PRK11716 80 SHLPPILDRFRAEHPLVEIKLT-------------TGDAADAVEKVQSGEADLAIAAKPET--LPASVA-FSPIDEIPLV 143 (269)
T ss_pred HHHHHHHHHHHHHCCCeEEEEE-------------ECCHHHHHHHHHCCCccEEEEecCCC--CCcceE-EEEcccceEE
Confidence 34557888888876 4667776 33456789999999999998543211 111233 2566677777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 144 ~v~~~~ 149 (269)
T PRK11716 144 LIAPAL 149 (269)
T ss_pred EEEcCC
Confidence 776543
No 152
>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=58.29 E-value=31 Score=30.71 Aligned_cols=69 Identities=13% Similarity=0.186 Sum_probs=47.1
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
++-.+++..+.++. +.++++. .+....++..|.+|++|++++..... ...++. .|..+..++
T Consensus 13 ~~l~~~l~~f~~~~P~i~l~i~-------------~~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~ 75 (200)
T cd08465 13 LVLPALMRQLRAEAPGIDLAVS-------------QASREAMLAQVADGEIDLALGVFPEL---PEELHA-ETLFEERFV 75 (200)
T ss_pred HhhhHHHHHHHHHCCCcEEEEe-------------cCChHhHHHHHHCCCccEEEeccccC---CcCeeE-EEeeeccEE
Confidence 44457777776654 3566665 44678899999999999998643222 233443 477788888
Q ss_pred EEEEccC
Q psy1412 244 ILFKVPT 250 (504)
Q Consensus 244 ilv~~~~ 250 (504)
++++...
T Consensus 76 lv~~~~h 82 (200)
T cd08465 76 CLADRAT 82 (200)
T ss_pred EEEeCCC
Confidence 8887654
No 153
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=56.58 E-value=1.9e+02 Score=27.82 Aligned_cols=68 Identities=10% Similarity=0.090 Sum_probs=46.9
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+..+++..+.+.. +.++.+. .+..++++..|.+|++|+++..... ....+++ .|.....++
T Consensus 103 ~~l~~~~~~~~~~~p~v~i~~~-------------~~~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~~-~~l~~~~~~ 165 (296)
T PRK09906 103 NLLPKVLPMFRLRHPDTLIELV-------------SLITTQQEEKLRRGELDVGFMRHPV---YSDEIDY-LELLDEPLV 165 (296)
T ss_pred hHHHHHHHHHHHHCCCeEEEEE-------------eCCcHHHHHHHHcCCeeEEEecCCC---CCCCceE-EEEecccEE
Confidence 34456777777765 4455554 3456789999999999999864432 2333554 688888998
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
+++++.
T Consensus 166 ~v~~~~ 171 (296)
T PRK09906 166 VVLPVD 171 (296)
T ss_pred EEecCC
Confidence 888754
No 154
>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=55.39 E-value=1.5e+02 Score=28.46 Aligned_cols=64 Identities=14% Similarity=0.022 Sum_probs=39.7
Q ss_pred HHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEEEEEc
Q psy1412 169 DLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKV 248 (504)
Q Consensus 169 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv~~ 248 (504)
.++..+.++.+..+++. .++-..++..|.+|++|+++...... ...+. +.|+.+..+++++++
T Consensus 107 ~~l~~~~~~~~i~i~l~-------------~~~~~~~~~~l~~g~~d~~i~~~~~~---~~~l~-~~~l~~~~~~~v~~~ 169 (292)
T TIGR03298 107 PALAPVLAQEGVLLDLV-------------VEDQDHTAELLRSGEVLGAVTTQAKP---VQGCR-VVPLGAMRYLAVASP 169 (292)
T ss_pred HHHHHHHhCCCceEEEE-------------eCcchhHHHHHhCCCceEEEecCCCC---CCCce-EEecCCceEEEEECc
Confidence 45666666544444444 22334678999999999998543222 22344 367888888888764
Q ss_pred c
Q psy1412 249 P 249 (504)
Q Consensus 249 ~ 249 (504)
+
T Consensus 170 ~ 170 (292)
T TIGR03298 170 A 170 (292)
T ss_pred h
Confidence 3
No 155
>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=54.15 E-value=70 Score=27.74 Aligned_cols=61 Identities=15% Similarity=0.143 Sum_probs=34.1
Q ss_pred ccCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCccEE-cCC-ccCCcceEEEecCCCCCchHHH
Q psy1412 409 FVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCNLTQ-IGG-LLDSKGYGIATPKGSPWRDRIS 471 (504)
Q Consensus 409 ~~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~l~~-vg~-~~~~~~~g~a~~k~Spl~~~in 471 (504)
.+.+.+..++.|..|. .+++-+.....+. ... .+.. ... ......++++.+|+.+......
T Consensus 125 ~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~-~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (194)
T cd08432 125 RFDDSSLALQAAVAGLGVALAPRALVADDL-AAG-RLVRPFDLPLPSGGAYYLVYPPGRAESPAVA 188 (194)
T ss_pred EECCHHHHHHHHHhCCCeEEeeHHHhhhhh-cCC-ceEeccccccCCCCCEEEEeccccccchHHH
Confidence 3567788888888887 5566554333322 222 2221 222 2344677888888766544433
No 156
>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=53.24 E-value=23 Score=26.91 Aligned_cols=34 Identities=18% Similarity=0.339 Sum_probs=26.5
Q ss_pred cccchhHHHHHHHHhhccCC-CCCCcccccccceehcc
Q psy1412 309 QFSVSNSFWFITGTFLRQGS-GLNPKVLQQGSSRTLDT 345 (504)
Q Consensus 309 ~~~l~~~~w~~~~~l~~qg~-~~~p~~~~~~s~R~v~~ 345 (504)
..+..+++|+++.++...|. |..|.+. .+|++..
T Consensus 22 ~~~~~da~yfs~~t~tTvGyGDi~p~t~---~gr~~~~ 56 (79)
T PF07885_consen 22 KWSFIDALYFSFVTITTVGYGDIVPQTP---AGRIFTI 56 (79)
T ss_dssp TTSHHHHHHHHHHHHTT---SSSSTSSH---HHHHHHH
T ss_pred cCCHHHHHHHHHHHHhcccCCCccCCcc---chHHHHH
Confidence 45689999999999999997 5799877 8888776
No 157
>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=52.91 E-value=74 Score=30.85 Aligned_cols=128 Identities=20% Similarity=0.136 Sum_probs=67.1
Q ss_pred hhcccchhhhhccC----C-CCceeeeeecchhccchhHHHHHHHHHHHhcCCCcccCChHHHHHhhhcCC-eEEEee-c
Q psy1412 359 RYMESKKCILFLGG----Q-GDETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGD-YAFLME-S 431 (504)
Q Consensus 359 ~~~~~i~s~~dL~~----~-~~i~~g~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~-~A~i~e-~ 431 (504)
+..+++++++||.+ + .++.+|+....-...- .-..+.+...-.-..+...+..+++..+..|. ++.+.. .
