Query 037841
Match_columns 561
No_of_seqs 283 out of 2389
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 04:53:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037841.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037841hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1052 Glutamate-gated kainat 100.0 4.4E-59 9.5E-64 523.6 39.0 426 1-452 183-624 (656)
2 KOG1054 Glutamate-gated AMPA-t 100.0 4.1E-54 8.8E-59 437.2 20.5 426 1-453 387-846 (897)
3 KOG1053 Glutamate-gated NMDA-t 100.0 4.1E-47 8.9E-52 400.7 25.6 410 25-451 391-855 (1258)
4 KOG4440 NMDA selective glutama 100.0 3.1E-48 6.7E-53 395.9 15.8 417 26-456 383-861 (993)
5 PRK09495 glnH glutamine ABC tr 99.9 3E-22 6.5E-27 198.3 22.1 221 48-402 24-245 (247)
6 PRK10797 glutamate and asparta 99.9 5.4E-22 1.2E-26 202.2 22.8 225 47-402 38-273 (302)
7 PRK11260 cystine transporter s 99.9 1.1E-21 2.4E-26 196.5 22.2 225 46-402 38-263 (266)
8 PF00497 SBP_bac_3: Bacterial 99.9 5.2E-22 1.1E-26 192.0 16.8 223 51-401 1-225 (225)
9 PRK15007 putative ABC transpor 99.9 1.1E-20 2.4E-25 186.4 21.5 217 48-400 20-242 (243)
10 PRK11917 bifunctional adhesin/ 99.9 2.2E-20 4.8E-25 186.3 22.2 219 46-399 35-258 (259)
11 PRK15010 ABC transporter lysin 99.9 2.3E-20 5E-25 186.4 21.8 222 47-400 24-254 (260)
12 TIGR01096 3A0103s03R lysine-ar 99.9 4.9E-20 1.1E-24 182.4 22.2 218 49-399 24-250 (250)
13 TIGR02995 ectoine_ehuB ectoine 99.9 3.4E-20 7.3E-25 186.8 19.9 227 43-399 27-260 (275)
14 PRK15437 histidine ABC transpo 99.8 1.8E-19 3.8E-24 179.9 21.3 222 48-401 25-255 (259)
15 PRK09959 hybrid sensory histid 99.8 6.8E-19 1.5E-23 211.6 26.1 218 47-400 300-520 (1197)
16 PRK10859 membrane-bound lytic 99.8 9.9E-19 2.2E-23 189.3 19.6 226 43-402 37-268 (482)
17 TIGR03870 ABC_MoxJ methanol ox 99.8 1.1E-17 2.3E-22 165.7 16.9 208 50-398 1-241 (246)
18 COG0834 HisJ ABC-type amino ac 99.7 1.1E-16 2.3E-21 160.5 20.5 227 47-401 32-265 (275)
19 PRK09959 hybrid sensory histid 99.7 3.7E-17 7.9E-22 196.6 18.8 223 46-401 53-278 (1197)
20 PF00060 Lig_chan: Ligand-gate 99.7 3.3E-19 7.1E-24 162.2 0.6 107 178-284 1-115 (148)
21 TIGR02285 conserved hypothetic 99.7 5.6E-17 1.2E-21 162.6 16.5 231 48-402 17-263 (268)
22 TIGR03871 ABC_peri_MoxJ_2 quin 99.7 2.3E-16 5E-21 154.4 18.5 212 50-399 1-228 (232)
23 cd00134 PBPb Bacterial peripla 99.7 7E-16 1.5E-20 146.9 20.9 215 51-399 1-218 (218)
24 smart00062 PBPb Bacterial peri 99.7 1.4E-15 3.1E-20 144.5 20.7 216 50-399 1-219 (219)
25 COG4623 Predicted soluble lyti 99.4 1.2E-11 2.7E-16 122.8 14.4 222 48-403 22-250 (473)
26 smart00079 PBPe Eukaryotic hom 99.4 5.6E-12 1.2E-16 112.4 11.1 122 273-400 1-133 (134)
27 TIGR01098 3A0109s03R phosphate 99.1 2.8E-09 6.1E-14 105.8 14.7 199 48-385 31-254 (254)
28 PRK00489 hisG ATP phosphoribos 98.9 5.5E-09 1.2E-13 105.7 11.4 165 114-401 51-220 (287)
29 PF10613 Lig_chan-Glu_bd: Liga 98.6 1.9E-08 4.1E-13 76.7 1.2 61 63-125 1-65 (65)
30 TIGR03431 PhnD phosphonate ABC 98.3 1.2E-05 2.7E-10 81.3 15.1 115 274-394 127-258 (288)
31 PRK11553 alkanesulfonate trans 97.8 0.00029 6.3E-09 72.2 13.5 109 274-388 121-236 (314)
32 PF12974 Phosphonate-bd: ABC t 97.7 0.00041 8.8E-09 68.4 11.7 120 273-398 96-230 (243)
33 TIGR01729 taurine_ABC_bnd taur 97.2 0.001 2.2E-08 67.7 8.3 68 274-347 92-164 (300)
34 TIGR03427 ABC_peri_uca ABC tra 96.9 0.011 2.4E-07 60.9 12.5 67 274-347 98-170 (328)
35 PF13379 NMT1_2: NMT1-like fam 96.7 0.0066 1.4E-07 60.1 9.0 71 274-349 106-189 (252)
36 TIGR01728 SsuA_fam ABC transpo 96.5 0.034 7.4E-07 55.6 12.2 69 274-348 93-166 (288)
37 PF03466 LysR_substrate: LysR 96.3 0.14 3.1E-06 47.7 14.6 180 82-386 20-205 (209)
38 PF09084 NMT1: NMT1/THI5 like; 96.1 0.057 1.2E-06 51.8 11.3 58 274-337 85-147 (216)
39 COG3221 PhnD ABC-type phosphat 96.1 0.12 2.6E-06 52.4 13.8 109 273-387 135-260 (299)
40 cd08442 PBP2_YofA_SoxR_like Th 96.1 0.68 1.5E-05 42.2 18.0 70 81-164 13-82 (193)
41 cd05466 PBP2_LTTR_substrate Th 96.1 0.54 1.2E-05 42.4 17.2 69 82-164 14-82 (197)
42 TIGR02122 TRAP_TAXI TRAP trans 95.9 0.051 1.1E-06 55.5 10.4 58 274-337 133-197 (320)
43 cd08412 PBP2_PAO1_like The C-t 95.9 1 2.2E-05 41.3 18.1 71 80-164 12-82 (198)
44 cd08438 PBP2_CidR The C-termin 95.8 1.2 2.6E-05 40.6 18.2 70 81-164 13-82 (197)
45 PRK11233 nitrogen assimilation 95.7 0.48 1E-05 48.1 16.7 69 81-163 105-173 (305)
46 cd08418 PBP2_TdcA The C-termin 95.7 0.92 2E-05 41.6 17.4 72 81-164 13-84 (201)
47 cd08468 PBP2_Pa0477 The C-term 95.7 1.1 2.4E-05 41.5 18.0 74 81-165 13-86 (202)
48 cd08440 PBP2_LTTR_like_4 TThe 95.5 1.8 4E-05 39.2 18.6 70 81-164 13-82 (197)
49 PRK11151 DNA-binding transcrip 95.5 0.97 2.1E-05 45.8 17.7 71 81-165 104-174 (305)
50 TIGR00363 lipoprotein, YaeC fa 95.3 1 2.2E-05 44.7 16.8 119 272-397 106-249 (258)
51 cd08421 PBP2_LTTR_like_1 The C 95.3 1.8 4E-05 39.5 17.8 70 81-164 13-82 (198)
52 cd08459 PBP2_DntR_NahR_LinR_li 95.3 0.74 1.6E-05 42.5 15.2 70 81-164 13-82 (201)
53 cd08415 PBP2_LysR_opines_like 95.3 1.7 3.7E-05 39.6 17.5 70 81-164 13-82 (196)
54 CHL00180 rbcR LysR transcripti 95.3 1.6 3.4E-05 44.3 18.6 74 81-165 108-181 (305)
55 cd08426 PBP2_LTTR_like_5 The C 95.2 1.7 3.7E-05 39.8 17.2 70 81-164 13-82 (199)
56 PRK12679 cbl transcriptional r 95.2 2.4 5.1E-05 43.3 19.7 207 48-399 92-305 (316)
57 PRK12684 transcriptional regul 95.1 1.3 2.7E-05 45.3 17.4 206 48-399 92-304 (313)
58 cd08417 PBP2_Nitroaromatics_li 95.1 1.6 3.4E-05 40.1 16.6 70 81-164 13-82 (200)
59 cd08463 PBP2_DntR_like_4 The C 95.0 2.2 4.7E-05 39.8 17.5 72 81-165 13-84 (203)
60 TIGR00787 dctP tripartite ATP- 95.0 0.55 1.2E-05 46.6 13.8 104 272-387 126-232 (257)
61 PRK09791 putative DNA-binding 94.8 1.3 2.8E-05 44.8 16.4 87 48-165 94-180 (302)
62 PRK11480 tauA taurine transpor 94.8 0.25 5.5E-06 50.8 11.2 67 273-345 113-184 (320)
63 cd08451 PBP2_BudR The C-termin 94.7 3.2 7E-05 37.8 18.7 70 82-164 15-84 (199)
64 cd08419 PBP2_CbbR_RubisCO_like 94.7 3.2 7E-05 37.7 17.7 69 82-164 13-81 (197)
65 cd08433 PBP2_Nac The C-teminal 94.6 3.2 7E-05 37.9 17.5 70 81-164 13-82 (198)
66 cd08462 PBP2_NodD The C-termin 94.6 1.6 3.5E-05 40.3 15.3 69 82-165 14-82 (200)
67 cd08466 PBP2_LeuO The C-termin 94.5 2.4 5.1E-05 38.9 16.3 70 81-164 13-82 (200)
68 cd08411 PBP2_OxyR The C-termin 94.5 2.9 6.3E-05 38.3 17.0 69 82-164 15-83 (200)
69 PRK11242 DNA-binding transcrip 94.5 2.7 5.9E-05 42.1 17.7 70 81-164 104-173 (296)
70 cd08441 PBP2_MetR The C-termin 94.4 3.3 7.2E-05 37.9 17.1 69 82-164 14-82 (198)
71 cd08461 PBP2_DntR_like_3 The C 94.3 2.2 4.8E-05 39.0 15.6 70 81-164 13-82 (198)
72 PRK12680 transcriptional regul 94.3 2.8 6.1E-05 43.1 17.5 85 48-164 92-176 (327)
73 cd08429 PBP2_NhaR The C-termin 94.2 3.9 8.4E-05 38.3 17.1 71 81-162 13-83 (204)
74 cd08420 PBP2_CysL_like C-termi 94.2 4.3 9.3E-05 36.8 18.3 70 81-164 13-82 (201)
75 TIGR02424 TF_pcaQ pca operon t 94.0 2.8 6.1E-05 42.2 16.7 86 48-164 92-177 (300)
76 PRK12681 cysB transcriptional 93.9 2.4 5.1E-05 43.6 16.2 85 48-164 92-176 (324)
77 cd08425 PBP2_CynR The C-termin 93.9 3.9 8.5E-05 37.3 16.4 69 82-164 15-83 (197)
78 PRK12683 transcriptional regul 93.9 4.4 9.6E-05 41.2 18.0 71 82-165 107-177 (309)
79 PRK10837 putative DNA-binding 93.9 5.4 0.00012 39.8 18.5 69 82-164 103-171 (290)
80 cd08435 PBP2_GbpR The C-termin 93.9 5 0.00011 36.5 18.8 72 81-164 13-84 (201)
81 cd08427 PBP2_LTTR_like_2 The C 93.7 4.7 0.0001 36.5 16.5 72 81-164 13-84 (195)
82 cd08460 PBP2_DntR_like_1 The C 93.7 1.8 3.8E-05 40.0 13.6 71 80-165 12-82 (200)
83 cd08413 PBP2_CysB_like The C-t 93.7 4.2 9.2E-05 37.4 16.2 71 81-164 13-83 (198)
84 cd08449 PBP2_XapR The C-termin 93.6 5.5 0.00012 36.2 17.3 72 81-164 13-84 (197)
85 cd08445 PBP2_BenM_CatM_CatR Th 93.5 4.5 9.9E-05 37.3 16.2 70 81-164 14-83 (203)
86 cd08430 PBP2_IlvY The C-termin 93.5 5.8 0.00013 36.1 18.1 71 81-164 13-83 (199)
87 PRK11063 metQ DL-methionine tr 93.4 2.2 4.8E-05 42.8 14.4 118 273-397 120-262 (271)
88 cd08434 PBP2_GltC_like The sub 93.3 6 0.00013 35.7 17.5 70 81-164 13-82 (195)
89 PF07885 Ion_trans_2: Ion chan 93.2 0.35 7.6E-06 38.5 6.7 56 211-266 21-78 (79)
90 cd08469 PBP2_PnbR The C-termin 93.2 4.9 0.00011 37.7 16.0 70 81-164 13-82 (221)
91 cd08464 PBP2_DntR_like_2 The C 93.0 6.4 0.00014 35.9 16.1 70 81-164 13-82 (200)
92 cd08437 PBP2_MleR The substrat 93.0 7.1 0.00015 35.6 17.3 72 81-164 13-84 (198)
93 cd08465 PBP2_ToxR The C-termin 93.0 3.4 7.4E-05 38.2 14.4 70 81-164 13-82 (200)
94 PF03480 SBP_bac_7: Bacterial 92.9 1.6 3.4E-05 44.0 12.7 105 271-387 125-232 (286)
95 cd08467 PBP2_SyrM The C-termin 92.9 6.5 0.00014 36.2 16.2 70 81-164 13-82 (200)
96 cd08443 PBP2_CysB The C-termin 92.9 7.5 0.00016 35.8 18.4 72 80-164 12-83 (198)
97 PRK10341 DNA-binding transcrip 92.9 4 8.7E-05 41.5 15.8 71 82-164 111-181 (312)
98 cd08448 PBP2_LTTR_aromatics_li 92.8 7.2 0.00016 35.3 17.1 70 81-164 13-82 (197)
99 cd08414 PBP2_LTTR_aromatics_li 92.8 7.3 0.00016 35.3 16.9 70 81-164 13-82 (197)
100 PRK11062 nhaR transcriptional 92.8 5.6 0.00012 40.1 16.6 73 80-163 105-177 (296)
101 cd08423 PBP2_LTTR_like_6 The C 92.8 7.1 0.00015 35.4 16.1 72 82-164 14-87 (200)
102 PRK09508 leuO leucine transcri 92.8 2.4 5.1E-05 43.2 13.9 70 81-164 125-194 (314)
103 cd08456 PBP2_LysR The C-termin 92.5 8 0.00017 35.1 16.9 70 81-164 13-82 (196)
104 cd08458 PBP2_NocR The C-termin 92.5 8.4 0.00018 35.2 16.6 70 81-164 13-82 (196)
105 PRK12682 transcriptional regul 92.5 11 0.00024 38.2 18.3 71 81-164 106-176 (309)
106 cd08444 PBP2_Cbl The C-termina 92.1 9.5 0.00021 35.0 17.1 73 80-165 12-84 (198)
107 cd08416 PBP2_MdcR The C-termin 91.6 10 0.00023 34.4 17.1 72 81-164 13-84 (199)
108 cd08457 PBP2_OccR The C-termin 91.5 11 0.00023 34.4 17.2 69 81-163 13-81 (196)
109 TIGR01256 modA molybdenum ABC 91.3 6.1 0.00013 37.7 14.1 72 309-386 132-204 (216)
110 cd08486 PBP2_CbnR The C-termin 91.2 6.8 0.00015 36.1 14.1 70 81-164 14-83 (198)
111 cd08453 PBP2_IlvR The C-termin 91.0 12 0.00026 34.1 16.9 73 81-164 13-85 (200)
112 cd08436 PBP2_LTTR_like_3 The C 90.9 12 0.00025 33.7 18.0 71 81-164 13-83 (194)
113 PF13531 SBP_bac_11: Bacterial 90.6 3.2 6.9E-05 40.0 11.5 194 80-397 10-226 (230)
114 COG1638 DctP TRAP-type C4-dica 89.9 0.52 1.1E-05 48.6 5.5 212 84-389 47-265 (332)
115 PRK11013 DNA-binding transcrip 89.8 18 0.00038 36.7 16.7 70 81-164 107-176 (309)
116 COG0725 ModA ABC-type molybdat 89.7 12 0.00025 37.3 14.6 115 274-398 124-252 (258)
117 PRK09906 DNA-binding transcrip 89.5 14 0.0003 37.0 15.6 70 82-165 104-173 (296)
118 TIGR03339 phn_lysR aminoethylp 89.2 24 0.00052 34.7 18.2 68 83-164 99-166 (279)
119 PF12727 PBP_like: PBP superfa 89.2 7.9 0.00017 36.6 12.6 100 273-383 82-190 (193)
120 PRK15421 DNA-binding transcrip 89.0 20 0.00043 36.6 16.5 69 82-164 103-171 (317)
121 cd08446 PBP2_Chlorocatechol Th 88.8 18 0.00039 32.8 17.2 70 81-164 14-83 (198)
122 PRK11482 putative DNA-binding 88.7 17 0.00037 37.0 15.7 83 48-165 116-198 (317)
123 COG0715 TauA ABC-type nitrate/ 88.6 2.4 5.1E-05 43.6 9.4 70 274-349 128-203 (335)
124 COG1910 Periplasmic molybdate- 88.0 13 0.00029 35.4 12.8 104 274-389 89-201 (223)
125 PRK09986 DNA-binding transcrip 87.8 31 0.00067 34.3 18.3 73 81-165 110-182 (294)
126 PRK11074 putative DNA-binding 87.5 34 0.00073 34.4 16.9 87 48-165 91-177 (300)
127 cd08485 PBP2_ClcR The C-termin 87.2 23 0.00051 32.4 17.1 69 81-163 14-82 (198)
128 PRK11716 DNA-binding transcrip 86.9 32 0.00069 33.5 16.2 69 82-163 81-149 (269)
129 cd08450 PBP2_HcaR The C-termin 86.8 23 0.00051 31.9 16.8 70 81-164 13-82 (196)
130 PRK10094 DNA-binding transcrip 86.3 40 0.00087 34.1 16.9 71 82-164 107-177 (308)
131 PRK09861 cytoplasmic membrane 85.1 25 0.00053 35.3 14.0 122 271-398 119-264 (272)
132 PRK10677 modA molybdate transp 82.8 22 0.00048 35.2 12.6 72 82-164 40-117 (257)
133 PF03401 TctC: Tripartite tric 82.7 31 0.00067 34.5 13.7 120 273-397 89-241 (274)
134 cd08452 PBP2_AlsR The C-termin 82.4 39 0.00084 30.7 17.4 70 81-164 13-82 (197)
135 PF14503 YhfZ_C: YhfZ C-termin 81.8 5.3 0.00011 38.8 7.3 104 283-399 113-224 (232)
136 COG2358 Imp TRAP-type uncharac 81.3 6.2 0.00013 40.3 8.0 59 274-338 129-194 (321)
137 PLN02245 ATP phosphoribosyl tr 80.8 14 0.0003 38.9 10.5 89 274-373 179-277 (403)
138 PRK03635 chromosome replicatio 79.2 56 0.0012 32.6 14.4 66 83-163 105-170 (294)
139 PRK14498 putative molybdopteri 78.4 21 0.00045 40.5 12.0 102 275-388 514-624 (633)
140 PRK11119 proX glycine betaine 78.4 12 0.00025 38.8 9.1 62 45-136 25-87 (331)
141 PRK13348 chromosome replicatio 77.6 79 0.0017 31.4 15.7 64 85-163 107-170 (294)
142 cd08431 PBP2_HupR The C-termin 74.9 63 0.0014 29.0 15.1 71 81-164 13-83 (195)
143 PLN03192 Voltage-dependent pot 72.7 6.6 0.00014 46.0 6.2 55 213-267 249-305 (823)
144 TIGR03414 ABC_choline_bnd chol 71.5 1.2E+02 0.0025 30.7 14.2 42 82-134 22-63 (290)
145 cd08481 PBP2_GcdR_like The C-t 70.8 77 0.0017 28.2 12.6 98 275-381 86-190 (194)
146 cd08447 PBP2_LTTR_aromatics_li 69.5 84 0.0018 28.1 17.4 70 81-164 13-82 (198)
147 cd08432 PBP2_GcdR_TrpI_HvrB_Am 69.4 83 0.0018 28.0 11.9 65 82-163 14-78 (194)
148 PRK13583 hisG ATP phosphoribos 65.4 71 0.0015 31.0 10.5 92 274-374 111-213 (228)
149 PF01634 HisG: ATP phosphoribo 65.3 8.5 0.00018 35.4 4.0 100 274-385 58-159 (163)
150 cd08422 PBP2_CrgA_like The C-t 65.0 50 0.0011 29.5 9.4 66 81-163 14-79 (197)
151 PRK01686 hisG ATP phosphoribos 64.8 82 0.0018 30.3 10.8 92 283-385 114-207 (215)
152 PF14981 FAM165: FAM165 family 64.0 14 0.0003 25.8 3.8 33 419-451 3-35 (51)
153 PRK11139 DNA-binding transcrip 63.0 1.7E+02 0.0036 29.2 14.2 101 275-383 181-286 (297)
154 PRK07377 hypothetical protein; 62.3 22 0.00047 33.0 6.0 62 48-133 74-135 (184)
155 cd01324 cbb3_Oxidase_CcoQ Cyto 60.1 10 0.00022 27.1 2.8 28 179-206 11-38 (48)
156 PRK10537 voltage-gated potassi 59.7 19 0.00042 38.1 6.0 54 210-263 164-219 (393)
157 PF12273 RCR: Chitin synthesis 58.9 7.4 0.00016 34.2 2.4 10 541-550 97-106 (130)
158 TIGR00070 hisG ATP phosphoribo 57.2 74 0.0016 29.8 8.8 67 274-349 101-167 (182)
159 KOG1419 Voltage-gated K+ chann 56.2 23 0.00049 38.5 5.7 88 180-267 235-324 (654)
160 cd08487 PBP2_BlaA The C-termin 55.0 1.5E+02 0.0033 26.2 12.2 64 82-162 14-77 (189)
161 cd08475 PBP2_CrgA_like_6 The C 53.7 1.6E+02 0.0035 26.1 10.9 66 81-162 14-79 (199)
162 PRK03601 transcriptional regul 51.6 42 0.0009 33.3 6.8 70 81-164 102-171 (275)
163 PF01102 Glycophorin_A: Glycop 49.7 25 0.00054 30.6 4.0 28 424-451 66-93 (122)
164 cd08439 PBP2_LrhA_like The C-t 49.3 55 0.0012 29.3 6.8 67 82-164 14-80 (185)
165 COG4521 TauA ABC-type taurine 47.5 88 0.0019 30.6 7.6 104 274-384 122-238 (334)
166 TIGR03298 argP transcriptional 47.4 2.9E+02 0.0063 27.2 15.9 64 85-163 107-170 (292)
167 PF05545 FixQ: Cbb3-type cytoc 47.4 21 0.00045 25.5 2.7 24 180-203 11-34 (49)
168 PF06305 DUF1049: Protein of u 47.1 65 0.0014 24.4 5.7 22 426-447 25-46 (68)
169 COG3181 Uncharacterized protei 45.5 1.4E+02 0.0031 30.5 9.4 123 270-397 130-284 (319)
170 PRK10216 DNA-binding transcrip 45.4 3.3E+02 0.0072 27.4 17.5 72 81-164 110-188 (319)
171 PRK07377 hypothetical protein; 44.5 2.7E+02 0.0058 26.0 11.9 39 295-338 99-137 (184)
172 cd08484 PBP2_LTTR_beta_lactama 43.6 2.3E+02 0.0051 25.0 11.1 99 275-381 84-185 (189)
173 TIGR02136 ptsS_2 phosphate bin 43.3 29 0.00062 34.9 4.1 73 82-164 49-127 (287)
174 cd08428 PBP2_IciA_ArgP The C-t 43.0 2.4E+02 0.0053 25.1 16.4 65 83-162 15-79 (195)
175 cd08479 PBP2_CrgA_like_9 The C 42.5 2.5E+02 0.0053 25.0 10.5 64 81-161 14-77 (198)
176 KOG0498 K+-channel ERG and rel 41.9 29 0.00062 39.6 4.1 71 214-284 294-371 (727)
177 PLN02317 arogenate dehydratase 41.8 86 0.0019 33.0 7.3 83 284-373 94-186 (382)
178 COG3114 CcmD Heme exporter pro 40.3 54 0.0012 24.8 3.9 23 431-453 24-46 (67)
179 KOG1420 Ca2+-activated K+ chan 39.9 17 0.00037 39.4 1.8 59 207-265 281-341 (1103)
180 PRK00072 hemC porphobilinogen 39.4 4.3E+02 0.0092 26.8 12.1 61 275-342 113-174 (295)
181 PF15050 SCIMP: SCIMP protein 38.8 80 0.0017 27.1 5.2 12 431-442 19-30 (133)
182 PRK10086 DNA-binding transcrip 38.6 3.7E+02 0.008 26.9 11.5 65 81-162 115-179 (311)
183 cd08478 PBP2_CrgA The C-termin 38.3 1.9E+02 0.0042 25.8 8.7 66 81-163 16-81 (199)
184 PRK11899 prephenate dehydratas 37.8 1.3E+02 0.0027 30.4 7.6 83 284-373 4-96 (279)
185 cd00494 HMBS Hydroxymethylbila 37.0 4.6E+02 0.01 26.5 11.7 60 275-342 109-170 (292)
186 cd08470 PBP2_CrgA_like_1 The C 35.3 2.5E+02 0.0053 25.0 8.9 65 81-162 14-78 (197)
187 cd08474 PBP2_CrgA_like_5 The C 35.3 3.2E+02 0.007 24.3 10.3 64 82-162 17-81 (202)
188 PF07204 Orthoreo_P10: Orthore 35.2 51 0.0011 27.0 3.4 23 425-447 43-65 (98)
189 PF12727 PBP_like: PBP superfa 34.0 49 0.0011 31.2 3.8 92 62-168 92-183 (193)
190 PF14979 TMEM52: Transmembrane 32.6 3.7E+02 0.0079 24.1 8.5 31 421-451 18-51 (154)
191 PRK01066 porphobilinogen deami 32.5 4.8E+02 0.01 25.4 11.0 60 275-342 124-185 (231)
192 PF03908 Sec20: Sec20; InterP 32.0 50 0.0011 27.0 3.1 24 179-202 68-91 (92)
193 PRK10752 sulfate transporter s 30.8 1.3E+02 0.0029 31.0 6.6 42 85-135 38-84 (329)
194 cd08471 PBP2_CrgA_like_2 The C 29.8 4E+02 0.0086 23.6 9.9 64 81-161 14-77 (201)
195 COG0040 HisG ATP phosphoribosy 29.5 3.4E+02 0.0074 27.4 8.9 101 274-387 107-211 (290)
196 PF14851 FAM176: FAM176 family 29.3 1.3E+02 0.0029 27.2 5.5 27 422-448 21-49 (153)
197 PRK11917 bifunctional adhesin/ 29.1 1E+02 0.0022 30.3 5.4 50 115-164 181-232 (259)
198 PF09084 NMT1: NMT1/THI5 like; 27.0 1.5E+02 0.0032 27.8 6.0 71 298-374 15-85 (216)
199 KOG3713 Voltage-gated K+ chann 25.5 79 0.0017 34.0 3.9 58 195-256 362-421 (477)
200 TIGR03730 tungstate_WtpA tungs 25.3 6.9E+02 0.015 24.9 11.1 29 307-339 176-204 (273)
201 PF03180 Lipoprotein_9: NLPA l 25.2 2.1E+02 0.0045 28.0 6.6 101 286-392 2-123 (237)
202 PF06679 DUF1180: Protein of u 25.2 98 0.0021 28.4 3.9 29 421-449 93-121 (163)
203 TIGR00212 hemC porphobilinogen 23.8 7.7E+02 0.017 25.0 12.1 60 275-342 109-170 (292)
204 PF01007 IRK: Inward rectifier 23.6 1.9E+02 0.0041 29.9 6.2 59 213-271 83-145 (336)
205 TIGR02976 phageshock_pspB phag 23.6 3.3E+02 0.0071 21.5 6.1 16 460-475 55-70 (75)
206 PF15179 Myc_target_1: Myc tar 23.4 1.2E+02 0.0026 28.2 4.1 38 414-451 13-51 (197)
207 TIGR03061 pip_yhgE_Nterm YhgE/ 22.7 4.9E+02 0.011 23.4 8.3 21 314-338 84-104 (164)
208 PF06667 PspB: Phage shock pro 22.3 3.8E+02 0.0083 21.2 6.2 11 462-472 57-67 (75)
209 PRK10859 membrane-bound lytic 21.9 8E+02 0.017 26.6 11.1 57 275-336 34-107 (482)
210 PF08374 Protocadherin: Protoc 21.4 3.2E+02 0.0069 26.2 6.6 36 416-451 31-66 (221)
211 PF10577 UPF0560: Uncharacteri 21.3 2.8E+02 0.006 32.0 7.2 22 259-280 130-151 (807)
212 PF10661 EssA: WXG100 protein 21.3 88 0.0019 28.1 2.8 29 175-203 115-143 (145)
213 COG4588 AcfC Accessory coloniz 21.2 3E+02 0.0064 26.4 6.2 74 82-167 34-114 (252)
214 PF10777 YlaC: Inner membrane 21.1 1.6E+02 0.0035 26.4 4.3 24 178-201 35-58 (155)
215 COG0107 HisF Imidazoleglycerol 20.8 1.2E+02 0.0027 29.4 3.8 47 78-133 182-228 (256)
216 TIGR01276 thiB thiamine ABC tr 20.6 8.4E+02 0.018 24.2 14.5 39 85-133 21-63 (309)
217 COG4736 CcoQ Cbb3-type cytochr 20.2 1.1E+02 0.0025 22.9 2.7 24 180-203 11-34 (60)
No 1
>KOG1052 consensus Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=4.4e-59 Score=523.61 Aligned_cols=426 Identities=34% Similarity=0.621 Sum_probs=373.1
Q ss_pred CcceecCCCCCCceecCCCCcccCCccceecCCCCCCCCCCCccCCCCceEEEEecCCCCCcceEEEeeCCCCCCCceEE
Q 037841 1 RGIGFWTPEKGLTQKLSSNSTTKSKLKPIIWPGDSTSDPKGWEVPTNEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVT 80 (561)
Q Consensus 1 ~~~g~w~~~~g~~~~~~~~~~~~~~~~~~~wpg~~~~~p~~~~~~~~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~ 80 (561)
+.||+|++..| ++|+|||.....|++|.++.+|++++|+++..+||..++... ....+.. .+.
T Consensus 183 ~~ig~W~~~~~---------------~~i~~~~~~~~~~~~~~~~~~~~~l~v~~~~~~P~~~~~~~~-~~~~~~~-~~~ 245 (656)
T KOG1052|consen 183 RRIGYWYPRGG---------------ENISWPGKDYFVPKGWFFPTNGKPLRVGVVTEPPFVDLVEDL-AILNGND-RIE 245 (656)
T ss_pred eeEEEecCCCC---------------ceeeccCCcccCcCCccccCCCceEEEEEeccCCceeeeecc-cccCCCC-ccc
Confidence 35899999998 589999999999999999999999999999777765444432 1333455 899
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
|+|+||++++++++||++++..++.+....+++|+|+|++++|.+|++|++ ++++++++|.+++|||.||++.++++++
T Consensus 246 G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~~g~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~ 324 (656)
T KOG1052|consen 246 GFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPNGNWDGLVGQLVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIV 324 (656)
T ss_pred eEEehHHHHHHHhCCCceEEEEcCCCCCCCCCCCChhHHHHHHhcCccccc-cceEEeecccccEEeccceEeccEEEEE
Confidence 999999999999999999998888776444466899999999999999999 8999999999999999999999999999
Q ss_pred EccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCCCCCc-----cCccchhHHHHHHHhhhcc-cccc
Q 037841 161 PIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDFRGPA-----RHQVGTSFWFSFSTMVFSQ-RERV 234 (561)
Q Consensus 161 p~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~~~-----~~~~~~~~~~~~~~l~~~~-~~~~ 234 (561)
++++.... .|.|++||++++|++++++++++++++|+++|+.+.++ .++ .....+++|+++++++.++ .+.|
T Consensus 325 ~~~~~~~~-~~~fl~Pf~~~vW~~i~~~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~p 402 (656)
T KOG1052|consen 325 RKPDSRSK-LWNFLAPFSPEVWLLILASLLLVGLLLWILERLSPYEL-PPRQIVTSLFSLLNCLWLTVGSLLQQGSDEIP 402 (656)
T ss_pred EecCCccc-ceEEecCCcHHHHHHHHHHHHHHHHHHHHHhccccccC-CccccceeEeecccchhhhhHHHhccCCCccc
Confidence 99987765 99999999999999999999999999999999998888 222 1133446799999999887 4688
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHh-CCCeeEEEeCchHHHHHHhc----CCCcc-c
Q 037841 235 ISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIK-RGDNVGYQKGSFVLGILKQL----GFDER-K 308 (561)
Q Consensus 235 ~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~-~~~~vg~~~gs~~~~~l~~~----~~~~~-~ 308 (561)
++.++|+++++||++++||+++|||+|+|+||+++..++|++++||++ ++..+|++.+++...++++. .+... +
T Consensus 403 ~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~~~~~~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 482 (656)
T KOG1052|consen 403 RSLSTRLLLGAWWLFVLILISSYTANLTAFLTVPRLRSPIDSLDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQR 482 (656)
T ss_pred cchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCcccCHHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCC
Confidence 999999999999999999999999999999999999999999999994 78899999999999999764 23344 6
Q ss_pred eeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcC-CcceEEeCcccccCceEEEecCCCCChhhHHHHHhhccc
Q 037841 309 LVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQH-CYKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILSVTE 387 (561)
Q Consensus 309 ~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~-~~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e 387 (561)
.+.+.+.+++.+++.+|.. ++++++.++.++.+.+.++. |+ ++++++.+...+++ ++||||||++.++++|+++.|
T Consensus 483 ~~~~~~~~e~~~~v~~~~~-~~~~~~~~~~~~~~~~~~~~~c~-~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e 559 (656)
T KOG1052|consen 483 SVPLASPEEGVERVRKGPS-GGYAFASDELYLAYLFLRDEICD-LTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQE 559 (656)
T ss_pred CccCCCHHHHHHHHHcCCC-CceEEEeccHHHHHHHhhcCCCc-eEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhcc
Confidence 7889999999999999986 55676777777766666655 75 99999999999999 999999999999999999999
Q ss_pred cchhHHHHHHHcccC---CCCCCCCCccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 037841 388 GDKMKEIEDAWFKKH---SSCPDASTVVSSRSLGLNSFWGLFLIAGIAAILALIIFLAVFVGQHRNVL 452 (561)
Q Consensus 388 ~G~~~~i~~kw~~~~---~~c~~~~~~~~~~~L~l~~~~g~F~il~~g~~lallvfl~E~~~~~~~~~ 452 (561)
.|++++++++|+.+. ..|.... +...|++++++|+|+++++|+++|+++|++|++|++++..
T Consensus 560 ~g~l~~~~~kw~~~~~~~~~~~~~~---~~~~l~~~~~~g~F~i~~~g~~lal~vfi~E~~~~~~~~~ 624 (656)
T KOG1052|consen 560 TGILQKLKRKWFSKKPCLPKCSQTE---KTKALDLESFWGLFLILLVGYLLALLVFILELLYSRRRTL 624 (656)
T ss_pred ccHHHHHHHHhccCCCCCCCCCCcc---cccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 999999999999765 4444433 6788999999999999999999999999999999988875
No 2
>KOG1054 consensus Glutamate-gated AMPA-type ion channel receptor subunit GluR2 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=4.1e-54 Score=437.20 Aligned_cols=426 Identities=21% Similarity=0.398 Sum_probs=349.4
Q ss_pred CcceecCCCCCCceecCCCCcccCCccceecCCCCCCCCCCCccCCCCceEEEEecCCCCCcceEEEeeCCC--CCCCce
Q 037841 1 RGIGFWTPEKGLTQKLSSNSTTKSKLKPIIWPGDSTSDPKGWEVPTNEKKLRIGVPVKKGFSYFVNVTIDPK--TQEPTS 78 (561)
Q Consensus 1 ~~~g~w~~~~g~~~~~~~~~~~~~~~~~~~wpg~~~~~p~~~~~~~~g~~LrVgv~~~~~~~pf~~~~~d~~--~~~~~~ 78 (561)
|.+|||.+..|++-..... +.+ ... -..+.+.+.|.+....|| +...++.. .++. +
T Consensus 387 rk~~~W~e~~~fv~~~t~a-----~~~------~d~-------~~~~n~tvvvttiL~spy---vm~kkn~~~~egn~-r 444 (897)
T KOG1054|consen 387 RKVGYWNEGEGFVPGSTVA-----QSR------NDQ-------ASKENRTVVVTTILESPY---VMLKKNHEQLEGNE-R 444 (897)
T ss_pred ceeeeecccCceeeccccc-----ccc------ccc-------cccccceEEEEEecCCch---hHHHhhHHHhcCCc-c
Confidence 6799999999999532110 000 000 012234455555434444 33333332 3455 8
Q ss_pred EEEehHHHHHHHHHHCCCceeEEEEecCCCCCC--CCCC-HHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccc
Q 037841 79 VTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGT--SSGS-YNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESG 155 (561)
Q Consensus 79 ~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~--~ngs-~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~ 155 (561)
+.|||+|++.+++++.++.+.+.++..+. +|. +.++ |+||++.|..|++|+++++++||..|.+.+|||.|++..+
T Consensus 445 yEGyCvdLa~~iAkhi~~~Y~l~iv~dgk-yGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REeviDFSKPfMslG 523 (897)
T KOG1054|consen 445 YEGYCVDLAAEIAKHIGIKYKLFIVGDGK-YGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLG 523 (897)
T ss_pred cceeHHHHHHHHHHhcCceEEEEEecCCc-ccccCCCcccccchhHHHhcCccceEEeeeeeehhhhhhhccccchhhcC
Confidence 99999999999999999866666665443 442 6777 9999999999999999999999999999999999999999
Q ss_pred eEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCC------CCC-------ccCccchhHHHH
Q 037841 156 VSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDF------RGP-------ARHQVGTSFWFS 222 (561)
Q Consensus 156 ~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~------~~~-------~~~~~~~~~~~~ 222 (561)
+++++++|++..+..+.|+.|+..++|+|++..++-+++++++..|..+-|+ +|+ ...++.+++||+
T Consensus 524 ISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~rg~~t~~~~~NeFgifNsLWFs 603 (897)
T KOG1054|consen 524 ISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTPSDPPNEFGIFNSLWFS 603 (897)
T ss_pred eEEEEeCcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccCchheeccccccCCCCCCCCCccchhhHHHHHH
Confidence 9999999999999999999999999999999999999999999887765442 332 124788999999
Q ss_pred HHHhhhcccc-ccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCC-eeEEEeCchHHHHHH
Q 037841 223 FSTMVFSQRE-RVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGD-NVGYQKGSFVLGILK 300 (561)
Q Consensus 223 ~~~l~~~~~~-~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~-~vg~~~gs~~~~~l~ 300 (561)
++++++|+.. .|++.++|++-.+||||.|||.++|||+|+++||+.+..+||.+.|||+++.+ .+|...+....++++
T Consensus 604 LgAFMQQG~DI~PRslSGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeFFr 683 (897)
T KOG1054|consen 604 LGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFR 683 (897)
T ss_pred HHHHHhcCCCCCccccccceeccchhhhhhhhhhhhhhHHHHHHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHHHh
Confidence 9999999976 67999999999999999999999999999999999999999999999998876 678888888888887
Q ss_pred hcCCC----------ccce-eecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcC-CcceEEeCcccccCceEEEe
Q 037841 301 QLGFD----------ERKL-VVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQH-CYKYTMVEPTFKTAGFGFAF 368 (561)
Q Consensus 301 ~~~~~----------~~~~-~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~-~~~l~~v~~~~~~~~~~~~~ 368 (561)
....+ .... +-+.+..|.++.+.+.+ |-+|++.+...-+|.-++. |+ -..++..+.+.++|++.
T Consensus 684 ~Skiavy~kMW~yM~SaepsVFv~t~aeGv~rVRksK---GkyAfLLEsTmNey~eqRkPCD-TMKVGgNLds~GYGiAT 759 (897)
T KOG1054|consen 684 RSKIAVYEKMWTYMKSAEPSVFVRTTAEGVARVRKSK---GKYAFLLESTMNEYIEQRKPCD-TMKVGGNLDSKGYGIAT 759 (897)
T ss_pred hhhHHHHHHHHHHHhcCCcceeeehhhhHHHHHHhcC---CceEeehHhhhhhhhhccCCcc-ceecccccCCcceeecC
Confidence 52211 0111 44556778888887766 6799999988888877665 98 45788889999999999
Q ss_pred cCCCCChhhHHHHHhhccccchhHHHHHHHcccCCCCCCCC--CccccccccccchhHHHHHHHHHHHHHHHHHHHHHHH
Q 037841 369 PLHSPLVHDVSKAILSVTEGDKMKEIEDAWFKKHSSCPDAS--TVVSSRSLGLNSFWGLFLIAGIAAILALIIFLAVFVG 446 (561)
Q Consensus 369 ~k~spl~~~in~~Il~l~e~G~~~~i~~kw~~~~~~c~~~~--~~~~~~~L~l~~~~g~F~il~~g~~lallvfl~E~~~ 446 (561)
||||.|+..+|-++++|.|.|+++++++||+.+.+.|.... ..++...|+|....|+||||..|+++|.++.++|++|
T Consensus 760 p~Gsslr~~vNLAvLkL~E~G~LdKLkNKWWYDkGeC~sg~~ds~~ktsaLsLSnVAGvFYIL~gGl~laMlvALiEF~y 839 (897)
T KOG1054|consen 760 PKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCY 839 (897)
T ss_pred CCCcccccchhhhhhhhcccchHHHhhhhhcccccccCCCCCCCCcchhhcchhhccceeeeehhhHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999998766 3334478999999999999999999999999999999
Q ss_pred Hhhcccc
Q 037841 447 QHRNVLR 453 (561)
Q Consensus 447 ~~~~~~~ 453 (561)
+.|...+
T Consensus 840 ksr~Eak 846 (897)
T KOG1054|consen 840 KSRAEAK 846 (897)
T ss_pred HhhHHHH
Confidence 8776644
No 3
>KOG1053 consensus Glutamate-gated NMDA-type ion channel receptor subunit GRIN2A and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=4.1e-47 Score=400.70 Aligned_cols=410 Identities=23% Similarity=0.432 Sum_probs=334.6
Q ss_pred CccceecCCCCCCCCCCCccCCCCceEEEEecCCCCCcceEEEe-eCCCCCC-----------------------C---c
Q 037841 25 KLKPIIWPGDSTSDPKGWEVPTNEKKLRIGVPVKKGFSYFVNVT-IDPKTQE-----------------------P---T 77 (561)
Q Consensus 25 ~~~~~~wpg~~~~~p~~~~~~~~g~~LrVgv~~~~~~~pf~~~~-~d~~~~~-----------------------~---~ 77 (561)
.++-.+||-- .+..... ....+|+|.+-+.+|| +.+. -||.++. . +
T Consensus 391 ~M~y~vWPr~---~~~~q~~-~d~~HL~VvTLeE~PF---Vive~vDP~t~~C~~ntvpc~s~~~~t~ss~~~~~~tvKk 463 (1258)
T KOG1053|consen 391 VMKYPVWPRY---HKFLQPV-PDKLHLTVVTLEERPF---VIVEDVDPLTQTCVRNTVPCRSQLNSTFSSGDEANRTVKK 463 (1258)
T ss_pred EEeccccccc---cCccCCC-CCcceeEEEEeccCCe---EEEecCCCCcCcCCCCCCcchhhhhhccCCCccCCchHHh
Confidence 4678889921 1111111 1235899999866654 5543 2332210 0 1
Q ss_pred eEEEehHHHHHHHHHHCCCceeEEEEecCCCCCC-CCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccce
Q 037841 78 SVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGT-SSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGV 156 (561)
Q Consensus 78 ~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~-~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~ 156 (561)
+.+||||||++.+++-+||+++.-.+..+ +.|+ .||.|+|||+.|..+++||++|+++|+++|++.+|||.||.++++
T Consensus 464 CCkGfCIDiLkKlA~~v~FtYDLYlVtnG-KhGkk~ng~WnGmIGev~~~rA~MAVgSltINeeRSevVDFSvPFveTgI 542 (1258)
T KOG1053|consen 464 CCKGFCIDILKKLARDVKFTYDLYLVTNG-KHGKKINGVWNGMIGEVVYQRADMAVGSLTINEERSEVVDFSVPFVETGI 542 (1258)
T ss_pred hhhhhhHHHHHHHHhhcCcceEEEEecCC-cccceecCcchhhHHHHHhhhhheeeeeeEechhhhccccccccccccce
Confidence 57899999999999999997776555533 4554 999999999999999999999999999999999999999999999
Q ss_pred EEEEEccCCCCCCcceeccccchhhHHHHHHHHHHH-HHHHhhhhcccCCC---------CCCCccCccchhHHHHHHHh
Q 037841 157 SMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFI-GFVVWALEHRVNED---------FRGPARHQVGTSFWFSFSTM 226 (561)
Q Consensus 157 ~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~-~~v~~~l~~~~~~~---------~~~~~~~~~~~~~~~~~~~l 226 (561)
.++|...+.. .+.-+||.||++.+|++++++++++ ++.++++|+..+-. -.+.+..+++.++|..+..+
T Consensus 543 sVmV~rsngt-vspsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp~FtigkaiwllwaLv 621 (1258)
T KOG1053|consen 543 SVMVARSNGT-VSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGPSFTIGKAIWLLWALV 621 (1258)
T ss_pred EEEEEecCCc-cCchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcCcccccccccCCCCCCCcceehhhHHHHHHHHH
Confidence 9999977654 4778999999999999999988765 45577888865322 22345789999999999888
Q ss_pred hhcc--ccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhC-------CCeeEEEeCchHHH
Q 037841 227 VFSQ--RERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKR-------GDNVGYQKGSFVLG 297 (561)
Q Consensus 227 ~~~~--~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~-------~~~vg~~~gs~~~~ 297 (561)
+... .+.|+...+|+++.+|-||++|+.++|||||+++|...++..++..+.|=.-+ +.+.|.+.++..++
T Consensus 622 FnnsVpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~vSGlsD~KfqrP~dq~PpFRFGTVpngSTE~ 701 (1258)
T KOG1053|consen 622 FNNSVPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDTVSGLSDPKFQRPHDQYPPFRFGTVPNGSTER 701 (1258)
T ss_pred hCCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccccCccccCCCcccccCCCCchhh
Confidence 8776 46889999999999999999999999999999999999999888888775311 34788888888888
Q ss_pred HHHhcCCCc--cceeec--CChHHHHHHhhccccCCceeEEeecchhHHHHHhcC--CcceEEeC--cccccCceEEEec
Q 037841 298 ILKQLGFDE--RKLVVY--NSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQH--CYKYTMVE--PTFKTAGFGFAFP 369 (561)
Q Consensus 298 ~l~~~~~~~--~~~~~~--~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~--~~~l~~v~--~~~~~~~~~~~~~ 369 (561)
++++ ++++ ..++.| ...+++++.|++|+ .||||.+...++|...+. |+ +..++ ..+...+||++++
T Consensus 702 niR~-Nyp~MHeYM~kyNq~~v~dal~sLK~gK----LDAFIyDaAVLnY~agkDegCK-LvTIGsgKvFAttGYGIal~ 775 (1258)
T KOG1053|consen 702 NIRS-NYPEMHEYMVKYNQPGVEDALESLKNGK----LDAFIYDAAVLNYMAGKDEGCK-LVTIGSGKVFATTGYGIALP 775 (1258)
T ss_pred hHHh-ccHHHHHHHHHhccCchHHHHHHHhccc----chhHHHHHHHHHHhhccCCCce-EEEecCCceeeecceeeecC
Confidence 8876 2332 223334 36789999999999 999999999999999876 97 55565 8899999999999
Q ss_pred CCCCChhhHHHHHhhccccchhHHHHHHHcccCCCCCCCCCccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 037841 370 LHSPLVHDVSKAILSVTEGDKMKEIEDAWFKKHSSCPDASTVVSSRSLGLNSFWGLFLIAGIAAILALIIFLAVFVGQHR 449 (561)
Q Consensus 370 k~spl~~~in~~Il~l~e~G~~~~i~~kw~~~~~~c~~~~~~~~~~~L~l~~~~g~F~il~~g~~lallvfl~E~~~~~~ 449 (561)
||||++..||.+|+++...|+|+++++.|+ ...|.+......+.+|++++|.|+||+|++|++|++++|+.|.+++++
T Consensus 776 k~Spwkr~IdlallQy~gdGeme~Le~~Wl--tgic~n~k~evmSsqLdIdnmaGvFymL~~amgLSllvfi~EHlvYw~ 853 (1258)
T KOG1053|consen 776 KNSPWKRQIDLALLQYLGDGEMEMLETLWL--TGICHNSKNEVMSSQLDIDNMAGVFYMLAVAMGLSLLVFIWEHLVYWK 853 (1258)
T ss_pred CCCcchhhHHHHHHHHhccchHHHHHHHHh--hcccccchhhhhhcccChhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999 688887777789999999999999999999999999999999876654
Q ss_pred cc
Q 037841 450 NV 451 (561)
Q Consensus 450 ~~ 451 (561)
-+
T Consensus 854 Lr 855 (1258)
T KOG1053|consen 854 LR 855 (1258)
T ss_pred hh
Confidence 44
No 4
>KOG4440 consensus NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=3.1e-48 Score=395.95 Aligned_cols=417 Identities=22% Similarity=0.372 Sum_probs=350.4
Q ss_pred ccceecCCCCCCCCCCCccCCCCceEEEEecCCCCCcceEEEeeCC-----------------------------CCC--
Q 037841 26 LKPIIWPGDSTSDPKGWEVPTNEKKLRIGVPVKKGFSYFVNVTIDP-----------------------------KTQ-- 74 (561)
Q Consensus 26 ~~~~~wpg~~~~~p~~~~~~~~g~~LrVgv~~~~~~~pf~~~~~d~-----------------------------~~~-- 74 (561)
=+.|||||+-+..|+|..+| .+|||-+...+ ||+|+..-. .+.