T Consensus 85 ~~dsp~~t~~eli~~ak~~p~~~~~g~~g~g~~~hl---~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~~ 161 (274)
T PF03401_consen 85 RADSPYKTLEELIEYAKANPGKLTFGSSGPGSSDHL---AAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSPG 161 (274)
T ss_dssp ETTSS-SSHHHHHHHHHCSCCC-EEEESSTTSHHHH---HHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEHH
T ss_pred eCCCccccHHHHHHHHHhCCCCeEEEecCCCchHHH---HHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecHH
Confidence 67889999999863 2 3588876511100000 00111111111122355677888888888888 665544 3
Q ss_pred chhhhhhhcC---------------CccEEcCC----cc-CCcceEEEecCCCC--CchHHHHHHHhhhccChhHHHHHh
Q psy1412 432 TMLDYEVQRN---------------CNLTQIGG----LL-DSKGYGIATPKGSP--WRDRISLAILELQEKGTIQMLYDK 489 (504)
Q Consensus 432 ~~~~y~~~~~---------------c~l~~vg~----~~-~~~~~g~a~~k~Sp--l~~~in~ail~l~e~G~l~~l~~k 489 (504)
....|..+.. .+.-...+ .+ ....+|++.|||-| .++.+..++.+..++-.+++..++
T Consensus 162 ~~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~ 241 (274)
T PF03401_consen 162 EALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEK 241 (274)
T ss_dssp HHHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHH
T ss_pred HHHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 3344443322 11111111 11 12233899999987 899999999999988766655433
No 158
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=52.19 E-value=22 Score=35.67 Aligned_cols=64 Identities=16% Similarity=0.251 Sum_probs=47.9
Q ss_pred HHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeeccccee-eeecccee
Q psy1412 168 IDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESV-IDFTKPFM 238 (504)
Q Consensus 168 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~-vdFs~p~~ 238 (504)
..+-+++.++.|-.+++...|++.-|. =..++.+|..|.+|+.+.+......+... --|+.||.
T Consensus 47 ~~fa~~v~ekt~G~l~i~vfP~~qLG~-------~~~~ie~l~~G~id~~~~s~~~l~~~~P~~~v~~lPfl 111 (332)
T COG1638 47 KKFAELVEEKTGGRLKIEVFPNSQLGG-------EAEMIEQLRSGTLDIGVVSLGFLAGLVPEFGVFDLPFL 111 (332)
T ss_pred HHHHHHHHHHhCCeEEEEECCCcccCc-------HHHHHHHHhcCCeeEEeccchhhcccCCcceeecCCee
Confidence 356777888999999999999888663 34699999999999998877665554332 23455554
No 159
>TIGR02136 ptsS_2 phosphate binding protein. Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons. This model separates members of the current family from the phosphate ABC transporter phosphate binding protein described by TIGRFAMs model TIGR00975.
Probab=49.94 E-value=29 Score=33.83 Aligned_cols=72 Identities=10% Similarity=0.086 Sum_probs=48.7
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccc-----e--eeeeccc
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARE-----S--VIDFTKP 236 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~-----~--~vdFs~p 236 (504)
.+-.+++.++.++. +.++++. .+..+.++..|.+|++|+++..-....+.. + -+. ..|
T Consensus 48 ~~lp~~l~~f~~~~P~i~v~i~-------------~~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~-~~~ 113 (287)
T TIGR02136 48 PLAEAAAEEFQKIHPGVSVTVQ-------------GAGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLI-EHK 113 (287)
T ss_pred HHHHHHHHHHHhhCCCceEEEc-------------cCCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCce-EEE
Confidence 34556777777766 4566665 456788999999999999886533332220 0 123 358
Q ss_pred eeeccEEEEEEccC
Q psy1412 237 FMNLGIGILFKVPT 250 (504)
Q Consensus 237 ~~~~g~~ilv~~~~ 250 (504)
+....++++++++.
T Consensus 114 l~~~~l~lvv~~~h 127 (287)
T TIGR02136 114 VAVDGLAVVVNKKN 127 (287)
T ss_pred EEEeeEEEEECCCC
Confidence 89999999987654
No 160
>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=49.45 E-value=47 Score=29.01 Aligned_cols=69 Identities=14% Similarity=0.161 Sum_probs=46.6
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .+....++..|.+|++|+++...... ...++ +.+..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~ 75 (196)
T cd08450 13 QWLPEVLPILREEHPDLDVELS-------------SLFSPQLAEALMRGKLDVAFMRPEIQ---SDGID-YQLLLKEPLI 75 (196)
T ss_pred hhHHHHHHHHHhhCCCcEEEEE-------------ecChHHHHHHHhcCCccEEEEeCCCC---CCCcE-EEEEEccceE
Confidence 44557777877765 4567766 34566799999999999998543221 22233 3677888888
Q ss_pred EEEEccC
Q psy1412 244 ILFKVPT 250 (504)
Q Consensus 244 ilv~~~~ 250 (504)
++++...
T Consensus 76 ~~~~~~~ 82 (196)
T cd08450 76 VVLPADH 82 (196)
T ss_pred EEecCCC
Confidence 8887654
No 161
>PF02879 PGM_PMM_II: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II; InterPro: IPR005845 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 2F7L_A 3PDK_B 1KFQ_B 1KFI_A 1C47_A 1VKL_B 1LXT_A 1JDY_B 3PMG_A 1C4G_B ....
Probab=48.29 E-value=42 Score=27.00 Aligned_cols=69 Identities=22% Similarity=0.352 Sum_probs=48.8
Q ss_pred ceehhHHHHHHHHHHcCceE-EEEEcCCCCCcc-c--cCCCCcchhhHHHHhhccccceecceeeecccceeee
Q psy1412 163 FEGFCIDLLKSIAAQVGFHF-VLRLVPDHTYGV-Y--DHETKEWNGIVKELMDKKADLAVASMTINYARESVID 232 (504)
Q Consensus 163 ~~G~~idll~~la~~l~f~~-~~~~~~~~~~G~-~--~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vd 232 (504)
..|-...++..+.+++|.++ ++..-+++.|+. . ++....+..+...+...++|+++ .+--..+|.-++|
T Consensus 29 ~~G~~~~~~~~ll~~lg~~~~~~n~~~d~~f~~~~~p~p~~~~l~~~~~~v~~~~ad~g~-~~DgDaDRl~~vd 101 (104)
T PF02879_consen 29 MNGAGSDILPRLLERLGCDVIELNCDPDPDFPNQHAPNPEEESLQRLIKIVRESGADLGI-AFDGDADRLGVVD 101 (104)
T ss_dssp TTSTTHHHHHHHHHHTTCEEEEESSS-STTGTTTSTSSTSTTTTHHHHHHHHHSTTSEEE-EE-TTSSBEEEEE
T ss_pred CCCHHHHHHHHHHHHcCCcEEEEecccccccccccccccccchhHHHHHHhhccCceEEE-EECCcCceeEEEC
Confidence 34778889999999999965 344456777865 3 34335788899999999999976 4555667766554
No 162
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=48.14 E-value=2.6e+02 Score=26.92 Aligned_cols=66 Identities=12% Similarity=0.036 Sum_probs=42.0
Q ss_pred hHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEEEE
Q psy1412 167 CIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILF 246 (504)
Q Consensus 167 ~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ilv 246 (504)
...++..+.++.+.++++. .+.-+..+..|.+|++|+++..-.. ....+. +.|+.+..+++++
T Consensus 105 l~~~l~~f~~~~~i~i~l~-------------~~~~~~~~~~l~~~~~d~~i~~~~~---~~~~l~-~~~l~~~~~~lv~ 167 (294)
T PRK03635 105 FLPALAPVLARSGVLLDLV-------------VEDQDHTAELLRRGEVVGAVTTEPQ---PVQGCR-VDPLGAMRYLAVA 167 (294)
T ss_pred HHHHHHHHHhCCCcEEEEE-------------ecCcHHHHHHHhCCCceEEEeccCC---CCCCce-eeecccceEEEEE
Confidence 3456777776644445554 2234568999999999999754222 222343 4688888888887
Q ss_pred Ecc
Q psy1412 247 KVP 249 (504)
Q Consensus 247 ~~~ 249 (504)
+..
T Consensus 168 ~~~ 170 (294)
T PRK03635 168 SPA 170 (294)
T ss_pred cch
Confidence 643
No 163
>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=44.72 E-value=58 Score=28.87 Aligned_cols=69 Identities=10% Similarity=0.031 Sum_probs=46.5
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++.++.++. +.++++. .++.+.++..|.+|++|+++.... . ....++ +.|+.+..+.
T Consensus 14 ~~l~~~l~~f~~~~P~v~i~i~-------------~~~~~~l~~~l~~g~~D~~~~~~~--~-~~~~~~-~~~l~~~~~~ 76 (198)
T cd08486 14 RSLPLLLRAFLTSTPTATVSLT-------------HMTKDEQVEGLLAGTIHVGFSRFF--P-RHPGIE-IVNIAQEDLY 76 (198)
T ss_pred HHHHHHHHHHHHhCCCeEEEEE-------------ECCHHHHHHHHHcCCceEEEecCC--C-CCCceE-EEEEeeccEE
Confidence 34457777777765 5566665 346778999999999999985321 1 222244 3577788888
Q ss_pred EEEEccC
Q psy1412 244 ILFKVPT 250 (504)
Q Consensus 244 ilv~~~~ 250 (504)
++++...
T Consensus 77 lv~~~~h 83 (198)
T cd08486 77 LAVHRSQ 83 (198)
T ss_pred EEecCCC
Confidence 8887653
No 164
>PRK07377 hypothetical protein; Provisional
Probab=44.27 E-value=67 Score=28.90 Aligned_cols=62 Identities=18% Similarity=0.221 Sum_probs=45.7
Q ss_pred CeEEEEEeecccCeEEEecCCCCCCCccceehhHHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccc
Q psy1412 135 NVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKA 214 (504)
Q Consensus 135 ~~~l~V~~~~~~P~~~~~~~~~~~~~~~~~G~~idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~ 214 (504)
..++|+|+.... .+ .+..-+..++.++.+.++++.+.|++..++ -+.+.+.|.+|++
T Consensus 74 s~~~Rlgv~~~~-----~~------~~~~~~~l~~~l~~~~~~y~~rlElv~y~~------------~~~l~~aL~~~eV 130 (184)
T PRK07377 74 SLVMRLGVLEIE-----TE------TSSVFDQLIDQLRTILDKYHLRLELVVYPD------------LQALEQALRDKEV 130 (184)
T ss_pred ccEEEEEEEecc-----cc------ccccHHHHHHHHHHHHHHhCceeeEEecCC------------HHHHHHHHhcCCc
Confidence 456888877551 11 122345567888999999999999987654 4679999999999
Q ss_pred cceec
Q psy1412 215 DLAVA 219 (504)
Q Consensus 215 D~av~ 219 (504)
|++.+
T Consensus 131 h~~c~ 135 (184)
T PRK07377 131 HAICL 135 (184)
T ss_pred cEEec
Confidence 98765
No 165
>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=41.87 E-value=84 Score=27.63 Aligned_cols=68 Identities=10% Similarity=0.131 Sum_probs=45.0
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.++. +.++++. .+....+...|.+|++|+++... ......+. +.++.+..+.+
T Consensus 14 ~l~~~l~~~~~~~P~v~i~i~-------------~~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~l 76 (197)
T cd08452 14 FLPPIVREYRKKFPSVKVELR-------------ELSSPDQVEELLKGRIDIGFLHP---PIQHTALH-IETVQSSPCVL 76 (197)
T ss_pred HHHHHHHHHHHHCCCcEEEEE-------------ecChHHHHHHHHCCCccEEEeeC---CCCCCCee-EEEeeeccEEE
Confidence 3457777777765 4566665 34567799999999999998532 22223344 35777788888
Q ss_pred EEEccC
Q psy1412 245 LFKVPT 250 (504)
Q Consensus 245 lv~~~~ 250 (504)
+++...
T Consensus 77 v~~~~h 82 (197)
T cd08452 77 ALPKQH 82 (197)
T ss_pred EEeCCC
Confidence 877543
No 166
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=40.14 E-value=56 Score=31.43 Aligned_cols=69 Identities=13% Similarity=0.257 Sum_probs=47.7
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +..++++ .+....++..|.+|++|++++...+. . ..+. ..|+.+..++
T Consensus 102 ~~l~~~l~~f~~~~P~v~v~~~-------------~~~~~~~~~~l~~g~~Dl~i~~~~~~--~-~~l~-~~~l~~~~~~ 164 (275)
T PRK03601 102 CMLTPWLGRLYQNQEALQFEAR-------------IAQRQSLVKQLHERQLDLLITTEAPK--M-DEFS-SQLLGHFTLA 164 (275)
T ss_pred HHHHHHHHHHHHhCCCcEEEEE-------------ECChHHHHHHHHcCCCCEEEEcCCCc--c-CCcc-EEEecceeEE
Confidence 45567777776654 5566665 34566799999999999999654332 2 2343 4588889999
Q ss_pred EEEEccC
Q psy1412 244 ILFKVPT 250 (504)
Q Consensus 244 ilv~~~~ 250 (504)
++++...
T Consensus 165 ~v~~~~~ 171 (275)
T PRK03601 165 LYTSAPS 171 (275)
T ss_pred EEecCch
Confidence 9987553
No 167
>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=39.54 E-value=2.5e+02 Score=24.26 Aligned_cols=62 Identities=11% Similarity=-0.055 Sum_probs=36.7
Q ss_pred cCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCccEEcCCccCCcceEEEecCCCCCchHHHHHH
Q psy1412 410 VSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCNLTQIGGLLDSKGYGIATPKGSPWRDRISLAI 474 (504)
Q Consensus 410 ~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~l~~vg~~~~~~~~g~a~~k~Spl~~~in~ai 474 (504)
+.+.+..+..+.+|. .+++-+....... . ...+..+.+ -....++++.+|+.+....+...+
T Consensus 130 ~~~~~~~~~~v~~G~Gi~~lp~~~~~~~~-~-~~~l~~l~~-~~~~~~~l~~~~~~~~s~~~~~~~ 192 (195)
T cd08428 130 VPSSEAFVDLAAQGLAYGMIPELQIEPEL-A-SGELIDLAP-GHLLRVTLYWHRWNLESGLMKRLS 192 (195)
T ss_pred ECCHHHHHHHHHhCCeeEeccHHHHHHHh-c-CCCEEEccC-cccccceEEEecccccCHHHHHhh
Confidence 567888888888888 5555443332222 2 234554433 234567888888876655554443
No 168
>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=39.21 E-value=75 Score=28.06 Aligned_cols=69 Identities=10% Similarity=-0.005 Sum_probs=44.5
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.++. +.++++. .+.-++++.+|.+|++|+++...... ...+. +.++.+..+.