T Consensus 383 d~~IiWpGg~~~KP~gi~~p---thLrivTi~~~---PFVYv~p~~sd~~c~eef~~~~d~~~k~~c~gpn~s~p~s~~~ 456 (993)
T KOG4440|consen 383 DRKIIWPGGETEKPRGIQMP---THLRIVTIHQE---PFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDSSPGSPRH 456 (993)
T ss_pred CceeecCCCCcCCCcccccc---ceeEEEEeccC---CeEEEecCCCCcchhhhccccCCcccceeecCCCCCCCCCccc
Confidence 36799999999999999998 67888887444 457766210 001
Q ss_pred --CCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCC--------C-CCCCHHHHHHHHHcCcccEEEeceeeecCcce
Q 037841 75 --EPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDG--------T-SSGSYNDLIYQVFLGEFDAAVGDITILLNRSN 143 (561)
Q Consensus 75 --~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g--------~-~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~ 143 (561)
.- +..|+|||++-.+++.+||+++..+++.+.-+. . ....|+|+++.|.+|.+||++++++|+++|.+
T Consensus 457 t~~f-CC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpERa~ 535 (993)
T KOG4440|consen 457 TVPF-CCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPERAQ 535 (993)
T ss_pred Ccch-hhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhCCccceEeeceeeChhhhh
Confidence 11 456999999999999999998888887543211 1 22369999999999999999999999999999
Q ss_pred eeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCC-CCC-------CccCcc
Q 037841 144 YVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNED-FRG-------PARHQV 215 (561)
Q Consensus 144 ~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~-~~~-------~~~~~~ 215 (561)
+++||.|+...|+.++.+++.+. +....|++||+..+|++++++..+++++++++.|..+-+ |.. .....+
T Consensus 536 yieFskPfkYqGitILeKk~~r~-Stl~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPFgRFk~~ds~~~ee~alnl 614 (993)
T KOG4440|consen 536 YIEFSKPFKYQGITILEKKEIRR-STLDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPFGRFKVNDSEEEEEDALNL 614 (993)
T ss_pred heeccCcccccceEEEeeCCCCC-chHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccceeeccCccchhhhcch
Confidence 99999999999999999977654 578899999999999999999999999999999876532 322 234589
Q ss_pred chhHHHHHHHhhhcc-cc-ccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCC----CeeEE
Q 037841 216 GTSFWFSFSTMVFSQ-RE-RVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRG----DNVGY 289 (561)
Q Consensus 216 ~~~~~~~~~~l~~~~-~~-~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~----~~vg~ 289 (561)
+.++||+++.++.+| ++ .|+|.++|++-++|+-|++|+.++|||+|+++|...+.+..++.+.|-.-.+ ...+.
T Consensus 615 ssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLdrPe~~ltGinDpRLRNps~nf~~aT 694 (993)
T KOG4440|consen 615 SSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLDRPEERLTGINDPRLRNPSDNFIYAT 694 (993)
T ss_pred hhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhhhhhheeecCccccccCCCCccccCcccceeEEE
Confidence 999999999999988 55 6799999999999999999999999999999999999999999888864222 35777
Q ss_pred EeCchHHHHHHhc-----CCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCcccccCce
Q 037841 290 QKGSFVLGILKQL-----GFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPTFKTAGF 364 (561)
Q Consensus 290 ~~gs~~~~~l~~~-----~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~~~~~~~ 364 (561)
..+|.+..|+++. -+..-.-..|.+.+|+++++.+|+ .+|++-+..-+++-.+++|+ +...++.|...++
T Consensus 695 Vk~SsVd~YFrRqVELS~MyR~ME~hNy~~A~eAiq~v~~gk----L~AFIWDS~rLEfEAs~~Ce-LvT~GeLFgRSgy 769 (993)
T KOG4440|consen 695 VKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDGK----LHAFIWDSARLEFEASQKCE-LVTTGELFGRSGY 769 (993)
T ss_pred ecCccHHHHHHHHhHHHHHHHhhhhcchhhHHHHHHHHHcCc----eeEEEeecceeeehhhcccc-eEecccccccccc
Confidence 8999999999751 122223457788899999999999 99999999999999999997 8889999999999
Q ss_pred EEEecCCCCChhhHHHHHhhccccchhHHHHHHHcccCC-CCCCCCCccccccccccchhHHHHHHHHHHHHHHHHHHHH
Q 037841 365 GFAFPLHSPLVHDVSKAILSVTEGDKMKEIEDAWFKKHS-SCPDASTVVSSRSLGLNSFWGLFLIAGIAAILALIIFLAV 443 (561)
Q Consensus 365 ~~~~~k~spl~~~in~~Il~l~e~G~~~~i~~kw~~~~~-~c~~~~~~~~~~~L~l~~~~g~F~il~~g~~lallvfl~E 443 (561)
|+.++|+||+.+.+..+|+++.|+|+|.++.++|+.... .|-. .....+..|+++++.|+|++.+.|+++++++.++|
T Consensus 770 GIGlqK~SPWt~~vtlaIL~~hEsGfMEkLDk~Wi~~Ggpq~c~-~~~k~PatLgl~NMagvFiLV~~Gia~GifLifiE 848 (993)
T KOG4440|consen 770 GIGLQKDSPWTQNVTLAILKSHESGFMEKLDKTWIRYGGPQECD-SRSKAPATLGLENMAGVFILVAGGIAAGIFLIFIE 848 (993)
T ss_pred ccccccCCCCcchhhHHHHHhhhcchHHHHHHHHHhcCCcchhh-hhccCcccccccccccEEEEEecchhheeeEEEEe
Confidence 999999999999999999999999999999999996533 2222 23347889999999999999999999999999999
Q ss_pred HHHHhhcccccCc
Q 037841 444 FVGQHRNVLRNSE 456 (561)
Q Consensus 444 ~~~~~~~~~~~~~ 456 (561)
..|+|++..+.++
T Consensus 849 v~Ykrh~~~k~kr 861 (993)
T KOG4440|consen 849 VAYKRHKDAKRKR 861 (993)
T ss_pred ehhhhhhhhhhHH
Confidence 9999887754333
No 5
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.90 E-value=3e-22 Score=198.34 Aligned_cols=221 Identities=24% Similarity=0.377 Sum_probs=189.5
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.++|+||+. .+|+||.+.+ ++ ++.|+++|+++++++++|.+ +++++. +|.+++.++.+|+
T Consensus 24 ~~~l~v~~~--~~~~P~~~~~------~g-~~~G~~vdl~~~ia~~lg~~--~~~~~~---------~~~~~~~~l~~G~ 83 (247)
T PRK09495 24 DKKLVVATD--TAFVPFEFKQ------GD-KYVGFDIDLWAAIAKELKLD--YTLKPM---------DFSGIIPALQTKN 83 (247)
T ss_pred CCeEEEEeC--CCCCCeeecC------CC-ceEEEeHHHHHHHHHHhCCc--eEEEeC---------CHHHHHHHHhCCC
Confidence 578999986 6789998742 34 79999999999999999974 555442 5999999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDF 207 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~ 207 (561)
+|+++++++.+++|.+.++||.||+.+++.+++++....
T Consensus 84 vDi~~~~~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~~~----------------------------------------- 122 (247)
T PRK09495 84 VDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNND----------------------------------------- 122 (247)
T ss_pred cCEEEecCccCHHHHhhccccchheecceEEEEECCCCC-----------------------------------------
Confidence 999987789999999999999999999999999855432
Q ss_pred CCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCee
Q 037841 208 RGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNV 287 (561)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~v 287 (561)
+++++|| +|++|
T Consensus 123 ------------------------------------------------------------------~~~~~dL--~g~~I 134 (247)
T PRK09495 123 ------------------------------------------------------------------IKSVKDL--DGKVV 134 (247)
T ss_pred ------------------------------------------------------------------CCChHHh--CCCEE
Confidence 6899999 68999
Q ss_pred EEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcC-CcceEEeCcccccCceEE
Q 037841 288 GYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQH-CYKYTMVEPTFKTAGFGF 366 (561)
Q Consensus 288 g~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~-~~~l~~v~~~~~~~~~~~ 366 (561)
|+..|+....++++. .+..+++.+++.++++++|..|+ +|+++.+...+.+++++. ...+..++.......+++
T Consensus 135 ~v~~g~~~~~~l~~~-~~~~~i~~~~~~~~~~~~L~~gr----vDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 209 (247)
T PRK09495 135 AVKSGTGSVDYAKAN-IKTKDLRQFPNIDNAYLELGTGR----ADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGI 209 (247)
T ss_pred EEecCchHHHHHHhc-CCCCceEEcCCHHHHHHHHHcCc----eeEEEeChHHHHHHHHhCCCCceEEecCcccccceEE
Confidence 999999888888763 45667888999999999999999 999999998888888765 335777777667778899
Q ss_pred EecCCCCChhhHHHHHhhccccchhHHHHHHHcccC
Q 037841 367 AFPLHSPLVHDVSKAILSVTEGDKMKEIEDAWFKKH 402 (561)
Q Consensus 367 ~~~k~spl~~~in~~Il~l~e~G~~~~i~~kw~~~~ 402 (561)
+++|++.+++.+|++|.++.++|.++++.++|+...
T Consensus 210 a~~~~~~l~~~~n~al~~~~~~g~~~~i~~k~~~~~ 245 (247)
T PRK09495 210 AFPKGSELREKVNGALKTLKENGTYAEIYKKWFGTE 245 (247)
T ss_pred EEcCcHHHHHHHHHHHHHHHHCCcHHHHHHHHcCCC
Confidence 999999999999999999999999999999999643
No 6
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.89 E-value=5.4e-22 Score=202.18 Aligned_cols=225 Identities=16% Similarity=0.229 Sum_probs=189.1
Q ss_pred CCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHH----HCCC-ceeEEEEecCCCCCCCCCCHHHHHH
Q 037841 47 NEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQ----ELPY-AVAYDFVPYGQPDGTSSGSYNDLIY 121 (561)
Q Consensus 47 ~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~----~l~f-~v~~~~v~~~~~~g~~ngs~~~li~ 121 (561)
..++|+||+. ++|+||.+.+ +++ +++||++|+++++++ ++|. .+++++++. +|..++.
T Consensus 38 ~~g~L~Vg~~--~~~pP~~f~~-----~~g-~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~---------~~~~~i~ 100 (302)
T PRK10797 38 KNGVIVVGHR--ESSVPFSYYD-----NQQ-KVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPI---------TSQNRIP 100 (302)
T ss_pred hCCeEEEEEc--CCCCCcceEC-----CCC-CEeeecHHHHHHHHHHHHHhhCCCCceEEEEEc---------ChHhHHH
Confidence 3577999998 7899999865 245 899999997777655 6764 368888884 4778999
Q ss_pred HHHcCcccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhc
Q 037841 122 QVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEH 201 (561)
Q Consensus 122 ~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~ 201 (561)
.|..|++|++++++++|++|.+.++||.||+.++..+++++.. .
T Consensus 101 ~L~~G~~Di~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~-~----------------------------------- 144 (302)
T PRK10797 101 LLQNGTFDFECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG-D----------------------------------- 144 (302)
T ss_pred HHHCCCccEEecCCccCcchhhcceecccEeeccEEEEEECCC-C-----------------------------------
Confidence 9999999999988999999999999999999999999998653 1
Q ss_pred ccCCCCCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHH
Q 037841 202 RVNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLI 281 (561)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~ 281 (561)
|++++||
T Consensus 145 ------------------------------------------------------------------------i~sl~dL- 151 (302)
T PRK10797 145 ------------------------------------------------------------------------IKDFADL- 151 (302)
T ss_pred ------------------------------------------------------------------------CCChHHc-
Confidence 6889999
Q ss_pred hCCCeeEEEeCchHHHHHHhcC---CCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhc--CCcceEEeC
Q 037841 282 KRGDNVGYQKGSFVLGILKQLG---FDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQ--HCYKYTMVE 356 (561)
Q Consensus 282 ~~~~~vg~~~gs~~~~~l~~~~---~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~--~~~~l~~v~ 356 (561)
.|++||+..|+...+++++.. .+..+++.+.+.++.+++|..|+ +||++.+...+...+.+ ..+.+.+++
T Consensus 152 -~Gk~V~v~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~Gr----vDa~i~d~~~~~~~~~~~~~~~~l~i~~ 226 (302)
T PRK10797 152 -KGKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGR----AVAFMMDDALLAGERAKAKKPDNWEIVG 226 (302)
T ss_pred -CCCEEEEeCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCC----ceEEEccHHHHHHHHHcCCCCcceEECC
Confidence 799999999999888886532 23467889999999999999999 99999998776654433 234577888
Q ss_pred cccccCceEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHcccC
Q 037841 357 PTFKTAGFGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWFKKH 402 (561)
Q Consensus 357 ~~~~~~~~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~~~~ 402 (561)
+.+...+++++++|+++ ++..+|++|.++.++|.+++|.++|++..
T Consensus 227 ~~~~~~~~~~a~~k~~~~L~~~in~~L~~l~~~G~l~~i~~kw~~~~ 273 (302)
T PRK10797 227 KPQSQEAYGCMLRKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFKNP 273 (302)
T ss_pred ccCCcCceeEEEeCCCHHHHHHHHHHHHHHHhCchHHHHHHHHcCCC
Confidence 77777789999999987 99999999999999999999999999753
No 7
>PRK11260 cystine transporter subunit; Provisional
Probab=99.89 E-value=1.1e-21 Score=196.51 Aligned_cols=225 Identities=20% Similarity=0.327 Sum_probs=193.0
Q ss_pred CCCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHc
Q 037841 46 TNEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFL 125 (561)
Q Consensus 46 ~~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~ 125 (561)
...+.|+||+. .+|+||.+.+ .++ .+.|+.+|+++++++++|. +++++.. +|.+++.++.+
T Consensus 38 ~~~~~l~v~~~--~~~~P~~~~~-----~~g-~~~G~~~dl~~~i~~~lg~--~~e~~~~---------~~~~~~~~l~~ 98 (266)
T PRK11260 38 KERGTLLVGLE--GTYPPFSFQG-----EDG-KLTGFEVEFAEALAKHLGV--KASLKPT---------KWDGMLASLDS 98 (266)
T ss_pred hcCCeEEEEeC--CCcCCceEEC-----CCC-CEEEehHHHHHHHHHHHCC--eEEEEeC---------CHHHHHHHHhc
Confidence 45789999986 6789998764 245 7999999999999999997 4555552 59999999999
Q ss_pred CcccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCC
Q 037841 126 GEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNE 205 (561)
Q Consensus 126 g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~ 205 (561)
|++|+++++++.+++|.+.+.||.||..+++.+++++.....
T Consensus 99 G~~D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~~~~-------------------------------------- 140 (266)
T PRK11260 99 KRIDVVINQVTISDERKKKYDFSTPYTVSGIQALVKKGNEGT-------------------------------------- 140 (266)
T ss_pred CCCCEEEeccccCHHHHhccccCCceeecceEEEEEcCCcCC--------------------------------------
Confidence 999999988899999999999999999999999998654322
Q ss_pred CCCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCC
Q 037841 206 DFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGD 285 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~ 285 (561)
+++++|| +|+
T Consensus 141 --------------------------------------------------------------------~~~~~dL--~g~ 150 (266)
T PRK11260 141 --------------------------------------------------------------------IKTAADL--KGK 150 (266)
T ss_pred --------------------------------------------------------------------CCCHHHc--CCC
Confidence 6889999 789
Q ss_pred eeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCcccccCceE
Q 037841 286 NVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPTFKTAGFG 365 (561)
Q Consensus 286 ~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~~~~~~~~ 365 (561)
+||+..|+....++++ .++..++..+++..+++++|.+|+ +|+++.+...+.+++++....+.+....+...+++
T Consensus 151 ~Igv~~G~~~~~~l~~-~~~~~~i~~~~~~~~~l~~L~~Gr----vD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 225 (266)
T PRK11260 151 KVGVGLGTNYEQWLRQ-NVQGVDVRTYDDDPTKYQDLRVGR----IDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESG 225 (266)
T ss_pred EEEEecCCcHHHHHHH-hCCCCceEecCCHHHHHHHHHcCC----CCEEEechHHHHHHHHhCCCcceecCCccccCceE
Confidence 9999999998888876 466677889999999999999999 99999999888888887654455556667778899
Q ss_pred EEecCCCC-ChhhHHHHHhhccccchhHHHHHHHcccC
Q 037841 366 FAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWFKKH 402 (561)
Q Consensus 366 ~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~~~~ 402 (561)
++++++++ |++.+|++|.++.++|.++++.++|+.+.
T Consensus 226 ~~v~~~~~~l~~~ln~~l~~~~~~g~~~~i~~k~~~~~ 263 (266)
T PRK11260 226 VALRKGNPDLLKAVNQAIAEMQKDGTLKALSEKWFGAD 263 (266)
T ss_pred EEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcCCc
Confidence 99999987 99999999999999999999999999653
No 8
>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=99.88 E-value=5.2e-22 Score=192.04 Aligned_cols=223 Identities=23% Similarity=0.375 Sum_probs=184.7
Q ss_pred EEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccE
Q 037841 51 LRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDA 130 (561)
Q Consensus 51 LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~ 130 (561)
||||+. .+|+||.+.+. ++ ++.|+++|+++++++++|+++++... +|.+++.+|.+|++|+
T Consensus 1 l~V~~~--~~~~P~~~~~~-----~~-~~~G~~~dl~~~i~~~~g~~~~~~~~-----------~~~~~~~~l~~g~~D~ 61 (225)
T PF00497_consen 1 LRVGVD--EDYPPFSYIDE-----DG-EPSGIDVDLLRAIAKRLGIKIEFVPM-----------PWSRLLEMLENGKADI 61 (225)
T ss_dssp EEEEEE--SEBTTTBEEET-----TS-EEESHHHHHHHHHHHHHTCEEEEEEE-----------EGGGHHHHHHTTSSSE
T ss_pred CEEEEc--CCCCCeEEECC-----CC-CEEEEhHHHHHHHHhhcccccceeec-----------cccccccccccccccc
Confidence 789996 58899999874 45 89999999999999999985555442 4899999999999999
Q ss_pred EEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCCCCC
Q 037841 131 AVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDFRGP 210 (561)
Q Consensus 131 ~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~~ 210 (561)
++++++.+++|.+.++||.||+....++++++.+...
T Consensus 62 ~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~~------------------------------------------- 98 (225)
T PF00497_consen 62 IIGGLSITPERAKKFDFSDPYYSSPYVLVVRKGDAPP------------------------------------------- 98 (225)
T ss_dssp EESSEB-BHHHHTTEEEESESEEEEEEEEEETTSTCS-------------------------------------------
T ss_pred ccccccccccccccccccccccchhheeeeccccccc-------------------------------------------
Confidence 9988999999999999999999999999999643211
Q ss_pred ccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCeeEEE
Q 037841 211 ARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGYQ 290 (561)
Q Consensus 211 ~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~vg~~ 290 (561)
...+++++|| +|.+||+.
T Consensus 99 ------------------------------------------------------------~~~~~~~~dl--~~~~i~~~ 116 (225)
T PF00497_consen 99 ------------------------------------------------------------IKTIKSLDDL--KGKRIGVV 116 (225)
T ss_dssp ------------------------------------------------------------TSSHSSGGGG--TTSEEEEE
T ss_pred ------------------------------------------------------------cccccchhhh--cCcccccc
Confidence 0126778899 68899999
Q ss_pred eCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCc-ceEEeCcccccCceEEEec
Q 037841 291 KGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCY-KYTMVEPTFKTAGFGFAFP 369 (561)
Q Consensus 291 ~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~-~l~~v~~~~~~~~~~~~~~ 369 (561)
.|+...+++++......+++.+.+.++++++|.+|+ +|+++.+...+.++++++.. ............++++++.
T Consensus 117 ~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~----~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 (225)
T PF00497_consen 117 RGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGR----IDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVR 192 (225)
T ss_dssp TTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTS----SSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEE
T ss_pred cchhHHHHhhhhccchhhhcccccHHHHHHHHhcCC----eeeeeccchhhhhhhhhcccccccccccccccceeEEeec
Confidence 999988888874222567788999999999999999 99999999999999998743 2323255556667777777
Q ss_pred CCCC-ChhhHHHHHhhccccchhHHHHHHHccc
Q 037841 370 LHSP-LVHDVSKAILSVTEGDKMKEIEDAWFKK 401 (561)
Q Consensus 370 k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~~~ 401 (561)
++.+ +.+.||++|.++.++|.+++|.+||+++
T Consensus 193 ~~~~~l~~~~n~~i~~l~~~G~~~~i~~ky~g~ 225 (225)
T PF00497_consen 193 KKNPELLEIFNKAIRELKQSGEIQKILKKYLGD 225 (225)
T ss_dssp TTTHHHHHHHHHHHHHHHHTTHHHHHHHHHHSS
T ss_pred ccccHHHHHHHHHHHHHHhCcHHHHHHHHHcCC
Confidence 7655 9999999999999999999999999963
No 9
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.87 E-value=1.1e-20 Score=186.44 Aligned_cols=217 Identities=21% Similarity=0.347 Sum_probs=181.1
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.++|+||+. ++|+||++.+. ++ ++.|+++|+++++++++|..+ +++. .+|..++.++.+|+
T Consensus 20 ~~~l~v~~~--~~~~P~~~~~~-----~g-~~~G~~~dl~~~i~~~lg~~~--~~~~---------~~~~~~~~~l~~g~ 80 (243)
T PRK15007 20 AETIRFATE--ASYPPFESIDA-----NN-QIVGFDVDLAQALCKEIDATC--TFSN---------QAFDSLIPSLKFRR 80 (243)
T ss_pred CCcEEEEeC--CCCCCceeeCC-----CC-CEEeeeHHHHHHHHHHhCCcE--EEEe---------CCHHHHhHHHhCCC
Confidence 468999997 68899998753 45 899999999999999999854 4443 26999999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDF 207 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~ 207 (561)
+|++++++..+++|.+.++||.||+..+.+++.+...
T Consensus 81 ~D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~v~~~~~------------------------------------------- 117 (243)
T PRK15007 81 VEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGK------------------------------------------- 117 (243)
T ss_pred cCEEEEcCccCHHHhcccceecCccccceEEEEeCCC-------------------------------------------
Confidence 9999887889999999999999999988887776331
Q ss_pred CCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCee
Q 037841 208 RGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNV 287 (561)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~v 287 (561)
+++++|| +|++|
T Consensus 118 ------------------------------------------------------------------~~~~~dL--~g~~I 129 (243)
T PRK15007 118 ------------------------------------------------------------------YTSVDQL--KGKKV 129 (243)
T ss_pred ------------------------------------------------------------------CCCHHHh--CCCeE
Confidence 4789999 68999
Q ss_pred EEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCcc-----cccC
Q 037841 288 GYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPT-----FKTA 362 (561)
Q Consensus 288 g~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~-----~~~~ 362 (561)
|+..|+...+++++. .+..+.+.+++.++.+.+|..|+ +|+++.+...+.+++++... +..++.. +...
T Consensus 130 gv~~g~~~~~~l~~~-~~~~~~~~~~~~~~~~~~L~~gr----vDa~i~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 203 (243)
T PRK15007 130 GVQNGTTHQKFIMDK-HPEITTVPYDSYQNAKLDLQNGR----IDAVFGDTAVVTEWLKDNPK-LAAVGDKVTDKDYFGT 203 (243)
T ss_pred EEecCcHHHHHHHHh-CCCCeEEEcCCHHHHHHHHHcCC----CCEEEeCHHHHHHHHhcCCC-ceeecCcccccccCCc
Confidence 999999988888763 55667788999999999999999 99999999888888877653 4443322 2234
Q ss_pred ceEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHcc
Q 037841 363 GFGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWFK 400 (561)
Q Consensus 363 ~~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~~ 400 (561)
+++++++++.+ |+..||++|.++.++|.++++.++|++
T Consensus 204 ~~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~i~~~w~~ 242 (243)
T PRK15007 204 GLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKWFQ 242 (243)
T ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 57899998865 999999999999999999999999984
No 10
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.86 E-value=2.2e-20 Score=186.31 Aligned_cols=219 Identities=14% Similarity=0.212 Sum_probs=180.5
Q ss_pred CCCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHC-CCceeEEEEecCCCCCCCCCCHHHHHHHHH
Q 037841 46 TNEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQEL-PYAVAYDFVPYGQPDGTSSGSYNDLIYQVF 124 (561)
Q Consensus 46 ~~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l-~f~v~~~~v~~~~~~g~~ngs~~~li~~l~ 124 (561)
.+.++|+||+. ++|+||.+.+. +++ ++.|+++|+++++++++ |..+++++.+. +|...+.+|.
T Consensus 35 ~~~g~l~vg~~--~~~pP~~~~~~----~~g-~~~G~~vdl~~~ia~~llg~~~~~~~~~~---------~~~~~~~~l~ 98 (259)
T PRK11917 35 KSKGQLIVGVK--NDVPHYALLDQ----ATG-EIKGFEIDVAKLLAKSILGDDKKIKLVAV---------NAKTRGPLLD 98 (259)
T ss_pred HhCCEEEEEEC--CCCCCceeeeC----CCC-ceeEeeHHHHHHHHHHhcCCCccEEEEEc---------ChhhHHHHHH
Confidence 34688999998 78999998642 245 89999999999999994 86666777663 4667778999
Q ss_pred cCcccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccC
Q 037841 125 LGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVN 204 (561)
Q Consensus 125 ~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~ 204 (561)
+|++|++++++++|++|.+.++||.||+.++.++++++...
T Consensus 99 ~g~~D~~~~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~~--------------------------------------- 139 (259)
T PRK11917 99 NGSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEKN--------------------------------------- 139 (259)
T ss_pred CCCccEEEecccCChhhhheeeeccCceeeceEEEEECCCC---------------------------------------
Confidence 99999999999999999999999999999999999996542
Q ss_pred CCCCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCC
Q 037841 205 EDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRG 284 (561)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~ 284 (561)
+++++|| +|
T Consensus 140 ---------------------------------------------------------------------~~s~~dL--~g 148 (259)
T PRK11917 140 ---------------------------------------------------------------------YKSLADM--KG 148 (259)
T ss_pred ---------------------------------------------------------------------CCCHHHh--CC
Confidence 6889999 69
Q ss_pred CeeEEEeCchHHHHHHhc---CCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCccccc
Q 037841 285 DNVGYQKGSFVLGILKQL---GFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPTFKT 361 (561)
Q Consensus 285 ~~vg~~~gs~~~~~l~~~---~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~~~~ 361 (561)
++||+..|+...+.+.+. .....+++.+++..+..++|..|+ +||++.+...+..+..+. ..++++.+..
T Consensus 149 ~~V~v~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~Gr----vDa~~~d~~~~~~~~~~~---~~~~~~~~~~ 221 (259)
T PRK11917 149 ANIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKR----VDAFSVDKSILLGYVDDK---SEILPDSFEP 221 (259)
T ss_pred CeEEEecCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCC----CcEEEecHHHHHHhhhcC---CeecCCcCCC
Confidence 999999999877766542 112345678889999999999999 999999987776655432 3566777777
Q ss_pred CceEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHc
Q 037841 362 AGFGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWF 399 (561)
Q Consensus 362 ~~~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~ 399 (561)
.+++++++|+++ +...+|++|.++.. .+++|.+||-
T Consensus 222 ~~~~~a~~k~~~~l~~~ln~~l~~~~~--~~~~i~~kw~ 258 (259)
T PRK11917 222 QSYGIVTKKDDPAFAKYVDDFVKEHKN--EIDALAKKWG 258 (259)
T ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHH--HHHHHHHHhC
Confidence 889999999988 99999999999854 8999999994
No 11
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.86 E-value=2.3e-20 Score=186.36 Aligned_cols=222 Identities=16% Similarity=0.263 Sum_probs=179.4
Q ss_pred CCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcC
Q 037841 47 NEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLG 126 (561)
Q Consensus 47 ~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g 126 (561)
..++|+||+. ++|+||.+.+. ++ ++.|+++||++++++++|.+ ++++. .+|..++.++..|
T Consensus 24 ~~~~l~v~~~--~~~pPf~~~~~-----~g-~~~G~~vdl~~~ia~~lg~~--~~~~~---------~~~~~~~~~l~~g 84 (260)
T PRK15010 24 LPETVRIGTD--TTYAPFSSKDA-----KG-DFVGFDIDLGNEMCKRMQVK--CTWVA---------SDFDALIPSLKAK 84 (260)
T ss_pred cCCeEEEEec--CCcCCceeECC-----CC-CEEeeeHHHHHHHHHHhCCc--eEEEe---------CCHHHHHHHHHCC
Confidence 3588999997 67899999752 45 89999999999999999975 55554 2699999999999
Q ss_pred cccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCC
Q 037841 127 EFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNED 206 (561)
Q Consensus 127 ~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~ 206 (561)
++|++++++..+++|.+.++||.||+.+..++++++....
T Consensus 85 ~~Di~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~---------------------------------------- 124 (260)
T PRK15010 85 KIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPI---------------------------------------- 124 (260)
T ss_pred CCCEEEecCcCCHHHHhhcccccceEeccEEEEEECCCCC----------------------------------------
Confidence 9999998899999999999999999999999999866532
Q ss_pred CCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCe
Q 037841 207 FRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN 286 (561)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~ 286 (561)
..+++|| +|++
T Consensus 125 -------------------------------------------------------------------~~~~~dl--~g~~ 135 (260)
T PRK15010 125 -------------------------------------------------------------------QPTLDSL--KGKH 135 (260)
T ss_pred -------------------------------------------------------------------CCChhHc--CCCE
Confidence 2468899 6899
Q ss_pred eEEEeCchHHHHHHhc-CCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHH-HHhcC-CcceEEeCccc----
Q 037841 287 VGYQKGSFVLGILKQL-GFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKL-LVGQH-CYKYTMVEPTF---- 359 (561)
Q Consensus 287 vg~~~gs~~~~~l~~~-~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~-~l~~~-~~~l~~v~~~~---- 359 (561)
||+..|+....++.+. .....+++.+++.++++++|.+|+ +|+++.+...+.+ +.++. ...+...++.+
T Consensus 136 Igv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~gr----iDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 211 (260)
T PRK15010 136 VGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGR----LDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKK 211 (260)
T ss_pred EEEecCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCC----ccEEEeCcHHHHHHHHhCCCCCceEEecCcccccc
Confidence 9999999887777542 122346677889999999999999 9999999877654 34432 33455554332
Q ss_pred -ccCceEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHcc
Q 037841 360 -KTAGFGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWFK 400 (561)
Q Consensus 360 -~~~~~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~~ 400 (561)
.....+++++++.+ |+..+|++|.++.++|.+++|.+||++
T Consensus 212 ~~~~~~~~a~~~~~~~L~~~ln~~l~~l~~~G~~~~i~~ky~~ 254 (260)
T PRK15010 212 YFGDGTGVGLRKDDAELTAAFNKALGELRQDGTYDKMAKKYFD 254 (260)
T ss_pred ccCCceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 22346789999876 999999999999999999999999995
No 12
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.86 E-value=4.9e-20 Score=182.45 Aligned_cols=218 Identities=23% Similarity=0.395 Sum_probs=184.6
Q ss_pred ceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcc
Q 037841 49 KKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEF 128 (561)
Q Consensus 49 ~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~ 128 (561)
+.|+||+. .+|+||.+.+ +++ +++|+++|+++++++.+|. ++++++ .+|.+++.++.+|++
T Consensus 24 ~~l~v~~~--~~~~P~~~~~-----~~g-~~~G~~~dl~~~i~~~lg~--~~~~~~---------~~~~~~~~~l~~G~~ 84 (250)
T TIGR01096 24 GSVRIGTE--TGYPPFESKD-----ANG-KLVGFDVDLAKALCKRMKA--KCKFVE---------QNFDGLIPSLKAKKV 84 (250)
T ss_pred CeEEEEEC--CCCCCceEEC-----CCC-CEEeehHHHHHHHHHHhCC--eEEEEe---------CCHHHHHHHHhCCCc
Confidence 68999996 6889998865 345 8999999999999999997 556555 269999999999999
Q ss_pred cEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCCC
Q 037841 129 DAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDFR 208 (561)
Q Consensus 129 D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~ 208 (561)
|++++++..+.+|.+.+.||.|++.++..++++.....
T Consensus 85 D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~------------------------------------------ 122 (250)
T TIGR01096 85 DAIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDL------------------------------------------ 122 (250)
T ss_pred CEEEecCccCHHHhhccccccchhcCCeEEEEECCCCc------------------------------------------
Confidence 99988788999999999999999999999999865432
Q ss_pred CCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCeeE
Q 037841 209 GPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVG 288 (561)
Q Consensus 209 ~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~vg 288 (561)
+.+++|| .|++||
T Consensus 123 -----------------------------------------------------------------~~~~~dl--~g~~i~ 135 (250)
T TIGR01096 123 -----------------------------------------------------------------AKTLEDL--DGKTVG 135 (250)
T ss_pred -----------------------------------------------------------------CCChHHc--CCCEEE
Confidence 3678899 588999
Q ss_pred EEeCchHHHHHHhcCCC-ccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCC--cceEEeCccccc----
Q 037841 289 YQKGSFVLGILKQLGFD-ERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHC--YKYTMVEPTFKT---- 361 (561)
Q Consensus 289 ~~~gs~~~~~l~~~~~~-~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~--~~l~~v~~~~~~---- 361 (561)
+..|+....++++. ++ ..+++.+.+.++++++|.+|+ +|+++.+...+.+++++.. +++.+++..+..
T Consensus 136 ~~~g~~~~~~l~~~-~~~~~~~~~~~s~~~~~~~L~~g~----vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 210 (250)
T TIGR01096 136 VQSGTTHEQYLKDY-FKPGVDIVEYDSYDNANMDLKAGR----IDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYF 210 (250)
T ss_pred EecCchHHHHHHHh-ccCCcEEEEcCCHHHHHHHHHcCC----CCEEEeCHHHHHHHHHhCCCCCceEEecccccccccc
Confidence 99999988888764 33 557788999999999999999 9999999999998887763 246666654332
Q ss_pred -CceEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHc
Q 037841 362 -AGFGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWF 399 (561)
Q Consensus 362 -~~~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~ 399 (561)
..++++++++++ |+..+|++|.++.++|.+++|.++|+
T Consensus 211 ~~~~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 211 GDGYGIGLRKGDTELKAAFNKALAAIRADGTYQKISKKWF 250 (250)
T ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHhhC
Confidence 247899999887 99999999999999999999999996
No 13
>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=99.85 E-value=3.4e-20 Score=186.75 Aligned_cols=227 Identities=19% Similarity=0.206 Sum_probs=184.1
Q ss_pred ccCCCCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCc-eeEEEEecCCCCCCCCCCHHHHHH
Q 037841 43 EVPTNEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYA-VAYDFVPYGQPDGTSSGSYNDLIY 121 (561)
Q Consensus 43 ~~~~~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~-v~~~~v~~~~~~g~~ngs~~~li~ 121 (561)
.-....++|+||+. +|+||.+.+. ++ .+.|+++||++++++++|+. +.++. .+|+.++.
T Consensus 27 ~~i~~~~~l~v~~~---~~pP~~~~~~-----~g-~~~G~~~dl~~~i~~~lg~~~~~~~~-----------~~w~~~~~ 86 (275)
T TIGR02995 27 EELKEQGFARIAIA---NEPPFTYVGA-----DG-KVSGAAPDVARAIFKRLGIADVNASI-----------TEYGALIP 86 (275)
T ss_pred HHHHhCCcEEEEcc---CCCCceeECC-----CC-ceecchHHHHHHHHHHhCCCceeecc-----------CCHHHHHH
Confidence 33345678999996 5788888653 34 78999999999999999974 33332 26999999
Q ss_pred HHHcCcccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhc
Q 037841 122 QVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEH 201 (561)
Q Consensus 122 ~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~ 201 (561)
.+.+|++|+++++++++++|...++||.||+.+..++++++.....
T Consensus 87 ~l~~G~~Di~~~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~~~---------------------------------- 132 (275)
T TIGR02995 87 GLQAGRFDAIAAGLFIKPERCKQVAFTQPILCDAEALLVKKGNPKG---------------------------------- 132 (275)
T ss_pred HHHCCCcCEEeecccCCHHHHhccccccceeecceeEEEECCCCCC----------------------------------
Confidence 9999999999888999999999999999999999999998765321
Q ss_pred ccCCCCCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHH
Q 037841 202 RVNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLI 281 (561)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~ 281 (561)
+++++||.
T Consensus 133 ------------------------------------------------------------------------i~~~~dl~ 140 (275)
T TIGR02995 133 ------------------------------------------------------------------------LKSYKDIA 140 (275)
T ss_pred ------------------------------------------------------------------------CCCHHHhc
Confidence 67888884
Q ss_pred h-CCCeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCC-cceEEeCccc
Q 037841 282 K-RGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHC-YKYTMVEPTF 359 (561)
Q Consensus 282 ~-~~~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~-~~l~~v~~~~ 359 (561)
. .|.+||+..|+...+++++.+.+..+++.+++.++++++|.+|+ +|+++.+...+.+++++.. .++..+.+..
T Consensus 141 ~~~g~~Igv~~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~gr----vDa~i~d~~~~~~~~~~~~~~~~~~~~~~~ 216 (275)
T TIGR02995 141 KNPDAKIAAPGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGR----ADAYSLTVLTINDLASKAGDPNVEVLAPFK 216 (275)
T ss_pred cCCCceEEEeCCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCC----CCEEecChHHHHHHHHhCCCCCceeecCcc
Confidence 3 36799999999999999886666667889999999999999999 9999999999888887642 1344333211
Q ss_pred ---ccCceEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHc
Q 037841 360 ---KTAGFGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWF 399 (561)
Q Consensus 360 ---~~~~~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~ 399 (561)
....++|+++++.+ |++.||++|.++.++|.+++|.++|-
T Consensus 217 ~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~~sG~~~~i~~ky~ 260 (275)
T TIGR02995 217 DAPVRYYGGAAFRPEDKELRDAFNVELAKLKESGEFAKIIAPYG 260 (275)
T ss_pred CCccccceeEEECCCCHHHHHHHHHHHHHHHhChHHHHHHHHhC
Confidence 11233788888766 99999999999999999999999994
No 14
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.84 E-value=1.8e-19 Score=179.86 Aligned_cols=222 Identities=18% Similarity=0.283 Sum_probs=177.7
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
..+|+||+. ++|+||.+.+. ++ ++.|+++||++++++++|.++++ +. .+|..++.++.+|+
T Consensus 25 ~~~l~v~~~--~~~~P~~~~~~-----~g-~~~G~~vdi~~~ia~~lg~~i~~--~~---------~pw~~~~~~l~~g~ 85 (259)
T PRK15437 25 PQNIRIGTD--PTYAPFESKNS-----QG-ELVGFDIDLAKELCKRINTQCTF--VE---------NPLDALIPSLKAKK 85 (259)
T ss_pred CCeEEEEeC--CCCCCcceeCC-----CC-CEEeeeHHHHHHHHHHcCCceEE--Ee---------CCHHHHHHHHHCCC
Confidence 578999986 57889988653 45 89999999999999999985555 44 25999999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDF 207 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~ 207 (561)
+|+++++++.+++|.+.++||.||..++.++++++..+.
T Consensus 86 ~D~~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~----------------------------------------- 124 (259)
T PRK15437 86 IDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDI----------------------------------------- 124 (259)
T ss_pred CCEEEecCCCCHHHhhhccccchhhcCceEEEEECCCCC-----------------------------------------
Confidence 999998899999999999999999999999999865432
Q ss_pred CCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCee
Q 037841 208 RGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNV 287 (561)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~v 287 (561)
..+++|| +|.+|
T Consensus 125 ------------------------------------------------------------------~~~~~dl--~g~~I 136 (259)
T PRK15437 125 ------------------------------------------------------------------QPTVESL--KGKRV 136 (259)
T ss_pred ------------------------------------------------------------------CCChHHh--CCCEE
Confidence 2468899 78999
Q ss_pred EEEeCchHHHHHHhcCC-CccceeecCChHHHHHHhhccccCCceeEEeecchhHHH-HHhcC-CcceEEeCc-----cc
Q 037841 288 GYQKGSFVLGILKQLGF-DERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKL-LVGQH-CYKYTMVEP-----TF 359 (561)
Q Consensus 288 g~~~gs~~~~~l~~~~~-~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~-~l~~~-~~~l~~v~~-----~~ 359 (561)
|+..|+....++++... ...+++.+.+.++.+++|..|+ +|+++.+...+.. ++.+. -..+.+.+. .+
T Consensus 137 gv~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~gr----vD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~ 212 (259)
T PRK15437 137 GVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGR----IDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKL 212 (259)
T ss_pred EEecCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCC----ccEEEechHHHHHHHHhCCCCCceEEecCccccccc
Confidence 99999998888876322 2356788889999999999999 9999998876643 33332 222433322 22
Q ss_pred ccCceEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHccc
Q 037841 360 KTAGFGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWFKK 401 (561)
Q Consensus 360 ~~~~~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~~~ 401 (561)
....++++++++.+ |++.+|++|.++..+|.+++|.++|++.
T Consensus 213 ~~~~~~ia~~~~~~~l~~~~n~~l~~~~~~G~~~~i~~k~~~~ 255 (259)
T PRK15437 213 FGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDF 255 (259)
T ss_pred cCcceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHHhcCC
Confidence 23446788887766 9999999999999999999999999963
No 15
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.83 E-value=6.8e-19 Score=211.58 Aligned_cols=218 Identities=16% Similarity=0.226 Sum_probs=183.1
Q ss_pred CCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcC
Q 037841 47 NEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLG 126 (561)
Q Consensus 47 ~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g 126 (561)
+.++|+||+. ++|+||.+.+. ++ ++.||++|+++++++++|. ++++++.. +|..+..++.+|
T Consensus 300 ~~~~l~v~~~--~~~pP~~~~d~-----~g-~~~G~~~Dll~~i~~~~g~--~~~~v~~~--------~~~~~~~~l~~g 361 (1197)
T PRK09959 300 QHPDLKVLEN--PYSPPYSMTDE-----NG-SVRGVMGDILNIITLQTGL--NFSPITVS--------HNIHAGTQLNPG 361 (1197)
T ss_pred HCCceEEEcC--CCCCCeeEECC-----CC-cEeeehHHHHHHHHHHHCC--eEEEEecC--------CHHHHHHHHHCC
Confidence 3678999987 88999999863 35 8999999999999999996 67777754 688899999999
Q ss_pred cccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCC
Q 037841 127 EFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNED 206 (561)
Q Consensus 127 ~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~ 206 (561)
++|++.+ +..+++|.+.++||.||+.+++++++++....