T Consensus 14 ~~l~~~l~~~~~~~P~i~l~~~-------------~~~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~-~~~l~~~~~~ 76 (198)
T cd08485 14 HTLPLLLRQLLSVAPSATVSLT-------------QMSKNRQIEALDAGTIDIGFGRFYPY---QEGVV-VRNVTNERLF 76 (198)
T ss_pred HHHHHHHHHHHHhCCCcEEEEE-------------ECCHHHHHHHHHcCCccEEEecCCCC---CCCeE-EEEeeccceE
Confidence 34456777776654 5666665 33456799999999999998643221 12233 3577777877
Q ss_pred EEEEccC
Q psy1412 244 ILFKVPT 250 (504)
Q Consensus 244 ilv~~~~ 250 (504)
+++++..
T Consensus 77 ~~~~~~~ 83 (198)
T cd08485 77 LGAQKSR 83 (198)
T ss_pred EEeCCCC
Confidence 7776543
No 169
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=38.84 E-value=70 Score=31.40 Aligned_cols=70 Identities=9% Similarity=0.153 Sum_probs=50.0
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
++-.+++..+.++. +.++++. .+....++..|.+|++|+++..... ....+.+ .|+....++
T Consensus 125 ~~l~~~l~~f~~~~P~i~l~i~-------------~~~~~~~~~~l~~g~~Di~i~~~~~---~~~~l~~-~~l~~~~~~ 187 (314)
T PRK09508 125 RLTSQIYNRIEQIAPNIHVVFK-------------SSLNQNIEHQLRYQETEFVISYEEF---DRPEFTS-VPLFKDELV 187 (314)
T ss_pred HHHHHHHHHHHHhCCCcEEEEE-------------eCcchhHHHHHhcCCccEEEecCCC---Cccccce-eeeecCceE
Confidence 45678888888876 5677776 3456779999999999999865432 1233444 477888999
Q ss_pred EEEEccCC
Q psy1412 244 ILFKVPTS 251 (504)
Q Consensus 244 ilv~~~~~ 251 (504)
++++...+
T Consensus 188 lv~~~~hp 195 (314)
T PRK09508 188 LVASKNHP 195 (314)
T ss_pred EEEcCCCC
Confidence 98876543
No 170
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=35.81 E-value=90 Score=30.26 Aligned_cols=66 Identities=11% Similarity=0.090 Sum_probs=35.8
Q ss_pred cCChHHHHHhhhcCC-eEEEeecchhhhhhhcCCccE-EcCCcc-CCcceEEEecCCCCCchHHHHHHHhh
Q psy1412 410 VSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRNCNLT-QIGGLL-DSKGYGIATPKGSPWRDRISLAILEL 477 (504)
Q Consensus 410 ~~~~~egi~~v~~g~-~A~i~e~~~~~y~~~~~c~l~-~vg~~~-~~~~~g~a~~k~Spl~~~in~ail~l 477 (504)
+.+.+..++.|.+|. .+++-+.....+. ... .+. .+.... ....+.++.+|+.+....+...+..+
T Consensus 220 ~~~~~~~~~~v~~g~gi~~lp~~~~~~~~-~~~-~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 288 (297)
T PRK11139 220 FSHSSMALQAAIHGQGVALGNRVLAQPEI-EAG-RLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWL 288 (297)
T ss_pred eCCHHHHHHHHHhCCCeEecchhhhHHHH-HCC-ceecccccCcCCCccEEEEeccccccChhHHHHHHHH
Confidence 566777777888887 5555443333332 222 111 122221 23578899998877655555544433
No 171
>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=35.56 E-value=99 Score=26.91 Aligned_cols=69 Identities=17% Similarity=0.211 Sum_probs=45.8
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.++++. .+..+.+...|.+|++|+++.... .....+. +.+.....++
T Consensus 13 ~~l~~~l~~~~~~~P~i~v~~~-------------~~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~ 75 (198)
T cd08447 13 SFLPRLLAAARAALPDVDLVLR-------------EMVTTDQIEALESGRIDLGLLRPP---FARPGLE-TRPLVREPLV 75 (198)
T ss_pred HHHHHHHHHHHHHCCCeEEEEE-------------eCCHHHHHHHHHcCCceEEEecCC---CCCCCee-EEEeecCceE
Confidence 44567778877765 4566665 346678999999999999985322 1222233 3577778888
Q ss_pred EEEEccC
Q psy1412 244 ILFKVPT 250 (504)
Q Consensus 244 ilv~~~~ 250 (504)
++++...
T Consensus 76 ~v~~~~~ 82 (198)
T cd08447 76 AAVPAGH 82 (198)
T ss_pred EEecCCC
Confidence 8876543
No 172
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=33.43 E-value=54 Score=28.52 Aligned_cols=27 Identities=22% Similarity=0.375 Sum_probs=21.2
Q ss_pred ccCchhHHHHHHHHHHHHHHHHHHHHh
Q psy1412 261 NPLAVEIWLYVLAAYLLVSFTLFVMAR 287 (504)
Q Consensus 261 ~Pf~~~vWl~i~~~~~~v~~~~~~i~r 287 (504)
.|.++.+|+.++++++++++++|.+.|
T Consensus 115 ~~~~~~i~~~i~g~ll~i~~giy~~~r 141 (145)
T PF10661_consen 115 KPISPTILLSIGGILLAICGGIYVVLR 141 (145)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677777788888888889988876
No 173
>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=33.17 E-value=10 Score=38.61 Aligned_cols=15 Identities=20% Similarity=0.235 Sum_probs=13.6
Q ss_pred CCccceeeEEEEeee
Q psy1412 1 MYDSVHVLAAGLALL 15 (504)
Q Consensus 1 ~~d~v~~~~tg~r~~ 15 (504)
+||||++++.+|+.+
T Consensus 279 ~~Dav~~~~~a~~~l 293 (368)
T cd06383 279 AYDAVLAVGEWPRRM 293 (368)
T ss_pred HHHHHHHhccccchh
Confidence 699999999999965
No 174
>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=32.59 E-value=38 Score=28.74 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=12.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHh
Q psy1412 265 VEIWLYVLAAYLLVSFTLFVMAR 287 (504)
Q Consensus 265 ~~vWl~i~~~~~~v~~~~~~i~r 287 (504)
|-+|++++++++++.++++++.|
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~r 24 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNR 24 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555555555543
No 175
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=32.34 E-value=1.1e+02 Score=26.60 Aligned_cols=66 Identities=12% Similarity=-0.007 Sum_probs=43.5
Q ss_pred hhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEEE
Q psy1412 166 FCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGI 244 (504)
Q Consensus 166 ~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~i 244 (504)
+-.+++..+.+.. +.++++. .+..+.+..+|.+|++|+++.... . ..+. +.+.....+++
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~~-------------~~~~~~~~~~l~~~~~Dl~i~~~~----~-~~~~-~~~l~~~~~~~ 74 (185)
T cd08439 14 ILPFLLNRFASVYPRLAIEVV-------------CKRTPRLMEMLERGEVDLALITHP----P-PGAS-ATILRRSPTVW 74 (185)
T ss_pred HHHHHHHHHHHHCCCeEEEEE-------------ECChHHHHHHHHCCCCcEEEEecc----C-CCCC-ceEEEEecCEE
Confidence 3456777776654 5667765 234567899999999999985321 1 1122 46777888888
Q ss_pred EEEccC
Q psy1412 245 LFKVPT 250 (504)
Q Consensus 245 lv~~~~ 250 (504)
++++..
T Consensus 75 v~~~~~ 80 (185)
T cd08439 75 YCAAGY 80 (185)
T ss_pred EECCCC
Confidence 877653
No 176
>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=31.47 E-value=74 Score=21.89 Aligned_cols=22 Identities=9% Similarity=0.404 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHH
Q psy1412 265 VEIWLYVLAAYLLVSFTLFVMA 286 (504)
Q Consensus 265 ~~vWl~i~~~~~~v~~~~~~i~ 286 (504)
.++|.++....+++++++|...
T Consensus 11 a~~~~l~~~~~~Figiv~wa~~ 32 (48)
T cd01324 11 ADSWGLLYLALFFLGVVVWAFR 32 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHHhC
Confidence 4689999989999999999874
No 177
>KOG1545|consensus
Probab=30.30 E-value=15 Score=36.58 Aligned_cols=84 Identities=23% Similarity=0.324 Sum_probs=51.2
Q ss_pred CcccccccCchhHH-HHHHHHHHHHHHHHHHHHhhCCCCccCCCCCCCCCCc-ccCcccchhHHHHHHHHhhccCCC-CC
Q psy1412 255 RLFSFMNPLAVEIW-LYVLAAYLLVSFTLFVMARFSPYEWSNPHPCLAESPI-VENQFSVSNSFWFITGTFLRQGSG-LN 331 (504)
Q Consensus 255 ~~~~fl~Pf~~~vW-l~i~~~~~~v~~~~~~i~r~~p~~~~~~~~~~~~~~~-~~~~~~l~~~~w~~~~~l~~qg~~-~~ 331 (504)
.+-++=+.|...+= +++++.++++++++|--.- .+.+.+. .....++-+++|+++-++...|.. -.
T Consensus 346 GLQILGqTl~aSmrElgLLIFFlfIgviLFsSav-----------YFAEade~~S~F~SIPdaFWwavVTMTTVGYGDm~ 414 (507)
T KOG1545|consen 346 GLQILGQTLRASMRELGLLIFFLFIGVILFSSAV-----------YFAEADEPESHFSSIPDAFWWAVVTMTTVGYGDMV 414 (507)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcee-----------eeeecCCCccCCCcCcccceEEEEEEEeeccccce
Confidence 33333344444443 4556666677777664221 1111111 223347889999999999988884 57
Q ss_pred Ccccccccceehcc----chhhhhh
Q psy1412 332 PKVLQQGSSRTLDT----ALDSKIE 352 (504)
Q Consensus 332 p~~~~~~s~R~v~~----An~Ltv~ 352 (504)
|-+. .+++|.. |-.||+.
T Consensus 415 P~Tv---gGKIVGslCAiaGVLTiA 436 (507)
T KOG1545|consen 415 PVTV---GGKIVGSLCAIAGVLTIA 436 (507)
T ss_pred eccc---CceehhhHHhhhhheEec
Confidence 8888 9999887 4466665
No 178
>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=29.37 E-value=4.1 Score=41.70 Aligned_cols=43 Identities=26% Similarity=0.565 Sum_probs=30.4
Q ss_pred CCccceeeEEEEeeecCCCccccchhhhhhhcccccCCCccccccc
Q psy1412 1 MYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT 46 (504)
Q Consensus 1 ~~d~v~~~~tg~r~~d~~~~~~~~~~~~~~~~~W~~g~~~~~~i~~ 46 (504)
+||||++++.|++.. .+....++.|+...+|..|..+.+.|+.
T Consensus 293 ~yDav~~~a~A~~~~---~~~~~~~~~c~~~~~w~~G~~i~~~l~~ 335 (384)
T cd06393 293 LYDAVHMVSVCYQRA---PQMTVNSLQCHRHKAWRFGGRFMNFIKE 335 (384)
T ss_pred hhhhHHHHHHHHhhh---hhcCCCCCCCCCCCCCcccHHHHHHHhh
Confidence 599999999998832 2222334578888899888767655654
No 179
>TIGR01276 thiB thiamine ABC transporter, periplasmic binding protein. This model finds the thiamine (and thiamine pyrophosphate) ABC transporter periplasmic binding protein ThiB in proteobacteria. Completed genomes having this protein (E. coli, Vibrio cholera, Haemophilus influenzae) also have the permease ThiP, described by TIGRFAMs equivalog model TIGR01253.
Probab=27.92 E-value=5.7e+02 Score=24.81 Aligned_cols=39 Identities=18% Similarity=0.202 Sum_probs=26.9
Q ss_pred HHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhh----ccccceec
Q psy1412 169 DLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMD----KKADLAVA 219 (504)
Q Consensus 169 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~----g~~D~av~ 219 (504)
.+++.+.++.|.+++++... +-..++..|.. ..+|++++
T Consensus 21 ~~~~~Fe~~~gi~V~~~~~~------------s~~~l~~kl~~e~~~~~~DVv~~ 63 (309)
T TIGR01276 21 VVKKAFEADCNCELKLVALE------------DGVSLLNRLRLEGKNSKADVVLG 63 (309)
T ss_pred HHHHHHHHHHCCEEEEEecC------------cHHHHHHHHHHcCCCCCCCEEEe
Confidence 57888888889998887432 12337777764 46888765
No 180
>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=27.42 E-value=43 Score=33.29 Aligned_cols=20 Identities=35% Similarity=0.464 Sum_probs=18.0
Q ss_pred ccchhhhHHHHHHHHHHHhh
Q psy1412 48 EPALMYDSVHVLAAGLALLD 67 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~ 67 (504)
.++.+|||++++++|++++.
T Consensus 276 ~~~~~yda~~~~~~A~~~a~ 295 (344)
T cd06348 276 FSAQAFDAVQVVAEALKRLN 295 (344)
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 57789999999999999885
No 181
>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=27.07 E-value=56 Score=32.50 Aligned_cols=33 Identities=27% Similarity=0.320 Sum_probs=25.9
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT 97 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~ 97 (504)
.++.+||+++++++|+++.. +..+..+.+.|++
T Consensus 286 ~~~~~yda~~~l~~A~~~ag-----------------~~~~~~i~~al~~ 318 (344)
T cd06345 286 MGASTYDSIYILAEAIERAG-----------------STDGDALVEALEK 318 (344)
T ss_pred cchHHHHHHHHHHHHHHHhc-----------------CCCHHHHHHHHHh
Confidence 67889999999999999753 1345678888775
No 182
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=26.91 E-value=74 Score=30.17 Aligned_cols=66 Identities=15% Similarity=0.160 Sum_probs=44.2
Q ss_pred HHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceec--ceeeecccce-----eeeeccceeeccEEE
Q psy1412 172 KSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVA--SMTINYARES-----VIDFTKPFMNLGIGI 244 (504)
Q Consensus 172 ~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~--~~tit~~R~~-----~vdFs~p~~~~g~~i 244 (504)
+.+.++.|++++++... ++..++..|..|++|++.. +..+-..+-. .+.........+..+
T Consensus 27 ~g~f~~~G~~ve~~~~~------------~g~~~~~al~~G~iD~a~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~l 94 (252)
T PF13379_consen 27 KGLFEKEGLDVEWVQFA------------SGADILEALAAGEIDIAFVLAPALIAIAKGAGGPDVDIVVLAGLSQNGNAL 94 (252)
T ss_dssp TTHHHHTTSCEEEEEES------------SHHHHHHHHHCTSSSEEEECTHHHHHHHTTTTT----EEEEEECSBSSEEE
T ss_pred cChHHHcCCEEEEEEcC------------CHHHHHHHHHcCCCCEEEechHHHHHHHcCCCCcccceEEeeccCCCceEE
Confidence 33667789999888653 6789999999999999887 1112223322 233334456678888
Q ss_pred EEEcc
Q psy1412 245 LFKVP 249 (504)
Q Consensus 245 lv~~~ 249 (504)
+++..