T Consensus 362 ~~D~i~~-~~~t~~r~~~~~fs~py~~~~~~~v~~~~~~~---------------------------------------- 400 (1197)
T PRK09959 362 GWDIIPG-AIYSEDRENNVLFAEAFITTPYVFVMQKAPDS---------------------------------------- 400 (1197)
T ss_pred CceEeec-ccCCccccccceeccccccCCEEEEEecCCCC----------------------------------------
Confidence 9999876 66899999999999999999999998754321
Q ss_pred CCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCe
Q 037841 207 FRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN 286 (561)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~ 286 (561)
+.+ +. +|++
T Consensus 401 -------------------------------------------------------------------~~~---~~-~g~~ 409 (1197)
T PRK09959 401 -------------------------------------------------------------------EQT---LK-KGMK 409 (1197)
T ss_pred -------------------------------------------------------------------ccc---cc-cCCE
Confidence 122 22 5889
Q ss_pred eEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCC-cc-eEEeCcccccCce
Q 037841 287 VGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHC-YK-YTMVEPTFKTAGF 364 (561)
Q Consensus 287 vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~-~~-l~~v~~~~~~~~~ 364 (561)
||+..|+...+++++. ++..+++.|++.++++++|.+|+ +||++.+...+.|+++++. .. +....+.+....+
T Consensus 410 vav~~g~~~~~~~~~~-~p~~~~~~~~~~~~~l~av~~G~----~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 484 (1197)
T PRK09959 410 VAIPYYYELHSQLKEM-YPEVEWIKVDNASAAFHKVKEGE----LDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASL 484 (1197)
T ss_pred EEEeCCcchHHHHHHH-CCCcEEEEcCCHHHHHHHHHcCC----CCEEehhhHHHHHHHHhcccccceeeecCCCCchhe
Confidence 9999999888888763 67788999999999999999999 9999999999999998752 22 3344444556678
Q ss_pred EEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHcc
Q 037841 365 GFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWFK 400 (561)
Q Consensus 365 ~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~~ 400 (561)
+|+++|+.| |...+|++|..+.++ .++++.+||++
T Consensus 485 ~~av~k~~~~L~~~lnk~l~~i~~~-~~~~i~~kW~~ 520 (1197)
T PRK09959 485 SFAFPRGEPELKDIINKALNAIPPS-EVLRLTEKWIK 520 (1197)
T ss_pred EEeeCCCCHHHHHHHHHHHHhCCHH-HHHHHHhhccc
Confidence 999999988 999999999999998 88899999995
No 16
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.81 E-value=9.9e-19 Score=189.29 Aligned_cols=226 Identities=17% Similarity=0.175 Sum_probs=179.0
Q ss_pred ccCCCCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHH
Q 037841 43 EVPTNEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQ 122 (561)
Q Consensus 43 ~~~~~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~ 122 (561)
..-.+.++||||+.. .|+.+.+. .+ ...||++|+++++++++|.++++ +... +|++++.+
T Consensus 37 ~~I~~~g~LrVg~~~----~P~~~~~~-----~~-~~~G~~~DLl~~ia~~LGv~~e~--v~~~--------~~~~ll~a 96 (482)
T PRK10859 37 EQIQERGELRVGTIN----SPLTYYIG-----ND-GPTGFEYELAKRFADYLGVKLEI--KVRD--------NISQLFDA 96 (482)
T ss_pred HHHHhCCEEEEEEec----CCCeeEec-----CC-CcccHHHHHHHHHHHHhCCcEEE--EecC--------CHHHHHHH
Confidence 333457889999973 24444432 22 45999999999999999985554 4322 79999999
Q ss_pred HHcCcccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcc
Q 037841 123 VFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHR 202 (561)
Q Consensus 123 l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~ 202 (561)
|.+|++|++++++++|++|.+.++||.||+....++++++....
T Consensus 97 L~~G~iDi~~~~lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~~~------------------------------------ 140 (482)
T PRK10859 97 LDKGKADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQPR------------------------------------ 140 (482)
T ss_pred HhCCCCCEEeccCcCChhhhccCcccCCceeeeEEEEEeCCCCC------------------------------------
Confidence 99999999988899999999999999999999999999865422
Q ss_pred cCCCCCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHh
Q 037841 203 VNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIK 282 (561)
Q Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~ 282 (561)
+++++||
T Consensus 141 -----------------------------------------------------------------------i~~l~dL-- 147 (482)
T PRK10859 141 -----------------------------------------------------------------------PRSLGDL-- 147 (482)
T ss_pred -----------------------------------------------------------------------CCCHHHh--
Confidence 6889999
Q ss_pred CCCeeEEEeCchHHHHHHhcC--CCccce--eecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCcc
Q 037841 283 RGDNVGYQKGSFVLGILKQLG--FDERKL--VVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPT 358 (561)
Q Consensus 283 ~~~~vg~~~gs~~~~~l~~~~--~~~~~~--~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~ 358 (561)
+|++||+..|+...+.+++.. ++..++ ..+.+.++++++|..|+ +|+++.+...+.+....+. ++.+....
T Consensus 148 ~Gk~I~V~~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~----iDa~v~d~~~~~~~~~~~p-~l~v~~~l 222 (482)
T PRK10859 148 KGGTLTVAAGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGK----IDYTIADSVEISLNQRYHP-ELAVAFDL 222 (482)
T ss_pred CCCeEEEECCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCC----CCEEEECcHHHHHHHHhCC-Cceeeeec
Confidence 699999999999888886532 333333 34578999999999999 9999999877765544444 35555444
Q ss_pred cccCceEEEecCC-CC-ChhhHHHHHhhccccchhHHHHHHHcccC
Q 037841 359 FKTAGFGFAFPLH-SP-LVHDVSKAILSVTEGDKMKEIEDAWFKKH 402 (561)
Q Consensus 359 ~~~~~~~~~~~k~-sp-l~~~in~~Il~l~e~G~~~~i~~kw~~~~ 402 (561)
....+++++++|+ .+ |+..+|++|.++.++|.++++.++|++..
T Consensus 223 ~~~~~~~~av~k~~~~~L~~~ln~~L~~i~~~G~l~~L~~kyfg~~ 268 (482)
T PRK10859 223 TDEQPVAWALPPSGDDSLYAALLDFFNQIKEDGTLARLEEKYFGHV 268 (482)
T ss_pred CCCceeEEEEeCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHhhhh
Confidence 4556789999994 55 99999999999999999999999999653
No 17
>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=99.77 E-value=1.1e-17 Score=165.74 Aligned_cols=208 Identities=17% Similarity=0.136 Sum_probs=157.0
Q ss_pred eEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHH---HHHHcC
Q 037841 50 KLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLI---YQVFLG 126 (561)
Q Consensus 50 ~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li---~~l~~g 126 (561)
+||||+. ++|+||.+.+ . .||++|+++++++++|++++ +++. +|++++ ..|.+|
T Consensus 1 ~l~vg~~--~~~pPf~~~~---------~-~Gfdvdl~~~ia~~lg~~~~--~~~~---------~~~~~~~~~~~L~~g 57 (246)
T TIGR03870 1 TLRVCAA--TKEAPYSTKD---------G-SGFENKIAAALAAAMGRKVV--FVWL---------AKPAIYLVRDGLDKK 57 (246)
T ss_pred CeEEEeC--CCCCCCccCC---------C-CcchHHHHHHHHHHhCCCeE--EEEe---------ccchhhHHHHHHhcC
Confidence 4899998 8999999852 2 59999999999999997544 4442 466655 699999
Q ss_pred cccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCC
Q 037841 127 EFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNED 206 (561)
Q Consensus 127 ~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~ 206 (561)
++|++++ ++++++| ++||.||+.++.++++++.+...
T Consensus 58 ~~Dii~~-~~~t~~r---~~fS~PY~~~~~~~v~~k~~~~~--------------------------------------- 94 (246)
T TIGR03870 58 LCDVVLG-LDTGDPR---VLTTKPYYRSSYVFLTRKDRNLD--------------------------------------- 94 (246)
T ss_pred CccEEEe-CCCChHH---HhcccCcEEeeeEEEEeCCCCCC---------------------------------------
Confidence 9999985 8888777 67999999999999999765322
Q ss_pred CCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHH--HHhCC
Q 037841 207 FRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKM--LIKRG 284 (561)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~d--L~~~~ 284 (561)
+++++| | .|
T Consensus 95 -------------------------------------------------------------------~~~~~d~~L--~g 105 (246)
T TIGR03870 95 -------------------------------------------------------------------IKSWNDPRL--KK 105 (246)
T ss_pred -------------------------------------------------------------------CCCccchhh--cc
Confidence 577754 6 68
Q ss_pred C-eeEEEeCchHHHHHHhcCCC------ccceeecC---------ChHHHHHHhhccccCCceeEEeecchhHHHHHhcC
Q 037841 285 D-NVGYQKGSFVLGILKQLGFD------ERKLVVYN---------SPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQH 348 (561)
Q Consensus 285 ~-~vg~~~gs~~~~~l~~~~~~------~~~~~~~~---------s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~ 348 (561)
+ +||+..|+..+.++++.... ..+++.+. +.++++++|..|+ +||++.+...+.+++.+.
T Consensus 106 ~~~vgv~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~Gr----vDa~i~~~~~~~~~~~~~ 181 (246)
T TIGR03870 106 VSKIGVIFGSPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVATGK----ADLAVAFAPEVARYVKAS 181 (246)
T ss_pred CceEEEecCChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHcCC----CCEEEeeHHhHHHHHHhC
Confidence 7 99999999999998864210 11122222 3578899999999 999999877777777654
Q ss_pred CcceE--EeCcccc---------cCceEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHH
Q 037841 349 CYKYT--MVEPTFK---------TAGFGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAW 398 (561)
Q Consensus 349 ~~~l~--~v~~~~~---------~~~~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw 398 (561)
...+. .+++... ...++++++|+.+ |++.||++|.++. |.+++|..+|
T Consensus 182 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l~--~~~~~i~~~y 241 (246)
T TIGR03870 182 PEPLRMTVIPDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKAK--PRIDAILKEE 241 (246)
T ss_pred CCCceEEeccccccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHhH--HHHHHHHHHc
Confidence 22232 2332211 1135899999988 9999999999998 4899999988
No 18
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.74 E-value=1.1e-16 Score=160.53 Aligned_cols=227 Identities=25% Similarity=0.335 Sum_probs=184.1
Q ss_pred CCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcC
Q 037841 47 NEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLG 126 (561)
Q Consensus 47 ~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g 126 (561)
....++||+.. ...+||.+.+.. .+ ++.||++|+++++++.++.....+++. .+|++++..+..|
T Consensus 32 ~~~~~~v~~~~-~~~~p~~~~~~~----~~-~~~G~dvdl~~~ia~~l~~~~~~~~~~---------~~~~~~~~~l~~g 96 (275)
T COG0834 32 ARGKLRVGTEA-TYAPPFEFLDAK----GG-KLVGFDVDLAKAIAKRLGGDKKVEFVP---------VAWDGLIPALKAG 96 (275)
T ss_pred hcCeEEEEecC-CCCCCcccccCC----CC-eEEeeeHHHHHHHHHHhCCcceeEEec---------cchhhhhHHHhcC
Confidence 46789999972 333588887642 15 899999999999999998643344444 3699999999999
Q ss_pred cccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCC
Q 037841 127 EFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNED 206 (561)
Q Consensus 127 ~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~ 206 (561)
++|+++.++++|++|.+.++||.||+.++..+++++.....
T Consensus 97 ~~D~~~~~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~~~--------------------------------------- 137 (275)
T COG0834 97 KVDIIIAGMTITPERKKKVDFSDPYYYSGQVLLVKKDSDIG--------------------------------------- 137 (275)
T ss_pred CcCEEEeccccCHHHhccccccccccccCeEEEEECCCCcC---------------------------------------
Confidence 99999999999999999999999999999999999776532
Q ss_pred CCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCe
Q 037841 207 FRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN 286 (561)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~ 286 (561)
+++++|| .|++
T Consensus 138 -------------------------------------------------------------------~~~~~DL--~gk~ 148 (275)
T COG0834 138 -------------------------------------------------------------------IKSLEDL--KGKK 148 (275)
T ss_pred -------------------------------------------------------------------cCCHHHh--CCCE
Confidence 5789999 6899
Q ss_pred eEEEeCch--HHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHH--HhcCCcceEEeCccccc-
Q 037841 287 VGYQKGSF--VLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLL--VGQHCYKYTMVEPTFKT- 361 (561)
Q Consensus 287 vg~~~gs~--~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~--l~~~~~~l~~v~~~~~~- 361 (561)
+|+..|+. ....... ..+...++.|++..+.+.+|..|+ +||++.+...+.+. ..+..............
T Consensus 149 v~v~~gt~~~~~~~~~~-~~~~~~~~~~~~~~~~~~al~~Gr----~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (275)
T COG0834 149 VGVQLGTTDEAEEKAKK-PGPNAKIVAYDSNAEALLALKNGR----ADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSV 223 (275)
T ss_pred EEEEcCcchhHHHHHhh-ccCCceEEeeCCHHHHHHHHHcCC----ccEEEcchHhhhhhhhhhcCCCCceeeeccCCCc
Confidence 99999999 4444444 344567899999999999999999 99999999998884 44443223333333333
Q ss_pred CceEEEecCC--CCChhhHHHHHhhccccchhHHHHHHHccc
Q 037841 362 AGFGFAFPLH--SPLVHDVSKAILSVTEGDKMKEIEDAWFKK 401 (561)
Q Consensus 362 ~~~~~~~~k~--spl~~~in~~Il~l~e~G~~~~i~~kw~~~ 401 (561)
.+++++++|+ ..+++.+|++|.++.++|.++++.++|+..
T Consensus 224 ~~~~~~~~~~~~~~l~~~in~~l~~l~~~G~~~~i~~kw~~~ 265 (275)
T COG0834 224 EYLGIALRKGDDPELLEAVNKALKELKADGTLQKISDKWFGP 265 (275)
T ss_pred ceeEEEeccCCcHHHHHHHHHHHHHHHhCccHHHHHHHhcCc
Confidence 6889999999 469999999999999999999999999963
No 19
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.74 E-value=3.7e-17 Score=196.65 Aligned_cols=223 Identities=13% Similarity=0.123 Sum_probs=186.5
Q ss_pred CCCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHc
Q 037841 46 TNEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFL 125 (561)
Q Consensus 46 ~~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~ 125 (561)
.+.++|+||+. ++|+|+.+... .++ ++.||++|+++.+++++|. +++++++. +|++++.++.+
T Consensus 53 ~~~~~l~vgv~--~~~~p~~~~~~----~~g-~~~G~~~D~l~~ia~~lG~--~~e~v~~~--------~~~~~l~~l~~ 115 (1197)
T PRK09959 53 ASKKNLVIAVH--KSQTATLLHTD----SQQ-RVRGINADYLNLLKRALNI--KLTLREYA--------DHQKAMDALEE 115 (1197)
T ss_pred hhCCeEEEEec--CCCCCCceeec----CCC-ccceecHHHHHHHHHhcCC--ceEEEeCC--------CHHHHHHHHHc
Confidence 35788999998 66666554431 245 8999999999999999996 77777754 79999999999
Q ss_pred CcccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCC
Q 037841 126 GEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNE 205 (561)
Q Consensus 126 g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~ 205 (561)
|++|++.+.++.+++|.+.++||.||+.+..++++++...
T Consensus 116 g~iDl~~~~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~~---------------------------------------- 155 (1197)
T PRK09959 116 GEVDIVLSHLVASPPLNDDIAATKPLIITFPALVTTLHDS---------------------------------------- 155 (1197)
T ss_pred CCCcEecCccccccccccchhcCCCccCCCceEEEeCCCC----------------------------------------
Confidence 9999998888999999999999999999999999987542
Q ss_pred CCCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCC
Q 037841 206 DFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGD 285 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~ 285 (561)
+++++++ .++
T Consensus 156 --------------------------------------------------------------------~~~~~~l--~~~ 165 (1197)
T PRK09959 156 --------------------------------------------------------------------MRPLTSS--KPV 165 (1197)
T ss_pred --------------------------------------------------------------------CCCcccc--cCe
Confidence 4677788 688
Q ss_pred eeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCC-cceEEeCc-ccccCc
Q 037841 286 NVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHC-YKYTMVEP-TFKTAG 363 (561)
Q Consensus 286 ~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~-~~l~~v~~-~~~~~~ 363 (561)
++++..|+...+++++ .++..+++.|++.++++++|..|+ +||++.+...+.++++++. ..+.+++. ......
T Consensus 166 ~i~~~~g~~~~~~~~~-~~p~~~i~~~~s~~~al~av~~G~----~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~ 240 (1197)
T PRK09959 166 NIARVANYPPDEVIHQ-SFPKATIISFTNLYQALASVSAGQ----NDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQY 240 (1197)
T ss_pred EEEEeCCCCCHHHHHH-hCCCCEEEeCCCHHHHHHHHHcCC----CCEEEccHHHHHHHHhcccccceEEEeeccCCCCc
Confidence 9999999999888887 478889999999999999999999 9999999999999998752 23444432 223344
Q ss_pred eEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHccc
Q 037841 364 FGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWFKK 401 (561)
Q Consensus 364 ~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~~~ 401 (561)
.+++++|+.+ |...+|++|..+.++|.. .+.++|+..
T Consensus 241 ~~~~~~~~~~~L~~~lnkal~~i~~~~~~-~i~~kW~~~ 278 (1197)
T PRK09959 241 NFFLTRKESVILNEVLNRFVDALTNEVRY-EVSQNWLDT 278 (1197)
T ss_pred eeEEEcCCcHHHHHHHHHHHHhCCHHHHH-HHHHhccCC
Confidence 6788999988 889999999999999877 899999964
No 20
>PF00060 Lig_chan: Ligand-gated ion channel; InterPro: IPR001320 The ability of synapses to modify their synaptic strength in response to activity is a fundamental property of the nervous system and may be an essential component of learning and memory. There are three classes of ionotropic glutamate receptor, namely NMDA (N-methyl-D-aspartate), AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole-4-propionic acid) and kainate receptors. They are believed to play critical roles in synaptic plasticity. At many synapses in the brain, transient activation of NMDA receptors leads to a persistent modification in the strength of synaptic transmission mediated by AMPA receptors and kainate receptors can act as the induction trigger for long-term changes in synaptic transmission [].; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 3FAT_A 3KFM_A 3KEI_A 3EN3_A 3EPE_B 3FAS_A 2F34_A 3C34_B 3S2V_A 3GBB_B ....
Probab=99.74 E-value=3.3e-19 Score=162.23 Aligned_cols=107 Identities=30% Similarity=0.620 Sum_probs=82.1
Q ss_pred chhhHHHHHHHHHHHHHHHhhhhcccCCCCCC-------CccCccchhHHHHHHHhhhcc-ccccccchhHHHHHHHHHH
Q 037841 178 TWDLWVTSGCFFIFIGFVVWALEHRVNEDFRG-------PARHQVGTSFWFSFSTMVFSQ-RERVISNLARFVVIVWYFV 249 (561)
Q Consensus 178 ~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~-~~~~~s~~~Ril~~~w~~~ 249 (561)
++++|++++++++++++++|++++..+.+++. ....++..++|++++++++++ ...|++.+.|++.++|+++
T Consensus 1 s~~vW~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~s~s~Ril~~~w~l~ 80 (148)
T PF00060_consen 1 SWSVWLLILLSILLVSLVLWLFERFSPYEWRKNQSSPPRRWRFSLSNSFWYTFGTLLQQGSSIRPRSWSGRILLAFWWLF 80 (148)
T ss_dssp -HHHHHHHHHHHHHHHTTGGGT------------------HHHHHHHHHHHCCCCCHHHHH------HHHHHHHHHHHHH
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccccCcccHHHHHHHHHHhhccccccccccchHHHHHHHHHHHH
Confidence 47899999999999999999999977766655 234578889999999999766 5678999999999999999
Q ss_pred HHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCC
Q 037841 250 VLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRG 284 (561)
Q Consensus 250 ~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~ 284 (561)
+++++++|+|+|+|+||.++++++|+|++||.+++
T Consensus 81 ~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~ 115 (148)
T PF00060_consen 81 SLILIASYTANLTSFLTVPKYEPPIDSLEDLANSG 115 (148)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHTSS-SSHHHHHTHS
T ss_pred HHHHHHHHHHHHHHHhcccCcCCCCCCHHHHHHCC
Confidence 99999999999999999999999999999998776
No 21
>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=99.73 E-value=5.6e-17 Score=162.65 Aligned_cols=231 Identities=13% Similarity=0.170 Sum_probs=166.3
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHC-CCceeEEEEecCCCCCCCCCCHHHHHHHHHcC
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQEL-PYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLG 126 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l-~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g 126 (561)
.++|++++. +|+||.+.+. ++ ...|+..++++++++++ ++.++++ . .+|.+++..+ .|
T Consensus 17 ~~~l~~~~~---~~pPf~~~~~-----~~-~~~G~~~~i~~~i~~~~~~~~~~~~--~---------~pw~r~l~~l-~~ 75 (268)
T TIGR02285 17 KEAITWIVN---DFPPFFIFSG-----PS-KGRGVFDVILQEIRRALPQYEHRFV--R---------VSFARSLKEL-QG 75 (268)
T ss_pred cceeEEEec---ccCCeeEeCC-----CC-CCCChHHHHHHHHHHHcCCCceeEE--E---------CCHHHHHHHH-hc
Confidence 478998885 7899988642 34 67999999999999998 7654444 3 2599999999 78
Q ss_pred cccEEEeceeeecCcceeeeccccccc-cceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCC
Q 037841 127 EFDAAVGDITILLNRSNYVDFTLPYTE-SGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNE 205 (561)
Q Consensus 127 ~~D~~vg~~~it~~R~~~vdfT~p~~~-~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~ 205 (561)
+.|.++.++++|++|.+.++||.||+. ...++++++.......
T Consensus 76 ~~d~~~~~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~~~------------------------------------ 119 (268)
T TIGR02285 76 KGGVCTVNLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAGVR------------------------------------ 119 (268)
T ss_pred CCCeEEeeccCCcchhhceeecCCccccCCceEEEccchhhhcc------------------------------------
Confidence 888777679999999999999999975 5788888865432100
Q ss_pred CCCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHh-CC
Q 037841 206 DFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIK-RG 284 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~-~~ 284 (561)
.+...-.++.+|.+ +|
T Consensus 120 ---------------------------------------------------------------~~~d~~~~~~~l~~l~g 136 (268)
T TIGR02285 120 ---------------------------------------------------------------DEQDGDVDLKKLLASKK 136 (268)
T ss_pred ---------------------------------------------------------------ccCCCCccHHHHhcCCC
Confidence 00000012333321 57
Q ss_pred CeeEEEeCchH----HHHHHhcCCC-ccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcC---CcceEEeC
Q 037841 285 DNVGYQKGSFV----LGILKQLGFD-ERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQH---CYKYTMVE 356 (561)
Q Consensus 285 ~~vg~~~gs~~----~~~l~~~~~~-~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~---~~~l~~v~ 356 (561)
+++|+..|+.. .+++++.+.. ..++..+++.++.+++|..|+ +|+++.+...+.+++++. ...+...+
T Consensus 137 ~~vgv~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~Gr----vD~~v~d~~~~~~~~~~~~~~~~~~~~~~ 212 (268)
T TIGR02285 137 KRLGVIASRSYGQQIDDILSDSGYQHNTRIIGNAAMGNLFKMLEKGR----VNYTLAYPPEKTYYEELNNGALPPLKFLP 212 (268)
T ss_pred eEEEEecceeccHHHHHHHHhCCcccceeeeccchHHHHHHHHHcCC----ccEEEeCcHHHHHHHHhccCCcCCeeEee
Confidence 78999887654 4445543322 124556677888999999999 999999999999888753 22344443
Q ss_pred ccc--ccCceEEEecCCC---CChhhHHHHHhhccccchhHHHHHHHcccC
Q 037841 357 PTF--KTAGFGFAFPLHS---PLVHDVSKAILSVTEGDKMKEIEDAWFKKH 402 (561)
Q Consensus 357 ~~~--~~~~~~~~~~k~s---pl~~~in~~Il~l~e~G~~~~i~~kw~~~~ 402 (561)
... ...+++++++|+. .++..||++|.+|.++|.+++|.++|++..
T Consensus 213 ~~~~~~~~~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~i~~k~~~~~ 263 (268)
T TIGR02285 213 VAGMPAHISVWVACPKTEWGRKVIADIDQALSELNVDPKYYKYFDRWLSPE 263 (268)
T ss_pred cCCCccceEEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhCCHh
Confidence 221 2235789999974 399999999999999999999999999643
No 22
>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=99.72 E-value=2.3e-16 Score=154.43 Aligned_cols=212 Identities=15% Similarity=0.116 Sum_probs=161.3
Q ss_pred eEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCccc
Q 037841 50 KLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFD 129 (561)
Q Consensus 50 ~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D 129 (561)
.||||+. ++|+||.+. ...|+++||++++++++|.++++++.+. .+..++..+.+|++|
T Consensus 1 ~l~v~~~--~~~~P~~~~----------~~~G~~~el~~~i~~~~g~~i~~~~~~~---------~~~~~~~~l~~g~~D 59 (232)
T TIGR03871 1 ALRVCAD--PNNLPFSNE----------KGEGFENKIAQLLADDLGLPLEYTWFPQ---------RRGFVRNTLNAGRCD 59 (232)
T ss_pred CeEEEeC--CCCCCccCC----------CCCchHHHHHHHHHHHcCCceEEEecCc---------chhhHHHHHhcCCcc
Confidence 4899987 789998752 3469999999999999998766655442 234456789999999
Q ss_pred EEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCCCC
Q 037841 130 AAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDFRG 209 (561)
Q Consensus 130 ~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~ 209 (561)
++++ +++|.+.++||.||...+.++++++.....
T Consensus 60 i~~~----~~~r~~~~~fs~py~~~~~~lv~~~~~~~~------------------------------------------ 93 (232)
T TIGR03871 60 VVIG----VPAGYEMVLTTRPYYRSTYVFVTRKDSLLD------------------------------------------ 93 (232)
T ss_pred EEEe----ccCccccccccCCcEeeeEEEEEeCCCccc------------------------------------------
Confidence 9876 467888899999999999999998764322
Q ss_pred CccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCeeEE
Q 037841 210 PARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGY 289 (561)
Q Consensus 210 ~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~vg~ 289 (561)
+++++|+.-.|.+||+
T Consensus 94 ----------------------------------------------------------------~~~~~d~~l~g~~V~v 109 (232)
T TIGR03871 94 ----------------------------------------------------------------VKSLDDPRLKKLRIGV 109 (232)
T ss_pred ----------------------------------------------------------------ccchhhhhhcCCeEEE
Confidence 6788883226889999
Q ss_pred EeCchHHHHHHhcCCCcccee---------ecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCcc--
Q 037841 290 QKGSFVLGILKQLGFDERKLV---------VYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPT-- 358 (561)
Q Consensus 290 ~~gs~~~~~l~~~~~~~~~~~---------~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~-- 358 (561)
..|+...+++++.+.. .++. ...+..+++.+|..|+ +||++.+...+.+++++....+.+....
T Consensus 110 ~~g~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~G~----~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~ 184 (232)
T TIGR03871 110 FAGTPPAHWLARHGLV-ENVVGYSLFGDYRPESPPGRMVEDLAAGE----IDVAIVWGPIAGYFAKQAGPPLVVVPLLPE 184 (232)
T ss_pred EcCChHHHHHHhcCcc-cccccccccccccccCCHHHHHHHHHcCC----cCEEEeccHHHHHHHHhCCCCceeeccccC
Confidence 9999999988764432 1222 1336789999999999 9999999888888777643234443321
Q ss_pred ----cccCceEEEecCCCC-ChhhHHHHHhhccccchhHHHHHHHc
Q 037841 359 ----FKTAGFGFAFPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWF 399 (561)
Q Consensus 359 ----~~~~~~~~~~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~ 399 (561)
....+++++++++.+ ++..+|++|.++. |.+++|.+||.
T Consensus 185 ~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~--~~~~~i~~kyg 228 (232)
T TIGR03871 185 DGGIPFDYRIAMGVRKGDKAWKDELNAVLDRRQ--AEIDAILREYG 228 (232)
T ss_pred CCCCCccceEEEEEecCCHHHHHHHHHHHHHHH--HHHHHHHHHcC
Confidence 123456888999876 9999999999975 47899999995
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=99.72 E-value=7e-16 Score=146.90 Aligned_cols=215 Identities=29% Similarity=0.449 Sum_probs=178.4
Q ss_pred EEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccE
Q 037841 51 LRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDA 130 (561)
Q Consensus 51 LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~ 130 (561)
|+||+. +.++||.+.+ +++ ...|+..++++.+.+++|. +++++.. .|.+++.++.+|++|+
T Consensus 1 l~i~~~--~~~~p~~~~~-----~~g-~~~G~~~~~~~~~~~~~g~--~~~~~~~---------~~~~~~~~l~~g~~D~ 61 (218)
T cd00134 1 LTVGTA--GTYPPFSFRD-----ANG-ELTGFDVDLAKAIAKELGV--KVKFVEV---------DWDGLITALKSGKVDL 61 (218)
T ss_pred CEEecC--CCCCCeeEEC-----CCC-CEEeeeHHHHHHHHHHhCC--eEEEEeC---------CHHHHHHHHhcCCcCE
Confidence 578887 7889998865 455 8999999999999999996 5555552 4899999999999999
Q ss_pred EEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCCCCC
Q 037841 131 AVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDFRGP 210 (561)
Q Consensus 131 ~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~~ 210 (561)
+++....+.+|...+.|+.|+.....++++++...
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------- 96 (218)
T cd00134 62 IAAGMTITPERAKQVDFSDPYYKSGQVILVKKGSP--------------------------------------------- 96 (218)
T ss_pred EeecCcCCHHHHhhccCcccceeccEEEEEECCCC---------------------------------------------
Confidence 99877778888888999999999999999996643
Q ss_pred ccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCeeEEE
Q 037841 211 ARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGYQ 290 (561)
Q Consensus 211 ~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~vg~~ 290 (561)
+.+++|| .|+++++.
T Consensus 97 ---------------------------------------------------------------~~~~~dl--~g~~i~~~ 111 (218)
T cd00134 97 ---------------------------------------------------------------IKSVKDL--KGKKVAVQ 111 (218)
T ss_pred ---------------------------------------------------------------CCChHHh--CCCEEEEE
Confidence 4689999 68999998
Q ss_pred eCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCcc--cccCceEEEe
Q 037841 291 KGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPT--FKTAGFGFAF 368 (561)
Q Consensus 291 ~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~--~~~~~~~~~~ 368 (561)
.|+....++.+. ....++..+.+.++.+++|.+|+ +|+++.+.....+...+....+.++... .....++++.
T Consensus 112 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~g~----~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 186 (218)
T cd00134 112 KGSTAEKYLKKA-LPEAKVVSYDDNAEALAALENGR----ADAVIVDEIALAALLKKHPPELKIVGPSIDLEPLGFGVAV 186 (218)
T ss_pred cCchHHHHHHHh-CCcccEEEeCCHHHHHHHHHcCC----ccEEEeccHHHHHHHHhcCCCcEEeccccCCCccceEEEE
Confidence 888888888764 23456788889999999999999 9999999999888877662236666553 4445567777
Q ss_pred cCCCC-ChhhHHHHHhhccccchhHHHHHHHc
Q 037841 369 PLHSP-LVHDVSKAILSVTEGDKMKEIEDAWF 399 (561)
Q Consensus 369 ~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~ 399 (561)
.++++ +...++++|.++.++|.++.+.++|+
T Consensus 187 ~~~~~~l~~~~~~~l~~~~~~g~~~~i~~~~~ 218 (218)
T cd00134 187 GKDNKELLDAVNKALKELRADGELKKISKKWF 218 (218)
T ss_pred cCCCHHHHHHHHHHHHHHHhCccHHHHHHhhC
Confidence 77774 99999999999999999999999996
No 24
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.70 E-value=1.4e-15 Score=144.50 Aligned_cols=216 Identities=30% Similarity=0.505 Sum_probs=180.8
Q ss_pred eEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCccc
Q 037841 50 KLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFD 129 (561)
Q Consensus 50 ~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D 129 (561)
+|+||+. +.++||.+.+ .++ ...|+..|+++.+.+++|. ++++.+. +|..++.++.+|++|
T Consensus 1 ~l~v~~~--~~~~p~~~~~-----~~g-~~~G~~~~~~~~~~~~~g~--~~~~~~~---------~~~~~~~~l~~g~~D 61 (219)
T smart00062 1 TLRVGTN--GDYPPFSFAD-----EDG-ELTGFDVDLAKAIAKELGL--KVEFVEV---------SFDNLLTALKSGKID 61 (219)
T ss_pred CEEEEec--CCCCCcEEEC-----CCC-CcccchHHHHHHHHHHhCC--eEEEEec---------cHHHHHHHHHCCccc
Confidence 4899997 7888988865 345 7899999999999999996 5555552 489999999999999
Q ss_pred EEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCCCC
Q 037841 130 AAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDFRG 209 (561)
Q Consensus 130 ~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~ 209 (561)
++++....+.+|...+.++.|+.....++++++..+
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------------------- 97 (219)
T smart00062 62 VVAAGMTITPERAKQVDFSDPYYKSGQVILVRKDSP-------------------------------------------- 97 (219)
T ss_pred EEeccccCCHHHHhheeeccceeeceeEEEEecCCC--------------------------------------------
Confidence 999877667888888999999999999999885532
Q ss_pred CccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCeeEE
Q 037841 210 PARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGY 289 (561)
Q Consensus 210 ~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~vg~ 289 (561)
+++++|| .|+++++
T Consensus 98 ----------------------------------------------------------------~~~~~dL--~g~~i~~ 111 (219)
T smart00062 98 ----------------------------------------------------------------IKSLEDL--KGKKVAV 111 (219)
T ss_pred ----------------------------------------------------------------CCChHHh--CCCEEEE
Confidence 6889999 6889999
Q ss_pred EeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCC-cceEEeCccccc-CceEEE
Q 037841 290 QKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHC-YKYTMVEPTFKT-AGFGFA 367 (561)
Q Consensus 290 ~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~-~~l~~v~~~~~~-~~~~~~ 367 (561)
..|+....++... .+..++..+.+..+.+.+|..|+ +|+++.......+...+.. ..+.++.+.... ..++++
T Consensus 112 ~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~g~----~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (219)
T smart00062 112 VAGTTGEELLKKL-YPEAKIVSYDSQAEALAALKAGR----ADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFA 186 (219)
T ss_pred ecCccHHHHHHHh-CCCceEEEcCCHHHHHHHhhcCc----ccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEE
Confidence 9998888888765 34456778888999999999999 9999999998888877651 246666665555 788999
Q ss_pred ecCCCC-ChhhHHHHHhhccccchhHHHHHHHc
Q 037841 368 FPLHSP-LVHDVSKAILSVTEGDKMKEIEDAWF 399 (561)
Q Consensus 368 ~~k~sp-l~~~in~~Il~l~e~G~~~~i~~kw~ 399 (561)
++++++ +.+.++++|.++.++|.++++.++|+
T Consensus 187 ~~~~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~ 219 (219)
T smart00062 187 VRKGDPELLDKINKALKELKADGTLKKIYEKWF 219 (219)
T ss_pred EECCCHHHHHHHHHHHHHHHhCchHHHHHhccC
Confidence 999987 89999999999999999999999985
No 25
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.35 E-value=1.2e-11 Score=122.77 Aligned_cols=222 Identities=14% Similarity=0.120 Sum_probs=179.1
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.++|||++...|. .+.. +++ ..+|+++++.+++++.||. +.++.+.. +.++++.+|.+|+
T Consensus 22 rGvLrV~tinsp~----sy~~-----~~~-~p~G~eYelak~Fa~yLgV--~Lki~~~~--------n~dqLf~aL~ng~ 81 (473)
T COG4623 22 RGVLRVSTINSPL----SYFE-----DKG-GPTGLEYELAKAFADYLGV--KLKIIPAD--------NIDQLFDALDNGN 81 (473)
T ss_pred cCeEEEEeecCcc----ceec-----cCC-CccchhHHHHHHHHHHhCC--eEEEEecC--------CHHHHHHHHhCCC
Confidence 6789999984333 3322 234 6789999999999999995 66666654 6899999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDF 207 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~ 207 (561)
+|++..++....+|.+.+.....|+..++.+|.++.+.+
T Consensus 82 ~DL~Aagl~~~~~~l~~~~~gP~y~svs~qlVyRkG~~R----------------------------------------- 120 (473)
T COG4623 82 ADLAAAGLLYNSERLKNFQPGPTYYSVSQQLVYRKGQYR----------------------------------------- 120 (473)
T ss_pred cceecccccCChhHhcccCCCCceecccHHHHhhcCCCC-----------------------------------------
Confidence 999999999999999988888889999999999977755
Q ss_pred CCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCee
Q 037841 208 RGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNV 287 (561)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~v 287 (561)
.+++++| +|..+
T Consensus 121 ------------------------------------------------------------------p~~l~~L--~g~~i 132 (473)
T COG4623 121 ------------------------------------------------------------------PRSLGQL--KGRQI 132 (473)
T ss_pred ------------------------------------------------------------------CCCHHHc--cCcee
Confidence 4889999 68889
Q ss_pred EEEeCchHHHHHHh---cCCCcccee--ecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCcccccC
Q 037841 288 GYQKGSFVLGILKQ---LGFDERKLV--VYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPTFKTA 362 (561)
Q Consensus 288 g~~~gs~~~~~l~~---~~~~~~~~~--~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~~~~~ 362 (561)
.+..|+...+.++. ..+|..... .-...++.++.+..|+ ++..+.+...+..+.+-+.+ +.+.-+.-...
T Consensus 133 ~v~~gs~~~~~l~~lk~~kyP~l~~k~d~~~~~~dLle~v~~Gk----ldytiads~~is~~q~i~P~-laVafd~tde~ 207 (473)
T COG4623 133 TVAKGSAHVEDLKLLKETKYPELIWKVDDKLGVEDLLEMVAEGK----LDYTIADSVEISLFQRVHPE-LAVAFDLTDEQ 207 (473)
T ss_pred eccCCcHHHHHHHHHHHhhcchhhhhhcccccHHHHHHHHhcCC----cceeeeccHHHHHHHHhCcc-ceeeeeccccc
Confidence 89999987666543 345543322 2236788999999999 99999999998888776664 65555555668
Q ss_pred ceEEEecCC--CCChhhHHHHHhhccccchhHHHHHHHcccCC
Q 037841 363 GFGFAFPLH--SPLVHDVSKAILSVTEGDKMKEIEDAWFKKHS 403 (561)
Q Consensus 363 ~~~~~~~k~--spl~~~in~~Il~l~e~G~~~~i~~kw~~~~~ 403 (561)
+.++++|.+ +.|...++..+..+.+.|.++++++|+++.-.
T Consensus 208 ~v~Wy~~~~dd~tL~a~ll~F~~~~~e~g~larleeky~gH~~ 250 (473)
T COG4623 208 PVAWYLPRDDDSTLSAALLDFLNEAKEDGLLARLEEKYLGHGD 250 (473)
T ss_pred CceeeccCCchHHHHHHHHHHHHHhhcchHHHHHHHHHhcccc
Confidence 899999996 45999999999999999999999999997543
No 26
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.35 E-value=5.6e-12 Score=112.43 Aligned_cols=122 Identities=32% Similarity=0.470 Sum_probs=105.8
Q ss_pred CcCCHHHHHhC-CCeeEEEeCchHHHHHHhcCCCc----------cceeecCChHHHHHHhhccccCCceeEEeecchhH
Q 037841 273 TITDVKMLIKR-GDNVGYQKGSFVLGILKQLGFDE----------RKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYG 341 (561)
Q Consensus 273 ~I~sl~dL~~~-~~~vg~~~gs~~~~~l~~~~~~~----------~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~ 341 (561)
||++++||..+ +.+||++.|+....++++..... .+++.+++..+++.+|..|+ ||++.+.+.+
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-----da~v~d~~~~ 75 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-----YAFLMESTYL 75 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-----CEEEeehHhH
Confidence 48899999532 26999999999999998753321 25678899999999999887 7999999999
Q ss_pred HHHHhcCCcceEEeCcccccCceEEEecCCCCChhhHHHHHhhccccchhHHHHHHHcc
Q 037841 342 KLLVGQHCYKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILSVTEGDKMKEIEDAWFK 400 (561)
Q Consensus 342 ~~~l~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~G~~~~i~~kw~~ 400 (561)
.+++++.|+ +.+++..+...+++++++||++|++.+|.+|.++.++|.++++.++|++
T Consensus 76 ~~~~~~~~~-~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~~l~~kw~~ 133 (134)
T smart00079 76 DYELSQNCD-LMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQKLENKWWK 133 (134)
T ss_pred HHHHhCCCC-eEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHHHHHHhhcc
Confidence 999888885 8888888888899999999999999999999999999999999999985
No 27
>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=99.06 E-value=2.8e-09 Score=105.77 Aligned_cols=199 Identities=20% Similarity=0.167 Sum_probs=141.5
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.++|+||+. +.+.|+ .+.+...++.+.+.+++|+++ +++... +|++++..+.+|+
T Consensus 31 ~~~l~vg~~--~~~~~~-------------~~~~~~~~l~~~l~~~~g~~v--~~~~~~--------~~~~~~~~l~~g~ 85 (254)
T TIGR01098 31 PKELNFGIL--PGENAS-------------NLTRRWEPLADYLEKKLGIKV--QLFVAT--------DYSAVIEAMRFGR 85 (254)
T ss_pred CCceEEEEC--CCCCHH-------------HHHHHHHHHHHHHHHHhCCcE--EEEeCC--------CHHHHHHHHHcCC
Confidence 467999997 555443 334556799999999999754 444432 7999999999999
Q ss_pred ccEEEeceeeec---Ccceeeecccccccc------ceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhh
Q 037841 128 FDAAVGDITILL---NRSNYVDFTLPYTES------GVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWA 198 (561)
Q Consensus 128 ~D~~vg~~~it~---~R~~~vdfT~p~~~~------~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~ 198 (561)
+|+++.+..... +|....+|+.||... ...+++++...
T Consensus 86 ~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~~--------------------------------- 132 (254)
T TIGR01098 86 VDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADSP--------------------------------- 132 (254)
T ss_pred ccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCCC---------------------------------
Confidence 999986553332 455667788775533 24677764431
Q ss_pred hhcccCCCCCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHH
Q 037841 199 LEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVK 278 (561)
Q Consensus 199 l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~ 278 (561)
|++++
T Consensus 133 ---------------------------------------------------------------------------i~~~~ 137 (254)
T TIGR01098 133 ---------------------------------------------------------------------------IKSLK 137 (254)
T ss_pred ---------------------------------------------------------------------------CCChH
Confidence 78999
Q ss_pred HHHhCCCeeEEEe-CchH-----HHHHHh-cCCC----ccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhc
Q 037841 279 MLIKRGDNVGYQK-GSFV-----LGILKQ-LGFD----ERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQ 347 (561)
Q Consensus 279 dL~~~~~~vg~~~-gs~~-----~~~l~~-~~~~----~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~ 347 (561)
|| +|++|++.. ++.. ..++.+ .+.+ ..++..+.+..+..++|..|+ +||++...+.+..+..+
T Consensus 138 dL--~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~----~Da~~~~~~~~~~~~~~ 211 (254)
T TIGR01098 138 DL--KGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGK----VDAATNNSSAIGRLKKR 211 (254)
T ss_pred Hh--cCCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCC----CCeEEecHHHHHHHHHh
Confidence 99 689999864 3321 234443 2322 135555566788999999999 99999999888877766
Q ss_pred CC---cceEEeCcccccCceEEEecCC-CC-ChhhHHHHHhhc
Q 037841 348 HC---YKYTMVEPTFKTAGFGFAFPLH-SP-LVHDVSKAILSV 385 (561)
Q Consensus 348 ~~---~~l~~v~~~~~~~~~~~~~~k~-sp-l~~~in~~Il~l 385 (561)
+. ..+.++.+.....+.+++++|+ .+ +.+.++++|..+
T Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 212 GPSDMKKVRVIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred CccchhheEEEEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 52 2577887666666779999999 54 999999999764
No 28
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.93 E-value=5.5e-09 Score=105.69 Aligned_cols=165 Identities=14% Similarity=0.149 Sum_probs=133.4
Q ss_pred CCHHHHHHHHHcCcccEEEeceeeecCcceeeecccc--ccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHH
Q 037841 114 GSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLP--YTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIF 191 (561)
Q Consensus 114 gs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p--~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~ 191 (561)
.++.+++..|.+|++|+++++...+.+|.+.++|+.| |....+++++|...+
T Consensus 51 ~~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~~-------------------------- 104 (287)
T PRK00489 51 LRPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDSD-------------------------- 104 (287)
T ss_pred ECcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCCC--------------------------
Confidence 3579999999999999999999989999888999887 777778888885542
Q ss_pred HHHHHhhhhcccCCCCCCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccC
Q 037841 192 IGFVVWALEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQ 271 (561)
Q Consensus 192 ~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~ 271 (561)
T Consensus 105 -------------------------------------------------------------------------------- 104 (287)
T PRK00489 105 -------------------------------------------------------------------------------- 104 (287)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCcCCHHHHHhCCCeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcc
Q 037841 272 PTITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYK 351 (561)
Q Consensus 272 ~~I~sl~dL~~~~~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~ 351 (561)
|++++|| +|+++++..+....+++++.+. ..+++.+++..+. ++..|. +||+++.......+.++ .
T Consensus 105 --i~sl~DL--~Gk~ia~~~~~~~~~~l~~~gi-~~~iv~~~gs~ea--a~~~G~----aDaivd~~~~~~~l~~~---~ 170 (287)
T PRK00489 105 --WQGVEDL--AGKRIATSYPNLTRRYLAEKGI-DAEVVELSGAVEV--APRLGL----ADAIVDVVSTGTTLRAN---G 170 (287)
T ss_pred --CCChHHh--CCCEEEEcCcHHHHHHHHHcCC-ceEEEECCCchhh--hhcCCc----ccEEEeeHHHHHHHHHC---C
Confidence 6889999 6999999889999999988766 3466777755554 566688 99998877777766553 3
Q ss_pred eEEeCcccccCceEEEecC--CCC-ChhhHHHHHhhccccchhHHHHHHHccc
Q 037841 352 YTMVEPTFKTAGFGFAFPL--HSP-LVHDVSKAILSVTEGDKMKEIEDAWFKK 401 (561)
Q Consensus 352 l~~v~~~~~~~~~~~~~~k--~sp-l~~~in~~Il~l~e~G~~~~i~~kw~~~ 401 (561)
+.++ +.+.....+++.+| .+| ....++.++.++ .|.+..+..+||+.
T Consensus 171 L~~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g~l~a~~~k~~~~ 220 (287)
T PRK00489 171 LKIV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QGVLRARESKYLMM 220 (287)
T ss_pred CEEE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HHHHHhhceEEEEE
Confidence 6666 56666678999999 566 778899999999 59999999999964
No 29
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=98.56 E-value=1.9e-08 Score=76.71 Aligned_cols=61 Identities=30% Similarity=0.538 Sum_probs=42.4
Q ss_pred ceEEEeeC--CCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCC--CCCCHHHHHHHHHc
Q 037841 63 YFVNVTID--PKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGT--SSGSYNDLIYQVFL 125 (561)
Q Consensus 63 pf~~~~~d--~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~--~ngs~~~li~~l~~ 125 (561)
||+....+ ..+++. ++.|||+||++++++.+||++++..++.+ ..|. +||+|+|++++|.+
T Consensus 1 Pfvm~~~~~~~~~g~~-~~eGyciDll~~la~~l~F~y~i~~~~Dg-~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 1 PFVMLKEDGENLTGND-RYEGYCIDLLEELAEELNFTYEIYLVPDG-KYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp TTBEE-TTSSGSBGGG-GEESHHHHHHHHHHHHHT-EEEEEE-TTS---EEBETTSEBEHHHHHHHT
T ss_pred CeEEEecCCcccCCCc-cEEEEHHHHHHHHHHHcCCeEEEEECCCC-CCcCcCCCCcCcCHHHHhcC
Confidence 55665554 334556 99999999999999999996555555433 3443 78999999999864
No 30
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=98.32 E-value=1.2e-05 Score=81.34 Aligned_cols=115 Identities=18% Similarity=0.154 Sum_probs=75.5
Q ss_pred cCCHHHHHhCCCeeEEEe-CchHH-----HHH-HhcCCCcc---ceeecC-ChHHHHHHhhccccCCceeEEeecchhHH
Q 037841 274 ITDVKMLIKRGDNVGYQK-GSFVL-----GIL-KQLGFDER---KLVVYN-SPEECHELFQKGSANGGIAAAFEEIPYGK 342 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~-gs~~~-----~~l-~~~~~~~~---~~~~~~-s~~~~~~~l~~g~~~~gv~a~i~~~~~~~ 342 (561)
|++++|| +|++|++.. ++... ..+ +..+.... +.+.+. +..+...+|..|+ +||++.+...+.
T Consensus 127 i~sl~DL--~Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~G~----vDa~~~~~~~~~ 200 (288)
T TIGR03431 127 IKSLEDL--KGKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVANGT----VDAATTNDENLD 200 (288)
T ss_pred CCcHHHh--CCCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHcCC----CCeEeccHHHHH
Confidence 7899999 689999863 33322 122 33333221 234454 6788999999999 999999888777
Q ss_pred HHHhcC-C---cceEEeCcccccCceEEEecCCC-C-ChhhHHHHHhhccccchhHHH
Q 037841 343 LLVGQH-C---YKYTMVEPTFKTAGFGFAFPLHS-P-LVHDVSKAILSVTEGDKMKEI 394 (561)
Q Consensus 343 ~~l~~~-~---~~l~~v~~~~~~~~~~~~~~k~s-p-l~~~in~~Il~l~e~G~~~~i 394 (561)
.+.++. . ..+.++...-.....+++++++- + +.+.++++|.++.+++..+++
T Consensus 201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~~~ 258 (288)
T TIGR03431 201 RMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDKACFE 258 (288)
T ss_pred HHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcHHHHH
Confidence 776532 1 12444322111223568889984 3 999999999999998665543
No 31
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.81 E-value=0.00029 Score=72.22 Aligned_cols=109 Identities=21% Similarity=0.252 Sum_probs=63.8
Q ss_pred cCCHHHHHhCCCeeEEEeCchHHHHH----HhcCCCccce-eecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcC
Q 037841 274 ITDVKMLIKRGDNVGYQKGSFVLGIL----KQLGFDERKL-VVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQH 348 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~gs~~~~~l----~~~~~~~~~~-~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~ 348 (561)
|++++|| .|++|++..|+..+..+ ++.+.+...+ ..+.+..+...+|..|+ +||++...++......+.
T Consensus 121 i~s~~dL--~Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~G~----vDa~~~~ep~~~~~~~~~ 194 (314)
T PRK11553 121 IKTVADL--KGHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQGN----VDAWAIWDPYYSAALLQG 194 (314)
T ss_pred CCCHHHh--CCCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcCC----CCEEEEcCcHHHHHHhcC
Confidence 6899999 68999998887666554 3444443222 23446677889999999 999988877776665543
Q ss_pred CcceEEeCcccccCceEEEecCC--CCChhhHHHHHhhcccc
Q 037841 349 CYKYTMVEPTFKTAGFGFAFPLH--SPLVHDVSKAILSVTEG 388 (561)
Q Consensus 349 ~~~l~~v~~~~~~~~~~~~~~k~--spl~~~in~~Il~l~e~ 388 (561)
..++...+..+......+++.+. ....+.+++.+..+.++
T Consensus 195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~~l~a~~~A 236 (314)
T PRK11553 195 GVRVLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLTEA 236 (314)
T ss_pred CcEEeecCcccCcCceEEEEcHHHHHHCHHHHHHHHHHHHHH
Confidence 32232223333333323333322 11334455555444444
No 32
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=97.67 E-value=0.00041 Score=68.36 Aligned_cols=120 Identities=22% Similarity=0.201 Sum_probs=76.2
Q ss_pred CcCCHHHHHhCCCeeEEEeCchH------HHHH-HhcCCCc---cceeecCChHHHHHHhhccccCCceeEEeecchhHH
Q 037841 273 TITDVKMLIKRGDNVGYQKGSFV------LGIL-KQLGFDE---RKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGK 342 (561)
Q Consensus 273 ~I~sl~dL~~~~~~vg~~~gs~~------~~~l-~~~~~~~---~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~ 342 (561)
+|++++|| .|+++++...+.. ...| ++.+.+. .+.+...+.+..+.+|.+|+ +||.+......+
T Consensus 96 ~i~~l~dL--~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~----~Da~~~~~~~~~ 169 (243)
T PF12974_consen 96 PITSLADL--KGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGK----ADAAAIPSDAFE 169 (243)
T ss_dssp S--SHHHH--GGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTS----SSEEEEEHHHHH
T ss_pred CCCChhhc--CCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCC----ccEEEEechhHH
Confidence 38999999 6999998654421 2334 4555542 23445568888999999999 999998887777
Q ss_pred HHHhcC---CcceEEeCcccccCceEEEecCCCC--ChhhHHHHHhhccccchhHHHHHHH
Q 037841 343 LLVGQH---CYKYTMVEPTFKTAGFGFAFPLHSP--LVHDVSKAILSVTEGDKMKEIEDAW 398 (561)
Q Consensus 343 ~~l~~~---~~~l~~v~~~~~~~~~~~~~~k~sp--l~~~in~~Il~l~e~G~~~~i~~kw 398 (561)
.+.... .++++++...-......+++.++-| .++.|-.+++.+..+-.-.++.+.+
T Consensus 170 ~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~~~~~l~~~ 230 (243)
T PF12974_consen 170 RLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPEGKAILDAF 230 (243)
T ss_dssp HHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHHHHHHHHHT
T ss_pred HHHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChhhHHHHHhc
Confidence 776653 4457777544333445677777755 8899999999998754444444443
No 33
>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=97.21 E-value=0.001 Score=67.69 Aligned_cols=68 Identities=26% Similarity=0.243 Sum_probs=48.0
Q ss_pred cCCHHHHHhCCCeeEEEeCchHHH----HHHhcCCCccceee-cCChHHHHHHhhccccCCceeEEeecchhHHHHHhc
Q 037841 274 ITDVKMLIKRGDNVGYQKGSFVLG----ILKQLGFDERKLVV-YNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQ 347 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~gs~~~~----~l~~~~~~~~~~~~-~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~ 347 (561)
|++++|| .|++||+..++..+. +|+..+.+...+.. .-...+...+|..|+ +||++...++.....++
T Consensus 92 I~s~~DL--kGK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~G~----vDa~~~~~p~~~~~~~~ 164 (300)
T TIGR01729 92 IEKPEDL--KGKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNLKPPQIVAAWQRGD----IDAAYVWPPALSELLKS 164 (300)
T ss_pred CCChhHc--CCCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEecCcHHHHHHHHcCC----cCEEEEecHHHHHHHhc
Confidence 7999999 699999987765443 44444554333222 224667899999999 99999988877655544
No 34
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=96.91 E-value=0.011 Score=60.87 Aligned_cols=67 Identities=21% Similarity=0.180 Sum_probs=50.2
Q ss_pred cCCHHHHHhCCCeeEEEeCchHHHHH----HhcCCCc--cceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhc
Q 037841 274 ITDVKMLIKRGDNVGYQKGSFVLGIL----KQLGFDE--RKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQ 347 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~gs~~~~~l----~~~~~~~--~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~ 347 (561)
|++++|| +|++||+..|+..+-+| ++.+.+. .+++.. ...+...++.+|+ +||+....++......+
T Consensus 98 i~svaDL--KGKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~-~~~d~~aAl~~G~----VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 98 GKSLADL--KGQKVNLVELSVSHYLLARALESVGLSEKDVKVVNT-SDADIVAAFITKD----VTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred CCCHHHc--CCCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeC-ChHHHHHHHhcCC----CcEEEEcCchHHHHHhC
Confidence 7999999 79999999887765444 4455553 344444 4577889999999 99999988887665554
No 35
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=96.73 E-value=0.0066 Score=60.13 Aligned_cols=71 Identities=27% Similarity=0.289 Sum_probs=49.7
Q ss_pred cCCHHHHHh-----CCCeeEE-EeCchHH----HHHHhcCCCc---cceeecCChHHHHHHhhccccCCceeEEeecchh
Q 037841 274 ITDVKMLIK-----RGDNVGY-QKGSFVL----GILKQLGFDE---RKLVVYNSPEECHELFQKGSANGGIAAAFEEIPY 340 (561)
Q Consensus 274 I~sl~dL~~-----~~~~vg~-~~gs~~~----~~l~~~~~~~---~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~ 340 (561)
+++++||.+ .|++|++ ..|+... .+|++.+.+. .+++.++. .+...+|..|+ +|+++...++
T Consensus 106 ~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~----iDa~~~~eP~ 180 (252)
T PF13379_consen 106 IKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGE----IDAAVLWEPF 180 (252)
T ss_dssp TCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-----SEEEEETTH
T ss_pred ccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCC----cCEEEecCCH
Confidence 799999965 5778998 4555433 3455555544 56666666 89999999999 9999999999
Q ss_pred HHHHHhcCC
Q 037841 341 GKLLVGQHC 349 (561)
Q Consensus 341 ~~~~l~~~~ 349 (561)
......+.-
T Consensus 181 ~~~~~~~g~ 189 (252)
T PF13379_consen 181 ASQAEAKGI 189 (252)
T ss_dssp HHHHHHTTS
T ss_pred HHHHHhccC
Confidence 888876653
No 36
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=96.45 E-value=0.034 Score=55.58 Aligned_cols=69 Identities=25% Similarity=0.395 Sum_probs=48.5
Q ss_pred cCCHHHHHhCCCeeEEEeCchHHH----HHHhcCCCccce-eecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcC
Q 037841 274 ITDVKMLIKRGDNVGYQKGSFVLG----ILKQLGFDERKL-VVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQH 348 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~gs~~~~----~l~~~~~~~~~~-~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~ 348 (561)
|++++|| .|++|++..++.... ++++.+.+.... ..+.+..+...++..|+ +|+++...++...+..+.
T Consensus 93 i~s~~dL--~Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~----vda~~~~~p~~~~~~~~~ 166 (288)
T TIGR01728 93 IRTVADL--KGKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQ----VDAWAIWEPWGSALVEEG 166 (288)
T ss_pred CCCHHHc--CCCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCC----CCEEEeccchHhHHhhcc
Confidence 7899999 699999877765443 344445543332 23345678899999999 999999888776665543
No 37
>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=96.25 E-value=0.14 Score=47.66 Aligned_cols=180 Identities=14% Similarity=0.111 Sum_probs=114.2
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-.+++..+.++.+ .+.+++.. ++..+++++|.+|++|++++.... ....+ -..++....++++++
T Consensus 20 ~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~~~~ 85 (209)
T PF03466_consen 20 LLPPLLAEFRERHP-NIRIEIRE---------GDSDELIEALRSGELDLAITFGPP---PPPGL-ESEPLGEEPLVLVVS 85 (209)
T ss_dssp THHHHHHHHHHHST-TEEEEEEE---------ESHHHHHHHHHTTSSSEEEESSSS---SSTTE-EEEEEEEEEEEEEEE
T ss_pred HHHHHHHHHHHHCC-CcEEEEEe---------ccchhhhHHHhcccccEEEEEeec---ccccc-ccccccceeeeeeee
Confidence 55688999999998 46777665 357899999999999999874443 22222 246777888999998
Q ss_pred ccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCCCCCccCccchhHHHHHHHhhhccccccccchhHH
Q 037841 162 IKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARF 241 (561)
Q Consensus 162 ~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ri 241 (561)
...+...
T Consensus 86 ~~~pl~~------------------------------------------------------------------------- 92 (209)
T PF03466_consen 86 PDHPLAQ------------------------------------------------------------------------- 92 (209)
T ss_dssp TTSGGGT-------------------------------------------------------------------------
T ss_pred ccccccc-------------------------------------------------------------------------
Confidence 6653210
Q ss_pred HHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCeeEEEe-CchHHHHH----HhcCCCccceeecCChH
Q 037841 242 VVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGYQK-GSFVLGIL----KQLGFDERKLVVYNSPE 316 (561)
Q Consensus 242 l~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~vg~~~-gs~~~~~l----~~~~~~~~~~~~~~s~~ 316 (561)
.. .-+++|| .+.++.... +......+ ++.+........+++.+
T Consensus 93 -----------------------------~~-~i~~~dL--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 (209)
T PF03466_consen 93 -----------------------------KK-PITLEDL--ADYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFE 140 (209)
T ss_dssp -----------------------------TS-SSSGGGG--TTSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHH
T ss_pred -----------------------------cc-cchhhhh--hhccccccccccccccccccccccccccccccccccchh
Confidence 01 2378999 466655543 44444433 44455554556788999
Q ss_pred HHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCc-ccccCceEEEecCCCCChhhHHHHHhhcc
Q 037841 317 ECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEP-TFKTAGFGFAFPLHSPLVHDVSKAILSVT 386 (561)
Q Consensus 317 ~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~-~~~~~~~~~~~~k~spl~~~in~~Il~l~ 386 (561)
.....+..|. ..+++-........ ...--....+.+ .+. ..++++.+++.+....+...+..+.
T Consensus 141 ~~~~~v~~g~----gi~~~p~~~~~~~~-~~~~l~~~~~~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~l~ 205 (209)
T PF03466_consen 141 SILSLVASGD----GIAILPDSLAQDEL-ESGELVFLPLPDPPLP-RPIYLVWRKDRPLSPAIQWFIDLLR 205 (209)
T ss_dssp HHHHHHHTTS----EBEEEEHHHHHHHH-HCTTEEEEEESSSTEE-EEEEEEEETTGTTHHHHHHHHHHHH
T ss_pred hhcccccccc----ceeecCcccccccc-cCCCEEEEECCCCCCc-eEEEEEEECCCCCCHHHHHHHHHHH
Confidence 9999999988 55555444333333 222101223344 444 7788899998776666666555443
No 38
>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=96.14 E-value=0.057 Score=51.79 Aligned_cols=58 Identities=28% Similarity=0.419 Sum_probs=39.6
Q ss_pred cCCHHHHHhCCCeeEEEeCchHH----HHHHhcCCCccceeecC-ChHHHHHHhhccccCCceeEEeec
Q 037841 274 ITDVKMLIKRGDNVGYQKGSFVL----GILKQLGFDERKLVVYN-SPEECHELFQKGSANGGIAAAFEE 337 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~gs~~~----~~l~~~~~~~~~~~~~~-s~~~~~~~l~~g~~~~gv~a~i~~ 337 (561)
|++++|| .|++||+..++... .+|++.+.+...+..+. ...+...+|.+|+ +||++..
T Consensus 85 i~~~~DL--kGK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~g~----vDa~~~~ 147 (216)
T PF09084_consen 85 IKSPADL--KGKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLSGQ----VDAAILW 147 (216)
T ss_dssp -SSGGGG--TTSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHTTS----SSEEEEE
T ss_pred CCCHHHh--CCCEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhcCC----CCEEEEc
Confidence 7999999 69999998876544 44455666555544433 3566677999999 9998833
No 39
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=96.12 E-value=0.12 Score=52.42 Aligned_cols=109 Identities=16% Similarity=0.136 Sum_probs=75.1
Q ss_pred CcCCHHHHHhCCCeeEEEeCchHH------HHHHhcC-CC---ccceeecCC-hHHHHHHhhccccCCceeEEeecchhH
Q 037841 273 TITDVKMLIKRGDNVGYQKGSFVL------GILKQLG-FD---ERKLVVYNS-PEECHELFQKGSANGGIAAAFEEIPYG 341 (561)
Q Consensus 273 ~I~sl~dL~~~~~~vg~~~gs~~~------~~l~~~~-~~---~~~~~~~~s-~~~~~~~l~~g~~~~gv~a~i~~~~~~ 341 (561)
+|++++|| +|+++++..-+..- .+|.+.+ .+ .-.-+.+.. -+.++.+|.+|+ +|+........
T Consensus 135 ~i~sl~dl--kgk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~a~~aV~nG~----vDva~~~~~~~ 208 (299)
T COG3221 135 PIKSLEDL--KGKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDAAVLAVANGQ----VDVAAVNSSAR 208 (299)
T ss_pred CcchHHHh--cCCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHHHHHHHHcCC----ceEEeccHHHH
Confidence 48999999 79999995443322 2333333 22 112344444 778899999999 99998888777
Q ss_pred HHHHhcCC----cceEEeCcccccCceEEEecCCCC--ChhhHHHHHhhccc
Q 037841 342 KLLVGQHC----YKYTMVEPTFKTAGFGFAFPLHSP--LVHDVSKAILSVTE 387 (561)
Q Consensus 342 ~~~l~~~~----~~l~~v~~~~~~~~~~~~~~k~sp--l~~~in~~Il~l~e 387 (561)
........ +++.++...-.-....++++++-| +++.|..+++.+.+
T Consensus 209 ~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 209 GLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred hhhhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 77666552 367777544334444577888755 99999999999986
No 40
>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=96.08 E-value=0.68 Score=42.20 Aligned_cols=70 Identities=17% Similarity=0.149 Sum_probs=48.3
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..++...+.+|++|+++... ......+ ...+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~-~~~~l~~~~~~~v~ 78 (193)
T cd08442 13 VRLPPLLAAYHARYP-KVDLSLST---------GTTGALIQAVLEGRLDGAFVAG---PVEHPRL-EQEPVFQEELVLVS 78 (193)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe---------CCcHHHHHHHHCCCccEEEEeC---CCCCCCc-EEEEeecCcEEEEe
Confidence 455788999999987 35666655 3567899999999999998532 2222222 24566777888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (193)
T cd08442 79 PKGH 82 (193)
T ss_pred cCCC
Confidence 7554
No 41
>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=96.08 E-value=0.54 Score=42.41 Aligned_cols=69 Identities=20% Similarity=0.337 Sum_probs=47.5
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-.++++.+.++.+ .+++++... +..+++..+.+|++|++++.... ....++ ..++....++++++
T Consensus 14 ~l~~~i~~~~~~~p-~i~i~~~~~---------~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~~~ 79 (197)
T cd05466 14 LLPPLLAAFRQRYP-GVELSLVEG---------GSSELLEALLEGELDLAIVALPV---DDPGLE-SEPLFEEPLVLVVP 79 (197)
T ss_pred HhHHHHHHHHHHCC-CCEEEEEEC---------ChHHHHHHHHcCCceEEEEcCCC---CCCcce-EeeeeccceEEEec
Confidence 45677888888876 367776652 45689999999999999874433 223333 34566778888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 80 ~~~ 82 (197)
T cd05466 80 PDH 82 (197)
T ss_pred CCC
Confidence 554
No 42
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=95.92 E-value=0.051 Score=55.54 Aligned_cols=58 Identities=29% Similarity=0.335 Sum_probs=40.7
Q ss_pred cCCHHHHHhCCCeeEEEeC-chH----HHHHHhcCCCccc--eeecCChHHHHHHhhccccCCceeEEeec
Q 037841 274 ITDVKMLIKRGDNVGYQKG-SFV----LGILKQLGFDERK--LVVYNSPEECHELFQKGSANGGIAAAFEE 337 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~g-s~~----~~~l~~~~~~~~~--~~~~~s~~~~~~~l~~g~~~~gv~a~i~~ 337 (561)
+++++|| .++++++... +.. ..+++..+..... .+.+.+..+...+|..|+ +|+++..
T Consensus 133 i~sl~dL--~gk~v~~~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~----vDa~~~~ 197 (320)
T TIGR02122 133 IKTVADL--KGKRVAVGAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGK----IDAAFYT 197 (320)
T ss_pred CCcHHHc--CCCEEecCCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCC----ccEEEEe
Confidence 7899999 5788877533 332 3345555554322 356778888999999999 9999887
No 43
>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=95.85 E-value=1 Score=41.27 Aligned_cols=71 Identities=15% Similarity=0.165 Sum_probs=50.2
Q ss_pred EEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEE
Q 037841 80 TGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMI 159 (561)
Q Consensus 80 ~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~iv 159 (561)
.++-.+++..+.++.+ .+++++.. ++..+++.++.+|++|+++.... .....+ ...++....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~~ 77 (198)
T cd08412 12 PYYLPGLLRRFREAYP-GVEVRVVE---------GNQEELEEGLRSGELDLALTYDL---DLPEDI-AFEPLARLPPYVW 77 (198)
T ss_pred hhhhHHHHHHHHHHCC-CcEEEEEE---------CCHHHHHHHHHcCCCcEEEEcCC---CCCccc-ceeeeeccceEEE
Confidence 3566789999999987 45666655 35788999999999999986321 112233 2467778888888
Q ss_pred EEccC
Q 037841 160 VPIKD 164 (561)
Q Consensus 160 vp~~~ 164 (561)
++...
T Consensus 78 ~~~~~ 82 (198)
T cd08412 78 LPADH 82 (198)
T ss_pred ecCCC
Confidence 87554
No 44
>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=95.77 E-value=1.2 Score=40.64 Aligned_cols=70 Identities=16% Similarity=0.262 Sum_probs=49.0
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+..++++.+.+..+ .+++++.. ++..+++..|.+|++|+++..... ....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~---------~~~~~~~~~L~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 78 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVE---------YGGKKVEQAVLNGELDVGITVLPV---DEEEFD-SQPLCNEPLVAVL 78 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEE---------cCcHHHHHHHHcCCCCEEEEeccc---ccCCce-eEEeccccEEEEe
Confidence 456688999999987 46776665 356789999999999999863322 122232 3566778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (197)
T cd08438 79 PRGH 82 (197)
T ss_pred cCCC
Confidence 8554
No 45
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=95.74 E-value=0.48 Score=48.15 Aligned_cols=69 Identities=16% Similarity=0.156 Sum_probs=46.0
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+...++..+.++.+ .+.+++.. ++..++...|.+|++|+++..-... ...+ ...++.+..+++++
T Consensus 105 ~~~~~~l~~~~~~~p-~i~l~~~~---------~~~~~~~~~l~~g~~Di~i~~~~~~---~~~~-~~~~l~~~~~~lv~ 170 (305)
T PRK11233 105 SLTMPLLQAVRAEFP-GIVLYLHE---------NSGATLNEKLMNGQLDMAVIYEHSP---VAGL-SSQPLLKEDLFLVG 170 (305)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEE---------CCcHHHHHHHHCCCCCEEEEcCCcC---CCCc-EEEEEeeeeEEEEE
Confidence 344568888988876 45665544 2457888999999999998532211 1222 34577778888888
Q ss_pred Ecc
Q 037841 161 PIK 163 (561)
Q Consensus 161 p~~ 163 (561)
+..
T Consensus 171 ~~~ 173 (305)
T PRK11233 171 TQD 173 (305)
T ss_pred cCc
Confidence 744
No 46
>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=95.72 E-value=0.92 Score=41.62 Aligned_cols=72 Identities=17% Similarity=0.230 Sum_probs=48.8
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..++..++.+|++|++++..... .....+ -..+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~-~~~~l~~~~~~~v~ 80 (201)
T cd08418 13 TLMPAVINRFKEQFP-DVQISIYE---------GQLSSLLPELRDGRLDFAIGTLPDE-MYLKEL-ISEPLFESDFVVVA 80 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe---------CcHHHHHHHHHcCCCcEEEEecCCC-CCCcce-eEEeecCCceEEEe
Confidence 456688889999887 46777664 3578999999999999998632111 111223 23566677888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 81 ~~~~ 84 (201)
T cd08418 81 RKDH 84 (201)
T ss_pred CCCC
Confidence 7543
No 47
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=95.72 E-value=1.1 Score=41.53 Aligned_cols=74 Identities=14% Similarity=0.108 Sum_probs=49.9
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+..+++..+.++.+ .+++++.. ++..++++.|.+|++|++++.......-...+.+ .+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~-~~l~~~~~~~~~ 81 (202)
T cd08468 13 AVMPRLMARLEELAP-SVRLNLVH---------AEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEE-RDWWEDTYVVIA 81 (202)
T ss_pred HHhHHHHHHHHhhCC-CCEEEEEE---------CChHhHHHHHHCCCccEEEecccccccCCCCEEE-EEEecCcEEEEE
Confidence 456688999999887 36666665 3578999999999999998633221000123333 467777888888
Q ss_pred EccCC
Q 037841 161 PIKDS 165 (561)
Q Consensus 161 p~~~~ 165 (561)
+...+
T Consensus 82 ~~~hp 86 (202)
T cd08468 82 SRDHP 86 (202)
T ss_pred eCCCC
Confidence 75543
No 48
>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=95.51 E-value=1.8 Score=39.18 Aligned_cols=70 Identities=17% Similarity=0.161 Sum_probs=48.7
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..++.+.+.+|++|+++..... ....+ -+.++.+..+++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~~~ 78 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRD---------VSAEQVIEAVRSGEVDFGIGSEPE---ADPDL-EFEPLLRDPFVLVC 78 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEe---------CChHHHHHHHHcCCccEEEEeCCC---CCCCe-eEEEeecccEEEEe
Confidence 456788999999887 45666654 356889999999999999863221 22222 23567778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (197)
T cd08440 79 PKDH 82 (197)
T ss_pred cCCC
Confidence 7554
No 49
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=95.45 E-value=0.97 Score=45.77 Aligned_cols=71 Identities=14% Similarity=0.135 Sum_probs=49.9
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-..++..+.+..+- +++++.. ++-+++++++.+|++|+++...... ... -...++....+++++
T Consensus 104 ~~~~~~l~~~~~~~P~-v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~-l~~~~l~~~~~~~~~ 169 (305)
T PRK11151 104 YLLPHIIPMLHQTFPK-LEMYLHE---------AQTHQLLAQLDSGKLDCAILALVKE---SEA-FIEVPLFDEPMLLAV 169 (305)
T ss_pred HHHHHHHHHHHHHCCC-cEEEEEe---------CCHHHHHHHHHcCCccEEEEecCCC---CCC-eEEEEeccCcEEEEe
Confidence 3555778888888873 6666655 3568999999999999998643221 122 245788888999998
Q ss_pred EccCC
Q 037841 161 PIKDS 165 (561)
Q Consensus 161 p~~~~ 165 (561)
++..+
T Consensus 170 ~~~hp 174 (305)
T PRK11151 170 YEDHP 174 (305)
T ss_pred cCCCC
Confidence 85543
No 50
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=95.34 E-value=1 Score=44.74 Aligned_cols=119 Identities=13% Similarity=0.072 Sum_probs=68.1
Q ss_pred CCcCCHHHHHhCCCeeEEEeCchHHH----HHHhcCCC------------------c--cceeecCChHHHHHHhhcccc
Q 037841 272 PTITDVKMLIKRGDNVGYQKGSFVLG----ILKQLGFD------------------E--RKLVVYNSPEECHELFQKGSA 327 (561)
Q Consensus 272 ~~I~sl~dL~~~~~~vg~~~gs~~~~----~l~~~~~~------------------~--~~~~~~~s~~~~~~~l~~g~~ 327 (561)
.++++++||. .|.+|++..+..... .|++.|.- . .+++.. ...+...++.+|+
T Consensus 106 ~~~~sl~dlk-~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel-~~~~~~~al~~g~- 182 (258)
T TIGR00363 106 KKIKNVNELQ-DGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITEL-ETSQLPRALDDPK- 182 (258)
T ss_pred cCCCCHHHcC-CCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEc-CHHHHHHHhhccc-
Confidence 3489999993 489999987654332 35665542 2 233333 3455678999999
Q ss_pred CCceeEEeecchhHHHHHhcC-CcceEEeCcccccCceEEEecCCCCChhhHHHHHhhccccchhHHHHHH
Q 037841 328 NGGIAAAFEEIPYGKLLVGQH-CYKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILSVTEGDKMKEIEDA 397 (561)
Q Consensus 328 ~~gv~a~i~~~~~~~~~l~~~-~~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~G~~~~i~~k 397 (561)
+|+++...+++...-..- -+.+ .....-...-..++++.+.-=.+.+.+.+..+.....-+.|.++
T Consensus 183 ---vDaa~v~~~~~~~agl~~~~~~i-~~e~~~~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~ 249 (258)
T TIGR00363 183 ---VDLAVINTTYAGQVGLNPQDDGV-FVEDKDSPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQKH 249 (258)
T ss_pred ---ccEEEEChHHHHHcCCCcCcCce-eecCCCCCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence 999999888766552221 1112 11111112224566666533445666666666655455555555
No 51
>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=95.33 E-value=1.8 Score=39.54 Aligned_cols=70 Identities=19% Similarity=0.257 Sum_probs=48.6
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..+++.++.+|++|+++.... .....+. ..+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~ 78 (198)
T cd08421 13 EFLPEDLASFLAAHP-DVRIDLEE---------RLSADIVRAVAEGRADLGIVAGN---VDAAGLE-TRPYRTDRLVVVV 78 (198)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe---------cCcHHHHHHHhcCCceEEEEecC---CCCCCcE-EEEeecCcEEEEe
Confidence 345678899999887 45666654 35678999999999999986322 2223333 4667788888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
++..
T Consensus 79 ~~~~ 82 (198)
T cd08421 79 PRDH 82 (198)
T ss_pred CCCC
Confidence 7554
No 52
>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=95.33 E-value=0.74 Score=42.47 Aligned_cols=70 Identities=19% Similarity=0.143 Sum_probs=48.9
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++.+++...|.+|++|+++..... ....+ .+.|.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~v~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~l-~~~~l~~~~~~~v~ 78 (201)
T cd08459 13 YFLPRLLAALREVAP-GVRIETVR---------LPVDELEEALESGEIDLAIGYLPD---LGAGF-FQQRLFRERYVCLV 78 (201)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe---------cCccCHHHHhhCCCceEEEEcCCC---Ccccc-eEEEeecCceEEEE
Confidence 455688999999987 35666654 345688899999999999863321 12223 34678888888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (201)
T cd08459 79 RKDH 82 (201)
T ss_pred cCCC
Confidence 8554
No 53
>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=95.29 E-value=1.7 Score=39.59 Aligned_cols=70 Identities=11% Similarity=0.150 Sum_probs=49.1
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.+..+ .+++++.. ++..++..++.+|++|+++..... ....+ .+.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~v~ 78 (196)
T cd08415 13 SLLPRAIARFRARHP-DVRISLHT---------LSSSTVVEAVLSGQADLGLASLPL---DHPGL-ESEPLASGRAVCVL 78 (196)
T ss_pred cccHHHHHHHHHHCC-CcEEEEEe---------cchHHHHHHHHcCCccEEEEeCCC---CCCcc-eeeeecccceEEEE
Confidence 456688999999887 45666655 356789999999999999863221 12222 35677778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (196)
T cd08415 79 PPGH 82 (196)
T ss_pred cCCC
Confidence 7543
No 54
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=95.28 E-value=1.6 Score=44.33 Aligned_cols=74 Identities=16% Similarity=0.206 Sum_probs=49.3
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.+..+ .+.+++.. ++...++..|.+|++|+++..-......... -...++....+++++
T Consensus 108 ~~~~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~-~~~~~l~~~~~~~v~ 176 (305)
T CHL00180 108 YLMPRLIGLFRQRYP-QINVQLQV---------HSTRRIAWNVANGQIDIAIVGGEVPTELKKI-LEITPYVEDELALII 176 (305)
T ss_pred hHHHHHHHHHHHHCC-CceEEEEe---------CCHHHHHHHHHcCCccEEEEcCccCcccccc-eeEEEeccCcEEEEE
Confidence 345678888888877 35666544 3578899999999999998632211111112 235677788889998
Q ss_pred EccCC
Q 037841 161 PIKDS 165 (561)
Q Consensus 161 p~~~~ 165 (561)
+...+
T Consensus 177 ~~~~p 181 (305)
T CHL00180 177 PKSHP 181 (305)
T ss_pred CCCCc
Confidence 86543
No 55
>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=95.21 E-value=1.7 Score=39.82 Aligned_cols=70 Identities=16% Similarity=0.156 Sum_probs=47.9
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++.. ++..+++.++.+|++|+++..... ....+. +.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 78 (199)
T cd08426 13 ELLPSLIARFRQRYP-GVFFTVDV---------ASTADVLEAVLSGEADIGLAFSPP---PEPGIR-VHSRQPAPIGAVV 78 (199)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEe---------CCcHHHHHHHHCCCccEEEecCCC---CCCCeE-EEeeccCcEEEEe
Confidence 345678888888877 45666654 346789999999999999863221 112232 4667788888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~h 82 (199)
T cd08426 79 PPGH 82 (199)
T ss_pred cCCC
Confidence 7554
No 56
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=95.19 E-value=2.4 Score=43.35 Aligned_cols=207 Identities=13% Similarity=0.113 Sum_probs=127.7
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.+.||||+. +.+ ...+-.++++.+.++.+ .+.+++.. ++.++++.+|.+|+
T Consensus 92 ~g~lrIg~~--~~~-----------------~~~~l~~~l~~f~~~~P-~i~l~l~~---------~~~~~~~~~L~~g~ 142 (316)
T PRK12679 92 SGVLTIATT--HTQ-----------------ARYSLPEVIKAFRELFP-EVRLELIQ---------GTPQEIATLLQNGE 142 (316)
T ss_pred CceEEEEec--hHh-----------------hhcchHHHHHHHHHHCC-CeEEEEec---------CCHHHHHHHHHcCC
Confidence 467999996 222 23456788999998887 35566544 35778999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDF 207 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~ 207 (561)
+|+++...... . ...+. ..++.....++++++..+..
T Consensus 143 ~Dl~i~~~~~~-~-~~~l~-~~~l~~~~~~~v~~~~hpl~---------------------------------------- 179 (316)
T PRK12679 143 ADIGIASERLS-N-DPQLV-AFPWFRWHHSLLVPHDHPLT---------------------------------------- 179 (316)
T ss_pred CCEEEecccCC-C-CCCce-EEEccCCcEEEEecCCCccc----------------------------------------
Confidence 99998632211 1 12233 35777888888887654321
Q ss_pred CCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCe-
Q 037841 208 RGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN- 286 (561)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~- 286 (561)
....-+++||. +.+
T Consensus 180 ---------------------------------------------------------------~~~~i~~~~L~--~~~~ 194 (316)
T PRK12679 180 ---------------------------------------------------------------QITPLTLESIA--KWPL 194 (316)
T ss_pred ---------------------------------------------------------------cCCCCCHHHHh--CCCe
Confidence 00124788885 443
Q ss_pred eEEEeCchH----HHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeC--cccc
Q 037841 287 VGYQKGSFV----LGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVE--PTFK 360 (561)
Q Consensus 287 vg~~~gs~~----~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~--~~~~ 360 (561)
+.+..+... ..++...+.........++.+...+++..|. --+++-.. +... . +.. .+..+. ....
T Consensus 195 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~----Gi~~lp~~-~~~~-~-~~~-~L~~~~~~~~~~ 266 (316)
T PRK12679 195 ITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGL----GIGLVAEQ-SSGE-Q-EES-NLIRLDTRHLFD 266 (316)
T ss_pred EEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcCC----cEEEeccc-cccc-c-cCC-cEEEEECcccCC
Confidence 334444333 3445555554444556678888899999987 34444433 2332 2 222 243332 2234
Q ss_pred cCceEEEecCCCCChhhHHHHHhhccccchhHHHHHHHc
Q 037841 361 TAGFGFAFPLHSPLVHDVSKAILSVTEGDKMKEIEDAWF 399 (561)
Q Consensus 361 ~~~~~~~~~k~spl~~~in~~Il~l~e~G~~~~i~~kw~ 399 (561)
...++++.+++.+....+...+..+.+.-....+.++-+
T Consensus 267 ~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~ 305 (316)
T PRK12679 267 ANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKRQVM 305 (316)
T ss_pred CceEEEEEeCCchhhHHHHHHHHHHhcccCHHHHHHHHh
Confidence 456788999998888888888877776666677777765
No 57
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=95.15 E-value=1.3 Score=45.30 Aligned_cols=206 Identities=12% Similarity=0.058 Sum_probs=121.3
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.+.|+||+. +.+ ...+-.+++..+.++.+ .+.+++.. ++..+++..|.+|+
T Consensus 92 ~g~l~Ig~~--~~~-----------------~~~~l~~~l~~~~~~~p-~i~l~~~~---------~~~~~~~~~L~~g~ 142 (313)
T PRK12684 92 QGNLTIATT--HTQ-----------------ARYALPAAIKEFKKRYP-KVRLSILQ---------GSPTQIAEMVLHGQ 142 (313)
T ss_pred CCeEEEEec--hHH-----------------HHHHhHHHHHHHHHHCC-CceEEEEe---------CChHHHHHHHHCCC
Confidence 467999986 222 22345678888888887 35666654 35789999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDF 207 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~ 207 (561)
+|+++..-.... ...+ -..++....++++++...+..
T Consensus 143 ~D~~i~~~~~~~--~~~l-~~~~l~~~~~~~v~~~~~pl~---------------------------------------- 179 (313)
T PRK12684 143 ADLAIATEAIAD--YKEL-VSLPCYQWNHCVVVPPDHPLL---------------------------------------- 179 (313)
T ss_pred cCEEEeecCCCC--CCCc-eEEEeccceEEEEeCCCCccc----------------------------------------
Confidence 999985311111 1122 246677788888887554321
Q ss_pred CCCccCccchhHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCC-e
Q 037841 208 RGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGD-N 286 (561)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~-~ 286 (561)
...--+++||. +. -
T Consensus 180 ---------------------------------------------------------------~~~~i~~~dL~--~~~~ 194 (313)
T PRK12684 180 ---------------------------------------------------------------ERKPLTLEDLA--QYPL 194 (313)
T ss_pred ---------------------------------------------------------------cCCCcCHHHHh--cCCc
Confidence 00124678885 44 3
Q ss_pred eEEEeCchHHH----HHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeC--cccc
Q 037841 287 VGYQKGSFVLG----ILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVE--PTFK 360 (561)
Q Consensus 287 vg~~~gs~~~~----~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~--~~~~ 360 (561)
+.+..++..+. ++...+.........++.+...+++..|- -.+++... ...... . ..+..++ ....
T Consensus 195 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gv~~lp~~-~~~~~~-~--~~l~~~~i~~~~~ 266 (313)
T PRK12684 195 ITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGL----GVGIVADM-AFDPER-D--RNLRAIDAGHLFG 266 (313)
T ss_pred EecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhCC----ceEEeehh-hccccc-c--CCeEEEECCCCCc
Confidence 44444544333 44444554444566778888999999987 34444432 222221 1 1244332 2333
Q ss_pred cCceEEEecCCCCChhhHHHHHhhccccchhHHHHHHHc
Q 037841 361 TAGFGFAFPLHSPLVHDVSKAILSVTEGDKMKEIEDAWF 399 (561)
Q Consensus 361 ~~~~~~~~~k~spl~~~in~~Il~l~e~G~~~~i~~kw~ 399 (561)
...++++.+++.++...+...+..+.+. +..++..+.+
T Consensus 267 ~~~~~l~~~~~~~~~~~~~~f~~~l~~~-~~~~~~~~~~ 304 (313)
T PRK12684 267 SSTTRLGLRRGAYLRGYVYTFIELFAPT-LNRKLVEQAL 304 (313)
T ss_pred ceeEEEEEECCCcCCHHHHHHHHHHHHH-hCHHHHHHHh
Confidence 4567889999987776666666555443 4455555544
No 58
>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=95.08 E-value=1.6 Score=40.06 Aligned_cols=70 Identities=23% Similarity=0.238 Sum_probs=48.6
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++...+...+.+|++|+++.... .....+ ...++....+++++
T Consensus 13 ~~~~~~i~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v~ 78 (200)
T cd08417 13 LLLPPLLARLRQEAP-GVRLRFVP---------LDRDDLEEALESGEIDLAIGVFP---ELPPGL-RSQPLFEDRFVCVA 78 (200)
T ss_pred HHHHHHHHHHHhhCC-CeEEEecc---------CCHHHHHHHHHcCCCCEEEeecc---cCCCcc-chhhhhcCceEEEe
Confidence 455678888888886 34555543 35789999999999999986322 222233 34677888899998
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (200)
T cd08417 79 RKDH 82 (200)
T ss_pred cCCC
Confidence 8554
No 59
>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=95.00 E-value=2.2 Score=39.85 Aligned_cols=72 Identities=15% Similarity=0.233 Sum_probs=49.8
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+.+++...+ +.++++.+|.+|++|++++.... ..+.++ ..++.+...++++
T Consensus 13 ~~~~~~l~~~~~~~P-~~~v~~~~~~--------~~~~l~~~L~~g~lDl~i~~~~~---~~~~l~-~~~l~~~~~~lv~ 79 (203)
T cd08463 13 LFLPELVARFRREAP-GARLEIHPLG--------PDFDYERALASGELDLVIGNWPE---PPEHLH-LSPLFSDEIVCLM 79 (203)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEeCC--------cchhHHHHHhcCCeeEEEecccc---CCCCcE-EeEeecCceEEEE
Confidence 466789999999887 3566665422 45789999999999999863221 112233 3567778888888
Q ss_pred EccCC
Q 037841 161 PIKDS 165 (561)
Q Consensus 161 p~~~~ 165 (561)
++..+
T Consensus 80 ~~~h~ 84 (203)
T cd08463 80 RADHP 84 (203)
T ss_pred eCCCC
Confidence 86643
No 60
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=94.96 E-value=0.55 Score=46.58 Aligned_cols=104 Identities=13% Similarity=0.072 Sum_probs=68.5
Q ss_pred CCcCCHHHHHhCCCeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHH-HhcCCc
Q 037841 272 PTITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLL-VGQHCY 350 (561)
Q Consensus 272 ~~I~sl~dL~~~~~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~-l~~~~~ 350 (561)
.+|++++|| +|+++.+..++...+.++.++. ..+ ..+..|...+|++|. +|+++........+ +.+..+
T Consensus 126 ~~i~s~~Dl--~G~kir~~~~~~~~~~~~~~Ga---~~v-~~~~~e~~~aL~~G~----vDg~~~~~~~~~~~~~~ev~~ 195 (257)
T TIGR00787 126 KPITKPEDL--KGLKIRIPNSPMNEAQFKALGA---NPE-PMAFSEVYTALQTGV----VDGQENPLSNVYSSKFYEVQK 195 (257)
T ss_pred CccCChHHh--CCCEEecCCCHHHHHHHHHcCC---ccc-ccCHHHHHHHHHcCC----cccccCCHHHHhhcchhhhcc
Confidence 569999999 7999999777778888888753 323 667789999999999 99988765433221 112233
Q ss_pred ceEEeCcccccCceEEEecCC--CCChhhHHHHHhhccc
Q 037841 351 KYTMVEPTFKTAGFGFAFPLH--SPLVHDVSKAILSVTE 387 (561)
Q Consensus 351 ~l~~v~~~~~~~~~~~~~~k~--spl~~~in~~Il~l~e 387 (561)
.++..+ .......+++.++ ..|-+...++|....+
T Consensus 196 y~~~~~--~~~~~~~~~~n~~~~~~L~~e~q~~i~~a~~ 232 (257)
T TIGR00787 196 YLSMTN--HGYLGYLVVVNKAFWKSLPPDLQAVVKEAAK 232 (257)
T ss_pred hheecC--CcccceEEEEeHHHHhcCCHHHHHHHHHHHH
Confidence 232222 2334556777776 3366677666665543
No 61
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=94.82 E-value=1.3 Score=44.79 Aligned_cols=87 Identities=14% Similarity=0.156 Sum_probs=58.4
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.+.|+||++ +.. ...+-.+++..+.+..+ .+++++.. ++..++..+|.+|+
T Consensus 94 ~g~l~I~~~--~~~-----------------~~~~l~~~l~~~~~~~p-~i~~~~~~---------~~~~~~~~~l~~g~ 144 (302)
T PRK09791 94 AGQINIGMG--ASI-----------------ARSLMPAVISRFHQQHP-QVKVRIME---------GQLVSMINELRQGE 144 (302)
T ss_pred ceEEEEEec--hHH-----------------HHhhhHHHHHHHHHHCC-CeEEEEEe---------CChHHHHHHHHCCC
Confidence 477999997 221 22355678889998887 46666554 35789999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccCC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDS 165 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~ 165 (561)
+|+++...... .....+. ..|+....+++++++..+
T Consensus 145 ~Di~i~~~~~~-~~~~~~~-~~~l~~~~~~l~~~~~~~ 180 (302)
T PRK09791 145 LDFTINTYYQG-PYDHEFT-FEKLLEKQFAVFCRPGHP 180 (302)
T ss_pred ccEEEEecCCc-cccccee-EEEeccceEEEEEcCCCC
Confidence 99988621111 1122343 367888899999885543
No 62
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=94.81 E-value=0.25 Score=50.75 Aligned_cols=67 Identities=24% Similarity=0.276 Sum_probs=47.3
Q ss_pred CcCCHHHHHhCCCeeEEEeCchHH----HHHHhcCCCccceeecC-ChHHHHHHhhccccCCceeEEeecchhHHHHH
Q 037841 273 TITDVKMLIKRGDNVGYQKGSFVL----GILKQLGFDERKLVVYN-SPEECHELFQKGSANGGIAAAFEEIPYGKLLV 345 (561)
Q Consensus 273 ~I~sl~dL~~~~~~vg~~~gs~~~----~~l~~~~~~~~~~~~~~-s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l 345 (561)
+|++++|| +|++||+..++... .+|++.+.+...+..+. ...+...+|.+|+ +||++...++.....