T Consensus 95 vv~~~ 99 (252)
T PF13379_consen 95 VVRND 99 (252)
T ss_dssp EECGG
T ss_pred EEcCc
Confidence 88764
No 183
>PF12916 DUF3834: Protein of unknown function (DUF3834); InterPro: IPR024533 This family is likely to be related to solute-binding lipo-proteins.; PDB: 3MST_A.
Probab=26.70 E-value=73 Score=29.06 Aligned_cols=44 Identities=25% Similarity=0.327 Sum_probs=27.0
Q ss_pred ehhHHHH-HHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecc
Q psy1412 165 GFCIDLL-KSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVAS 220 (504)
Q Consensus 165 G~~idll-~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~ 220 (504)
|=.-|++ +++.+.-|.+.|++..+ .|..++.++.+|++|.|+-+
T Consensus 77 GsaADvl~Ral~d~~~~~~EvVytd------------D~~~i~~Ml~~g~vdsAVv~ 121 (201)
T PF12916_consen 77 GSAADVLTRALLDLKGIKAEVVYTD------------DMSEIVKMLNEGEVDSAVVG 121 (201)
T ss_dssp TSHHHHHHHHHHHHH--T-EEEE---------------HHHHHHHHHTT-E--EEEE
T ss_pred ccHHHHHHHHHHhhccccceeEEec------------CHHHHHHHHhcCceeeeeec
Confidence 5555654 56667778899998754 59999999999999998744
No 184
>PRK10918 phosphate ABC transporter periplasmic substrate-binding protein PstS; Provisional
Probab=26.56 E-value=1.3e+02 Score=30.31 Aligned_cols=50 Identities=16% Similarity=0.279 Sum_probs=37.7
Q ss_pred CCcchhhHHHHhhccccceecceeeecccceee-eeccceeeccEEEEEEcc
Q psy1412 199 TKEWNGIVKELMDKKADLAVASMTINYARESVI-DFTKPFMNLGIGILFKVP 249 (504)
Q Consensus 199 ~g~w~gli~~l~~g~~D~av~~~tit~~R~~~v-dFs~p~~~~g~~ilv~~~ 249 (504)
.|+=.| +.++.+|.+|++.++..++.+..+.. -+..|....++++++..+
T Consensus 61 ~GSG~G-i~~~~~g~vd~a~ssr~l~~~E~~~~~~~~~pva~daIaivvN~~ 111 (346)
T PRK10918 61 IGSSGG-VKQIIANTVDFGASDAPLSDEKLAQEGLFQFPTVIGGVVLAVNIP 111 (346)
T ss_pred CccHHH-HHHHHhCCCcEEecCccCCHHHHhhcCCeeeeEEEEEEEEEEeCC
Confidence 456566 58899999999999999986533211 245789999999999865
No 185
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.49 E-value=94 Score=26.22 Aligned_cols=29 Identities=17% Similarity=0.308 Sum_probs=24.0
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHhhCCCC
Q psy1412 264 AVEIWLYVLAAYLLVSFTLFVMARFSPYE 292 (504)
Q Consensus 264 ~~~vWl~i~~~~~~v~~~~~~i~r~~p~~ 292 (504)
+...|++.++.+++-.++=+++.|+.+..
T Consensus 4 t~~~W~~a~igLvvGi~IG~li~Rlt~~~ 32 (138)
T COG3105 4 TFMTWEYALIGLVVGIIIGALIARLTNRK 32 (138)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHcchh
Confidence 45789999999998888889999987543
No 186
>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=25.63 E-value=2.6 Score=43.05 Aligned_cols=45 Identities=22% Similarity=0.513 Sum_probs=29.5
Q ss_pred CCccceeeEEEEeeecCCCccccchh----hh--hhhcccccCCCccccccc
Q psy1412 1 MYDSVHVLAAGLALLDKSSVIKTSNL----SC--DLEVPWRDGLSLYNYINT 46 (504)
Q Consensus 1 ~~d~v~~~~tg~r~~d~~~~~~~~~~----~~--~~~~~W~~g~~~~~~i~~ 46 (504)
+||||.+++.|++.+. .....+.++ .| +...+|..|..+.++|+.
T Consensus 276 ~yDaV~~~A~A~~~l~-~~~~~~~~~~~~~~C~~~~~~~W~~G~~l~~~ik~ 326 (372)
T cd06387 276 THDAILVIAEAFRYLR-RQRVDVSRRGSAGDCLANPAVPWSQGIDIERALKM 326 (372)
T ss_pred HHHHHHHHHHHHHHHH-hcCCCcccCCCCCCcCCCCCCCccchHHHHHHHHh
Confidence 5999999999998642 122222222 55 345689888888777765
No 187
>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=25.02 E-value=2e+02 Score=29.35 Aligned_cols=38 Identities=18% Similarity=0.039 Sum_probs=27.5
Q ss_pred cccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhh
Q psy1412 47 AEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINT 97 (504)
Q Consensus 47 ~~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~ 97 (504)
..++..||||.+.|+||++..+.+. -..+..+.+.|++
T Consensus 285 ~~aa~fyDaVLLYa~AL~EtL~~G~-------------~~~~~~I~~~m~N 322 (380)
T cd06369 285 DYVAAYHDGVLLFGHVLKKFLESQE-------------GVQTFSFINEFRN 322 (380)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCC-------------CCCcHHHHHHHhC
Confidence 3789999999999999998763221 0233667777776
No 188
>KOG3713|consensus
Probab=24.98 E-value=45 Score=34.73 Aligned_cols=53 Identities=15% Similarity=0.325 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHhhCCCCccCCCCCCCCCCcccCcccchhHHHHHHHHhhccCC-CCCCcccccccceehcc
Q psy1412 275 YLLVSFTLFVMARFSPYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGS-GLNPKVLQQGSSRTLDT 345 (504)
Q Consensus 275 ~~~v~~~~~~i~r~~p~~~~~~~~~~~~~~~~~~~~~l~~~~w~~~~~l~~qg~-~~~p~~~~~~s~R~v~~ 345 (504)
+++-+.+++.+||-.|.. +-.+|=-++|+++-++...|+ +..|++. .|+++++
T Consensus 356 I~iFStlvY~~Ek~~~~~---------------~FtSIPa~~WWaiVTMTTVGYGDm~P~T~---~Gklvas 409 (477)
T KOG3713|consen 356 IVIFSTLVYFAEKDEPDT---------------KFTSIPAGFWWAVVTMTTVGYGDMVPVTV---LGKLVAS 409 (477)
T ss_pred HHHHHHHHHHhhhcCCCC---------------CCccccchhheeeEEEeeecccCcccccc---chHHHHH
Confidence 334445666666644322 344677899999999999998 5799999 9999987
No 189
>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=24.01 E-value=74 Score=32.04 Aligned_cols=36 Identities=11% Similarity=0.121 Sum_probs=28.3
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhhceE
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTLDL 100 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~~~i 100 (504)
.++.+||||.+++.|+++.. ..++..+.++|.+.++
T Consensus 252 ~~a~aY~av~~~a~Ai~~AG-----------------s~d~~aV~~aL~~~~~ 287 (347)
T TIGR03863 252 LDYAAWLAVRAVGEAVTRTR-----------------SADPATLRDYLLSDEF 287 (347)
T ss_pred HHHHHHHHHHHHHHHHHHhc-----------------CCCHHHHHHHHcCCCc
Confidence 57889999999999999874 2456788888876443
No 190
>TIGR00975 3a0107s03 phosphate ABC transporter, phosphate-binding protein. This family represents one type of (periplasmic, in Gram-negative bacteria) phosphate-binding protein found in phosphate ABC (ATP-binding cassette) transporters. This protein is accompanied, generally in the same operon, by an ATP binding protein and (usually) two permease proteins.