T Consensus 113 ~I~s~~DL--kGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~Al~~G~----VDAa~~~~p~~~~~~ 184 (320)
T PRK11480 113 TISKPEDL--IGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQPPAIIAAWQRGD----IDGAYVWAPAVNALE 184 (320)
T ss_pred CCCChHHc--CCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECCcHHHHHHHHcCC----cCEEEEcchHHHHHH
Confidence 38999999 69999997665443 34566666544433322 4577889999999 999888777765443
No 63
>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=94.73 E-value=3.2 Score=37.80 Aligned_cols=70 Identities=16% Similarity=0.191 Sum_probs=48.3
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+--++++.+.++.+ .+.+++.. ++..++...+.+|++|+++...... ....+ .+.++....++++++
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~ 81 (199)
T cd08451 15 LVPGLIRRFREAYP-DVELTLEE---------ANTAELLEALREGRLDAAFVRPPVA--RSDGL-VLELLLEEPMLVALP 81 (199)
T ss_pred ccHHHHHHHHHHCC-CcEEEEec---------CChHHHHHHHHCCCccEEEEecCCC--CCCce-eEEEeecccEEEEec
Confidence 56678999999987 35666654 3567899999999999998632211 11222 346677788888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 82 ~~~ 84 (199)
T cd08451 82 AGH 84 (199)
T ss_pred CCC
Confidence 554
No 64
>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=94.71 E-value=3.2 Score=37.67 Aligned_cols=69 Identities=16% Similarity=0.182 Sum_probs=47.0
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+..+++..+.++.+ .+.+++.. +...++..++.+|++|+++....... ..+ ...++....++++++
T Consensus 13 ~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~~~~ 78 (197)
T cd08419 13 FAPRLLGAFCRRHP-GVEVSLRV---------GNREQVLERLADNEDDLAIMGRPPED---LDL-VAEPFLDNPLVVIAP 78 (197)
T ss_pred HhhHHHHHHHHHCC-CceEEEEE---------CCHHHHHHHHhcCCccEEEecCCCCC---CCe-EEEEeccCCEEEEec
Confidence 45577888888876 35666654 35678899999999999985322211 112 346777788888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 79 ~~~ 81 (197)
T cd08419 79 PDH 81 (197)
T ss_pred CCC
Confidence 544
No 65
>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=94.63 E-value=3.2 Score=37.90 Aligned_cols=70 Identities=19% Similarity=0.216 Sum_probs=47.8
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.+..+ .+++++.. ++-.++...|.+|++|+++... ......+ -..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~ 78 (198)
T cd08433 13 VLAVPLLRAVRRRYP-GIRLRIVE---------GLSGHLLEWLLNGRLDLALLYG---PPPIPGL-STEPLLEEDLFLVG 78 (198)
T ss_pred hcchHHHHHHHHHCC-CcEEEEEe---------cCcHHHHHHHhCCCCcEEEEeC---CCCCCCe-eEEEeccccEEEEe
Confidence 345678899999887 46666654 2456889999999999998632 2222222 34677778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (198)
T cd08433 79 PADA 82 (198)
T ss_pred cCCC
Confidence 7554
No 66
>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=94.58 E-value=1.6 Score=40.31 Aligned_cols=69 Identities=19% Similarity=0.223 Sum_probs=46.5
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-..++..+.++.+ .+.+++.. ++. ++++.|.+|++|++++.-... ...+. ..|+....++++++
T Consensus 14 ~l~~~i~~~~~~~P-~i~l~i~~---------~~~-~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~ 78 (200)
T cd08462 14 LLPPVIERVAREAP-GVRFELLP---------PDD-QPHELLERGEVDLLIAPERFM---SDGHP-SEPLFEEEFVCVVW 78 (200)
T ss_pred HHHHHHHHHHHHCC-CCEEEEec---------CCh-hHHHHHhcCCeeEEEecCCCC---CCCce-eeeeeccceEEEEc
Confidence 45577888888887 35666654 244 899999999999998632211 12232 44677788888887
Q ss_pred ccCC
Q 037841 162 IKDS 165 (561)
Q Consensus 162 ~~~~ 165 (561)
...+
T Consensus 79 ~~hp 82 (200)
T cd08462 79 ADNP 82 (200)
T ss_pred CCCC
Confidence 5543
No 67
>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=94.55 E-value=2.4 Score=38.93 Aligned_cols=70 Identities=16% Similarity=0.105 Sum_probs=49.2
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++++ .+++++.. ++..++..+|.+|++|+++... ......+ -+.++....+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~~~~---------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~-~~~~l~~~~~~lv~ 78 (200)
T cd08466 13 LLLPRLLARLKQLAP-NISLRESP---------SSEEDLFEDLRLQEVDLVIDYV---PFRDPSF-KSELLFEDELVCVA 78 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec---------CchHhHHHHHHcCCccEEEecc---cCCCCCc-eeeeecccceEEEE
Confidence 455688889999887 46666654 3577899999999999998632 1112223 24577788899998
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (200)
T cd08466 79 RKDH 82 (200)
T ss_pred eCCC
Confidence 8554
No 68
>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=94.54 E-value=2.9 Score=38.29 Aligned_cols=69 Identities=17% Similarity=0.209 Sum_probs=46.9
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-.+++..+.++.+ .+++++.. ++..+++..+.+|++|+++..... ....+ -..++.+..++++++
T Consensus 15 ~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~v~~ 80 (200)
T cd08411 15 LLPRLLPALRQAYP-KLRLYLRE---------DQTERLLEKLRSGELDAALLALPV---DEPGL-EEEPLFDEPFLLAVP 80 (200)
T ss_pred hhHHHHHHHHHHCC-CcEEEEEe---------CcHHHHHHHHHcCCccEEEEeccC---CCCCc-eEEEeeccceEEEec
Confidence 55688889988887 35666654 357889999999999999863211 11222 234566778888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 81 ~~~ 83 (200)
T cd08411 81 KDH 83 (200)
T ss_pred CCC
Confidence 544
No 69
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=94.46 E-value=2.7 Score=42.11 Aligned_cols=70 Identities=11% Similarity=0.055 Sum_probs=49.3
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+..+++..+.++.+ .+.+++.. ++..+++..+.+|++|+++... +.....+ .+.++....+++++
T Consensus 104 ~~l~~~l~~~~~~~p-~~~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~l-~~~~l~~~~~~~~~ 169 (296)
T PRK11242 104 YLIGPLIDAFHARYP-GITLTIRE---------MSQERIEALLADDELDVGIAFA---PVHSPEI-EAQPLFTETLALVV 169 (296)
T ss_pred hhhHHHHHHHHHHCC-CCEEEEEe---------CCHHHHHHHHHCCCCcEEEEec---CCCCcce-eEEEeeeccEEEEE
Confidence 355678888988876 46666654 3578899999999999998632 2222233 34677788888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
++..
T Consensus 170 ~~~~ 173 (296)
T PRK11242 170 GRHH 173 (296)
T ss_pred cCCC
Confidence 8654
No 70
>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=94.44 E-value=3.3 Score=37.88 Aligned_cols=69 Identities=17% Similarity=0.247 Sum_probs=46.4
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-..++..+.++.+ .+++++.. ++..++...|.+|++|+++..-.. ....+. ..++....++++++
T Consensus 14 ~~~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~ 79 (198)
T cd08441 14 WLMPVLDQFRERWP-DVELDLSS---------GFHFDPLPALLRGELDLVITSDPL---PLPGIA-YEPLFDYEVVLVVA 79 (198)
T ss_pred hhHHHHHHHHHhCC-CeEEEEEe---------CCchhHHHHHHcCCceEEEecCCc---CCCCcE-EEEccCCcEEEEEc
Confidence 44578899999987 35666654 346789999999999999863221 112222 34667777888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 80 ~~~ 82 (198)
T cd08441 80 PDH 82 (198)
T ss_pred CCC
Confidence 543
No 71
>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=94.33 E-value=2.2 Score=39.03 Aligned_cols=70 Identities=19% Similarity=0.115 Sum_probs=47.7
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++.. ++..++...+.+|++|+++.... .....+ -+.++....+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Di~i~~~~---~~~~~~-~~~~l~~~~~~lv~ 78 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRD---------LESDNLEAQLERGEVDLALTTPE---YAPDGL-RSRPLFEERYVCVT 78 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEee---------CCcccHHHHHhcCCCcEEEecCc---cCCccc-eeeeeecCcEEEEE
Confidence 455788899999887 45666654 23467889999999999986321 112223 25677778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (198)
T cd08461 79 RRGH 82 (198)
T ss_pred cCCC
Confidence 7553
No 72
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=94.28 E-value=2.8 Score=43.12 Aligned_cols=85 Identities=12% Similarity=0.064 Sum_probs=58.2
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.+.||||+. +.. ...+-.++++.+.++.+ .+++++.. ++.++++.+|.+|+
T Consensus 92 ~g~lrIg~~--~~~-----------------~~~~l~~~l~~f~~~~P-~v~i~l~~---------~~~~~~~~~l~~g~ 142 (327)
T PRK12680 92 QGQLTLTTT--HTQ-----------------ARFVLPPAVAQIKQAYP-QVSVHLQQ---------AAESAALDLLGQGD 142 (327)
T ss_pred ceEEEEEec--chh-----------------HHHhhHHHHHHHHHHCC-CcEEEEEe---------CChHHHHHHHHCCC
Confidence 467999997 221 12355688999999998 46676655 35789999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKD 164 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~ 164 (561)
+|+++..... ....... ..|+....++++++...
T Consensus 143 ~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~l~~~~~h 176 (327)
T PRK12680 143 ADIAIVSTAG--GEPSAGI-AVPLYRWRRLVVVPRGH 176 (327)
T ss_pred CcEEEEecCC--CCCCcce-EEEeeccceEEEEeCCC
Confidence 9999853211 1112222 46788888888888654
No 73
>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=94.18 E-value=3.9 Score=38.27 Aligned_cols=71 Identities=13% Similarity=0.176 Sum_probs=47.3
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.+..+ .+++++.. ++..+++..|.+|++|+++........-...+ ...|+.+..+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~---------~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~~~ 81 (204)
T cd08429 13 SIAYRLLEPAMDLHE-PIRLVCRE---------GKLEQLLADLALHRLDMVLADRPMPSSLDVKG-YSHRLGECGVSFFA 81 (204)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe---------CCHHHHHHHHHcCCccEEEecCCCccccchhe-eeccccccceEEEe
Confidence 456788899999887 46676665 46889999999999999885322111100111 24577777777776
Q ss_pred Ec
Q 037841 161 PI 162 (561)
Q Consensus 161 p~ 162 (561)
+.
T Consensus 82 ~~ 83 (204)
T cd08429 82 AP 83 (204)
T ss_pred cC
Confidence 54
No 74
>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=94.17 E-value=4.3 Score=36.83 Aligned_cols=70 Identities=16% Similarity=0.247 Sum_probs=47.7
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++-.+++.+|.+|++|+++...... ...+. +.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~~~l~~~~---------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~ 78 (201)
T cd08420 13 YLLPRLLARFRKRYP-EVRVSLTI---------GNTEEIAERVLDGEIDLGLVEGPVD---HPDLI-VEPFAEDELVLVV 78 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe---------CCcHHHHHHHHCCCccEEEecCCCC---CcceE-EEeecCccEEEEe
Confidence 455688899998886 35666654 2457889999999999998643221 22222 3567778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (201)
T cd08420 79 PPDH 82 (201)
T ss_pred cCCC
Confidence 7554
No 75
>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=94.01 E-value=2.8 Score=42.20 Aligned_cols=86 Identities=17% Similarity=0.215 Sum_probs=57.4
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.+.|+||+. +.. ...+-.+++..+.++.+ .+.+.+.. ++..+++.++.+|+
T Consensus 92 ~~~l~I~~~--~~~-----------------~~~~~~~~l~~~~~~~P-~~~i~~~~---------~~~~~~~~~l~~g~ 142 (300)
T TIGR02424 92 GPTVRIGAL--PTV-----------------AARLMPEVVKRFLARAP-RLRVRIMT---------GPNAYLLDQLRVGA 142 (300)
T ss_pred CceEEEecc--cHH-----------------HHhhhHHHHHHHHHhCC-CcEEEEEe---------CchHHHHHHHHCCC
Confidence 567999986 221 12345678888888888 46676665 35678999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKD 164 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~ 164 (561)
+|++++..... .....+ -..|......+++++...
T Consensus 143 ~D~~i~~~~~~-~~~~~~-~~~~l~~~~~~~~~~~~h 177 (300)
T TIGR02424 143 LDLVVGRLGAP-ETMQGL-SFEHLYNEPVVFVVRAGH 177 (300)
T ss_pred CCEEEEecCCc-ccccce-eeeeecCCceEEEEcCCC
Confidence 99998633221 111223 245677788888887554
No 76
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=93.95 E-value=2.4 Score=43.58 Aligned_cols=85 Identities=21% Similarity=0.200 Sum_probs=56.0
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.+.|+||+. +.+ ...+-.+++..+.++.+ .+.+++.. ++.++++.++.+|+
T Consensus 92 ~g~l~Ig~~--~~~-----------------~~~~l~~~l~~f~~~~P-~i~i~i~~---------~~~~~~~~~L~~g~ 142 (324)
T PRK12681 92 KGSLYIATT--HTQ-----------------ARYALPPVIKGFIERYP-RVSLHMHQ---------GSPTQIAEAAAKGN 142 (324)
T ss_pred CCeEEEEec--hhH-----------------HHHhhHHHHHHHHHHCC-CcEEEEEe---------CCHHHHHHHHHcCC
Confidence 467999996 222 12345678888888887 46666655 46889999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKD 164 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~ 164 (561)
+|+++.... ......+. ..++.....+++++...
T Consensus 143 iDl~i~~~~--~~~~~~l~-~~~l~~~~~~~v~~~~h 176 (324)
T PRK12681 143 ADFAIATEA--LHLYDDLI-MLPCYHWNRSVVVPPDH 176 (324)
T ss_pred CCEEEecCc--ccCCCCeE-EEEeccceeEEEeCCCC
Confidence 999986321 11122232 34666677788877543
No 77
>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=93.93 E-value=3.9 Score=37.28 Aligned_cols=69 Identities=10% Similarity=0.100 Sum_probs=47.8
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-.+++..+.++.+ .+.+++.. ++..++...+.+|++|+++.... .....+ ...++....++++++
T Consensus 15 ~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~~v~~ 80 (197)
T cd08425 15 LIGPLIDRFHARYP-GIALSLRE---------MPQERIEAALADDRLDLGIAFAP---VRSPDI-DAQPLFDERLALVVG 80 (197)
T ss_pred hhHHHHHHHHHHCC-CcEEEEEE---------CcHHHHHHHHHcCCccEEEEecC---CCCCCc-EEEEeccccEEEEec
Confidence 44678899988887 46777665 24678899999999999985322 122222 245677788888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
+..
T Consensus 81 ~~~ 83 (197)
T cd08425 81 ATH 83 (197)
T ss_pred CCC
Confidence 554
No 78
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=93.92 E-value=4.4 Score=41.19 Aligned_cols=71 Identities=18% Similarity=0.230 Sum_probs=47.9
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-..++..+.++.+ .+.+++.. ++.++++..|.+|++|+++...... ....+.+ .|+....++++++
T Consensus 107 ~l~~~i~~f~~~~P-~i~l~~~~---------~~~~~~~~~L~~~~~D~~i~~~~~~--~~~~l~~-~~l~~~~~~~v~~ 173 (309)
T PRK12683 107 ALPKVVRQFKEVFP-KVHLALRQ---------GSPQEIAEMLLNGEADIGIATEALD--REPDLVS-FPYYSWHHVVVVP 173 (309)
T ss_pred HHHHHHHHHHHHCC-CceEEEEe---------CCHHHHHHHHHcCCccEEEecCCCC--CCCCceE-EEcccCeEEEEec
Confidence 44578888888887 35666655 4689999999999999998532111 1123333 4677778888888
Q ss_pred ccCC
Q 037841 162 IKDS 165 (561)
Q Consensus 162 ~~~~ 165 (561)
...+
T Consensus 174 ~~hp 177 (309)
T PRK12683 174 KGHP 177 (309)
T ss_pred CCCC
Confidence 5543
No 79
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=93.90 E-value=5.4 Score=39.82 Aligned_cols=69 Identities=13% Similarity=0.172 Sum_probs=46.2
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-.+++..+.+..+ .+.+++.. ++..+++..+.+|++|+++...... ...+ ...++....++++++
T Consensus 103 ~~~~~l~~~~~~~P-~i~i~v~~---------~~~~~~~~~l~~g~~Di~i~~~~~~---~~~~-~~~~l~~~~~~lv~~ 168 (290)
T PRK10837 103 ILPAMIARYRRDYP-QLPLELSV---------GNSQDVINAVLDFRVDIGLIEGPCH---SPEL-ISEPWLEDELVVFAA 168 (290)
T ss_pred hhHHHHHHHHHHCC-CceEEEEE---------CCHHHHHHHHHhCCceEEEecCCCC---CCce-eEEEeecceEEEEEc
Confidence 45677888888886 35666654 3567899999999999998632211 1222 235666777888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 169 ~~h 171 (290)
T PRK10837 169 PDS 171 (290)
T ss_pred CCC
Confidence 554
No 80
>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=93.86 E-value=5 Score=36.52 Aligned_cols=72 Identities=13% Similarity=0.199 Sum_probs=49.1
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.+..+ .+++++.. ++..++.+++.+|++|+++.... ...+...+ ...++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~-~~~~l~~~~~~~~~ 80 (201)
T cd08435 13 VLLPPAIARLLARHP-RLTVRVVE---------GTSDELLEGLRAGELDLAIGRLA-DDEQPPDL-ASEELADEPLVVVA 80 (201)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe---------CCHHHHHHHHHcCCccEEEEecC-cccCCCCc-EEEEcccCcEEEEE
Confidence 345688889988887 46666654 35688999999999999986321 11112223 34577788889988
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 81 ~~~~ 84 (201)
T cd08435 81 RPGH 84 (201)
T ss_pred eCCC
Confidence 8654
No 81
>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=93.74 E-value=4.7 Score=36.52 Aligned_cols=72 Identities=21% Similarity=0.279 Sum_probs=47.8
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.+..+ .+++++.. ++.+++++.+.+|++|+++...... .....+ .+.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~-~~~~l~~~~~~~v~ 80 (195)
T cd08427 13 GLLPRALARLRRRHP-DLEVHIVP---------GLSAELLARVDAGELDAAIVVEPPF-PLPKDL-VWTPLVREPLVLIA 80 (195)
T ss_pred HHhHHHHHHHHHHCC-CceEEEEe---------CCcHHHHHHHHCCCCCEEEEcCCCC-ccccCc-eEEEcccCcEEEEE
Confidence 345678888888887 35666654 3568899999999999998632111 101222 34567778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 81 ~~~~ 84 (195)
T cd08427 81 PAEL 84 (195)
T ss_pred CCCC
Confidence 7543
No 82
>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=93.71 E-value=1.8 Score=40.00 Aligned_cols=71 Identities=20% Similarity=0.220 Sum_probs=48.8
Q ss_pred EEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEE
Q 037841 80 TGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMI 159 (561)
Q Consensus 80 ~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~iv 159 (561)
..+-.+++..+.++.+ .+++++.. ++. ++++++.+|++|++++.... ....+. ..++.+..++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~v~l~~---------~~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v 76 (200)
T cd08460 12 AAFGPALLAAVAAEAP-GVRLRFVP---------ESD-KDVDALREGRIDLEIGVLGP---TGPEIR-VQTLFRDRFVGV 76 (200)
T ss_pred HHHHHHHHHHHHHHCC-CCEEEEec---------Cch-hHHHHHHCCCccEEEecCCC---CCcchh-eeeeeccceEEE
Confidence 3566788999999987 46666654 234 78899999999999863221 122333 467778888888
Q ss_pred EEccCC
Q 037841 160 VPIKDS 165 (561)
Q Consensus 160 vp~~~~ 165 (561)
++...+
T Consensus 77 ~~~~hp 82 (200)
T cd08460 77 VRAGHP 82 (200)
T ss_pred EeCCCC
Confidence 885543
No 83
>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=93.67 E-value=4.2 Score=37.41 Aligned_cols=71 Identities=23% Similarity=0.247 Sum_probs=48.9
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..++.+++.+|++|+++..... .....+. +.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~---------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~ 79 (198)
T cd08413 13 YVLPPVIAAFRKRYP-KVKLSLHQ---------GTPSQIAEMVLKGEADIAIATEAL--DDHPDLV-TLPCYRWNHCVIV 79 (198)
T ss_pred hhccHHHHHHHHhCC-ceEEEEEe---------CCHHHHHHHHHcCCCCEEEEccCC--CCCCCcE-EEEeeeeeEEEEe
Confidence 355688999999987 36666655 357789999999999999852211 1112233 4667778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 80 ~~~h 83 (198)
T cd08413 80 PPGH 83 (198)
T ss_pred cCCC
Confidence 8554
No 84
>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=93.60 E-value=5.5 Score=36.16 Aligned_cols=72 Identities=11% Similarity=0.033 Sum_probs=48.5
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-..++..+.++.+ .+++++.. ++..+++..+.+|++|++++...... ....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~-~~~l~~~~~~~v~ 80 (197)
T cd08449 13 GGLGPALRRFKRQYP-NVTVRFHE---------LSPEAQKAALLSKRIDLGFVRFADTL-NDPPLA-SELLWREPMVVAL 80 (197)
T ss_pred hhHHHHHHHHHHHCC-CeEEEEEE---------CCHHHHHHHHhCCCccEEEecccccC-CCCCce-EEEEEEeeEEEEe
Confidence 456788999999987 46666654 35788999999999999986332210 112222 3567777888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 81 ~~~~ 84 (197)
T cd08449 81 PEEH 84 (197)
T ss_pred cCCC
Confidence 7543
No 85
>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=93.52 E-value=4.5 Score=37.26 Aligned_cols=70 Identities=16% Similarity=0.248 Sum_probs=48.6
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++.. ++..+++..+.+|++|++++..... ...+ ...++....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~ 79 (203)
T cd08445 14 GLLPELIRRFRQAAP-DVEIELIE---------MTTVQQIEALKEGRIDVGFGRLRIE---DPAI-RRIVLREEPLVVAL 79 (203)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe---------CChHHHHHHHHcCCCcEEEecCCCC---CCCc-eeEEEEeccEEEEe
Confidence 466788899999887 45666654 3568999999999999998632211 1223 24566778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 80 ~~~h 83 (203)
T cd08445 80 PAGH 83 (203)
T ss_pred eCCC
Confidence 8554
No 86
>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=93.50 E-value=5.8 Score=36.08 Aligned_cols=71 Identities=23% Similarity=0.259 Sum_probs=48.0
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..+++.++.+|++|+++...... ....+. ..++.+..+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~l~-~~~l~~~~~~~~~ 79 (199)
T cd08430 13 SFLPPILERFRAQHP-QVEIKLHT---------GDPADAIDKVLNGEADIAIAARPDK--LPARLA-FLPLATSPLVFIA 79 (199)
T ss_pred eeccHHHHHHHHHCC-CceEEEEe---------CCHHHHHHHHHCCCCCEEEEecCCC--CCcccE-EEeeccceEEEEE
Confidence 455678999999997 46666654 3578899999999999998632111 112232 3566677788888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 80 ~~~~ 83 (199)
T cd08430 80 PNIA 83 (199)
T ss_pred eCCc
Confidence 7543
No 87
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=93.45 E-value=2.2 Score=42.76 Aligned_cols=118 Identities=14% Similarity=0.115 Sum_probs=63.7
Q ss_pred CcCCHHHHHhCCCeeEEEeCc-hH---HHHHHhcCC------------------C--ccceeecCChHHHHHHhhccccC
Q 037841 273 TITDVKMLIKRGDNVGYQKGS-FV---LGILKQLGF------------------D--ERKLVVYNSPEECHELFQKGSAN 328 (561)
Q Consensus 273 ~I~sl~dL~~~~~~vg~~~gs-~~---~~~l~~~~~------------------~--~~~~~~~~s~~~~~~~l~~g~~~ 328 (561)
.|++++||. .|.+|++.... .. ..+|++.|. . ..+++.. ...+...++.+|+
T Consensus 120 ~i~si~DL~-~Gk~IAip~d~~n~~r~L~lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~-~~~~~~~al~~g~-- 195 (271)
T PRK11063 120 KIKSLDELQ-DGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVEL-EAPQLPRSLDDAQ-- 195 (271)
T ss_pred CCCCHHHhc-CCCEEEecCCCccHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEEC-cHHHHHHhccccc--
Confidence 489999993 48999997532 22 224454333 1 1233333 4556778899999
Q ss_pred CceeEEeecchhHHHHHhcC-CcceEEeCcccccCceEEEecCCCCChhhHHHHHhhccccchhHHHHHH
Q 037841 329 GGIAAAFEEIPYGKLLVGQH-CYKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILSVTEGDKMKEIEDA 397 (561)
Q Consensus 329 ~gv~a~i~~~~~~~~~l~~~-~~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~G~~~~i~~k 397 (561)
+|+++...+++...-... -+.+ .....-...-..++++++.-=-+.+.+.+..+.....-+.|.++
T Consensus 196 --vDaa~i~~~~a~~a~~~~~~~~l-~~e~~~~~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~~ 262 (271)
T PRK11063 196 --IALAVINTTYASQIGLTPAKDGI-FVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANKV 262 (271)
T ss_pred --ccEEEEChHHHHHcCCCCCCCee-EECCCCCCeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence 999999988877543222 1222 22211111223566666533334454445444444444455544
No 88
>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=93.31 E-value=6 Score=35.70 Aligned_cols=70 Identities=21% Similarity=0.400 Sum_probs=47.5
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-..++..+.++.+ .+++++.. ++..+++.++.+|++|+++.... .....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~l~-~~~l~~~~~~~v~ 78 (195)
T cd08434 13 SLVPDLIRAFRKEYP-NVTFELHQ---------GSTDELLDDLKNGELDLALCSPV---PDEPDIE-WIPLFTEELVLVV 78 (195)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEec---------CcHHHHHHHHHcCCccEEEEccC---CCCCCee-EEEeecceEEEEe
Confidence 455678888888886 35666554 34678899999999999986322 2223333 3567778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
++..
T Consensus 79 ~~~~ 82 (195)
T cd08434 79 PKDH 82 (195)
T ss_pred cCCC
Confidence 7554
No 89
>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=93.21 E-value=0.35 Score=38.47 Aligned_cols=56 Identities=20% Similarity=0.307 Sum_probs=46.7
Q ss_pred ccCccchhHHHHHHHhhhcc-c-cccccchhHHHHHHHHHHHHHHHHHhHhhheeeeE
Q 037841 211 ARHQVGTSFWFSFSTMVFSQ-R-ERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLT 266 (561)
Q Consensus 211 ~~~~~~~~~~~~~~~l~~~~-~-~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt 266 (561)
...++.+++|+++.++...| + ..|.+...|++.+++.+.++.+.....+.+++.++
T Consensus 21 ~~~~~~da~yfs~~t~tTvGyGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l~ 78 (79)
T PF07885_consen 21 EKWSFIDALYFSFVTITTVGYGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVLT 78 (79)
T ss_dssp STTSHHHHHHHHHHHHTT---SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHhcccCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35678999999999999777 4 46788889999999999999999999999887653
No 90
>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=93.20 E-value=4.9 Score=37.71 Aligned_cols=70 Identities=14% Similarity=0.150 Sum_probs=48.9
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+..+++..+.++.+ .+++++.. ++..++.+.+.+|++|++++... .....+. ..|......++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~---------~~~~~~~~~l~~g~~Di~i~~~~---~~~~~l~-~~~l~~~~~~~v~ 78 (221)
T cd08469 13 VLLPALVRRLETEAP-GIDLRIRP---------VTRLDLAEQLDLGRIDLVIGIFE---QIPPRFR-RRTLFDEDEVWVM 78 (221)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEee---------CChhhHHHHHHCCCccEEEecCC---CCCccce-eeeeeccceEEEE
Confidence 355678888888887 46666654 35678999999999999986322 1223333 4577788888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (221)
T cd08469 79 RKDH 82 (221)
T ss_pred eCCC
Confidence 8554
No 91
>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=92.99 E-value=6.4 Score=35.90 Aligned_cols=70 Identities=16% Similarity=0.097 Sum_probs=47.1
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-..++..+.++.+ .+++++.. ++..+++..+.+|++|+++..... ....+ -..+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~v~ 78 (200)
T cd08464 13 WLAPPLLAALRAEAP-GVRLVFRQ---------VDPFNVGDMLDRGEIDLAIGVFGE---LPAWL-KREVLYTEGYACLF 78 (200)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec---------CCcccHHHHHhcCcccEEEecCCC---Ccccc-eeeeecccceEEEE
Confidence 456678889998887 46666654 245678899999999999863221 12222 34577777888887
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (200)
T cd08464 79 DPQQ 82 (200)
T ss_pred eCCC
Confidence 7443
No 92
>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=92.99 E-value=7.1 Score=35.64 Aligned_cols=72 Identities=15% Similarity=0.161 Sum_probs=49.6
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++...+++.+.+|++|+++... ........++ ..++.+..+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~-~~~~~~~~l~-~~~l~~~~~~~~~ 80 (198)
T cd08437 13 YYFPKLAKDLIKTGL-MIQIDTYE---------GGSAELLEQLLQGDLDIALLGS-LTPLENSALH-SKIIKTQHFMIIV 80 (198)
T ss_pred HHhHHHHHHHHHhCC-ceEEEEEE---------cCHHHHHHHHHcCCCCEEEecC-CCCCCcccce-EEEeecceEEEEe
Confidence 355688899999988 46777665 3578899999999999998632 1111223333 4567778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 81 ~~~h 84 (198)
T cd08437 81 SKDH 84 (198)
T ss_pred cCCC
Confidence 7554
No 93
>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=92.98 E-value=3.4 Score=38.18 Aligned_cols=70 Identities=17% Similarity=0.154 Sum_probs=48.4
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++.. ++..+++++|.+|++|++++..... ...++. .+.....+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~---------~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~lv~ 78 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQ---------ASREAMLAQVADGEIDLALGVFPEL---PEELHA-ETLFEERFVCLA 78 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEec---------CChHhHHHHHHCCCccEEEeccccC---CcCeeE-EEeeeccEEEEE
Confidence 455688899988887 45666554 3678999999999999998633221 122333 456677788888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~h 82 (200)
T cd08465 79 DRAT 82 (200)
T ss_pred eCCC
Confidence 7553
No 94
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=92.94 E-value=1.6 Score=44.02 Aligned_cols=105 Identities=13% Similarity=0.087 Sum_probs=66.4
Q ss_pred CCCcCCHHHHHhCCCeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHH-HhcCC
Q 037841 271 QPTITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLL-VGQHC 349 (561)
Q Consensus 271 ~~~I~sl~dL~~~~~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~-l~~~~ 349 (561)
..+|++++|| +|.++.+..+......++.+|... +.. ...|...+|++|. +|++.......... +.+.+
T Consensus 125 ~~pi~s~~Dl--kG~kiR~~~~~~~~~~~~~lGa~p---v~i-p~~evy~aLq~G~----vDg~~~~~~~~~~~~~~ev~ 194 (286)
T PF03480_consen 125 KKPIRSPEDL--KGLKIRVPGSPVMSDFFEALGASP---VPI-PWSEVYQALQQGV----VDGAENSASSIYSLGLYEVA 194 (286)
T ss_dssp SS--SSGGGG--TTEEEEETSSHHHHHHHHHCTSEE---EE--TGGGHHHHHHTTS----SSEEEEEHHHHHHTTGGGTS
T ss_pred ccCCccHhhH--hhCeEEecCCHHHHHHHHHcCCee---ecC-cHHHHHHHHhcCC----cCeEecCHHHHHhcChhhhC
Confidence 3579999999 799998866777788888877532 333 5668999999999 99999877655322 12336
Q ss_pred cceEEeCcccccCceEEEecCCCC--ChhhHHHHHhhccc
Q 037841 350 YKYTMVEPTFKTAGFGFAFPLHSP--LVHDVSKAILSVTE 387 (561)
Q Consensus 350 ~~l~~v~~~~~~~~~~~~~~k~sp--l~~~in~~Il~l~e 387 (561)
+ +..... ....+..+++.+..- |-++..++|.+..+
T Consensus 195 ~-y~~~~~-~~~~~~~~~~n~~~w~~L~~e~q~~l~~~~~ 232 (286)
T PF03480_consen 195 K-YFTDTN-HGWSPYAVIMNKDWWDSLPDEDQEALDDAAD 232 (286)
T ss_dssp S-EEEEEE-EEEEEEEEEEEHHHHHHS-HHHHHHHHHHHH
T ss_pred C-eeEeec-ccCcceEEEEcHHHHhcCCHHHHHHHHHHHH
Confidence 5 333322 444556777777632 55555555554443
No 95
>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=92.93 E-value=6.5 Score=36.20 Aligned_cols=70 Identities=13% Similarity=0.112 Sum_probs=48.3
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..++++.|.+|++|+++.... .....+. ..+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~ 78 (200)
T cd08467 13 ALLPRLAPRLRERAP-GLDLRLCP---------IGDDLAERGLEQGTIDLAVGRFA---VPPDGLV-VRRLYDDGFACLV 78 (200)
T ss_pred HHHHHHHHHHHhhCC-CCEEEEec---------CCcccHHHHhhCCCcCEEEecCC---CCCccce-eEEeeeccEEEEE
Confidence 456788899999988 46676654 24568899999999999985321 1112233 3567788888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~h 82 (200)
T cd08467 79 RHGH 82 (200)
T ss_pred cCCC
Confidence 7543
No 96
>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=92.92 E-value=7.5 Score=35.76 Aligned_cols=72 Identities=21% Similarity=0.205 Sum_probs=49.3
Q ss_pred EEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEE
Q 037841 80 TGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMI 159 (561)
Q Consensus 80 ~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~iv 159 (561)
..+-.+++..+.++.+ .+++++.. ++..++...+.+|++|+++..... .....+. ..++....++++
T Consensus 12 ~~~l~~~l~~f~~~~P-~~~i~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~v 78 (198)
T cd08443 12 RYVLPPVIKGFIERYP-RVSLQMHQ---------GSPTQIAEMVSKGLVDFAIATEAL--HDYDDLI-TLPCYHWNRCVV 78 (198)
T ss_pred eeECcHHHHHHHHHCC-CeEEEEEe---------CCHHHHHHHHHCCCccEEEEeccc--cccCCce-EeeeeeceEEEE
Confidence 4566788999999887 35666654 356789999999999999852211 1112232 456777888888
Q ss_pred EEccC
Q 037841 160 VPIKD 164 (561)
Q Consensus 160 vp~~~ 164 (561)
++...
T Consensus 79 ~~~~h 83 (198)
T cd08443 79 VKRDH 83 (198)
T ss_pred EcCCC
Confidence 87554
No 97
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=92.90 E-value=4 Score=41.49 Aligned_cols=71 Identities=14% Similarity=0.204 Sum_probs=49.2
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-.+++..+.+..+ .+++++.. ++..+++.+|.+|++|+++...... ..... -...|+....++++++
T Consensus 111 ~l~~~l~~~~~~~p-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~-l~~~~l~~~~~~lv~~ 178 (312)
T PRK10341 111 FMSDMINKFKEVFP-KAQVSMYE---------AQLSSFLPAIRDGRLDFAIGTLSNE-MKLQD-LHVEPLFESEFVLVAS 178 (312)
T ss_pred hHHHHHHHHHHhCC-CCEEEEEe---------CCHHHHHHHHHcCCCcEEEecCCcc-cccCC-eeEEEEecccEEEEEc
Confidence 44588888888887 36677665 3578999999999999998532211 11122 2356777888899988
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 179 ~~~ 181 (312)
T PRK10341 179 KSR 181 (312)
T ss_pred CCC
Confidence 553
No 98
>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=92.80 E-value=7.2 Score=35.28 Aligned_cols=70 Identities=13% Similarity=0.063 Sum_probs=48.8
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..++...+.+|++|+++... ......+ .+.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~~~~Di~i~~~---~~~~~~~-~~~~l~~~~~~~~~ 78 (197)
T cd08448 13 RGLPRILRAFRAEYP-GIEVALHE---------MSSAEQIEALLRGELDLGFVHS---RRLPAGL-SARLLHREPFVCCL 78 (197)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe---------CCHHHHHHHHHcCCcceEEEeC---CCCCcCc-eEEEEecCcEEEEe
Confidence 456788999999887 46666655 3578899999999999987522 1222223 34567778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~h 82 (197)
T cd08448 79 PAGH 82 (197)
T ss_pred eCCC
Confidence 7553
No 99
>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=92.80 E-value=7.3 Score=35.27 Aligned_cols=70 Identities=10% Similarity=0.160 Sum_probs=47.9
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.+..+ .+++++.. ++..++...+.+|++|+++..... ....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~p-~i~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 78 (197)
T cd08414 13 GLLPRLLRRFRARYP-DVELELRE---------MTTAEQLEALRAGRLDVGFVRPPP---DPPGLA-SRPLLREPLVVAL 78 (197)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec---------CChHHHHHHHHcCCccEEEEcCCC---CCCCee-EEEEeeccEEEEe
Confidence 345678888888876 35666554 356889999999999999863222 122232 4567778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (197)
T cd08414 79 PADH 82 (197)
T ss_pred cCCC
Confidence 7554
No 100
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=92.79 E-value=5.6 Score=40.08 Aligned_cols=73 Identities=15% Similarity=0.173 Sum_probs=46.3
Q ss_pred EEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEE
Q 037841 80 TGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMI 159 (561)
Q Consensus 80 ~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~iv 159 (561)
.++-.+++..+.++.+ .+++++.. ++.+++...+.+|++|+++............+ ...|+....++++
T Consensus 105 ~~~l~~~l~~f~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l-~~~~l~~~~~~~~ 173 (296)
T PRK11062 105 KRLVSRVLLTAVPEDE-SIHLRCFE---------STHEMLLEQLSQHKLDMILSDCPVDSTQQEGL-FSKKLGECGVSFF 173 (296)
T ss_pred HhhHHHHHHHHHhcCC-ceEEEEEe---------CCHHHHHHHHHcCCCCEEEecCCCccccccch-hhhhhhccCcceE
Confidence 3566788888888776 35555543 36789999999999999885322111111222 3456667777777
Q ss_pred EEcc
Q 037841 160 VPIK 163 (561)
Q Consensus 160 vp~~ 163 (561)
++.+
T Consensus 174 ~~~~ 177 (296)
T PRK11062 174 CTNP 177 (296)
T ss_pred ecCC
Confidence 6644
No 101
>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=92.78 E-value=7.1 Score=35.44 Aligned_cols=72 Identities=13% Similarity=0.130 Sum_probs=48.5
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeee--cCcceeeeccccccccceEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITIL--LNRSNYVDFTLPYTESGVSMI 159 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it--~~R~~~vdfT~p~~~~~~~iv 159 (561)
+-.+++..+.+..+ .+++++.. ++..++...+.+|++|+++...... ......+ ...+.....++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~-~~~~l~~~~~~~~ 82 (200)
T cd08423 14 LLPPALAALRARHP-GLEVRLRE---------AEPPESLDALRAGELDLAVVFDYPVTPPPDDPGL-TRVPLLDDPLDLV 82 (200)
T ss_pred hhhHHHHHHHHhCC-CCeEEEEe---------CCHHHHHHHHhcCCccEEEEeccccccCCCCCCc-EEEEeccCcEEEE
Confidence 45678888999887 46666655 3467889999999999998632110 0122223 3566778888888
Q ss_pred EEccC
Q 037841 160 VPIKD 164 (561)
Q Consensus 160 vp~~~ 164 (561)
++...
T Consensus 83 ~~~~~ 87 (200)
T cd08423 83 LPADH 87 (200)
T ss_pred ecCCC
Confidence 87554
No 102
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=92.75 E-value=2.4 Score=43.22 Aligned_cols=70 Identities=9% Similarity=0.121 Sum_probs=49.4
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+.+++.. ++...++.+|.+|++|+++..... ....+.+ .++....+++++
T Consensus 125 ~~l~~~l~~f~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Di~i~~~~~---~~~~l~~-~~l~~~~~~lv~ 190 (314)
T PRK09508 125 RLTSQIYNRIEQIAP-NIHVVFKS---------SLNQNIEHQLRYQETEFVISYEEF---DRPEFTS-VPLFKDELVLVA 190 (314)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe---------CcchhHHHHHhcCCccEEEecCCC---Cccccce-eeeecCceEEEE
Confidence 456788999999987 46676655 356789999999999999874321 1223333 466778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 191 ~~~h 194 (314)
T PRK09508 191 SKNH 194 (314)
T ss_pred cCCC
Confidence 8554
No 103
>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=92.50 E-value=8 Score=35.06 Aligned_cols=70 Identities=11% Similarity=0.024 Sum_probs=48.1
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++...+++++.+|++|+++..... ....+ -+.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~~~ 78 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHT---------RDSPTVEQWLSAQQCDLGLVSTLH---EPPGI-ERERLLRIDGVCVL 78 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEe---------CCHHHHHHHHHcCCccEEEEecCC---CCCCe-eEEEeeccCeEEEe
Confidence 456788999999987 46777665 356788999999999999853211 11222 24566777888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (196)
T cd08456 79 PPGH 82 (196)
T ss_pred cCCC
Confidence 7543
No 104
>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=92.48 E-value=8.4 Score=35.24 Aligned_cols=70 Identities=16% Similarity=0.142 Sum_probs=47.8
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..++...+.+|++|+++...... ...+ -+.++.+...++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~ 78 (196)
T cd08458 13 SFMSGVIQTFIADRP-DVSVYLDT---------VPSQTVLELVSLQHYDLGISILAGD---YPGL-TTEPVPSFRAVCLL 78 (196)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEec---------cChHHHHHHHHcCCCCEEEEeccCC---CCCc-eEEEeccCceEEEe
Confidence 355688999999987 46666654 3567899999999999998632221 1222 23567777888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~h 82 (196)
T cd08458 79 PPGH 82 (196)
T ss_pred cCCC
Confidence 7543
No 105
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=92.45 E-value=11 Score=38.17 Aligned_cols=71 Identities=23% Similarity=0.278 Sum_probs=48.7
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.+..+ .+++++.. ++.++++..+.+|++|++++.... .....++ +.|+.....++++
T Consensus 106 ~~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~l~-~~~l~~~~~~~~~ 172 (309)
T PRK12682 106 YVLPRVVAAFRKRYP-KVNLSLHQ---------GSPDEIARMVISGEADIGIATESL--ADDPDLA-TLPCYDWQHAVIV 172 (309)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEec---------CCHHHHHHHHHcCCccEEEecCcc--cCCCcce-EEEeeeeeEEEEe
Confidence 455688889988887 35566544 356889999999999999863221 1112333 3577788888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 173 ~~~~ 176 (309)
T PRK12682 173 PPDH 176 (309)
T ss_pred cCCC
Confidence 8654
No 106
>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=92.11 E-value=9.5 Score=35.00 Aligned_cols=73 Identities=18% Similarity=0.247 Sum_probs=50.0
Q ss_pred EEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEE
Q 037841 80 TGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMI 159 (561)
Q Consensus 80 ~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~iv 159 (561)
.++-.+++..+.++.+ .+++++.. ++..++++.+.+|++|+++..-.. .....+ .+.++....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~ 78 (198)
T cd08444 12 RYALPWVVQAFKEQFP-NVHLVLHQ---------GSPEEIASMLANGQADIGIATEAL--ENHPEL-VSFPYYDWHHHII 78 (198)
T ss_pred hhhhhHHHHHHHHHCC-CeEEEEEe---------CCHHHHHHHHHCCCccEEEecccc--CCCcCc-EEeeccccceeEE
Confidence 3466788999999987 46666654 356789999999999999862111 111223 2467777888888
Q ss_pred EEccCC
Q 037841 160 VPIKDS 165 (561)
Q Consensus 160 vp~~~~ 165 (561)
++...+
T Consensus 79 ~~~~hp 84 (198)
T cd08444 79 VPVGHP 84 (198)
T ss_pred ecCCCc
Confidence 885543
No 107
>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=91.55 E-value=10 Score=34.37 Aligned_cols=72 Identities=18% Similarity=0.201 Sum_probs=47.9
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++.. +...++...+.+|++|+++..... ......+ -+.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~l-~~~~l~~~~~~~v~ 80 (199)
T cd08416 13 NTVPRIIMGLKLRRP-ELDIELTL---------GSNKDLLKKLKDGELDAILVATPE-GLNDPDF-EVVPLFEDDIFLAV 80 (199)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEEE---------cCcHHHHHHHhCCCCCEEEEecCC-cCCCCCe-EEEEeecceEEEEE
Confidence 456788899999987 35666654 245688999999999999863221 0011222 24566777888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 81 ~~~h 84 (199)
T cd08416 81 PATS 84 (199)
T ss_pred CCCC
Confidence 7554
No 108
>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=91.55 E-value=11 Score=34.42 Aligned_cols=69 Identities=16% Similarity=0.150 Sum_probs=46.6
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++-.++...+.+|++|+++.... .....+. ..++.+..+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~~~ 78 (196)
T cd08457 13 GFLPRFLAAFLRLRP-NLHLSLMG---------LSSSQVLEAVASGRADLGIADGP---LEERQGF-LIETRSLPAVVAV 78 (196)
T ss_pred cccHHHHHHHHHHCC-CeEEEEEe---------cCcHHHHHHHHcCCccEEEeccC---CCCCCcE-EEEeccCCeEEEe
Confidence 455688999999987 46666655 23468889999999999986322 1122222 3456677788887
Q ss_pred Ecc
Q 037841 161 PIK 163 (561)
Q Consensus 161 p~~ 163 (561)
+..
T Consensus 79 ~~~ 81 (196)
T cd08457 79 PMG 81 (196)
T ss_pred eCC
Confidence 754
No 109
>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=91.29 E-value=6.1 Score=37.69 Aligned_cols=72 Identities=8% Similarity=-0.026 Sum_probs=39.8
Q ss_pred eeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCccc-ccCceEEEecCCCCChhhHHHHHhhcc
Q 037841 309 LVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPTF-KTAGFGFAFPLHSPLVHDVSKAILSVT 386 (561)
Q Consensus 309 ~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~~-~~~~~~~~~~k~spl~~~in~~Il~l~ 386 (561)
+....+..+..+.+.+|+ +++.+......... .... ....++... ....+++++.|+++=.+.-.+.|..+.
T Consensus 132 ~~~~~~~~~~~~~~~~Ge----~~~~~~~~~~~~~~-~~~~-~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl~ 204 (216)
T TIGR01256 132 LVYGEDVRQALQFVETGN----APAGIVALSDVIPS-KKVG-SVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYLK 204 (216)
T ss_pred eeecCcHHHHHHHHHcCC----CCEEeeehhhhccc-CCcc-EEEEeCccccCCccccEEEEECCCChHHHHHHHHHHc
Confidence 334446677888999999 88877655333221 1222 233444432 233457888888775444444444333
No 110
>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=91.21 E-value=6.8 Score=36.13 Aligned_cols=70 Identities=7% Similarity=0.127 Sum_probs=48.3
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..+++++|.+|++|+++.... .....++ +.++....+++++
T Consensus 14 ~~l~~~l~~f~~~~P-~v~i~i~~---------~~~~~l~~~l~~g~~D~~~~~~~---~~~~~~~-~~~l~~~~~~lv~ 79 (198)
T cd08486 14 RSLPLLLRAFLTSTP-TATVSLTH---------MTKDEQVEGLLAGTIHVGFSRFF---PRHPGIE-IVNIAQEDLYLAV 79 (198)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEE---------CCHHHHHHHHHcCCceEEEecCC---CCCCceE-EEEEeeccEEEEe
Confidence 345688899999887 46666655 36789999999999999985321 1112222 4556677888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 80 ~~~h 83 (198)
T cd08486 80 HRSQ 83 (198)
T ss_pred cCCC
Confidence 8543
No 111
>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=91.01 E-value=12 Score=34.10 Aligned_cols=73 Identities=12% Similarity=0.109 Sum_probs=48.1
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..++..++.+|++|+++............+ -+.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~ 81 (200)
T cd08453 13 SVLPELVRRFREAYP-DVELQLRE---------ATSDVQLEALLAGEIDAGIVIPPPGASAPPAL-AYRPLLSEPLVLAV 81 (200)
T ss_pred HHHHHHHHHHHHhCC-CceEEEEe---------CCHHHHHHHHHcCCCCEEEEecCcccCCCcce-eEEEeeeCceEEEE
Confidence 355688889988887 35666654 35678899999999999986321111011222 24667778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 82 ~~~h 85 (200)
T cd08453 82 PAAW 85 (200)
T ss_pred ECCC
Confidence 8554
No 112
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=90.90 E-value=12 Score=33.74 Aligned_cols=71 Identities=14% Similarity=0.119 Sum_probs=48.4
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+.+++.. ++..++...+.+|++|+++..... .....+ ...++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~~ 79 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQ---------AGSDDLLAAVREGRLDLAFVGLPE--RRPPGL-ASRELAREPLVAVV 79 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec---------CCHHHHHHHHHcCCccEEEEecCC--CCCCCc-EEEEeecceEEEEe
Confidence 456788899998887 46666654 356789999999999999863322 122223 23566777888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 80 ~~~~ 83 (194)
T cd08436 80 APDH 83 (194)
T ss_pred cCCC
Confidence 7554
No 113
>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=90.56 E-value=3.2 Score=40.04 Aligned_cols=194 Identities=15% Similarity=0.135 Sum_probs=111.9
Q ss_pred EEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcC-cccEEEeceeeecCcc---eeee--ccccccc
Q 037841 80 TGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLG-EFDAAVGDITILLNRS---NYVD--FTLPYTE 153 (561)
Q Consensus 80 ~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g-~~D~~vg~~~it~~R~---~~vd--fT~p~~~ 153 (561)
.+..-++.+.+.++.|+++++.+. +-.++..+|..| +.|+.+.+-....++. ..+. -..|+..
T Consensus 10 ~~~~~~l~~~f~~~~g~~v~v~~~-----------~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~ 78 (230)
T PF13531_consen 10 APALEELAEAFEKQPGIKVEVSFG-----------GSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLAR 78 (230)
T ss_dssp HHHHHHHHHHHHHHHCEEEEEEEE-----------CHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEE
T ss_pred HHHHHHHHHHHHhccCCeEEEEEC-----------ChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCccccccc
Confidence 345567888888888865544443 346788888877 7898877532221111 2333 5678888
Q ss_pred cceEEEEEccCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCCCCCccCccchhHHHHHHHhhhccccc
Q 037841 154 SGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQRER 233 (561)
Q Consensus 154 ~~~~ivvp~~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 233 (561)
+.+++++++..+..
T Consensus 79 ~~~vl~~~~~~~~~------------------------------------------------------------------ 92 (230)
T PF13531_consen 79 SPLVLAVPKGNPKG------------------------------------------------------------------ 92 (230)
T ss_dssp EEEEEEEETTSTTS------------------------------------------------------------------
T ss_pred CceEEEeccCcccc------------------------------------------------------------------
Confidence 99999999765322
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCeeEEEeCc------hHHHHHHhcC---C
Q 037841 234 VISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGYQKGS------FVLGILKQLG---F 304 (561)
Q Consensus 234 ~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~vg~~~gs------~~~~~l~~~~---~ 304 (561)
+.+++||.+.+.+|++.... .....+.+.+ .
T Consensus 93 ----------------------------------------~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~~g~~~~ 132 (230)
T PF13531_consen 93 ----------------------------------------IRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAAAGGQEL 132 (230)
T ss_dssp ----------------------------------------TTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHHHTHCHH
T ss_pred ----------------------------------------cCCHHHHhhccCEEEecCcccChhhHHHHHHHHHcccHHH
Confidence 68889998766688886531 1223333332 1
Q ss_pred C---cccee-ecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceE--EeCccccc--CceEEEecCCCCChh
Q 037841 305 D---ERKLV-VYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYT--MVEPTFKT--AGFGFAFPLHSPLVH 376 (561)
Q Consensus 305 ~---~~~~~-~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~--~v~~~~~~--~~~~~~~~k~spl~~ 376 (561)
- ..++. ..++..+....+..|+ +++.+......... +....+. ..++.+.. ..+.+++-++++=.+
T Consensus 133 ~~~l~~~~~~~~~~~~~~~~~v~~g~----~d~~~~~~s~~~~~--~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~ 206 (230)
T PF13531_consen 133 LDALQKNIVQYVPSTSQVLSAVASGE----ADAGIVYESQAIFA--RQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPE 206 (230)
T ss_dssp HHHHHHTEEEEESSHHHHHHHHHTTS----SSEEEEEHHHHHHC--TSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHH
T ss_pred HHHHHHhCcccccchHHHHHHHHcCC----CcceeeHHHHHHHh--hcCCCeEEEECCchhcCCCEEEEEEEecCCCCHH
Confidence 0 12333 5567788888999998 88888765554322 2222233 33444442 346778888776555
Q ss_pred hHHHHHhhccccchhHHHHHH
Q 037841 377 DVSKAILSVTEGDKMKEIEDA 397 (561)
Q Consensus 377 ~in~~Il~l~e~G~~~~i~~k 397 (561)
.-...+..|... .-+++..+
T Consensus 207 ~a~~f~~~L~s~-~~q~~l~~ 226 (230)
T PF13531_consen 207 AARAFIDFLLSP-EGQQILAK 226 (230)
T ss_dssp HHHHHHHHHTSH-HHHHHHHH
T ss_pred HHHHHHHHHCCH-HHHHHHHH
Confidence 555555444433 34444433
No 114
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=89.92 E-value=0.52 Score=48.63 Aligned_cols=212 Identities=15% Similarity=0.133 Sum_probs=120.1
Q ss_pred HHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcce-eeeccccccccceEEEEEc
Q 037841 84 IDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSN-YVDFTLPYTESGVSMIVPI 162 (561)
Q Consensus 84 idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~-~vdfT~p~~~~~~~ivvp~ 162 (561)
-.+-+++.++.|-.+.+++.|.+.- |+=.+++++|.+|.+|+.+.+......+.. .--|+.||...+.
T Consensus 47 ~~fa~~v~ekt~G~l~i~vfP~~qL-----G~~~~~ie~l~~G~id~~~~s~~~l~~~~P~~~v~~lPflf~d~------ 115 (332)
T COG1638 47 KKFAELVEEKTGGRLKIEVFPNSQL-----GGEAEMIEQLRSGTLDIGVVSLGFLAGLVPEFGVFDLPFLFRDE------ 115 (332)
T ss_pred HHHHHHHHHHhCCeEEEEECCCccc-----CcHHHHHHHHhcCCeeEEeccchhhcccCCcceeecCCeeeCCH------
Confidence 3556788899999888888776654 467899999999999999887655554432 3345556544221
Q ss_pred cCCCCCCcceeccccchhhHHHHHHHHHHHHHHHhhhhcccCCCCCCCccCccchhHHHHHHHhhhccccccccchhHHH
Q 037841 163 KDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWALEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFV 242 (561)
Q Consensus 163 ~~~~~~~~~~fl~PF~~~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~Ril 242 (561)
+ ....++. .++.=-+.-.+---+
T Consensus 116 -~----~~~~~~~---~~~g~~l~~~~e~~g------------------------------------------------- 138 (332)
T COG1638 116 -E----HARRVLD---SEFGEELLKSLEAKG------------------------------------------------- 138 (332)
T ss_pred -H----HHHHHHc---cHHHHHHHHHHHHcC-------------------------------------------------
Confidence 1 0111111 111111111110000
Q ss_pred HHHHHHHHHHHHHHhHhhheeeeEeeccCCCcCCHHHHHhCCCeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHh
Q 037841 243 VIVWYFVVLVLTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELF 322 (561)
Q Consensus 243 ~~~w~~~~lil~~~Yta~LtS~Lt~~~~~~~I~sl~dL~~~~~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l 322 (561)
+...+.|..-.-+ ...-..||++.+|| +|.++-+.........++.+|-....+ ...|...+|
T Consensus 139 --------~~~l~~~~~G~R~---~t~~k~PI~~peDl--kGlkiRv~~s~~~~~~~~a~GA~P~pm----~f~Evy~aL 201 (332)
T COG1638 139 --------LKGLAFWENGFRQ---FTSNKRPIKTPEDL--KGLKIRVPQSPLLLAMFKALGANPTPM----PFAEVYTAL 201 (332)
T ss_pred --------CEEEEEecCceee---eecCCCCCCChHHh--CCCeeecCCCHHHHHHHHHcCCCCCCC----CHHHHHHHH
Confidence 0000001100001 11112379999999 799999988888889999877543222 566889999
Q ss_pred hccccCCceeEEeecchhHHHH----HhcCCcceEEeCcccccCceEEEecCC--CCChhhHHHHHhhccccc
Q 037841 323 QKGSANGGIAAAFEEIPYGKLL----VGQHCYKYTMVEPTFKTAGFGFAFPLH--SPLVHDVSKAILSVTEGD 389 (561)
Q Consensus 323 ~~g~~~~gv~a~i~~~~~~~~~----l~~~~~~l~~v~~~~~~~~~~~~~~k~--spl~~~in~~Il~l~e~G 389 (561)
++|. +|+.-.....+... .++|+ +..+ ....+..+.+.+. .-|-+...++|++..+..
T Consensus 202 qtGv----VDGqEnp~~~i~~~k~~EVqky~---t~tn--H~~~~~~~~~s~~~w~~L~~e~q~il~~aa~e~ 265 (332)
T COG1638 202 QTGV----VDGQENPLSNIYSAKLYEVQKYL---TLTN--HIYLPLAVLVSKAFWDSLPEEDQTILLEAAKEA 265 (332)
T ss_pred HcCC----cccccCCHHHHhhccHHHHhHHh---hhcc--ccccceeeEEcHHHHhcCCHHHHHHHHHHHHHH
Confidence 9999 99876665443211 11222 1111 1223345666666 237778888887766554
No 115
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=89.78 E-value=18 Score=36.66 Aligned_cols=70 Identities=10% Similarity=0.055 Sum_probs=45.7
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.+..+ .+++++... +-.++...+.+|++|+++...... ...+ ...++.....++++
T Consensus 107 ~~l~~~l~~~~~~~P-~v~i~i~~~---------~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~ 172 (309)
T PRK11013 107 SLLPGLCQPFLARYP-DVSLNIVPQ---------ESPLLEEWLSAQRHDLGLTETLHT---PAGT-ERTELLTLDEVCVL 172 (309)
T ss_pred hhHHHHHHHHHHHCC-CCeEEEEeC---------CHHHHHHHHHcCCCCEEEEcCCCC---CCCc-eeeeecceeEEEEE
Confidence 356688888888886 466766652 456788999999999998632211 1222 23455566677777
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 173 ~~~~ 176 (309)
T PRK11013 173 PAGH 176 (309)
T ss_pred cCCC
Confidence 7554
No 116
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=89.66 E-value=12 Score=37.30 Aligned_cols=115 Identities=17% Similarity=0.231 Sum_probs=69.5
Q ss_pred cCCHHHHHhC-CCeeEEE------eCchHHHHHHhcCCC---ccceeecCChHHHHHHhhccccCCceeEEeecchhHHH
Q 037841 274 ITDVKMLIKR-GDNVGYQ------KGSFVLGILKQLGFD---ERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKL 343 (561)
Q Consensus 274 I~sl~dL~~~-~~~vg~~------~gs~~~~~l~~~~~~---~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~ 343 (561)
+..+++|.+. +.++++- .|.+..+.|+..+.- ..+++...+.++.+..+..|. +|+.+.-...+..
T Consensus 124 ~~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~----ad~g~vy~sd~~~ 199 (258)
T COG0725 124 IESLEDLLERPDVRLAIGDPKTVPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAYVETGE----ADAGFVYVSDALL 199 (258)
T ss_pred cccHHHHhcCcCcEEEecCCCCCCchHHHHHHHHHhchhhhccccEEecCcHHHHHHHHHcCC----CCeEEEEEEhhhc
Confidence 3447777763 5577773 466778888775432 347788888899999999999 8877665543222
Q ss_pred HHhcCCcceEEeCccccc-CceEEEecCCCCC---hhhHHHHHhhccccchhHHHHHHH
Q 037841 344 LVGQHCYKYTMVEPTFKT-AGFGFAFPLHSPL---VHDVSKAILSVTEGDKMKEIEDAW 398 (561)
Q Consensus 344 ~l~~~~~~l~~v~~~~~~-~~~~~~~~k~spl---~~~in~~Il~l~e~G~~~~i~~kw 398 (561)
. ..-..+..++..... ..+.+++.+++.- ...|-+.+.. ..-+++.++|
T Consensus 200 ~--~~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s----~~a~~il~~~ 252 (258)
T COG0725 200 S--KKVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLS----PEAQEILEKY 252 (258)
T ss_pred c--CCceEEEEcccccCCCeEEEEEEEcCCCCHHHHHHHHHHHhC----HHHHHHHHHc
Confidence 2 122223444444333 5567778887664 5555555543 2334455544
No 117
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=89.51 E-value=14 Score=37.00 Aligned_cols=70 Identities=14% Similarity=0.186 Sum_probs=50.0
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+..+++..+.++.+ .+.+.+.. ++.++++..+.+|++|+++..... ....++ +.|+....++++++
T Consensus 104 ~l~~~~~~~~~~~p-~v~i~~~~---------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~-~~~l~~~~~~~v~~ 169 (296)
T PRK09906 104 LLPKVLPMFRLRHP-DTLIELVS---------LITTQQEEKLRRGELDVGFMRHPV---YSDEID-YLELLDEPLVVVLP 169 (296)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEe---------CCcHHHHHHHHcCCeeEEEecCCC---CCCCce-EEEEecccEEEEec
Confidence 45678888888887 46666554 246789999999999999864322 223343 36888889999988
Q ss_pred ccCC
Q 037841 162 IKDS 165 (561)
Q Consensus 162 ~~~~ 165 (561)
+..+
T Consensus 170 ~~~p 173 (296)
T PRK09906 170 VDHP 173 (296)
T ss_pred CCCc
Confidence 6543
No 118
>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=89.19 E-value=24 Score=34.71 Aligned_cols=68 Identities=12% Similarity=0.135 Sum_probs=46.6
Q ss_pred hHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEEc
Q 037841 83 CIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPI 162 (561)
Q Consensus 83 ~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~ 162 (561)
-.+++..+.++.+ .+++++.. ++..+++..+.+|++|+++...... ...+ -..|+....++++++.
T Consensus 99 ~~~~l~~~~~~~p-~v~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~lv~s~ 164 (279)
T TIGR03339 99 VLDLVARFRQRYP-GIEVSVRI---------GNSQEVLQALQSYRVDVAVSSEVVD---DPRL-DRVVLGNDPLVAVVHR 164 (279)
T ss_pred HHHHHHHHHHHCC-CcEEEEEE---------CCHHHHHHHHHcCCCcEEEEecccC---CCce-EEEEcCCceEEEEECC
Confidence 4567888888877 35666654 3567899999999999998632222 1222 2356777888888875
Q ss_pred cC
Q 037841 163 KD 164 (561)
Q Consensus 163 ~~ 164 (561)
+.
T Consensus 165 ~~ 166 (279)
T TIGR03339 165 QH 166 (279)
T ss_pred CC
Confidence 54
No 119
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=89.19 E-value=7.9 Score=36.62 Aligned_cols=100 Identities=14% Similarity=0.060 Sum_probs=63.3
Q ss_pred CcCCHHHHHhCCCeeE-EEeCchHHHHHHh----cCCCccceee----cCChHHHHHHhhccccCCceeEEeecchhHHH
Q 037841 273 TITDVKMLIKRGDNVG-YQKGSFVLGILKQ----LGFDERKLVV----YNSPEECHELFQKGSANGGIAAAFEEIPYGKL 343 (561)
Q Consensus 273 ~I~sl~dL~~~~~~vg-~~~gs~~~~~l~~----~~~~~~~~~~----~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~ 343 (561)
.|++++||.+.+.++. -..||-.+.+|.+ .+.+...+.- ..+-.+...++..|. .|+.+.....+..
T Consensus 82 ~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G~----AD~G~g~~~~A~~ 157 (193)
T PF12727_consen 82 GITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASGK----ADAGIGIRAAAEE 157 (193)
T ss_pred cCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcCC----CCEEeehHHHHHh
Confidence 4899999977676544 4667877777654 3344433333 346677899999999 9998876555432
Q ss_pred HHhcCCcceEEeCcccccCceEEEecCCCCChhhHHHHHh
Q 037841 344 LVGQHCYKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAIL 383 (561)
Q Consensus 344 ~l~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il 383 (561)
+ ..- .|.-+ ....+-+++++..-..+.+.+.|.
T Consensus 158 ~--~gL-~Fvpl----~~E~~dlv~~~~~~~~~~vq~ll~ 190 (193)
T PF12727_consen 158 F--YGL-DFVPL----AEERYDLVIRREDLEDPAVQALLD 190 (193)
T ss_pred h--cCC-CcEEc----cccceEEEEEhhHcCCHHHHHHHH
Confidence 1 111 13222 335677888888666666655554
No 120
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=88.98 E-value=20 Score=36.56 Aligned_cols=69 Identities=16% Similarity=0.219 Sum_probs=47.5
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-.+++..+.++.+ .+.+++.. +.-.++...|.+|++|+++..-. .....+.+ .++....++++++
T Consensus 103 ~l~~~l~~~~~~~P-~i~l~~~~---------~~~~~~~~~L~~g~~Dl~i~~~~---~~~~~~~~-~~l~~~~~~lv~~ 168 (317)
T PRK15421 103 WLTPALENFHKNWP-QVEMDFKS---------GVTFDPQPALQQGELDLVMTSDI---LPRSGLHY-SPMFDYEVRLVLA 168 (317)
T ss_pred HHHHHHHHHHHHCC-CceEEEEe---------CccHHHHHHHHCCCcCEEEecCc---ccCCCceE-EEeccceEEEEEc
Confidence 34677888888877 46666654 24568899999999999986321 12233433 6777888888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 169 ~~h 171 (317)
T PRK15421 169 PDH 171 (317)
T ss_pred CCC
Confidence 554
No 121
>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=88.85 E-value=18 Score=32.82 Aligned_cols=70 Identities=11% Similarity=0.128 Sum_probs=48.4
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++.. ++..++..++.+|++|+++..... ....+ -+.++....+++++
T Consensus 14 ~~l~~~i~~~~~~~P-~v~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~v~ 79 (198)
T cd08446 14 DTVPRLLRAFLTARP-DVTVSLHN---------MTKDEQIEALRAGRIHIGFGRFYP---VEPDI-AVENVAQERLYLAV 79 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEee---------CCHHHHHHHHHCCCccEEEEecCC---CCCCc-eeEEeeeccEEEEE
Confidence 355688899999887 46676654 357889999999999999853211 11222 24567778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 80 ~~~~ 83 (198)
T cd08446 80 PKSH 83 (198)
T ss_pred eCCC
Confidence 8554
No 122
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=88.70 E-value=17 Score=37.04 Aligned_cols=83 Identities=8% Similarity=0.086 Sum_probs=55.5
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.+.++||+. +.. ...+-..++..+.+..+ .+.++.. ..++++..|.+|+
T Consensus 116 ~~~l~Ig~~--~~~-----------------~~~~l~~~l~~f~~~~P-~i~i~~~-----------~~~~~~~~l~~g~ 164 (317)
T PRK11482 116 QRTITIATT--PSV-----------------GALVMPVIYQAIKTHYP-QLLLRNI-----------PISDAENQLSQFQ 164 (317)
T ss_pred CceEEEEec--HHH-----------------HHHHHHHHHHHHHHHCC-CCEEEEe-----------cchhHHHHHHCCC
Confidence 467999997 222 11356678888888887 3454422 3467899999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccCC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDS 165 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~ 165 (561)
+|++++.... ....+. +.++....++++++...+
T Consensus 165 ~Dl~i~~~~~---~~~~~~-~~~l~~~~~~lv~~~~hp 198 (317)
T PRK11482 165 TDLIIDTHSC---SNRTIQ-HHVLFTDNVVLVCRQGHP 198 (317)
T ss_pred cCEEEeccCC---CCCceE-EEEEecCcEEEEEeCCCC
Confidence 9999864322 223343 367788888998886543
No 123
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=88.61 E-value=2.4 Score=43.57 Aligned_cols=70 Identities=23% Similarity=0.275 Sum_probs=50.0
Q ss_pred cCCHHHHHhCCCeeEEEeCch-HH----HHHHhcCCCcccee-ecCChHHHHHHhhccccCCceeEEeecchhHHHHHhc
Q 037841 274 ITDVKMLIKRGDNVGYQKGSF-VL----GILKQLGFDERKLV-VYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQ 347 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~gs~-~~----~~l~~~~~~~~~~~-~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~ 347 (561)
|++++|| +|+++|+..++. .. ..|.+.|.+..... ..-.+.+...++..|+ +||++...++......+
T Consensus 128 i~~~adl--kGk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~g~----vda~~~~ep~~~~~~~~ 201 (335)
T COG0715 128 IKSVADL--KGKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAAGQ----VDAFVVWEPWNAAAEGE 201 (335)
T ss_pred cccccCC--CCceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhcCC----cceEEecCCchhhhhcc
Confidence 7889999 799999988774 33 33344565544433 2334558888999999 99988888887776666
Q ss_pred CC
Q 037841 348 HC 349 (561)
Q Consensus 348 ~~ 349 (561)
.-
T Consensus 202 ~~ 203 (335)
T COG0715 202 GG 203 (335)
T ss_pred CC
Confidence 53
No 124
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=88.00 E-value=13 Score=35.41 Aligned_cols=104 Identities=12% Similarity=0.108 Sum_probs=62.1
Q ss_pred cCCHHHHHhCCCee-EEEeCchHHHHHHh----cCCCccceeecC----ChHHHHHHhhccccCCceeEEeecchhHHHH
Q 037841 274 ITDVKMLIKRGDNV-GYQKGSFVLGILKQ----LGFDERKLVVYN----SPEECHELFQKGSANGGIAAAFEEIPYGKLL 344 (561)
Q Consensus 274 I~sl~dL~~~~~~v-g~~~gs~~~~~l~~----~~~~~~~~~~~~----s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~ 344 (561)
|++++||.+.+.++ --..||-.+..|.+ .+.....+.-|. +-.....++..|+ +|+-+.-+ +.
T Consensus 89 i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~----AD~GvGlr----~~ 160 (223)
T COG1910 89 ISSLEDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGR----ADAGVGLR----HA 160 (223)
T ss_pred cccHHHHhhcCcEEEecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHcCC----CCccccHH----HH
Confidence 89999998666543 23567777766654 333333444443 4455688999999 99988844 44
Q ss_pred HhcCCcceEEeCcccccCceEEEecCCCCChhhHHHHHhhccccc
Q 037841 345 VGQHCYKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILSVTEGD 389 (561)
Q Consensus 345 l~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~G 389 (561)
..++.-+|.- +....+-|+.+|+.--.+.+...+..|...+
T Consensus 161 A~~~gL~Fip----l~~E~YD~virke~~~~~~vr~fi~~L~s~~ 201 (223)
T COG1910 161 AEKYGLDFIP----LGDEEYDFVIRKERLDKPVVRAFIKALKSEG 201 (223)
T ss_pred HHHcCCceEE----cccceEEEEEehhHccCHHHHHHHHHhcccc
Confidence 4444323432 3445677889997544444444444444433
No 125
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=87.83 E-value=31 Score=34.34 Aligned_cols=73 Identities=18% Similarity=0.126 Sum_probs=48.4
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.++++.+.++.+ .+.+++.. .+-++++.++.+|++|+++.... .......+.+ .|+....+++++
T Consensus 110 ~~l~~~l~~f~~~~p-~i~l~i~~---------~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~~-~~l~~~~~~~v~ 177 (294)
T PRK09986 110 GRLRPAMRHFLKENP-NVEWLLRE---------LSPSMQMAALERRELDAGIWRMA-DLEPNPGFTS-RRLHESAFAVAV 177 (294)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEe---------CCHHHHHHHHHcCCCCEEEecCC-ccCCCCCeEE-EEeecccEEEEE
Confidence 345677888888887 35666654 24578899999999999985211 0112233433 667778888888
Q ss_pred EccCC
Q 037841 161 PIKDS 165 (561)
Q Consensus 161 p~~~~ 165 (561)
+...+
T Consensus 178 ~~~~~ 182 (294)
T PRK09986 178 PEEHP 182 (294)
T ss_pred cCCCC
Confidence 86653
No 126
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=87.48 E-value=34 Score=34.39 Aligned_cols=87 Identities=11% Similarity=0.057 Sum_probs=56.0
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
.+.++||+. +.+ ...+..+++..+.++.+ .+++.+.. ++..+++..+.+|+
T Consensus 91 ~g~l~Ig~~--~~~-----------------~~~~l~~~l~~~~~~~p-~i~i~i~~---------~~~~~~~~~l~~g~ 141 (300)
T PRK11074 91 RGQLSIAVD--NIV-----------------RPDRTRQLIVDFYRHFD-DVELIIRQ---------EVFNGVWDALADGR 141 (300)
T ss_pred CceEEEEEc--Ccc-----------------chhHHHHHHHHHHHhCC-CceEEEEe---------hhhhHHHHHHHCCC
Confidence 468999986 222 12345688889998888 35565554 35678999999999
Q ss_pred ccEEEeceeeecCcceeeeccccccccceEEEEEccCC
Q 037841 128 FDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIKDS 165 (561)
Q Consensus 128 ~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~~~ 165 (561)
+|++++.... ......+ -..++....+++++++..+
T Consensus 142 ~Dl~i~~~~~-~~~~~~l-~~~~l~~~~~~~v~~~~hp 177 (300)
T PRK11074 142 VDIAIGATRA-IPVGGRF-AFRDMGMLSWACVVSSDHP 177 (300)
T ss_pred CCEEEecCcc-CCccccc-ceeecccceEEEEEcCCCc
Confidence 9999873211 1111122 2455677778888875543
No 127
>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=87.25 E-value=23 Score=32.35 Aligned_cols=69 Identities=13% Similarity=0.044 Sum_probs=46.0
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++-++++.++.+|++|+++...... ...+. +.++....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~~~ 79 (198)
T cd08485 14 HTLPLLLRQLLSVAP-SATVSLTQ---------MSKNRQIEALDAGTIDIGFGRFYPY---QEGVV-VRNVTNERLFLGA 79 (198)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEE---------CCHHHHHHHHHcCCccEEEecCCCC---CCCeE-EEEeeccceEEEe
Confidence 355678888888887 46666654 3567899999999999998632111 12232 3566677777776
Q ss_pred Ecc
Q 037841 161 PIK 163 (561)
Q Consensus 161 p~~ 163 (561)
+..
T Consensus 80 ~~~ 82 (198)
T cd08485 80 QKS 82 (198)
T ss_pred CCC
Confidence 644
No 128
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=86.92 E-value=32 Score=33.53 Aligned_cols=69 Identities=22% Similarity=0.228 Sum_probs=46.7
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+..+++..+.++.+ .+++++.. ++..+++.++.+|++|+++..... .....+. ..+.....++++++
T Consensus 81 ~~~~~l~~~~~~~p-~i~l~i~~---------~~~~~~~~~l~~~~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~ 147 (269)
T PRK11716 81 HLPPILDRFRAEHP-LVEIKLTT---------GDAADAVEKVQSGEADLAIAAKPE--TLPASVA-FSPIDEIPLVLIAP 147 (269)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEE---------CCHHHHHHHHHCCCccEEEEecCC--CCCcceE-EEEcccceEEEEEc
Confidence 45688999999987 36666655 356899999999999999853221 1111222 35566777888876
Q ss_pred cc
Q 037841 162 IK 163 (561)
Q Consensus 162 ~~ 163 (561)
..
T Consensus 148 ~~ 149 (269)
T PRK11716 148 AL 149 (269)
T ss_pred CC
Confidence 44
No 129
>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=86.80 E-value=23 Score=31.88 Aligned_cols=70 Identities=14% Similarity=0.150 Sum_probs=48.8
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.++++.+.++.+ .+++++.. ++..+++..+.+|++|+++...... ...+ ...++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~ 78 (196)
T cd08450 13 QWLPEVLPILREEHP-DLDVELSS---------LFSPQLAEALMRGKLDVAFMRPEIQ---SDGI-DYQLLLKEPLIVVL 78 (196)
T ss_pred hhHHHHHHHHHhhCC-CcEEEEEe---------cChHHHHHHHhcCCccEEEEeCCCC---CCCc-EEEEEEccceEEEe
Confidence 456788999999988 46676665 3467899999999999998532111 1223 24567778888888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (196)
T cd08450 79 PADH 82 (196)
T ss_pred cCCC
Confidence 7554
No 130
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=86.30 E-value=40 Score=34.09 Aligned_cols=71 Identities=11% Similarity=0.137 Sum_probs=47.9
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-.+++..+.++++. +.+++.. ++..++.+.|.+|++|++++. .-.......+ -..++....++++++
T Consensus 107 ~l~~~l~~~~~~~P~-i~l~l~~---------~~~~~~~~~l~~g~~D~~i~~-~~~~~~~~~l-~~~~l~~~~~~~v~~ 174 (308)
T PRK10094 107 AVAQLLAWLNERYPF-TQFHISR---------QIYMGVWDSLLYEGFSLAIGV-TGTEALANTF-SLDPLGSVQWRFVMA 174 (308)
T ss_pred HHHHHHHHHHHhCCC-cEEEEEe---------ehhhhHHHHHhCCCccEEEec-ccCccccCCe-eEEEecceeEEEEEC
Confidence 345889999999984 6676655 356788999999999998862 1111112223 345777778888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 175 ~~h 177 (308)
T PRK10094 175 ADH 177 (308)
T ss_pred CCC
Confidence 554
No 131
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=85.09 E-value=25 Score=35.26 Aligned_cols=122 Identities=10% Similarity=0.059 Sum_probs=63.3
Q ss_pred CCCcCCHHHHHhCCCeeEEEeC--chHHHH--HHhcC---------C-----------CccceeecCChHHHHHHhhccc
Q 037841 271 QPTITDVKMLIKRGDNVGYQKG--SFVLGI--LKQLG---------F-----------DERKLVVYNSPEECHELFQKGS 326 (561)
Q Consensus 271 ~~~I~sl~dL~~~~~~vg~~~g--s~~~~~--l~~~~---------~-----------~~~~~~~~~s~~~~~~~l~~g~ 326 (561)
..++++++||. .|.+|++.++ ...+.+ |+..+ . ...+++.. ...+...+|.+|.
T Consensus 119 s~~iksl~DL~-~Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~-~~~q~~~al~dg~ 196 (272)
T PRK09861 119 SKKIKTVAQIK-EGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMEL-EGAQLPRVLDDPK 196 (272)
T ss_pred ccCCCCHHHcC-CCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEc-CHHHhHhhccCcc
Confidence 44589999994 5889999863 333332 23322 1 11222222 3456788898988
Q ss_pred cCCceeEEeecchhHHHHHhcCCcceEEeCcccccCceEEEecCCCCChhhHHHHHhhccccchhHHHHHHH
Q 037841 327 ANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILSVTEGDKMKEIEDAW 398 (561)
Q Consensus 327 ~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~G~~~~i~~kw 398 (561)
+|+++....++...-.+--..-......-......++++.+.-=.+.+.+.+..+.....-+.|.++|
T Consensus 197 ----vD~a~i~~~~~~~ag~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 264 (272)
T PRK09861 197 ----VDVAIISTTYIQQTGLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETIF 264 (272)
T ss_pred ----cCEEEEchhHHHHcCCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 99998888776541111111111111111112234556554334455666666665554444555543
No 132
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=82.83 E-value=22 Score=35.18 Aligned_cols=72 Identities=15% Similarity=0.137 Sum_probs=42.4
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc-ccEEEeceeeecCcc---eee-ecc-ccccccc
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE-FDAAVGDITILLNRS---NYV-DFT-LPYTESG 155 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~-~D~~vg~~~it~~R~---~~v-dfT-~p~~~~~ 155 (561)
..-++.+.+.++.|.++.+++-. + ..+..++.+|. +|+.+.+-.-..++. ..+ ..+ .+|....
T Consensus 40 ~~~~l~~~Fe~~~g~~v~~~~~~----------S-g~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~n~ 108 (257)
T PRK10677 40 ALQDIAAQYKKEKGVDVVSSFAS----------S-STLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLGNS 108 (257)
T ss_pred HHHHHHHHHHhhhCCeEEEEecc----------c-HHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeecCE
Confidence 34466777777777655554421 2 36777888877 899877432211111 112 111 3577788
Q ss_pred eEEEEEccC
Q 037841 156 VSMIVPIKD 164 (561)
Q Consensus 156 ~~ivvp~~~ 164 (561)
+++++++..
T Consensus 109 lvl~~~~~~ 117 (257)
T PRK10677 109 LVVVAPKAS 117 (257)
T ss_pred EEEEEECCC
Confidence 899998664
No 133
>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=82.68 E-value=31 Score=34.53 Aligned_cols=120 Identities=22% Similarity=0.241 Sum_probs=72.2
Q ss_pred CcCCHHHHHh---C-CC--eeEEE-eCchHH---HHH-HhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhH
Q 037841 273 TITDVKMLIK---R-GD--NVGYQ-KGSFVL---GIL-KQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYG 341 (561)
Q Consensus 273 ~I~sl~dL~~---~-~~--~vg~~-~gs~~~---~~l-~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~ 341 (561)
+++|++||++ . .. .+|.. .|+..+ ..| +..+.+ .+.++|+..-+.+.+|..|. +|+.+......
T Consensus 89 p~~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~G~~~~~~allgG~----vd~~~~~~~~~ 163 (274)
T PF03401_consen 89 PYKTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYDGGAEALTALLGGH----VDAAFGSPGEA 163 (274)
T ss_dssp S-SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-SSHHHHHHHHHTTS----SSEEEEEHHHH
T ss_pred ccccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeCCccHHHHHHhCCe----eeEEeecHHHH
Confidence 3788999863 2 22 55553 233222 223 345653 46789999999999999999 99998876555
Q ss_pred HHHHhcC-CcceEEeC--------c--cc---------ccCceEEEecCCCC--ChhhHHHHHhhccccchhHHHHHH
Q 037841 342 KLLVGQH-CYKYTMVE--------P--TF---------KTAGFGFAFPLHSP--LVHDVSKAILSVTEGDKMKEIEDA 397 (561)
Q Consensus 342 ~~~l~~~-~~~l~~v~--------~--~~---------~~~~~~~~~~k~sp--l~~~in~~Il~l~e~G~~~~i~~k 397 (561)
..+++.. -+-+.+.. + ++ .....++++|||-| .++.+..++.+..++-.+++..++
T Consensus 164 ~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~ 241 (274)
T PF03401_consen 164 LPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEK 241 (274)
T ss_dssp HHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHH
T ss_pred HHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 5444432 11111111 0 11 12334889999987 899999999999998777665554
No 134
>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=82.38 E-value=39 Score=30.73 Aligned_cols=70 Identities=13% Similarity=0.158 Sum_probs=47.7
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++..++..+|.+|++|+++.. .......+. +.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~---~~~~~~~~~-~~~l~~~~~~lv~ 78 (197)
T cd08452 13 EFLPPIVREYRKKFP-SVKVELRE---------LSSPDQVEELLKGRIDIGFLH---PPIQHTALH-IETVQSSPCVLAL 78 (197)
T ss_pred hHHHHHHHHHHHHCC-CcEEEEEe---------cChHHHHHHHHCCCccEEEee---CCCCCCCee-EEEeeeccEEEEE
Confidence 345688899999887 46666655 356789999999999999852 122222333 3566677788888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~h 82 (197)
T cd08452 79 PKQH 82 (197)
T ss_pred eCCC
Confidence 7543
No 135
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=81.82 E-value=5.3 Score=38.82 Aligned_cols=104 Identities=19% Similarity=0.175 Sum_probs=51.2
Q ss_pred CCCeeEEEeCchHHHHHHhcCCCccc--eeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEe--Cc-
Q 037841 283 RGDNVGYQKGSFVLGILKQLGFDERK--LVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMV--EP- 357 (561)
Q Consensus 283 ~~~~vg~~~gs~~~~~l~~~~~~~~~--~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v--~~- 357 (561)
.|.+||+-..|.-+..|.+..+...+ ++.. +..+++++|.+|. +||++-+..- .-.. .- .+... ..
T Consensus 113 dGmRVGiD~~S~Dq~~LT~~~~~gk~Ve~Vei-~Y~q~~~~l~~g~----IDA~IWN~d~--i~~~-~~-~l~~~~l~~~ 183 (232)
T PF14503_consen 113 DGMRVGIDPSSIDQKILTEAEFEGKNVEFVEI-PYNQLLELLRSGE----IDAAIWNYDE--IEDK-NF-GLKYVPLKDD 183 (232)
T ss_dssp ---EEEE-TT-HHHHHHHHHHHTTS--EEEE---HHHHHHHHHHTS------EEEEE--H--HCCH-HC-TEEEEE--SS
T ss_pred eeeEeecCCCCccHHHHHHHHhCCCceEEEEe-cHHHHHHHHHCCC----ccEEEECCcc--cccc-cC-CeeEEeCCch
Confidence 47799998888888888664444333 3333 4668899999999 9999988761 1111 11 12222 11
Q ss_pred -c-cccCceEEEecCCCCC-hhhHHHHHhhccccchhHHHHHHHc
Q 037841 358 -T-FKTAGFGFAFPLHSPL-VHDVSKAILSVTEGDKMKEIEDAWF 399 (561)
Q Consensus 358 -~-~~~~~~~~~~~k~spl-~~~in~~Il~l~e~G~~~~i~~kw~ 399 (561)
. .......++++|+.+. ...+.+.| ....+..++++-.
T Consensus 184 ~~~~~~seAVivi~~~~~~i~~ll~~~i----d~~~vl~iQ~~V~ 224 (232)
T PF14503_consen 184 PMSKDASEAVIVIRKDNEPIKALLRKLI----DVEKVLEIQKKVL 224 (232)
T ss_dssp CHHHHTT-EEEEEETT-HHHHHHHHHH------HHHHHHHHHHHH
T ss_pred HHHHhcCeeEEEEeCCCHHHHHHHHHhc----CHHHHHHHHHHHH
Confidence 1 1344557888888763 33333333 3334555555544
No 136
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=81.34 E-value=6.2 Score=40.27 Aligned_cols=59 Identities=27% Similarity=0.334 Sum_probs=38.9
Q ss_pred cCCHHHHHhCCCeeEEE-eCch----HHHHHHhcCCCccceeecC--ChHHHHHHhhccccCCceeEEeecc
Q 037841 274 ITDVKMLIKRGDNVGYQ-KGSF----VLGILKQLGFDERKLVVYN--SPEECHELFQKGSANGGIAAAFEEI 338 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~-~gs~----~~~~l~~~~~~~~~~~~~~--s~~~~~~~l~~g~~~~gv~a~i~~~ 338 (561)
|++++|| .|++|.+- .||- .+..|+.+++......... ...+..+++.+|+ +||++...
T Consensus 129 Ikti~DL--~GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~~~~~~a~~~~~l~~g~----iDA~~~~~ 194 (321)
T COG2358 129 IKTIADL--KGKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAESADALKNGT----IDAAFYVA 194 (321)
T ss_pred cceehhc--CCCEEeecCCCCccHHHHHHHHHHcCCCCcchhhhhhcCchhhHHHhhCCc----ccEEEEec
Confidence 8999999 79999873 2333 3455566666544332212 2234488899999 99987754
No 137
>PLN02245 ATP phosphoribosyl transferase
Probab=80.83 E-value=14 Score=38.88 Aligned_cols=89 Identities=15% Similarity=0.066 Sum_probs=56.4
Q ss_pred cCCHHHHHhCC---------CeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHH
Q 037841 274 ITDVKMLIKRG---------DNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLL 344 (561)
Q Consensus 274 I~sl~dL~~~~---------~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~ 344 (561)
+++++||. | ++|+...-...++||++.+....+++..+-.-|. +-..|- .|++++-.......
T Consensus 179 ~~s~~dL~--g~~~~~~~~~~RIATkYp~ltr~ff~~~Gv~~v~Iv~l~GAvE~--AP~lGl----ADaIvDIVsTGtTL 250 (403)
T PLN02245 179 INSLKELA--QMPQWTEERPLRVVTGFTYLGPKFMKDNGFKHVTFSTADGALEA--APAMGI----ADAILDLVSSGTTL 250 (403)
T ss_pred cCCHHHhc--ccccccccCceEEEeCCHHHHHHHHHHcCCCeEEEEECcCceec--ccccCc----hhhhcchhccHHHH
Confidence 68888985 4 5888877788899999988765555555433333 334454 66666655554444
Q ss_pred HhcCCcceEEeC-cccccCceEEEecCCCC
Q 037841 345 VGQHCYKYTMVE-PTFKTAGFGFAFPLHSP 373 (561)
Q Consensus 345 l~~~~~~l~~v~-~~~~~~~~~~~~~k~sp 373 (561)
.++. +.+++ +.+......++.+|++.
T Consensus 251 raNg---Lk~i~~~~Il~S~A~LIan~~sl 277 (403)
T PLN02245 251 RENN---LKEIEGGVVLESQAVLVASRRAL 277 (403)
T ss_pred HHCC---CEEccCceEEEEEEEEEEecchh
Confidence 3333 56674 55566666677777754
No 138
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=79.18 E-value=56 Score=32.62 Aligned_cols=66 Identities=14% Similarity=0.016 Sum_probs=44.5
Q ss_pred hHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEEc
Q 037841 83 CIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPI 162 (561)
Q Consensus 83 ~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~ 162 (561)
-..++..+.++. .+++++.. ++-.+++..+.+|++|+++..- ...... ..+.++.+..++++++.
T Consensus 105 l~~~l~~f~~~~--~i~i~l~~---------~~~~~~~~~l~~~~~d~~i~~~---~~~~~~-l~~~~l~~~~~~lv~~~ 169 (294)
T PRK03635 105 FLPALAPVLARS--GVLLDLVV---------EDQDHTAELLRRGEVVGAVTTE---PQPVQG-CRVDPLGAMRYLAVASP 169 (294)
T ss_pred HHHHHHHHHhCC--CcEEEEEe---------cCcHHHHHHHhCCCceEEEecc---CCCCCC-ceeeecccceEEEEEcc
Confidence 345677777763 56677665 2456889999999999997532 112222 25677888899999874
Q ss_pred c
Q 037841 163 K 163 (561)
Q Consensus 163 ~ 163 (561)
.