Probab=22.89 E-value=1.6e+02 Score=29.12 Aligned_cols=48 Identities=13% Similarity=0.242 Sum_probs=35.7
Q ss_pred CCcchhhHHHHhhccccceecceeeecccc-----eeeeeccceeeccEEEEEEcc
Q psy1412 199 TKEWNGIVKELMDKKADLAVASMTINYARE-----SVIDFTKPFMNLGIGILFKVP 249 (504)
Q Consensus 199 ~g~w~gli~~l~~g~~D~av~~~tit~~R~-----~~vdFs~p~~~~g~~ilv~~~ 249 (504)
.|+=.| +.+|.+|.+|++.++..++++-. ..++ .|+...++++++..+
T Consensus 34 ~GSg~G-i~~l~~g~~dia~ssr~l~~~E~~~~~~~~~~--~pva~dai~vivn~~ 86 (314)
T TIGR00975 34 IGSGAG-IAQFAAGTVDFGASDAPLSEADLASRGSGLLQ--FPTVIGAIVVTYNLP 86 (314)
T ss_pred CCCHHH-HHHHHcCCCCEEecCCCCCHHHHHhhcCCcEE--eeEEeeeEEEEEeCC
Confidence 345455 68889999999999988885432 2333 488999999999864
No 191
>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=22.80 E-value=50 Score=28.03 Aligned_cols=23 Identities=13% Similarity=0.348 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCC
Q psy1412 268 WLYVLAAYLLVSFTLFVMARFSP 290 (504)
Q Consensus 268 Wl~i~~~~~~v~~~~~~i~r~~p 290 (504)
|++++++++++.++++++.+++.
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~r 24 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNR 24 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHH
Confidence 78888888888788888777754
No 192
>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=22.32 E-value=1.1e+02 Score=26.50 Aligned_cols=69 Identities=13% Similarity=0.095 Sum_probs=44.7
Q ss_pred ehhHHHHHHHHHHc-CceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccceeeeeccceeeccEE
Q psy1412 165 GFCIDLLKSIAAQV-GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIG 243 (504)
Q Consensus 165 G~~idll~~la~~l-~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~~~vdFs~p~~~~g~~ 243 (504)
.+-.+++..+.+.. +.++++. .+..+.++.+|.+|++|+++...... ....+. +.+..+..++
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~i~-------------~~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~~-~~~l~~~~~~ 76 (195)
T cd08431 13 QPLYPLIAEFYQLNKATRIRLS-------------EEVLGGTWDALASGRADLVIGATGEL--PPGGVK-TRPLGEVEFV 76 (195)
T ss_pred HHHHHHHHHHHHHCCCCceEEE-------------EeccchHHHHHhCCCCCEEEEecCCC--CCCceE-EEecccceEE
Confidence 45568888888876 4667775 33456789999999999998532111 112233 3566667777
Q ss_pred EEEEcc
Q psy1412 244 ILFKVP 249 (504)
Q Consensus 244 ilv~~~ 249 (504)
++++..
T Consensus 77 ~v~~~~ 82 (195)
T cd08431 77 FAVAPN 82 (195)
T ss_pred EEEcCC
Confidence 776643
No 193
>PHA02650 hypothetical protein; Provisional
Probab=21.98 E-value=2.1e+02 Score=21.94 Aligned_cols=28 Identities=7% Similarity=0.237 Sum_probs=15.9
Q ss_pred ccCchhHHHHHHHHHHHHHHHHHHHHhh
Q psy1412 261 NPLAVEIWLYVLAAYLLVSFTLFVMARF 288 (504)
Q Consensus 261 ~Pf~~~vWl~i~~~~~~v~~~~~~i~r~ 288 (504)
.++.+..|+.++++.+++.++.++.-+.
T Consensus 45 ~~~~~~~~ii~i~~v~i~~l~~flYLK~ 72 (81)
T PHA02650 45 SWFNGQNFIFLIFSLIIVALFSFFVFKG 72 (81)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666666655555555555554444
No 194
>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=21.83 E-value=1.8e+02 Score=24.80 Aligned_cols=50 Identities=16% Similarity=0.288 Sum_probs=33.4
Q ss_pred HHHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhcccccee
Q psy1412 168 IDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAV 218 (504)
Q Consensus 168 idll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av 218 (504)
.+.+++.++..|+++.-++..++.=|.... -..+..|+..+..|++|..+
T Consensus 24 ~~~l~~~a~~~g~~i~~~~~D~~~SG~~~~-Rp~l~~ll~~~~~g~vd~vv 73 (140)
T cd03770 24 KAILEEYAKENGLENIRHYIDDGFSGTTFD-RPGFNRMIEDIEAGKIDIVI 73 (140)
T ss_pred HHHHHHHHHHCCCEEEEEEEcCCCcCCcCC-CHHHHHHHHHHHcCCCCEEE
Confidence 456777888889986444443332333211 34689999999999999765
No 195
>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=21.55 E-value=92 Score=30.56 Aligned_cols=34 Identities=18% Similarity=0.244 Sum_probs=27.1
Q ss_pred ccchhhhHHHHHHHHHHHhhhcCCcccccCCCCCCCcccCchhHHHHhhhc
Q psy1412 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTL 98 (504)
Q Consensus 48 ~~~~~yDav~~~a~a~~~~~~~~~~~~~~~~c~~~~~~~~G~~l~~~l~~~ 98 (504)
.+..+||+++++++|+++.. +.++..+.+.|++.
T Consensus 274 ~~~~~yda~~~~~~al~~~~-----------------~~~~~~v~~~l~~~ 307 (334)
T cd06342 274 YAPYAYDAANVLAEAIKKAG-----------------STDPAKVADALRKV 307 (334)
T ss_pred hHHHHHHHHHHHHHHHHHhC-----------------CCCHHHHHHHHHhC
Confidence 67899999999999998752 24567888888753
No 196
>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=21.49 E-value=4.3 Score=41.88 Aligned_cols=46 Identities=28% Similarity=0.460 Sum_probs=30.0
Q ss_pred CCccceeeEEEEeeec-CCCccccchhhhhh--hcccccCCCccccccc
Q psy1412 1 MYDSVHVLAAGLALLD-KSSVIKTSNLSCDL--EVPWRDGLSLYNYINT 46 (504)
Q Consensus 1 ~~d~v~~~~tg~r~~d-~~~~~~~~~~~~~~--~~~W~~g~~~~~~i~~ 46 (504)
+||||.+++.|++.+. .........+.|.. ...|..|..++++|+.