T Consensus 170 ~ 170 (294)
T PRK03635 170 A 170 (294)
T ss_pred h
Confidence 4
No 139
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=78.42 E-value=21 Score=40.47 Aligned_cols=102 Identities=12% Similarity=0.093 Sum_probs=57.1
Q ss_pred CCHHHHHhCCCeeEE-EeCchHHHHHH----hcCCCccc----eeecCChHHHHHHhhccccCCceeEEeecchhHHHHH
Q 037841 275 TDVKMLIKRGDNVGY-QKGSFVLGILK----QLGFDERK----LVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLV 345 (561)
Q Consensus 275 ~sl~dL~~~~~~vg~-~~gs~~~~~l~----~~~~~~~~----~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l 345 (561)
.+++||.+.+.++.+ ..|+..+..+. +.++.... ....++.+....++..|. +++.+.-.+...
T Consensus 514 isl~dL~~~~~plI~~~~gs~~r~~le~~l~~~Gi~~~~i~~~~~e~~s~~~i~~~V~~G~----~d~Gi~i~~~~~--- 586 (633)
T PRK14498 514 EGIEDLVRKDVRFVNRQRGSGTRILLDYHLKELAIDPERINGYDREEKTHMAVAAAVAQGR----ADAGLGIRAAAK--- 586 (633)
T ss_pred CCHHHhccCCcEEEecCCCchHHHHHHHHHHHcCCCHHHCCCcccccCCHHHHHHHHHcCC----CcchHhHHHHHH---
Confidence 579999643326665 45656555544 44554322 345678889999999997 665554333211
Q ss_pred hcCCcceEEeCcccccCceEEEecCCCCChhhHHHHHhhcccc
Q 037841 346 GQHCYKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILSVTEG 388 (561)
Q Consensus 346 ~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~ 388 (561)
..... +..+. ...++++.+++..........+..+.+.
T Consensus 587 ~~~l~-~i~l~----~~~~~l~~~~~~~~s~a~~aFl~~l~~~ 624 (633)
T PRK14498 587 ALGLD-FIPLA----EEEYDLLIPKERLEKPAVRAFLEALKSP 624 (633)
T ss_pred HcCCC-Ceeee----eEEEEEEEEhhHccCHHHHHHHHHHcCH
Confidence 11111 22222 1246788888766666666655555443
No 140
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=78.40 E-value=12 Score=38.76 Aligned_cols=62 Identities=13% Similarity=0.138 Sum_probs=43.7
Q ss_pred CCCCceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCce-eEEEEecCCCCCCCCCCHHHHHHHH
Q 037841 45 PTNEKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAV-AYDFVPYGQPDGTSSGSYNDLIYQV 123 (561)
Q Consensus 45 ~~~g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v-~~~~v~~~~~~g~~ngs~~~li~~l 123 (561)
|..++++++|+. +|. -.-+.-.|++.+.+.+||.+ ++. .. +-.-+...|
T Consensus 25 ~~~~~~V~~~~~---~W~----------------~~~~~t~v~~~iLe~~GY~V~e~~--~~---------~~~~~~~al 74 (331)
T PRK11119 25 PGKGITVQPAQS---TIA----------------EETFQTLLVSRALEKLGYDVNKPK--EV---------DYNVFYTSI 74 (331)
T ss_pred CCCCeEEEEeec---Ccc----------------HHHHHHHHHHHHHHHcCCceeeec--cc---------CcHHHHHHH
Confidence 446899999996 552 11245578888889899966 443 32 236778889
Q ss_pred HcCcccEEEecee
Q 037841 124 FLGEFDAAVGDIT 136 (561)
Q Consensus 124 ~~g~~D~~vg~~~ 136 (561)
.+|++|+.+....
T Consensus 75 a~GdiDv~~~~W~ 87 (331)
T PRK11119 75 ANGDATFTAVNWF 87 (331)
T ss_pred HcCCCeEehhhcc
Confidence 9999999876443
No 141
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=77.64 E-value=79 Score=31.45 Aligned_cols=64 Identities=9% Similarity=0.039 Sum_probs=41.4
Q ss_pred HHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEEcc
Q 037841 85 DVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIK 163 (561)
Q Consensus 85 dl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~ 163 (561)
..+..+.+. + .+.+++.. ++.++++..|.+|++|+++..... ....+. +.++....++++++..
T Consensus 107 ~~l~~~~~~-~-~i~i~~~~---------~~~~~~~~~L~~~~~d~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~ 170 (294)
T PRK13348 107 PALAAVLAG-E-RILLELIV---------DDQDHTFALLERGEVVGCVSTQPK---PMRGCL-AEPLGTMRYRCVASPA 170 (294)
T ss_pred HHHHHHHhC-C-CeEEEEEE---------cchHHHHHHHhcCCeEEEEecCCc---ccCCcc-cccccccceEEEEccc
Confidence 445555444 2 45666554 356889999999999998753211 223444 5777888888888744
No 142
>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=74.92 E-value=63 Score=29.01 Aligned_cols=71 Identities=15% Similarity=0.030 Sum_probs=47.5
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++.. ++.++++.++.+|++|+++...... ....+ .+.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~-~~~~l~~~~~~~v~ 79 (195)
T cd08431 13 QPLYPLIAEFYQLNK-ATRIRLSE---------EVLGGTWDALASGRADLVIGATGEL--PPGGV-KTRPLGEVEFVFAV 79 (195)
T ss_pred HHHHHHHHHHHHHCC-CCceEEEE---------eccchHHHHHhCCCCCEEEEecCCC--CCCce-EEEecccceEEEEE
Confidence 456789999999987 35666655 2456888999999999998632111 11122 34566677788888
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 80 ~~~h 83 (195)
T cd08431 80 APNH 83 (195)
T ss_pred cCCC
Confidence 7543
No 143
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=72.70 E-value=6.6 Score=45.95 Aligned_cols=55 Identities=16% Similarity=0.295 Sum_probs=47.0
Q ss_pred CccchhHHHHHHHhhhcc-cc-ccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEe
Q 037841 213 HQVGTSFWFSFSTMVFSQ-RE-RVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTV 267 (561)
Q Consensus 213 ~~~~~~~~~~~~~l~~~~-~~-~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~ 267 (561)
.++..++|+++.++...| ++ .|.+...|++.++++++++++.++..+++++++..
T Consensus 249 ~~Yi~slYwai~TmtTVGYGDi~p~t~~E~i~~i~~ml~g~~~~a~~ig~i~~li~~ 305 (823)
T PLN03192 249 IRYISAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE 305 (823)
T ss_pred HHHHHHHHHHHHHHhhccCCCcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356678999999999776 33 56899999999999999999999999999997654
No 144
>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.
Probab=71.47 E-value=1.2e+02 Score=30.68 Aligned_cols=42 Identities=14% Similarity=0.101 Sum_probs=31.8
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEec
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGD 134 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~ 134 (561)
+...|++.+.+.+||++++. . ++-.-+...|.+|++|+.+..
T Consensus 22 ~~~~i~~~iLE~~Gy~Ve~~--~---------~~~~~~~~al~~GdiD~~~e~ 63 (290)
T TIGR03414 22 ATTALASVLLEGLGYQPKVT--L---------LSVPVTYAGLKDGDLDVFLGN 63 (290)
T ss_pred HHHHHHHHHHHHcCCcceeE--E---------ccHHHHHHHHHcCCceEeccc
Confidence 44578888888899977653 3 235677888999999998864
No 145
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=70.80 E-value=77 Score=28.21 Aligned_cols=98 Identities=8% Similarity=-0.010 Sum_probs=51.0
Q ss_pred CCHHHHHhCCCeeEEEe-C-chHHHHHHhcCCCcc---ceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCC
Q 037841 275 TDVKMLIKRGDNVGYQK-G-SFVLGILKQLGFDER---KLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHC 349 (561)
Q Consensus 275 ~sl~dL~~~~~~vg~~~-g-s~~~~~l~~~~~~~~---~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~ 349 (561)
-+++||. +.++.... . .....++.+.+.... ....+++.+...+.+..|. ..+++.... +.......
T Consensus 86 ~~~~dl~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gi~~~p~~~-~~~~~~~~- 157 (194)
T cd08481 86 AAPADLA--HLPLLQQTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGL----GVALLPRFL-IEEELARG- 157 (194)
T ss_pred CcHHHHh--hCceEecCCCCcCHHHHHHHcCCCCCCccCceEeccHHHHHHHHHhCC----CeEEecHHH-HHHHHHCC-
Confidence 4688885 44443322 1 234556666554321 1245577888899999887 444444433 33332222
Q ss_pred cceEEe-C-cccccCceEEEecCCCCChhhHHHH
Q 037841 350 YKYTMV-E-PTFKTAGFGFAFPLHSPLVHDVSKA 381 (561)
Q Consensus 350 ~~l~~v-~-~~~~~~~~~~~~~k~spl~~~in~~ 381 (561)
. +... . +......++++.+++.+....+...
T Consensus 158 ~-l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 190 (194)
T cd08481 158 R-LVVPFNLPLTSDKAYYLVYPEDKAESPPVQAF 190 (194)
T ss_pred C-EEeecCccccCCCeEEEEeCcccccCHHHHHH
Confidence 1 2222 2 2223456788888876655544443
No 146
>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=69.54 E-value=84 Score=28.14 Aligned_cols=70 Identities=19% Similarity=0.099 Sum_probs=47.4
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
.+-.+++..+.++.+ .+++++.. ++.+++..++.+|++|+++... ......+ ...++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~---------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~v~ 78 (198)
T cd08447 13 SFLPRLLAAARAALP-DVDLVLRE---------MVTTDQIEALESGRIDLGLLRP---PFARPGL-ETRPLVREPLVAAV 78 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe---------CCHHHHHHHHHcCCceEEEecC---CCCCCCe-eEEEeecCceEEEe
Confidence 456788899999987 35666544 3578999999999999998532 1112222 23566677788887
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 79 ~~~~ 82 (198)
T cd08447 79 PAGH 82 (198)
T ss_pred cCCC
Confidence 7543
No 147
>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=69.36 E-value=83 Score=28.00 Aligned_cols=65 Identities=6% Similarity=-0.051 Sum_probs=40.8
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-..++..+.++.+ .+++++... . .+..+.+|++|+++... +.....+ .+.+.....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~~---------~---~~~~l~~g~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~v~~ 76 (194)
T cd08432 14 WLIPRLARFQARHP-DIDLRLSTS---------D---RLVDFAREGIDLAIRYG---DGDWPGL-EAERLMDEELVPVCS 76 (194)
T ss_pred HHHHHhHHHHHHCC-CeEEEEEec---------C---CccccccccccEEEEec---CCCCCCc-ceEEccCCcEEEecC
Confidence 44567788888877 466666541 1 35678899999998522 1111222 356677778888877
Q ss_pred cc
Q 037841 162 IK 163 (561)
Q Consensus 162 ~~ 163 (561)
..
T Consensus 77 ~~ 78 (194)
T cd08432 77 PA 78 (194)
T ss_pred HH
Confidence 43
No 148
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=65.38 E-value=71 Score=31.04 Aligned_cols=92 Identities=12% Similarity=0.090 Sum_probs=52.9
Q ss_pred cCCHHHHHh--------CC--CeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHH
Q 037841 274 ITDVKMLIK--------RG--DNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKL 343 (561)
Q Consensus 274 I~sl~dL~~--------~~--~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~ 343 (561)
+++++||.. .| .+|+...-...++||++.+.+..+++...-.-|. +-..|- .|++++-......
T Consensus 111 ~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf~~~Gv~~~~Iv~l~GsvEl--aP~~Gl----AD~IvDivsTG~T 184 (228)
T PRK13583 111 VDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFLSQKGVQDYRIVESLGATEG--APANGS----AEIIVDITSTGET 184 (228)
T ss_pred cCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHHHHcCCceeEEEECCCceec--ccccCc----chhhhhhhchhHH
Confidence 567777741 13 4788777778899998877754344444333222 223344 5666665555444
Q ss_pred HHhcCCcceEEeC-cccccCceEEEecCCCCC
Q 037841 344 LVGQHCYKYTMVE-PTFKTAGFGFAFPLHSPL 374 (561)
Q Consensus 344 ~l~~~~~~l~~v~-~~~~~~~~~~~~~k~spl 374 (561)
. +.+. +.+++ +.+......++.++.|.+
T Consensus 185 L-r~Ng--L~~i~~~~Il~SsA~LI~n~~s~~ 213 (228)
T PRK13583 185 L-RANH--LKILSDGVILRSQACLVRARKADW 213 (228)
T ss_pred H-HHCC--CEEecCceEEEEEEEEEEeccccc
Confidence 3 3332 56775 455666667777887643
No 149
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=65.29 E-value=8.5 Score=35.35 Aligned_cols=100 Identities=12% Similarity=0.078 Sum_probs=57.5
Q ss_pred cCCHHHHHhCCCeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceE
Q 037841 274 ITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYT 353 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~ 353 (561)
+.+++||.+ +.+|+...-...+.||++.+.+..-+....+.|-+ -..|- +|++++-.......-++. +.
T Consensus 58 ~~~~~~l~~-~~rIATkyp~l~~~yf~~~g~~~~ii~l~GsvE~a---p~~gl----AD~IvDiv~TG~TLr~Ng---L~ 126 (163)
T PF01634_consen 58 YKSVEDLKA-GLRIATKYPNLTRRYFAEKGINVEIIKLSGSVELA---PPLGL----ADAIVDIVETGTTLRANG---LK 126 (163)
T ss_dssp GCCGGGGSS-TEEEEES-HHHHHHHHHHCT-EEEEEE-SS-TTHH---HHTTS----SSEEEEEESSSHHHHHTT---EE
T ss_pred CCCHHHhcc-CCEEEECCHHHHHHHHHHcCCcEEEEEccCCcccc---CCCCC----CCEEEEeccCcHHHHHCC---CE
Confidence 577888831 77898877778899999877544333344454433 33455 788888777665554443 45
Q ss_pred EeCcccccCceEEEecCCCC--ChhhHHHHHhhc
Q 037841 354 MVEPTFKTAGFGFAFPLHSP--LVHDVSKAILSV 385 (561)
Q Consensus 354 ~v~~~~~~~~~~~~~~k~sp--l~~~in~~Il~l 385 (561)
.+.. +......++..+.+. -.+.+++.+.+|
T Consensus 127 ~i~~-i~~s~a~LI~n~~~~~~k~~~i~~l~~~l 159 (163)
T PF01634_consen 127 EIET-ILESSARLIANKASLKEKEEKIDELVTRL 159 (163)
T ss_dssp EEEE-EEEEEEEEEEEHHHHHHCHHHHHHHHHHH
T ss_pred EeEE-EEEEEEEEEEcCccchhhHHHHHHHHHHH
Confidence 5544 444555666666653 223455555444
No 150
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=64.98 E-value=50 Score=29.47 Aligned_cols=66 Identities=11% Similarity=0.068 Sum_probs=40.0
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++... +.+. .+.+|++|+++... +.....+. +.++....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~~-----------~~~~-~l~~~~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~ 76 (197)
T cd08422 14 LHLAPLLAEFLARYP-DVRLELVLS-----------DRLV-DLVEEGFDLAIRIG---ELPDSSLV-ARRLGPVRRVLVA 76 (197)
T ss_pred HHHHHHHHHHHHhCC-ceEEEEecC-----------cccc-chhhcCccEEEEeC---CCCCcchh-hhhhhccCcEEEE
Confidence 456688899999987 456665431 1233 35568899998632 11222232 4566777788887
Q ss_pred Ecc
Q 037841 161 PIK 163 (561)
Q Consensus 161 p~~ 163 (561)
+..
T Consensus 77 ~~~ 79 (197)
T cd08422 77 SPA 79 (197)
T ss_pred CHH
Confidence 643
No 151
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=64.79 E-value=82 Score=30.34 Aligned_cols=92 Identities=12% Similarity=0.026 Sum_probs=56.5
Q ss_pred CCCeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCcccccC
Q 037841 283 RGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPTFKTA 362 (561)
Q Consensus 283 ~~~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~~~~~ 362 (561)
.+.+|+...-...++||++.+.+ .+++...-.-|. +-..|- .|++++-........++. +.++.+ +...
T Consensus 114 ~~~rIATkYp~it~~yf~~~gv~-~~iv~l~GsvE~--aP~~Gl----AD~IvDivsTG~TLr~Ng---L~~ie~-Il~s 182 (215)
T PRK01686 114 PRLRVATKYPNIARRYFAEKGEQ-VEIIKLYGSVEL--APLVGL----ADAIVDIVETGNTLRANG---LVEVEE-IMDI 182 (215)
T ss_pred CCCEEEeCCHHHHHHHHHHcCCe-EEEEECcCceee--ccccCC----ccEEEEeecChHHHHHCc---CEEeeE-EEee
Confidence 56789887788889999887775 455544433333 233455 788887776666654444 445544 4445
Q ss_pred ceEEEecCCCCC--hhhHHHHHhhc
Q 037841 363 GFGFAFPLHSPL--VHDVSKAILSV 385 (561)
Q Consensus 363 ~~~~~~~k~spl--~~~in~~Il~l 385 (561)
...++.++.|.. .+.++..+.++
T Consensus 183 ~A~LI~n~~s~~~k~~~i~~l~~~l 207 (215)
T PRK01686 183 SARLIVNRASLKLKREEIRPLIEKL 207 (215)
T ss_pred EEEEEEecccchhhHHHHHHHHHHH
Confidence 556777777652 24555555554
No 152
>PF14981 FAM165: FAM165 family
Probab=63.96 E-value=14 Score=25.80 Aligned_cols=33 Identities=18% Similarity=0.239 Sum_probs=28.6
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 037841 419 LNSFWGLFLIAGIAAILALIIFLAVFVGQHRNV 451 (561)
Q Consensus 419 l~~~~g~F~il~~g~~lallvfl~E~~~~~~~~ 451 (561)
++++-.++||+..-.++.++.|..--+|++++.
T Consensus 3 L~~vPlLlYILaaKtlilClaFAgvK~yQ~krl 35 (51)
T PF14981_consen 3 LDNVPLLLYILAAKTLILCLAFAGVKMYQRKRL 35 (51)
T ss_pred hhhchHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 567888999999999999999999888887665
No 153
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=63.02 E-value=1.7e+02 Score=29.16 Aligned_cols=101 Identities=8% Similarity=0.002 Sum_probs=52.3
Q ss_pred CCHHHHHhCCCeeEE-EeCchHHHHHHhcCCCc---cceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCc
Q 037841 275 TDVKMLIKRGDNVGY-QKGSFVLGILKQLGFDE---RKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCY 350 (561)
Q Consensus 275 ~sl~dL~~~~~~vg~-~~gs~~~~~l~~~~~~~---~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~ 350 (561)
.+++||. +.+... ..+....+++...+... .....+++.+...+++..|. ..+++. ............-
T Consensus 181 i~~~dL~--~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----gi~~lp-~~~~~~~~~~~~l 253 (297)
T PRK11139 181 KTPEDLA--RHTLLHDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQ----GVALGN-RVLAQPEIEAGRL 253 (297)
T ss_pred CCHHHhh--cCceEeecCcccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhCC----CeEecc-hhhhHHHHHCCce
Confidence 5788885 444433 33344556666544421 11245677877888888877 344443 3334333333221
Q ss_pred ceEEeCccc-ccCceEEEecCCCCChhhHHHHHh
Q 037841 351 KYTMVEPTF-KTAGFGFAFPLHSPLVHDVSKAIL 383 (561)
Q Consensus 351 ~l~~v~~~~-~~~~~~~~~~k~spl~~~in~~Il 383 (561)
...+.+.. ....+.++.+|+.+....+...+.
T Consensus 254 -~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~ 286 (297)
T PRK11139 254 -VCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQ 286 (297)
T ss_pred -ecccccCcCCCccEEEEeccccccChhHHHHHH
Confidence 11223222 234678888887665555444443
No 154
>PRK07377 hypothetical protein; Provisional
Probab=62.30 E-value=22 Score=32.98 Aligned_cols=62 Identities=21% Similarity=0.200 Sum_probs=46.0
Q ss_pred CceEEEEecCCCCCcceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCc
Q 037841 48 EKKLRIGVPVKKGFSYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGE 127 (561)
Q Consensus 48 g~~LrVgv~~~~~~~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~ 127 (561)
..++|+|+... . + ..+ ..-+-.++.++.+.++++. +.|+++++ +-+.+.+++.+|+
T Consensus 74 s~~~Rlgv~~~--~------~-----~~~-~~~~~l~~~l~~~~~~y~~--rlElv~y~--------~~~~l~~aL~~~e 129 (184)
T PRK07377 74 SLVMRLGVLEI--E------T-----ETS-SVFDQLIDQLRTILDKYHL--RLELVVYP--------DLQALEQALRDKE 129 (184)
T ss_pred ccEEEEEEEec--c------c-----ccc-ccHHHHHHHHHHHHHHhCc--eeeEEecC--------CHHHHHHHHhcCC
Confidence 46799998732 0 1 111 3445577888999999986 67778876 6899999999999
Q ss_pred ccEEEe
Q 037841 128 FDAAVG 133 (561)
Q Consensus 128 ~D~~vg 133 (561)
+|++.+
T Consensus 130 Vh~~c~ 135 (184)
T PRK07377 130 VHAICL 135 (184)
T ss_pred ccEEec
Confidence 998876
No 155
>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=60.07 E-value=10 Score=27.11 Aligned_cols=28 Identities=29% Similarity=0.496 Sum_probs=22.7
Q ss_pred hhhHHHHHHHHHHHHHHHhhhhcccCCC
Q 037841 179 WDLWVTSGCFFIFIGFVVWALEHRVNED 206 (561)
Q Consensus 179 ~~vW~~~~~~~i~~~~v~~~l~~~~~~~ 206 (561)
.++|.++..+.+++|+++|.+..+..+.
T Consensus 11 a~~~~l~~~~~~Figiv~wa~~p~~k~~ 38 (48)
T cd01324 11 ADSWGLLYLALFFLGVVVWAFRPGRKKA 38 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcchh
Confidence 3678999999999999999997665443
No 156
>PRK10537 voltage-gated potassium channel; Provisional
Probab=59.71 E-value=19 Score=38.09 Aligned_cols=54 Identities=20% Similarity=0.273 Sum_probs=41.1
Q ss_pred CccCccchhHHHHHHHhhhcc--ccccccchhHHHHHHHHHHHHHHHHHhHhhhee
Q 037841 210 PARHQVGTSFWFSFSTMVFSQ--RERVISNLARFVVIVWYFVVLVLTQSYTASLTS 263 (561)
Q Consensus 210 ~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS 263 (561)
++..++.+++|+++.++...| ...|.+..+|++.+++.++++.+..+..+.++.
T Consensus 164 ~~~~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~ 219 (393)
T PRK10537 164 PPIESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFG 219 (393)
T ss_pred cCCCCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455689999999998888665 335688889999999999888766555555544
No 157
>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=58.93 E-value=7.4 Score=34.25 Aligned_cols=10 Identities=30% Similarity=0.411 Sum_probs=4.8
Q ss_pred ccCCCcchhh
Q 037841 541 VELTNPDQEI 550 (561)
Q Consensus 541 ~~~~~~~~~~ 550 (561)
.++..|.+.+
T Consensus 97 ~~~~~P~~~~ 106 (130)
T PF12273_consen 97 PELQPPPHAY 106 (130)
T ss_pred cccCCCCccc
Confidence 4445554444
No 158
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=57.16 E-value=74 Score=29.80 Aligned_cols=67 Identities=18% Similarity=0.230 Sum_probs=45.0
Q ss_pred cCCHHHHHhCCCeeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCC
Q 037841 274 ITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHC 349 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~ 349 (561)
+++.+|| .+.+|+.......++||.+.+.+ .+++...-.-|. +-..|- +|++++-......+.++..
T Consensus 101 ~~~~~~l--~~~rIATkyp~i~~~~f~~~Gi~-v~ii~l~GsvE~--aP~~Gl----aD~IvDiv~TG~TL~~NgL 167 (182)
T TIGR00070 101 ISSVEDL--KGKRIATKYPNLARRYFEKKGID-VEIIKLNGSVEL--APLLGL----ADAIVDIVSTGTTLRENGL 167 (182)
T ss_pred CCChHHh--CCCEEEECCHHHHHHHHHHcCCe-EEEEECcceeec--ccCCCc----eeEEEEEeCCHHHHHHCCC
Confidence 5788898 58899988888899999987774 344444433333 223566 8888887777666555443
No 159
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=56.18 E-value=23 Score=38.45 Aligned_cols=88 Identities=14% Similarity=0.220 Sum_probs=66.8
Q ss_pred hhHHHHHHHHHHHHHHHhhhhcccCCCCCCCccCccchhHHHHHHHhhhcc--ccccccchhHHHHHHHHHHHHHHHHHh
Q 037841 180 DLWVTSGCFFIFIGFVVWALEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQ--RERVISNLARFVVIVWYFVVLVLTQSY 257 (561)
Q Consensus 180 ~vW~~~~~~~i~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~Ril~~~w~~~~lil~~~Y 257 (561)
..|...++.+++.++++++.|.-...+-....-.++-.++|+..-++.-.| ...|....+|++.+.+-++++-+-+.=
T Consensus 235 Tt~YIGFL~LIfsSflVYLaEKd~~~e~~n~~F~TyADALWWG~ITltTIGYGDk~P~TWlGr~laa~fsligiSFFALP 314 (654)
T KOG1419|consen 235 TTWYIGFLVLIFSSFLVYLAEKDAQGEGTNDEFPTYADALWWGVITLTTIGYGDKTPQTWLGRLLAACFSLIGISFFALP 314 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccccccccccchhHHHHHHhhheeEEeeccCCcCcccchhHHHHHHHHHHHHHHHhcc
Confidence 457777788888999999999874433222233468889999999988776 457799999999999988888777777
Q ss_pred HhhheeeeEe
Q 037841 258 TASLTSLLTV 267 (561)
Q Consensus 258 ta~LtS~Lt~ 267 (561)
.+.|-|=++.
T Consensus 315 AGILGSGfAL 324 (654)
T KOG1419|consen 315 AGILGSGFAL 324 (654)
T ss_pred cccccchhhh
Confidence 7777775443
No 160
>cd08487 PBP2_BlaA The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold. This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is
Probab=54.99 E-value=1.5e+02 Score=26.22 Aligned_cols=64 Identities=8% Similarity=0.028 Sum_probs=37.3
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-..++..+.++++ .+++++... . .+. .+.+|++|+++... +.....+. +.++....++++++
T Consensus 14 ~l~~~l~~f~~~~P-~i~l~i~~~---------~--~~~-~~~~~~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~v~~ 76 (189)
T cd08487 14 WLLPRLAEFRQLHP-FIELRLRTN---------N--NVV-DLATEGLDFAIRFG---EGLWPATH-NERLLDAPLSVLCS 76 (189)
T ss_pred HHhHHHHHHHHHCC-CceEEeeec---------C--Ccc-ccccCCcCEEEEec---CCCCCCce-eeeeccCceeeeeC
Confidence 34466788888887 466665431 1 123 35567899998532 21122232 46677777777776
Q ss_pred c
Q 037841 162 I 162 (561)
Q Consensus 162 ~ 162 (561)
.
T Consensus 77 ~ 77 (189)
T cd08487 77 P 77 (189)
T ss_pred H
Confidence 3
No 161
>cd08475 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=53.66 E-value=1.6e+02 Score=26.14 Aligned_cols=66 Identities=9% Similarity=0.001 Sum_probs=38.6
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++.. ..++.+.+.. ++|+++... .. .....+ -+.+.....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~-----------~~~~~~~l~~-~~D~~i~~~-~~-~~~~~l-~~~~l~~~~~~~v~ 77 (199)
T cd08475 14 LCVAPLLLELARRHP-ELELELSF-----------SDRFVDLIEE-GIDLAVRIG-EL-ADSTGL-VARRLGTQRMVLCA 77 (199)
T ss_pred hhHHHHHHHHHHHCC-CeEEEEEe-----------ccchhhHhhc-CccEEEEeC-CC-CCCCCe-EEEEcccceEEEEE
Confidence 456688899999987 45666542 1244556655 499998421 11 111123 24556667777777
Q ss_pred Ec
Q 037841 161 PI 162 (561)
Q Consensus 161 p~ 162 (561)
+.
T Consensus 78 ~~ 79 (199)
T cd08475 78 SP 79 (199)
T ss_pred CH
Confidence 63
No 162
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=51.59 E-value=42 Score=33.28 Aligned_cols=70 Identities=7% Similarity=0.011 Sum_probs=50.5
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.+..+ .+++++.. +...++++.|.+|++|+++...... ...+ ...|+....+++++
T Consensus 102 ~~l~~~l~~f~~~~P-~v~v~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~l-~~~~l~~~~~~~v~ 167 (275)
T PRK03601 102 CMLTPWLGRLYQNQE-ALQFEARI---------AQRQSLVKQLHERQLDLLITTEAPK---MDEF-SSQLLGHFTLALYT 167 (275)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEE---------CChHHHHHHHHcCCCCEEEEcCCCc---cCCc-cEEEecceeEEEEe
Confidence 456788899988887 35666655 3567899999999999999643222 1223 45678888899999
Q ss_pred EccC
Q 037841 161 PIKD 164 (561)
Q Consensus 161 p~~~ 164 (561)
+...
T Consensus 168 ~~~~ 171 (275)
T PRK03601 168 SAPS 171 (275)
T ss_pred cCch
Confidence 8554
No 163
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=49.74 E-value=25 Score=30.58 Aligned_cols=28 Identities=21% Similarity=0.150 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 037841 424 GLFLIAGIAAILALIIFLAVFVGQHRNV 451 (561)
Q Consensus 424 g~F~il~~g~~lallvfl~E~~~~~~~~ 451 (561)
-+.+|+|+.+++.++++++-++.+|+++
T Consensus 66 i~~Ii~gv~aGvIg~Illi~y~irR~~K 93 (122)
T PF01102_consen 66 IIGIIFGVMAGVIGIILLISYCIRRLRK 93 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHS-
T ss_pred eeehhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3455666655555555555555444433
No 164
>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=49.30 E-value=55 Score=29.31 Aligned_cols=67 Identities=13% Similarity=-0.034 Sum_probs=46.4
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVP 161 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp 161 (561)
+-.+++..+.++.+ .+++++.. +...++..+|.+|++|+++... . . ..+ .+.++....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~~~~Dl~i~~~---~-~-~~~-~~~~l~~~~~~~v~~ 77 (185)
T cd08439 14 ILPFLLNRFASVYP-RLAIEVVC---------KRTPRLMEMLERGEVDLALITH---P-P-PGA-SATILRRSPTVWYCA 77 (185)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEE---------CChHHHHHHHHCCCCcEEEEec---c-C-CCC-CceEEEEecCEEEEC
Confidence 45678888888887 36666655 2457899999999999998632 1 1 112 246677788888887
Q ss_pred ccC
Q 037841 162 IKD 164 (561)
Q Consensus 162 ~~~ 164 (561)
...
T Consensus 78 ~~~ 80 (185)
T cd08439 78 AGY 80 (185)
T ss_pred CCC
Confidence 554
No 165
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=47.46 E-value=88 Score=30.63 Aligned_cols=104 Identities=21% Similarity=0.170 Sum_probs=63.0
Q ss_pred cCCHHHHHhCCCeeEEEeCchHHH----HHHhcCCCccceeecC-ChHHHHHHhhccccCCceeEEeecchhHHHHHhcC
Q 037841 274 ITDVKMLIKRGDNVGYQKGSFVLG----ILKQLGFDERKLVVYN-SPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQH 348 (561)
Q Consensus 274 I~sl~dL~~~~~~vg~~~gs~~~~----~l~~~~~~~~~~~~~~-s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~ 348 (561)
|...+||+ |++|++.--|..+- -|+..+.+..+...++ .+.+...+.++|. +|+.....+.+..+.+..
T Consensus 122 I~kpeDL~--GK~iavPFvSTtHysLLaaLkhw~idp~~V~IlNl~Pp~IaAAwqRGD----IDgAyVW~PAl~el~ksG 195 (334)
T COG4521 122 IEKPEDLI--GKRIAVPFVSTTHYSLLAALKHWGIDPGQVEILNLQPPAIAAAWQRGD----IDGAYVWAPALSELKKSG 195 (334)
T ss_pred cCChHHhc--cCeeccceeehhHHHHHHHHHHcCCCccceeEeccCCHHHHHHHHcCC----CCceeeccHhHHHHhhcC
Confidence 88999995 99999865544332 2344556655555544 5667889999999 999888888777665433
Q ss_pred Ccce---EEeCcccccCceEEEecCC----CC-ChhhHHHHHhh
Q 037841 349 CYKY---TMVEPTFKTAGFGFAFPLH----SP-LVHDVSKAILS 384 (561)
Q Consensus 349 ~~~l---~~v~~~~~~~~~~~~~~k~----sp-l~~~in~~Il~ 384 (561)
+-+ ..++..-....-+++++|+ .| ....|-+..+.
T Consensus 196 -kVltDs~qvgqwgaPTfdvwVvrkdfAekhPe~v~aFakv~~d 238 (334)
T COG4521 196 -KVLTDSEQVGQWGAPTFDVWVVRKDFAEKHPEVVAAFAKVALD 238 (334)
T ss_pred -cEeccHHHhhccCCCceeeEEeehHhhHhChHHHHHHHHHHHH
Confidence 111 1122222222236777776 34 55555555443
No 166
>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=47.40 E-value=2.9e+02 Score=27.24 Aligned_cols=64 Identities=14% Similarity=0.071 Sum_probs=41.7
Q ss_pred HHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEEcc
Q 037841 85 DVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPIK 163 (561)
Q Consensus 85 dl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~~ 163 (561)
.++..+.++. .+.+.... ++-..+++.|.+|++|+++..... ....+. +.++.+..++++++++
T Consensus 107 ~~l~~~~~~~--~i~i~l~~---------~~~~~~~~~l~~g~~d~~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~~ 170 (292)
T TIGR03298 107 PALAPVLAQE--GVLLDLVV---------EDQDHTAELLRSGEVLGAVTTQAK---PVQGCR-VVPLGAMRYLAVASPA 170 (292)
T ss_pred HHHHHHHhCC--CceEEEEe---------CcchhHHHHHhCCCceEEEecCCC---CCCCce-EEecCCceEEEEECch
Confidence 4567777664 45666554 244678899999999999864222 122333 4677788888888744
No 167
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=47.37 E-value=21 Score=25.48 Aligned_cols=24 Identities=38% Similarity=0.562 Sum_probs=19.5
Q ss_pred hhHHHHHHHHHHHHHHHhhhhccc
Q 037841 180 DLWVTSGCFFIFIGFVVWALEHRV 203 (561)
Q Consensus 180 ~vW~~~~~~~i~~~~v~~~l~~~~ 203 (561)
..|.+++++.+++|+++|...++.
T Consensus 11 ~~~~~v~~~~~F~gi~~w~~~~~~ 34 (49)
T PF05545_consen 11 RSIGTVLFFVFFIGIVIWAYRPRN 34 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHHcccc
Confidence 467788888899999999997654
No 168
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=47.10 E-value=65 Score=24.38 Aligned_cols=22 Identities=14% Similarity=0.179 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 037841 426 FLIAGIAAILALIIFLAVFVGQ 447 (561)
Q Consensus 426 F~il~~g~~lallvfl~E~~~~ 447 (561)
+...++|.+++.++.+...+..
T Consensus 25 l~~f~~G~llg~l~~~~~~~~~ 46 (68)
T PF06305_consen 25 LIAFLLGALLGWLLSLPSRLRL 46 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3334455555555555544433
No 169
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.54 E-value=1.4e+02 Score=30.54 Aligned_cols=123 Identities=14% Similarity=0.066 Sum_probs=79.2
Q ss_pred cCCCcCCHHHHHhC---CC-eeEEEeC---chH----HHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecc
Q 037841 270 LQPTITDVKMLIKR---GD-NVGYQKG---SFV----LGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEI 338 (561)
Q Consensus 270 ~~~~I~sl~dL~~~---~~-~vg~~~g---s~~----~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~ 338 (561)
...+.+|++||++. +. .+.+..+ +.. ..+.+..+. +.+.++|+...+.+.+|.-|. +++.+...
T Consensus 130 ~~s~~~t~~dlv~~~k~~p~~v~~~~~g~Gs~dhl~~~~~~k~~Gi-~~~~Vpy~g~gea~taLlgg~----v~a~~~~~ 204 (319)
T COG3181 130 ADSPYKTLKDLVAYAKADPGSVIGGGSGLGSADHLAGALFAKAAGI-KITYVPYKGGGEALTALLGGH----VDAGSTNL 204 (319)
T ss_pred CCCCcccHHHHHHHHHhCCCeEEecCCCCCcHHHHHHHHHHHHhCC-ceeEEeecCccHHHHHHhcCc----eeeeecCh
Confidence 34458999999742 11 1222111 111 222344565 668899999999999999999 99999987
Q ss_pred hhHHHHHhcC-Cc--------ceEEeCc----------ccccCceEEEecCCCC--ChhhHHHHHhhccccchhHHHHHH
Q 037841 339 PYGKLLVGQH-CY--------KYTMVEP----------TFKTAGFGFAFPLHSP--LVHDVSKAILSVTEGDKMKEIEDA 397 (561)
Q Consensus 339 ~~~~~~l~~~-~~--------~l~~v~~----------~~~~~~~~~~~~k~sp--l~~~in~~Il~l~e~G~~~~i~~k 397 (561)
.-..-+.+.. .+ ++...++ .+.....++..|+|-| ....++.++.++.++..+++..++
T Consensus 205 se~~~~vksG~lr~Lav~s~eRl~~~pdvPT~~E~G~~~~~~~wrgvfap~g~~~e~~~~~~~a~kk~l~s~e~~~~~~~ 284 (319)
T COG3181 205 SELLSQVKSGTLRLLAVFSEERLPGLPDVPTLKEQGYDVVMSIWRGVFAPAGTPDEIIAKLSAALKKALASPEWQKRLKE 284 (319)
T ss_pred hhhhhhhccCceEEEEeechhhcCCCCCCCChHhcCCceeeeeeeEEEeCCCCCHHHHHHHHHHHHHHhcCHHHHHHHHh
Confidence 6666555542 11 1111111 1223445788999966 899999999999999877665554
No 170
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=45.41 E-value=3.3e+02 Score=27.35 Aligned_cols=72 Identities=11% Similarity=0.014 Sum_probs=44.8
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecC-------cceeeeccccccc
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLN-------RSNYVDFTLPYTE 153 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~-------R~~~vdfT~p~~~ 153 (561)
.+-.+++..+.+..+ .+++++... +. +..+.+.+|++|+++..-..... ....+ -+.+...
T Consensus 110 ~~~~~~l~~f~~~~P-~v~v~i~~~---------~~-~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~~~~~-~~~~l~~ 177 (319)
T PRK10216 110 IMLNALSKRIYQRYP-QATIKLRNW---------DY-DSLDAITRGEVDIGFTGRESHPRSRELLSLLPLAI-DFEVLFS 177 (319)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEEeC---------Cc-chHHHHhcCCccEEEecCCCCcccccccccccccc-ceeeeee
Confidence 355688899988887 466776541 23 36899999999999863211100 01112 2455556
Q ss_pred cceEEEEEccC
Q 037841 154 SGVSMIVPIKD 164 (561)
Q Consensus 154 ~~~~ivvp~~~ 164 (561)
...++++++..
T Consensus 178 ~~~~~v~~~~h 188 (319)
T PRK10216 178 DLPCVWLRKDH 188 (319)
T ss_pred cceEEEEeCCC
Confidence 77888887554
No 171
>PRK07377 hypothetical protein; Provisional
Probab=44.55 E-value=2.7e+02 Score=26.01 Aligned_cols=39 Identities=21% Similarity=0.224 Sum_probs=30.4
Q ss_pred HHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecc
Q 037841 295 VLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEI 338 (561)
Q Consensus 295 ~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~ 338 (561)
.+++++++ .-+..++.|.+.+++.+++.+|+ +++.+...
T Consensus 99 l~~~~~~y-~~rlElv~y~~~~~l~~aL~~~e----Vh~~c~~~ 137 (184)
T PRK07377 99 LRTILDKY-HLRLELVVYPDLQALEQALRDKE----VHAICLES 137 (184)
T ss_pred HHHHHHHh-CceeeEEecCCHHHHHHHHhcCC----ccEEecCC
Confidence 45566664 33567899999999999999999 99887643
No 172
>cd08484 PBP2_LTTR_beta_lactamase The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topol
Probab=43.59 E-value=2.3e+02 Score=25.03 Aligned_cols=99 Identities=11% Similarity=-0.050 Sum_probs=49.3
Q ss_pred CCHHHHHhCCCeeEEEeC-chHHHHHHhcCCCccc--eeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcc
Q 037841 275 TDVKMLIKRGDNVGYQKG-SFVLGILKQLGFDERK--LVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYK 351 (561)
Q Consensus 275 ~sl~dL~~~~~~vg~~~g-s~~~~~l~~~~~~~~~--~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~ 351 (561)
.+++||. +.++..... .....++++.+..... ...+++.+...+++..|. --+++... .......+..-
T Consensus 84 ~~~~~L~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gi~~lp~~-~~~~~~~~~~l- 155 (189)
T cd08484 84 SEPADLA--NETLLRSYRADEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGA----GVALAPPS-MFSRELASGAL- 155 (189)
T ss_pred CChhHhh--cCceEecCCCchHHHHHHHcCCCCCcccCcccccHHHHHHHHHhCC----CeEEecHH-hHHHHHHCCCE-
Confidence 3578884 444433222 2244556654443211 234677888889999887 44444433 33332222211
Q ss_pred eEEeCcccccCceEEEecCCCCChhhHHHH
Q 037841 352 YTMVEPTFKTAGFGFAFPLHSPLVHDVSKA 381 (561)
Q Consensus 352 l~~v~~~~~~~~~~~~~~k~spl~~~in~~ 381 (561)
...+........++++.+|+.+....+...
T Consensus 156 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f 185 (189)
T cd08484 156 VQPFKITVSTGSYWLTRLKSKPETPAMSAF 185 (189)
T ss_pred EeecccccCCCCEEEEeccccccchhhHHH
Confidence 112232223345677788876554444433
No 173
>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=43.32 E-value=29 Score=34.93 Aligned_cols=73 Identities=12% Similarity=0.104 Sum_probs=48.8
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCc-----ceeee-ccccccccc
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNR-----SNYVD-FTLPYTESG 155 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R-----~~~vd-fT~p~~~~~ 155 (561)
+-.+++..+.++.+ .+++++.. ++..+++++|.+|++|+++..-...++. .+..+ -..++....
T Consensus 49 ~lp~~l~~f~~~~P-~i~v~i~~---------~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~~~~l~~~~ 118 (287)
T TIGR02136 49 LAEAAAEEFQKIHP-GVSVTVQG---------AGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLIEHKVAVDG 118 (287)
T ss_pred HHHHHHHHHHhhCC-CceEEEcc---------CCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCceEEEEEEee
Confidence 45678888888887 35555544 3678999999999999987532222111 00111 245788889
Q ss_pred eEEEEEccC
Q 037841 156 VSMIVPIKD 164 (561)
Q Consensus 156 ~~ivvp~~~ 164 (561)
++++++...
T Consensus 119 l~lvv~~~h 127 (287)
T TIGR02136 119 LAVVVNKKN 127 (287)
T ss_pred EEEEECCCC
Confidence 999998654
No 174
>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=43.03 E-value=2.4e+02 Score=25.07 Aligned_cols=65 Identities=6% Similarity=0.004 Sum_probs=41.1
Q ss_pred hHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEEEc
Q 037841 83 CIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIVPI 162 (561)
Q Consensus 83 ~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivvp~ 162 (561)
-..++..+.++ + .+++++.. ++.+++.+.+.+|++|+++..- ......+ .+.++.....+++++.
T Consensus 15 l~~~l~~f~~~-~-~v~l~l~~---------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~ 79 (195)
T cd08428 15 FLPALAPVLKR-E-RILLDLIV---------DDEDRTHDLLRDGEVVGCISTQ---AQPMQGC-RSDYLGSMDYLLVASP 79 (195)
T ss_pred hHHHHHHHHhC-c-CeEEEEEe---------CCchhHHHHHHcCcceEEEEec---CCCCCCc-eeEEeeeeeEEEEECC
Confidence 34567777777 3 56777665 2567889999999999876421 1112222 3456666677777653
No 175
>cd08479 PBP2_CrgA_like_9 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=42.51 E-value=2.5e+02 Score=25.00 Aligned_cols=64 Identities=5% Similarity=-0.060 Sum_probs=39.2
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-..++..+.++.+ .+++++...+ ...++.+|++|+++.. .......+. +.++.....++++
T Consensus 14 ~~l~~~l~~f~~~~P-~i~i~~~~~~------------~~~~l~~g~~Dl~i~~---~~~~~~~l~-~~~l~~~~~~~~~ 76 (198)
T cd08479 14 RHIAPALSDFAKRYP-ELEVQLELTD------------RPVDLVEEGFDLDIRV---GDLPDSSLI-ARKLAPNRRILCA 76 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEecC------------ccccccccCccEEEEc---CCCCCccce-eeeccCCceEEEE
Confidence 456788999999988 4666665311 1347889999998752 111222332 3455566666666
Q ss_pred E
Q 037841 161 P 161 (561)
Q Consensus 161 p 161 (561)
+
T Consensus 77 ~ 77 (198)
T cd08479 77 S 77 (198)
T ss_pred C
Confidence 5
No 176
>KOG0498 consensus K+-channel ERG and related proteins, contain PAS/PAC sensor domain [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=41.88 E-value=29 Score=39.59 Aligned_cols=71 Identities=14% Similarity=0.200 Sum_probs=56.9
Q ss_pred ccchhHHHHHHHhhhc--cccccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEe-----eccCCCcCCHHHHHhCC
Q 037841 214 QVGTSFWFSFSTMVFS--QRERVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTV-----QQLQPTITDVKMLIKRG 284 (561)
Q Consensus 214 ~~~~~~~~~~~~l~~~--~~~~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~-----~~~~~~I~sl~dL~~~~ 284 (561)
.+..++|+.+++|.-- +...+.+....++.++.++++++|.++.-+|+++++.. .+++.+++++++-++..