T Consensus 300 ayDaV~~~A~A~~~l~~~~~~~~~~~~~c~~~~~~~w~~G~~ll~~i~~ 348 (400)
T cd06391 300 IYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKK 348 (400)
T ss_pred HHHHHHHHHHHHHHHHhhccccCCCCcccccCCCCCCCChHHHHHHHHh
Confidence 5999999999988642 22223334446654 4588888777666654
No 197
>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=21.21 E-value=1.9e+02 Score=26.19 Aligned_cols=66 Identities=15% Similarity=0.192 Sum_probs=41.5
Q ss_pred HHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeee-cccceee---eeccceeeccEEEEEEcc
Q psy1412 174 IAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTIN-YARESVI---DFTKPFMNLGIGILFKVP 249 (504)
Q Consensus 174 la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit-~~R~~~v---dFs~p~~~~g~~ilv~~~ 249 (504)
+-++-|.+++++... .....+..|..|++|++++..... ..|.+-. -+-..+......++++..
T Consensus 15 ~f~~~gl~ve~~~~~------------~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~ 82 (216)
T PF09084_consen 15 YFKEEGLDVEIVFFG------------GGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPNALVVRKD 82 (216)
T ss_dssp HHHHTTEEEEEEEES------------SHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCEEEEEETT
T ss_pred CCccCeEEEEEEEec------------ChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCceEEEEecc
Confidence 345567788888653 466799999999999998876532 2333322 222334445567777755
Q ss_pred CC
Q psy1412 250 TS 251 (504)
Q Consensus 250 ~~ 251 (504)
+.
T Consensus 83 s~ 84 (216)
T PF09084_consen 83 SG 84 (216)
T ss_dssp TS
T ss_pred CC
Confidence 43
No 198
>PF12849 PBP_like_2: 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.; PDB: 1QUL_A 1OIB_A 1A54_A 1IXH_A 1A40_A 1QUJ_A 1A55_A 1IXI_A 2ABH_A 1QUK_A ....
Probab=20.83 E-value=1e+02 Score=29.67 Aligned_cols=76 Identities=16% Similarity=0.170 Sum_probs=49.2
Q ss_pred ceehhHHHHHHHHHH-cCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeeecccc---e--------e
Q psy1412 163 FEGFCIDLLKSIAAQ-VGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARE---S--------V 230 (504)
Q Consensus 163 ~~G~~idll~~la~~-l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit~~R~---~--------~ 230 (504)
+..+.-++.+...+. -+.++.+.. .|+ ..-+.+|.+|++|+++.+-.++++-. . .
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~v~v~~------------~gS-~~g~~~l~~g~~di~~~sr~l~~~e~~~~~~~~~~~~~~ 86 (281)
T PF12849_consen 20 VAPIMEALAEAFERQYPGVKVTVES------------SGS-GAGIQALINGKVDIAISSRPLTAAEIASEGYNAKGQKWG 86 (281)
T ss_dssp THHHHHHHHHHHHHHSTTBEEEEEE------------E-H-HHHHHHHHTTSSSEEEESSHHHHHHHHHHTCCCCCHHHH
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEe------------CCC-HHHHHHHHhCCCEEEEeCCCCcHHHHhHhhhhhcccccc
Confidence 334444555555555 467777653 223 56788999999999998877764411 0 0
Q ss_pred ee-eccceeeccEEEEEEccCC
Q psy1412 231 ID-FTKPFMNLGIGILFKVPTS 251 (504)
Q Consensus 231 vd-Fs~p~~~~g~~ilv~~~~~ 251 (504)
.+ -..|+...++++++.++.+
T Consensus 87 ~~~~~~~va~d~i~iv~n~~np 108 (281)
T PF12849_consen 87 GGLVQIPVARDAIVIVVNKDNP 108 (281)
T ss_dssp CTEEEEEEEEEEEEEEEETTTT
T ss_pred cccEEEEEEEeeEEEEEcCCCc
Confidence 11 1379999999999997643
No 199
>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=20.75 E-value=1.9e+02 Score=27.56 Aligned_cols=49 Identities=12% Similarity=0.192 Sum_probs=37.4
Q ss_pred HHHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceeee
Q psy1412 169 DLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTIN 224 (504)
Q Consensus 169 dll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~tit 224 (504)
.+.+++.++-+=.+++...+.+..| ....++..+.+|.+|++.......
T Consensus 17 ~f~~~v~e~t~G~v~v~~~~~g~Lg-------~~~e~~~~v~~G~~d~~~~~~~~~ 65 (257)
T TIGR00787 17 KFAKLVNEKTNGEIKISVFPSSQLG-------SDRAMLEALQGGALDMTAPSSSKF 65 (257)
T ss_pred HHHHHHHHHcCCeEEEEEcCCCCCC-------ChHHHHHHHhCCCccEEecccccc
Confidence 5778888888888888877765433 456799999999999987655433
No 200
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=20.74 E-value=1.4e+02 Score=28.37 Aligned_cols=69 Identities=17% Similarity=0.213 Sum_probs=40.0
Q ss_pred HHHHHHHHcCceEEEEEcCCCCCccccCCCCcchhhHHHHhhccccceecceee-ec-ccceeeeeccceeeccEEEEEE
Q psy1412 170 LLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTI-NY-ARESVIDFTKPFMNLGIGILFK 247 (504)
Q Consensus 170 ll~~la~~l~f~~~~~~~~~~~~G~~~~~~g~w~gli~~l~~g~~D~av~~~ti-t~-~R~~~vdFs~p~~~~g~~ilv~ 247 (504)
.+....+..+.+..++.++ +....+.+|..|++|+++++-.+ .. ......-...++.....+++++
T Consensus 162 ~l~~~~~~~~~~~~~~~~~------------~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~ 229 (259)
T PRK11917 162 AIGEAAKKIGIDVKFSEFP------------DYPSIKAALDAKRVDAFSVDKSILLGYVDDKSEILPDSFEPQSYGIVTK 229 (259)
T ss_pred HHHHhhHhcCCceeEEecC------------CHHHHHHHHHcCCCcEEEecHHHHHHhhhcCCeecCCcCCCCceEEEEe
Confidence 3444444455555554433 35678899999999998877543 11 1111122234566666778877
Q ss_pred ccC
Q psy1412 248 VPT 250 (504)
Q Consensus 248 ~~~ 250 (504)
+.+
T Consensus 230 k~~ 232 (259)
T PRK11917 230 KDD 232 (259)
T ss_pred CCC
Confidence 654
No 201
>PRK11677 hypothetical protein; Provisional
Probab=20.63 E-value=1.2e+02 Score=26.07 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCC
Q psy1412 267 IWLYVLAAYLLVSFTLFVMARFSP 290 (504)
Q Consensus 267 vWl~i~~~~~~v~~~~~~i~r~~p 290 (504)
.|++.++++++..++=|++.|+.+
T Consensus 2 ~W~~a~i~livG~iiG~~~~R~~~ 25 (134)
T PRK11677 2 TWEYALIGLVVGIIIGAVAMRFGN 25 (134)
T ss_pred cHHHHHHHHHHHHHHHHHHHhhcc
Confidence 399999888888888888888754
No 202
>PRK13712 conjugal transfer protein TrbA; Provisional
Probab=20.15 E-value=87 Score=24.59 Aligned_cols=18 Identities=33% Similarity=0.979 Sum_probs=15.7
Q ss_pred chhHHHHHHHHhhccCCC
Q psy1412 312 VSNSFWFITGTFLRQGSG 329 (504)
Q Consensus 312 l~~~~w~~~~~l~~qg~~ 329 (504)
+-.++||..|++|.||..
T Consensus 52 l~~sl~flcgaimnq~aa 69 (115)
T PRK13712 52 LTASLWFLCGAIMNQGAA 69 (115)
T ss_pred ecHHHHHHHHHHHcCCce
Confidence 567899999999999874
Done!