T Consensus 294 kY~~aLyw~l~tLstvG~g~~~s~~~~E~iFsi~~mi~GllL~A~lIGNmt~~iqs~tsR~~~~r~k~rd~e~~m~~~ 371 (727)
T KOG0498|consen 294 KYVYALYWGLSTLSTVGYGLVHANNMGEKIFSIFIMLFGLLLFAYLIGNMTALLQSLTSRTEEMRDKMRDAEQWMSRR 371 (727)
T ss_pred HHHHHHHHHhhHhhhccCCccCCCCcHHHHHHHHHHHHhHHHHHHHHhhHHHhHHHHhHHHHHHHHHHHHHHHHHHhc
Confidence 5677999999999844 45667888899999999999999999999999998754 45566677777776443
No 177
>PLN02317 arogenate dehydratase
Probab=41.78 E-value=86 Score=33.00 Aligned_cols=83 Identities=13% Similarity=0.049 Sum_probs=58.1
Q ss_pred CCeeEEE--eCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchh--------HHHHHhcCCcceE
Q 037841 284 GDNVGYQ--KGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPY--------GKLLVGQHCYKYT 353 (561)
Q Consensus 284 ~~~vg~~--~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~--------~~~~l~~~~~~l~ 353 (561)
..+|+|+ .|+|.+.-.++. ++...++.+++.++.++++.+|. +|..+..... ....+.++ +++
T Consensus 94 ~~rVaylGp~GtfSe~AA~~~-f~~~e~vp~~sf~~vf~AVe~g~----ad~gVvPIENS~~GsV~~t~DlL~~~--~l~ 166 (382)
T PLN02317 94 KLRVAYQGVPGAYSEAAARKA-YPNCEAVPCEQFEAAFQAVELWL----ADRAVLPIENSLGGSIHRNYDLLLRH--RLH 166 (382)
T ss_pred CcEEEEECCCcCHHHHHHHHh-hCcCceeecCCHHHHHHHHHCCC----CCEEEEEEeccCccchHHHHHHHhcC--CCE
Confidence 3478884 678887776553 55567889999999999999999 6655443221 11222333 378
Q ss_pred EeCcccccCceEEEecCCCC
Q 037841 354 MVEPTFKTAGFGFAFPLHSP 373 (561)
Q Consensus 354 ~v~~~~~~~~~~~~~~k~sp 373 (561)
++++....-...++..+|..
T Consensus 167 IvgEv~l~I~h~Ll~~~g~~ 186 (382)
T PLN02317 167 IVGEVQLPVHHCLLALPGVR 186 (382)
T ss_pred EEEEEEEEeeeEEecCCCCC
Confidence 99999888888888777754
No 178
>COG3114 CcmD Heme exporter protein D [Intracellular trafficking and secretion]
Probab=40.28 E-value=54 Score=24.84 Aligned_cols=23 Identities=30% Similarity=0.384 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHhhcccc
Q 037841 431 IAAILALIIFLAVFVGQHRNVLR 453 (561)
Q Consensus 431 ~g~~lallvfl~E~~~~~~~~~~ 453 (561)
+..++++++.+++-++++++.++
T Consensus 24 ~~tll~l~~l~v~sv~qrr~iL~ 46 (67)
T COG3114 24 GMTLLPLAVLVVHSVLQRRAILR 46 (67)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566777788888888887765
No 179
>KOG1420 consensus Ca2+-activated K+ channel Slowpoke, alpha subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=39.93 E-value=17 Score=39.37 Aligned_cols=59 Identities=20% Similarity=0.313 Sum_probs=46.4
Q ss_pred CCCCccCccchhHHHHHHHhhhcccccc--ccchhHHHHHHHHHHHHHHHHHhHhhheeee
Q 037841 207 FRGPARHQVGTSFWFSFSTMVFSQRERV--ISNLARFVVIVWYFVVLVLTQSYTASLTSLL 265 (561)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~s~~~Ril~~~w~~~~lil~~~Yta~LtS~L 265 (561)
|......+++.+.++.+.+|...|.-.. ....+|++++++++++|.+-++|.-.++-..
T Consensus 281 f~n~hrltyw~cvyfl~vtmstvgygdvyc~t~lgrlfmvffil~glamfasyvpeiieli 341 (1103)
T KOG1420|consen 281 FQNNHRLTYWECVYFLMVTMSTVGYGDVYCKTTLGRLFMVFFILGGLAMFASYVPEIIELI 341 (1103)
T ss_pred ccCcccchhhheeeeeEEEeeeccccceeehhhhhHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 6666667888898888888776664333 7888999999999999999999977655443
No 180
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=39.36 E-value=4.3e+02 Score=26.84 Aligned_cols=61 Identities=13% Similarity=-0.003 Sum_probs=40.1
Q ss_pred CCHHHHHhCCCeeEEEeCchHHHHHHhcCCCccceeec-CChHHHHHHhhccccCCceeEEeecchhHH
Q 037841 275 TDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVY-NSPEECHELFQKGSANGGIAAAFEEIPYGK 342 (561)
Q Consensus 275 ~sl~dL~~~~~~vg~~~gs~~~~~l~~~~~~~~~~~~~-~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~ 342 (561)
.+++||- .|..||. +|.=+...-...+|+.+++.+ .+.+..+..|..|. .||++.-..-+.
T Consensus 113 ~~l~~Lp-~ga~IGT--sS~RR~aql~~~~Pdl~~~~iRGNV~TRL~KL~~g~----~DaivLA~AGL~ 174 (295)
T PRK00072 113 KSLDDLP-EGAVVGT--SSLRRQAQLLALRPDLEIKPLRGNVDTRLRKLDEGE----YDAIILAAAGLK 174 (295)
T ss_pred CChhHCC-CCCEEec--CcHHHHHHHHHHCcCCEEEECccCHHHHHHHhhCCC----CCEeehHhhHHH
Confidence 5788885 4556664 333333322234677777755 48899999999999 888887655443
No 181
>PF15050 SCIMP: SCIMP protein
Probab=38.76 E-value=80 Score=27.12 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=5.3
Q ss_pred HHHHHHHHHHHH
Q 037841 431 IAAILALIIFLA 442 (561)
Q Consensus 431 ~g~~lallvfl~ 442 (561)
++.+++|++|++
T Consensus 19 vS~~lglIlyCv 30 (133)
T PF15050_consen 19 VSVVLGLILYCV 30 (133)
T ss_pred HHHHHHHHHHHH
Confidence 444444444433
No 182
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=38.55 E-value=3.7e+02 Score=26.93 Aligned_cols=65 Identities=8% Similarity=0.006 Sum_probs=41.1
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++..+++..+.++.+ .+.+++.... ... .+.+|++|+++.... .....+ -..++....+++++
T Consensus 115 ~~l~~~l~~f~~~~P-~i~i~~~~~~---------~~~---~l~~~~~Di~i~~~~---~~~~~l-~~~~l~~~~~~lv~ 177 (311)
T PRK10086 115 CWLVPRLADFTRRYP-SISLTILTGN---------ENV---NFQRAGIDLAIYFDD---APSAQL-THHFLMDEEILPVC 177 (311)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEeCC---------ccc---CCccCCccEEEEeCC---CCCCCc-eEEEeecccEEEec
Confidence 456678889999987 4666665422 111 578899999986321 112222 34667777888887
Q ss_pred Ec
Q 037841 161 PI 162 (561)
Q Consensus 161 p~ 162 (561)
+.
T Consensus 178 ~~ 179 (311)
T PRK10086 178 SP 179 (311)
T ss_pred CH
Confidence 74
No 183
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene wh
Probab=38.28 E-value=1.9e+02 Score=25.79 Aligned_cols=66 Identities=11% Similarity=0.166 Sum_probs=41.4
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-.+++..+.++.+ .+++++.. ...+. ++.+|++|+++... ......+ .+.++....+++++
T Consensus 16 ~~l~~~l~~f~~~~P-~v~i~~~~-----------~~~~~-~l~~~~~D~~i~~~---~~~~~~l-~~~~l~~~~~~~v~ 78 (199)
T cd08478 16 HLLAPLIAKFRERYP-DIELELVS-----------NEGII-DLIERKTDVAIRIG---ELTDSTL-HARPLGKSRLRILA 78 (199)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe-----------ccccc-cchhccccEEEEec---CCCCCCc-eEEEcccccEEEEE
Confidence 345678899998887 46666542 12233 36789999998522 2222233 34577788888888
Q ss_pred Ecc
Q 037841 161 PIK 163 (561)
Q Consensus 161 p~~ 163 (561)
+..
T Consensus 79 ~~~ 81 (199)
T cd08478 79 SPD 81 (199)
T ss_pred CHH
Confidence 744
No 184
>PRK11899 prephenate dehydratase; Provisional
Probab=37.81 E-value=1.3e+02 Score=30.37 Aligned_cols=83 Identities=13% Similarity=0.117 Sum_probs=56.7
Q ss_pred CCeeEEE--eCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchh--------HHHHHhcCCcceE
Q 037841 284 GDNVGYQ--KGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPY--------GKLLVGQHCYKYT 353 (561)
Q Consensus 284 ~~~vg~~--~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~--------~~~~l~~~~~~l~ 353 (561)
..+|+++ .|+|.++-..+. ++...++++.+.++.++++..|. ++..+..... ....+.++ .++
T Consensus 4 ~~kvaylGp~GsfS~~Aa~~~-~~~~~~v~~~s~~~vf~av~~g~----~d~gVvPiENS~~G~V~~~~Dll~~~--~l~ 76 (279)
T PRK11899 4 TNRIAFQGEPGANSHLACRDA-FPDMEPLPCATFEDAFEAVESGE----ADLAMIPIENSLAGRVADIHHLLPES--GLH 76 (279)
T ss_pred CCEEEEECCCCCHHHHHHHHh-cCcCceeecCCHHHHHHHHHCCC----CCEEEEEeeccCCccHHHHHHHHhcC--CCE
Confidence 4468884 688887776664 45557889999999999999999 5544433211 11222222 378
Q ss_pred EeCcccccCceEEEecCCCC
Q 037841 354 MVEPTFKTAGFGFAFPLHSP 373 (561)
Q Consensus 354 ~v~~~~~~~~~~~~~~k~sp 373 (561)
++++.+..-...++..+|..
T Consensus 77 Iv~E~~l~I~h~Ll~~~~~~ 96 (279)
T PRK11899 77 IVGEYFLPIRHQLMALPGAT 96 (279)
T ss_pred EEEEEEEEeeEEEecCCCCC
Confidence 99998888888888777754
No 185
>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II. HMBS is found in all organisms except viruses.
Probab=36.97 E-value=4.6e+02 Score=26.55 Aligned_cols=60 Identities=18% Similarity=0.109 Sum_probs=39.4
Q ss_pred CCHHHHHhCCCeeEEEeCchHHH-HHHhcCCCccceeecC-ChHHHHHHhhccccCCceeEEeecchhHH
Q 037841 275 TDVKMLIKRGDNVGYQKGSFVLG-ILKQLGFDERKLVVYN-SPEECHELFQKGSANGGIAAAFEEIPYGK 342 (561)
Q Consensus 275 ~sl~dL~~~~~~vg~~~gs~~~~-~l~~~~~~~~~~~~~~-s~~~~~~~l~~g~~~~gv~a~i~~~~~~~ 342 (561)
.+++||- .|..||. +|.=+. .++. .+|..+++.+. +.+..++.|..|. .||++.-..-+.
T Consensus 109 ~~l~~Lp-~ga~IGT--sS~RR~aql~~-~rpdl~~~~iRGNV~TRL~KL~~ge----~DaiiLA~AGL~ 170 (292)
T cd00494 109 SSLEDLP-AGSVVGT--SSLRRQAQLKR-KRPDLKFEPLRGNVDTRLRKLDEGE----YDAIILAAAGLK 170 (292)
T ss_pred CChhHCC-CCCEEec--CCHHHHHHHHH-HCCCCEEEEcCCCHHHHHHHhcCCC----CCEeehHhhHHH
Confidence 4688885 4556664 333333 2333 36777777554 8899999999999 898887655444
No 186
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=35.33 E-value=2.5e+02 Score=24.97 Aligned_cols=65 Identities=12% Similarity=0.074 Sum_probs=38.6
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-..++..+.++.+ .+++++... +.+.+ +.+|++|+++.. .......+. +.+.....+++++
T Consensus 14 ~~l~~~l~~f~~~~P-~v~l~i~~~-----------~~~~~-~~~~~~D~~i~~---~~~~~~~~~-~~~l~~~~~~~v~ 76 (197)
T cd08470 14 RFIAPLVNDFMQRYP-KLEVDIELT-----------NRVVD-LVSEGFDLAIRL---GRLTDSSLM-ARRLASRRHYVCA 76 (197)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEec-----------CCccc-hhccCccEEEEc---CCCCccchh-hhhccCCceEEEE
Confidence 456788899999988 466665431 12333 446789999852 111112222 3566677777777
Q ss_pred Ec
Q 037841 161 PI 162 (561)
Q Consensus 161 p~ 162 (561)
+.
T Consensus 77 ~~ 78 (197)
T cd08470 77 SP 78 (197)
T ss_pred CH
Confidence 63
No 187
>cd08474 PBP2_CrgA_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=35.29 E-value=3.2e+02 Score=24.28 Aligned_cols=64 Identities=9% Similarity=0.151 Sum_probs=37.6
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccc-cceEEEE
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTE-SGVSMIV 160 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~-~~~~ivv 160 (561)
+-.+++..+.++.+ .+++++...+ .+.++.+|++|+++..... ....+. ..++.. ..+++++
T Consensus 17 ~l~~~l~~~~~~~P-~v~i~~~~~~------------~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~v~ 79 (202)
T cd08474 17 LLAPLLARFLARYP-DIRLELVVDD------------GLVDIVAEGFDAGIRLGES---VEKDMV-AVPLGPPLRMAVVA 79 (202)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEecC------------CcccccccCccEEEEcCCC---CCCCeE-EEEeccccceEEEe
Confidence 44578888888887 4666665311 1346778999999752111 112232 345555 4666666
Q ss_pred Ec
Q 037841 161 PI 162 (561)
Q Consensus 161 p~ 162 (561)
+.
T Consensus 80 ~~ 81 (202)
T cd08474 80 SP 81 (202)
T ss_pred CH
Confidence 53
No 188
>PF07204 Orthoreo_P10: Orthoreovirus membrane fusion protein p10; InterPro: IPR009854 This family consists of several Orthoreovirus membrane fusion protein p10 sequences. p10 is thought to be a multifunctional protein that plays a key role in virus-host interaction [].
Probab=35.17 E-value=51 Score=27.01 Aligned_cols=23 Identities=39% Similarity=0.431 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 037841 425 LFLIAGIAAILALIIFLAVFVGQ 447 (561)
Q Consensus 425 ~F~il~~g~~lallvfl~E~~~~ 447 (561)
.++..|.|+++.++++.+-+..+
T Consensus 43 pyLA~GGG~iLilIii~Lv~CC~ 65 (98)
T PF07204_consen 43 PYLAAGGGLILILIIIALVCCCR 65 (98)
T ss_pred HHhhccchhhhHHHHHHHHHHhh
Confidence 33444455555555533333333
No 189
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=34.00 E-value=49 Score=31.21 Aligned_cols=92 Identities=17% Similarity=0.214 Sum_probs=57.4
Q ss_pred cceEEEeeCCCCCCCceEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCc
Q 037841 62 SYFVNVTIDPKTQEPTSVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNR 141 (561)
Q Consensus 62 ~pf~~~~~d~~~~~~~~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R 141 (561)
++..++++++.++ .-++|+.+.+..+..- +-++ .+...-.+-.++...|..|++|++++ +.-.+.+
T Consensus 92 ~~~r~vnR~~GSG--------tR~l~d~~l~~~gi~~--~~i~---gy~~~~~th~~vA~aVa~G~AD~G~g-~~~~A~~ 157 (193)
T PF12727_consen 92 PGLRFVNRQPGSG--------TRILFDQLLAEEGIDP--EDIP---GYAQEANTHLAVAAAVASGKADAGIG-IRAAAEE 157 (193)
T ss_pred CCcEEEECCCCCH--------HHHHHHHHHHHcCCCh--hhCC---CccccccChHHHHHHHHcCCCCEEee-hHHHHHh
Confidence 3455666554222 3478888888776532 1111 01112235688999999999999987 4334444
Q ss_pred ceeeeccccccccceEEEEEccCCCCC
Q 037841 142 SNYVDFTLPYTESGVSMIVPIKDSKKR 168 (561)
Q Consensus 142 ~~~vdfT~p~~~~~~~ivvp~~~~~~~ 168 (561)
...++| .|.....+.+++++.....+
T Consensus 158 ~~gL~F-vpl~~E~~dlv~~~~~~~~~ 183 (193)
T PF12727_consen 158 FYGLDF-VPLAEERYDLVIRREDLEDP 183 (193)
T ss_pred hcCCCc-EEccccceEEEEEhhHcCCH
Confidence 456777 56777889999997764433
No 190
>PF14979 TMEM52: Transmembrane 52
Probab=32.57 E-value=3.7e+02 Score=24.14 Aligned_cols=31 Identities=23% Similarity=0.336 Sum_probs=17.2
Q ss_pred chhHHHHHHHHHHH---HHHHHHHHHHHHHhhcc
Q 037841 421 SFWGLFLIAGIAAI---LALIIFLAVFVGQHRNV 451 (561)
Q Consensus 421 ~~~g~F~il~~g~~---lallvfl~E~~~~~~~~ 451 (561)
++|-+|+++.++.+ .++.+.++.+.+.+|++
T Consensus 18 ~LWyIwLill~~~llLLCG~ta~C~rfCClrk~~ 51 (154)
T PF14979_consen 18 SLWYIWLILLIGFLLLLCGLTASCVRFCCLRKQA 51 (154)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 55666655554433 34444556667766664
No 191
>PRK01066 porphobilinogen deaminase; Provisional
Probab=32.49 E-value=4.8e+02 Score=25.42 Aligned_cols=60 Identities=18% Similarity=0.048 Sum_probs=37.7
Q ss_pred CCHHHHHhCCCeeEEEeCchHHH-HHHhcCCCccceeecC-ChHHHHHHhhccccCCceeEEeecchhHH
Q 037841 275 TDVKMLIKRGDNVGYQKGSFVLG-ILKQLGFDERKLVVYN-SPEECHELFQKGSANGGIAAAFEEIPYGK 342 (561)
Q Consensus 275 ~sl~dL~~~~~~vg~~~gs~~~~-~l~~~~~~~~~~~~~~-s~~~~~~~l~~g~~~~gv~a~i~~~~~~~ 342 (561)
.++++|- .|-+||. |..+. ..-...+|..+++.+. +.+.-+..|..|. .||++.-..-+.
T Consensus 124 ~~l~~Lp-~ga~IGT---SS~RR~aql~~~rPdl~v~~iRGNV~TRL~KL~~ge----~DaiiLA~AGL~ 185 (231)
T PRK01066 124 YLSQPLP-RRPRIGS---SSLRREELLKLLFPSGIILDIRGTIEERLKLLEEKK----YDAIVVAKAAVL 185 (231)
T ss_pred CchhhCC-CCCEEeC---ChHHHHHHHHHHCCCCEEEeCcCCHHHHHHHhcCCC----CCchhhHHHHHH
Confidence 3567774 4546664 44433 2222346766766664 7888899999998 888877554443
No 192
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=32.01 E-value=50 Score=27.00 Aligned_cols=24 Identities=25% Similarity=0.278 Sum_probs=19.0
Q ss_pred hhhHHHHHHHHHHHHHHHhhhhcc
Q 037841 179 WDLWVTSGCFFIFIGFVVWALEHR 202 (561)
Q Consensus 179 ~~vW~~~~~~~i~~~~v~~~l~~~ 202 (561)
.+-|+..++++++++.++|++.+|
T Consensus 68 ~D~~li~~~~~~f~~~v~yI~~rR 91 (92)
T PF03908_consen 68 TDRILIFFAFLFFLLVVLYILWRR 91 (92)
T ss_pred HhHHHHHHHHHHHHHHHHHHhhhc
Confidence 355777788888888899988776
No 193
>PRK10752 sulfate transporter subunit; Provisional
Probab=30.84 E-value=1.3e+02 Score=30.99 Aligned_cols=42 Identities=19% Similarity=0.061 Sum_probs=27.4
Q ss_pred HHHHHHHHHC----CCceeEEEEecCCCCCCCCCCHHHHHHHHHcC-cccEEEece
Q 037841 85 DVFKAVIQEL----PYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLG-EFDAAVGDI 135 (561)
Q Consensus 85 dl~~~i~~~l----~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g-~~D~~vg~~ 135 (561)
++..++.++. |.++++...- ++-..+..+|.+| .+|+.+++.
T Consensus 38 ~~~~~f~~~~~~~tG~~V~v~~s~---------ggSg~l~~qI~~g~~aDV~~~a~ 84 (329)
T PRK10752 38 QYNKAFSAHWKQQTGDNVVIRQSH---------GGSGKQATSVINGIEADVVTLAL 84 (329)
T ss_pred HHHHHHHHHHHhccCCceEEEeCC---------CChHHHHHHHHcCCCCCEEEeCC
Confidence 6677777655 7766554322 2446788888865 689987754
No 194
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=29.82 E-value=4e+02 Score=23.61 Aligned_cols=64 Identities=8% Similarity=0.097 Sum_probs=37.2
Q ss_pred EehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCcceeeeccccccccceEEEE
Q 037841 81 GFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNRSNYVDFTLPYTESGVSMIV 160 (561)
Q Consensus 81 G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R~~~vdfT~p~~~~~~~ivv 160 (561)
++-..++..+.++.+ .+++++... +.+. .+.+|++|+++..... ....+. +.++.+..+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~~-----------~~~~-~~~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 76 (201)
T cd08471 14 LHVLPIITDFLDAYP-EVSVRLLLL-----------DRVV-NLLEEGVDVAVRIGHL---PDSSLV-ATRVGSVRRVVCA 76 (201)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEEc-----------Cccc-hhhcccccEEEEecCC---CCCCeE-EEEccccceEEEE
Confidence 345678889999887 466665531 1222 3457899998752111 112232 3456666777776
Q ss_pred E
Q 037841 161 P 161 (561)
Q Consensus 161 p 161 (561)
+
T Consensus 77 ~ 77 (201)
T cd08471 77 S 77 (201)
T ss_pred C
Confidence 5
No 195
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=29.48 E-value=3.4e+02 Score=27.41 Aligned_cols=101 Identities=12% Similarity=0.099 Sum_probs=58.8
Q ss_pred cCCHHHHHhCCC-eeEEEeCchHHHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcce
Q 037841 274 ITDVKMLIKRGD-NVGYQKGSFVLGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKY 352 (561)
Q Consensus 274 I~sl~dL~~~~~-~vg~~~gs~~~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l 352 (561)
.++.+||. |. +|+...-...++||++.+.+-.-+....+.| . +-..|- .||+++-.......-.+.+
T Consensus 107 ~~~~~~l~--~~~rIATkYp~l~~~yf~~~g~~~~Ii~l~GsvE-~--aP~~Gl----ADaIvDivsTG~TLkaNgL--- 174 (290)
T COG0040 107 YTSPEDLK--GRLRIATKYPNLARKYFAEKGIDVEIIKLSGSVE-L--APALGL----ADAIVDIVSTGTTLKANGL--- 174 (290)
T ss_pred ccChhHhc--CCceEEEccHHHHHHHHHHcCceEEEEEccCcEe-e--ccccCc----cceEEEeecCCHhHHHCCC---
Confidence 47788884 44 8888777778999988665432222333333 2 223455 7888887777666655555
Q ss_pred EEeCcccccCceEEEecCCCCCh---hhHHHHHhhccc
Q 037841 353 TMVEPTFKTAGFGFAFPLHSPLV---HDVSKAILSVTE 387 (561)
Q Consensus 353 ~~v~~~~~~~~~~~~~~k~spl~---~~in~~Il~l~e 387 (561)
..+ +.+......++.++...+. +.+++.+.++..
T Consensus 175 ~~i-d~i~~ssa~LI~n~~~~~~~k~~~i~~l~~rl~g 211 (290)
T COG0040 175 KEI-EVIYDSSARLIVNAKASLKDKQELIDQLVTRLKG 211 (290)
T ss_pred EEE-EEEEeeEEEEEeccccccchhHHHHHHHHHHHHH
Confidence 355 4445555556666432222 346666666643
No 196
>PF14851 FAM176: FAM176 family
Probab=29.26 E-value=1.3e+02 Score=27.21 Aligned_cols=27 Identities=15% Similarity=0.418 Sum_probs=15.8
Q ss_pred hhHHHHHHH--HHHHHHHHHHHHHHHHHh
Q 037841 422 FWGLFLIAG--IAAILALIIFLAVFVGQH 448 (561)
Q Consensus 422 ~~g~F~il~--~g~~lallvfl~E~~~~~ 448 (561)
-.++|+++| +|+++.|+++++.+.++.
T Consensus 21 ~~aLYFv~gVC~GLlLtLcllV~risc~~ 49 (153)
T PF14851_consen 21 RFALYFVSGVCAGLLLTLCLLVIRISCRP 49 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhheeec
Confidence 355666665 455556666666666643
No 197
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=29.12 E-value=1e+02 Score=30.29 Aligned_cols=50 Identities=14% Similarity=0.077 Sum_probs=31.8
Q ss_pred CHHHHHHHHHcCcccEEEeceeee-cCcc-eeeeccccccccceEEEEEccC
Q 037841 115 SYNDLIYQVFLGEFDAAVGDITIL-LNRS-NYVDFTLPYTESGVSMIVPIKD 164 (561)
Q Consensus 115 s~~~li~~l~~g~~D~~vg~~~it-~~R~-~~vdfT~p~~~~~~~ivvp~~~ 164 (561)
+..+.+.+|.+|++|+++++.... .... .......++....+++++++.+
T Consensus 181 ~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~k~~ 232 (259)
T PRK11917 181 DYPSIKAALDAKRVDAFSVDKSILLGYVDDKSEILPDSFEPQSYGIVTKKDD 232 (259)
T ss_pred CHHHHHHHHHcCCCcEEEecHHHHHHhhhcCCeecCCcCCCCceEEEEeCCC
Confidence 678899999999999998765321 1111 1122234455566788887554
No 198
>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=26.96 E-value=1.5e+02 Score=27.79 Aligned_cols=71 Identities=10% Similarity=0.188 Sum_probs=50.0
Q ss_pred HHHhcCCCccceeecCChHHHHHHhhccccCCceeEEeecchhHHHHHhcCCcceEEeCcccccCceEEEecCCCCC
Q 037841 298 ILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFEEIPYGKLLVGQHCYKYTMVEPTFKTAGFGFAFPLHSPL 374 (561)
Q Consensus 298 ~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~~~l~~~~~~l~~v~~~~~~~~~~~~~~k~spl 374 (561)
++++.+. +.+++.+....+..++|..|+ +|+.+......-....+.- .+.++..........+++++++.+
T Consensus 15 ~f~~~gl-~ve~~~~~~~~~~~~~l~~G~----~D~~~~~~~~~~~~~~~g~-~~~~i~~~~~~~~~~l~~~~~s~i 85 (216)
T PF09084_consen 15 YFKEEGL-DVEIVFFGGGGDVLEALASGK----ADIAVAGPDAVLFARAKGA-DIKIIAASYQSSPNALVVRKDSGI 85 (216)
T ss_dssp HHHHTTE-EEEEEEESSHHHHHHHHHTTS----HSEEEEECHHHHHHHHTTS-TEEEEEEEEEECCEEEEEETTTS-
T ss_pred CCccCeE-EEEEEEecChhHHHHHHhcCC----ceEEeccchHHHHHHhcCC-eeEEEEEecCCCceEEEEeccCCC
Confidence 4455444 346777888889999999999 9988887765554444444 377776666666778888888773
No 199
>KOG3713 consensus Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism]
Probab=25.50 E-value=79 Score=33.99 Aligned_cols=58 Identities=14% Similarity=0.239 Sum_probs=42.7
Q ss_pred HHhhhhcccCCCCCCCccCccchhHHHHHHHhhhcc--ccccccchhHHHHHHHHHHHHHHHHH
Q 037841 195 VVWALEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQ--RERVISNLARFVVIVWYFVVLVLTQS 256 (561)
Q Consensus 195 v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~Ril~~~w~~~~lil~~~ 256 (561)
+++++|+-. ..+.-.++-.++|+..-+|.--| ...|++..+|++...-.+++++..+.
T Consensus 362 lvY~~Ek~~----~~~~FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gklvas~cil~GVLvlAl 421 (477)
T KOG3713|consen 362 LVYFAEKDE----PDTKFTSIPAGFWWAVVTMTTVGYGDMVPVTVLGKLVASLCILCGVLVLAL 421 (477)
T ss_pred HHHHhhhcC----CCCCCccccchhheeeEEEeeecccCccccccchHHHHHHHHHHhHHHhhc
Confidence 345566533 33446678889999999988776 34779999999998888888776653
No 200
>TIGR03730 tungstate_WtpA tungstate ABC transporter binding protein WtpA. Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists.
Probab=25.29 E-value=6.9e+02 Score=24.92 Aligned_cols=29 Identities=24% Similarity=0.264 Sum_probs=23.1
Q ss_pred cceeecCChHHHHHHhhccccCCceeEEeecch
Q 037841 307 RKLVVYNSPEECHELFQKGSANGGIAAAFEEIP 339 (561)
Q Consensus 307 ~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~~~~ 339 (561)
.+++...+..+....+..|+ +|+.+.-..
T Consensus 176 ~k~~~~~~v~~~~~~v~sG~----aD~g~vY~S 204 (273)
T TIGR03730 176 SKIFIRPKEVELLSLLESGE----IDYAFIYKS 204 (273)
T ss_pred cceeecCchHhHHHHHHCCC----CcEEEEEee
Confidence 56777778888999999999 888776544
No 201
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=25.18 E-value=2.1e+02 Score=28.04 Aligned_cols=101 Identities=22% Similarity=0.303 Sum_probs=65.9
Q ss_pred eeEEEeCchH------HHHHHhcCCCccceeecCChHHHHHHhhccccCCceeEEee-cchhHHHHHhcCCcceEEeCcc
Q 037841 286 NVGYQKGSFV------LGILKQLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFE-EIPYGKLLVGQHCYKYTMVEPT 358 (561)
Q Consensus 286 ~vg~~~gs~~------~~~l~~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~-~~~~~~~~l~~~~~~l~~v~~~ 358 (561)
+||+..+... .+.+++.++ ..+++.+++..+.-++|..|+ +||-+. ..+|++.+.+++..++..+++.
T Consensus 2 kIG~~~~~~~~i~~~v~~~~~~~Gi-~vevv~f~D~~~~N~AL~~G~----iDaN~fQh~~yl~~~n~~~~~~L~~v~~~ 76 (237)
T PF03180_consen 2 KIGVTPGPDAEILEAVKEKLKKKGI-DVEVVEFSDYVQPNEALADGE----IDANFFQHIPYLEQFNKENGYNLVPVGPT 76 (237)
T ss_dssp EEEEETTCHHHHHHHHHHHHHHTTE-EEEEEEESSTTHHHHHHHTTS----SSEEEEEEHHHHHHHHHHHT--EEEEEEE
T ss_pred EEEEeCCCHHHHHHHHHHHHHhcCC-eEEEEEecchhhcChHHHCCC----cceeccCCHHHHHHHHHHCCCcEEEecce
Confidence 5777655432 233444553 457889999999999999999 998544 5688888888776668777764
Q ss_pred cccCceEEEecCCCCC--------------hhhHHHHHhhccccchhH
Q 037841 359 FKTAGFGFAFPLHSPL--------------VHDVSKAILSVTEGDKMK 392 (561)
Q Consensus 359 ~~~~~~~~~~~k~spl--------------~~~in~~Il~l~e~G~~~ 392 (561)
...++|++-.|-.-+ ..-..++|.-|.+.|++.
T Consensus 77 -~~~p~glYS~k~~sl~~lp~Ga~VaIpnD~sN~~RaL~lLq~aGLI~ 123 (237)
T PF03180_consen 77 -YIEPMGLYSKKYKSLDDLPDGATVAIPNDPSNQARALKLLQEAGLIT 123 (237)
T ss_dssp -EE---EEEESSSSSGGGS-TTEEEEEESSHHHHHHHHHHHHHTTSEE
T ss_pred -eEEeEEEeecccCchhhcCCCCEEEEeCCccchhHHHHHHHhCCeEE
Confidence 344566665443222 234678888888888764
No 202
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=25.15 E-value=98 Score=28.40 Aligned_cols=29 Identities=14% Similarity=0.094 Sum_probs=21.2
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 037841 421 SFWGLFLIAGIAAILALIIFLAVFVGQHR 449 (561)
Q Consensus 421 ~~~g~F~il~~g~~lallvfl~E~~~~~~ 449 (561)
-+.-.||++++.++++++.|++..+.-++
T Consensus 93 ~l~R~~~Vl~g~s~l~i~yfvir~~R~r~ 121 (163)
T PF06679_consen 93 MLKRALYVLVGLSALAILYFVIRTFRLRR 121 (163)
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 45667788888888888888887665544
No 203
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=23.78 E-value=7.7e+02 Score=24.96 Aligned_cols=60 Identities=15% Similarity=0.020 Sum_probs=39.4
Q ss_pred CCHHHHHhCCCeeEEEeCchHHHHH-HhcCCCccceeec-CChHHHHHHhhccccCCceeEEeecchhHH
Q 037841 275 TDVKMLIKRGDNVGYQKGSFVLGIL-KQLGFDERKLVVY-NSPEECHELFQKGSANGGIAAAFEEIPYGK 342 (561)
Q Consensus 275 ~sl~dL~~~~~~vg~~~gs~~~~~l-~~~~~~~~~~~~~-~s~~~~~~~l~~g~~~~gv~a~i~~~~~~~ 342 (561)
.+++||- .|-+||. |..+.-. -...+|..+++.+ .+.+..++.|..|. .||++.-..-+.
T Consensus 109 ~~l~~Lp-~ga~VGT---sS~RR~aql~~~rPdl~i~~iRGNV~TRL~KL~~g~----~DaiiLA~AGL~ 170 (292)
T TIGR00212 109 LSLDSLP-QGAKVGT---SSLRRKAQLKAIRPDLKIEPLRGNIDTRLRKLDEGE----YDAIILAEAGLK 170 (292)
T ss_pred CChhHCC-CCCEecc---CCHHHHHHHHHHCCCCEEEECcCCHHHHHHHhcCCC----CCEeehHhhHHH
Confidence 5688885 4545554 4444322 2224677777755 48899999999998 899887655544
No 204
>PF01007 IRK: Inward rectifier potassium channel; InterPro: IPR013521 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. Inwardly-rectifying potassium channels (Kir) are the principal class of two-TM domain potassium channels. They are characterised by the property of inward-rectification, which is described as the ability to allow large inward currents and smaller outward currents. Inwardly rectifying potassium channels (Kir) are responsible for regulating diverse processes including: cellular excitability, vascular tone, heart rate, renal salt flow, and insulin release []. To date, around twenty members of this superfamily have been cloned, which can be grouped into six families by sequence similarity, and these are designated Kir1.x-6.x [, ]. Cloned Kir channel cDNAs encode proteins of between ~370-500 residues, both N- and C-termini are thought to be cytoplasmic, and the N terminus lacks a signal sequence. Kir channel alpha subunits possess only 2TM domains linked with a P-domain. Thus, Kir channels share similarity with the fifth and sixth domains, and P-domain of the other families. It is thought that four Kir subunits assemble to form a tetrameric channel complex, which may be hetero- or homomeric [].; PDB: 3AT9_A 3AUW_D 3SYA_A 3ATE_A 3SYQ_A 3SYO_A 3ATB_A 3SYC_A 3AT8_A 3ATA_A ....
Probab=23.62 E-value=1.9e+02 Score=29.94 Aligned_cols=59 Identities=19% Similarity=0.168 Sum_probs=46.9
Q ss_pred CccchhHHHHHHHhhhcc-cc---ccccchhHHHHHHHHHHHHHHHHHhHhhheeeeEeeccC
Q 037841 213 HQVGTSFWFSFSTMVFSQ-RE---RVISNLARFVVIVWYFVVLVLTQSYTASLTSLLTVQQLQ 271 (561)
Q Consensus 213 ~~~~~~~~~~~~~l~~~~-~~---~~~s~~~Ril~~~w~~~~lil~~~Yta~LtS~Lt~~~~~ 271 (561)
.++..+|+|++.++.-.| +. .+....+-+++.+=.++++++.+.-++-+.+-++.|+..
T Consensus 83 ~~f~~aF~FSveT~tTIGYG~~~~~~~c~~a~~l~~~q~~~g~l~~a~~~Glvfar~srP~~R 145 (336)
T PF01007_consen 83 NSFTSAFLFSVETQTTIGYGSRYPTPECPYAIFLVTIQSLVGLLLDAFMTGLVFARFSRPKKR 145 (336)
T ss_dssp TTHHHHHHHHHHHHTT---SSSEB-CSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCCG
T ss_pred cchhhheeEEEEEEEEeccCCcccCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccc
Confidence 688999999999999666 32 346777888888888999999999999888888887754
No 205
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=23.61 E-value=3.3e+02 Score=21.51 Aligned_cols=16 Identities=25% Similarity=0.264 Sum_probs=7.7
Q ss_pred HHHHHHHHHHhhcccC
Q 037841 460 LSRIRIFLRIFVSKDL 475 (561)
Q Consensus 460 ~~~l~~~~~~~~~~~~ 475 (561)
.+.++.+.+..|...+
T Consensus 55 ~eRI~tLE~ILd~e~P 70 (75)
T TIGR02976 55 EERIDTLERILDAEHP 70 (75)
T ss_pred HHHHHHHHHHHcCCCc
Confidence 3344445555555443
No 206
>PF15179 Myc_target_1: Myc target protein 1
Probab=23.41 E-value=1.2e+02 Score=28.19 Aligned_cols=38 Identities=11% Similarity=0.193 Sum_probs=28.1
Q ss_pred cccccccchhHHHHHH-HHHHHHHHHHHHHHHHHHhhcc
Q 037841 414 SRSLGLNSFWGLFLIA-GIAAILALIIFLAVFVGQHRNV 451 (561)
Q Consensus 414 ~~~L~l~~~~g~F~il-~~g~~lallvfl~E~~~~~~~~ 451 (561)
.+.++++++..+|.+- ++|++++.+|+++-.|..|||.
T Consensus 13 ~~~f~~~~lIlaF~vSm~iGLviG~li~~LltwlSRRRA 51 (197)
T PF15179_consen 13 LENFDWEDLILAFCVSMAIGLVIGALIWALLTWLSRRRA 51 (197)
T ss_pred hhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3456777888888654 5888888888888777776665
No 207
>TIGR03061 pip_yhgE_Nterm YhgE/Pip N-terminal domain. This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057.
Probab=22.69 E-value=4.9e+02 Score=23.40 Aligned_cols=21 Identities=14% Similarity=0.099 Sum_probs=17.2
Q ss_pred ChHHHHHHhhccccCCceeEEeecc
Q 037841 314 SPEECHELFQKGSANGGIAAAFEEI 338 (561)
Q Consensus 314 s~~~~~~~l~~g~~~~gv~a~i~~~ 338 (561)
+.++..+++.+|+ +++++.=.
T Consensus 84 ~~~ea~~~l~~g~----~~~~ivIP 104 (164)
T TIGR03061 84 SAKEAEKGLADGK----YYMVITIP 104 (164)
T ss_pred CHHHHHHHhHcCc----EEEEEEEC
Confidence 7889999999999 88776543
No 208
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=22.26 E-value=3.8e+02 Score=21.15 Aligned_cols=11 Identities=36% Similarity=0.504 Sum_probs=4.8
Q ss_pred HHHHHHHHhhc
Q 037841 462 RIRIFLRIFVS 472 (561)
Q Consensus 462 ~l~~~~~~~~~ 472 (561)
.++.+.+..|.
T Consensus 57 RI~tLE~ILda 67 (75)
T PF06667_consen 57 RIETLERILDA 67 (75)
T ss_pred HHHHHHHHHcC
Confidence 33444444443
No 209
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=21.88 E-value=8e+02 Score=26.62 Aligned_cols=57 Identities=21% Similarity=0.361 Sum_probs=35.3
Q ss_pred CCHHHHHhCCC-eeEEEeC------------chHHHHHH----hcCCCccceeecCChHHHHHHhhccccCCceeEEee
Q 037841 275 TDVKMLIKRGD-NVGYQKG------------SFVLGILK----QLGFDERKLVVYNSPEECHELFQKGSANGGIAAAFE 336 (561)
Q Consensus 275 ~sl~dL~~~~~-~vg~~~g------------s~~~~~l~----~~~~~~~~~~~~~s~~~~~~~l~~g~~~~gv~a~i~ 336 (561)
++++.+.+++. +||+... ++..++++ .++. +.+++.+.+.++.+++|.+|+ +|.++.
T Consensus 34 ~~l~~I~~~g~LrVg~~~~P~~~~~~~~~~~G~~~DLl~~ia~~LGv-~~e~v~~~~~~~ll~aL~~G~----iDi~~~ 107 (482)
T PRK10859 34 NQLEQIQERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLGV-KLEIKVRDNISQLFDALDKGK----ADLAAA 107 (482)
T ss_pred ccHHHHHhCCEEEEEEecCCCeeEecCCCcccHHHHHHHHHHHHhCC-cEEEEecCCHHHHHHHHhCCC----CCEEec
Confidence 56777776665 5665322 12223333 3444 235556778899999999999 886544
No 210
>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].
Probab=21.40 E-value=3.2e+02 Score=26.23 Aligned_cols=36 Identities=22% Similarity=0.210 Sum_probs=25.0
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 037841 416 SLGLNSFWGLFLIAGIAAILALIIFLAVFVGQHRNV 451 (561)
Q Consensus 416 ~L~l~~~~g~F~il~~g~~lallvfl~E~~~~~~~~ 451 (561)
..+-+.+.-++-|+++.+.+.|+||+.-++.++|+.
T Consensus 31 ~~~~d~~~I~iaiVAG~~tVILVI~i~v~vR~CRq~ 66 (221)
T PF08374_consen 31 SRSKDYVKIMIAIVAGIMTVILVIFIVVLVRYCRQS 66 (221)
T ss_pred cccccceeeeeeeecchhhhHHHHHHHHHHHHHhhc
Confidence 344456666777788888888888888777655543
No 211
>PF10577 UPF0560: Uncharacterised protein family UPF0560; InterPro: IPR018890 This family of proteins has no known function.
Probab=21.32 E-value=2.8e+02 Score=32.02 Aligned_cols=22 Identities=27% Similarity=0.326 Sum_probs=18.4
Q ss_pred hhheeeeEeeccCCCcCCHHHH
Q 037841 259 ASLTSLLTVQQLQPTITDVKML 280 (561)
Q Consensus 259 a~LtS~Lt~~~~~~~I~sl~dL 280 (561)
++|+++||+.+....++++-.+
T Consensus 130 s~lta~LT~~s~~~e~~~FP~l 151 (807)
T PF10577_consen 130 SNLTAYLTVASSPLELDSFPYL 151 (807)
T ss_pred eeEEEEEecccchhhhcccccc
Confidence 5799999999888777777776
No 212
>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=21.29 E-value=88 Score=28.12 Aligned_cols=29 Identities=14% Similarity=0.307 Sum_probs=21.2
Q ss_pred cccchhhHHHHHHHHHHHHHHHhhhhccc
Q 037841 175 QPLTWDLWVTSGCFFIFIGFVVWALEHRV 203 (561)
Q Consensus 175 ~PF~~~vW~~~~~~~i~~~~v~~~l~~~~ 203 (561)
.|..+.+|+.++++++++|++++.+-|+.
T Consensus 115 ~~~~~~i~~~i~g~ll~i~~giy~~~r~~ 143 (145)
T PF10661_consen 115 KPISPTILLSIGGILLAICGGIYVVLRKV 143 (145)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46667777778778888888887776653
No 213
>COG4588 AcfC Accessory colonization factor AcfC, contains ABC-type periplasmic domain [General function prediction only]
Probab=21.19 E-value=3e+02 Score=26.35 Aligned_cols=74 Identities=16% Similarity=0.078 Sum_probs=42.1
Q ss_pred ehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEeceeeecCc--ceee-ec----ccccccc
Q 037841 82 FCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVGDITILLNR--SNYV-DF----TLPYTES 154 (561)
Q Consensus 82 ~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg~~~it~~R--~~~v-df----T~p~~~~ 154 (561)
--.|+.+...++.+-.|++.+-|- .+|.+- ..+.+|+.+|.-.....- ..+- +| -.|.+.-
T Consensus 34 aL~~vA~~~~ektg~kVnvt~GPq--------~tW~~k----AkknADilfgaseqsalaia~~~~~~fs~~~i~ply~R 101 (252)
T COG4588 34 ALKDVAKKYEEKTGIKVNVTAGPQ--------ATWNEK----AKKNADILFGASEQSALAIAEDHKDSFSEKNIQPLYLR 101 (252)
T ss_pred HHHHHHHHHHHHhCeEEEEecCCc--------chhhhh----hhccCceeecccHHHHHHHHHhccccccccccceeeee
Confidence 456778888899987666655432 267653 467899988743221100 0111 12 2466666
Q ss_pred ceEEEEEccCCCC
Q 037841 155 GVSMIVPIKDSKK 167 (561)
Q Consensus 155 ~~~ivvp~~~~~~ 167 (561)
.-.++|++.++.+
T Consensus 102 ~aiIlvkkgNPkn 114 (252)
T COG4588 102 PAIILVKKGNPKN 114 (252)
T ss_pred ceEEEecCCCccc
Confidence 6667777665543
No 214
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=21.10 E-value=1.6e+02 Score=26.40 Aligned_cols=24 Identities=4% Similarity=-0.032 Sum_probs=18.7
Q ss_pred chhhHHHHHHHHHHHHHHHhhhhc
Q 037841 178 TWDLWVTSGCFFIFIGFVVWALEH 201 (561)
Q Consensus 178 ~~~vW~~~~~~~i~~~~v~~~l~~ 201 (561)
.+.+|++..+.++.+.+++|.-+.
T Consensus 35 HP~L~~~M~~~y~~~~~lm~~spy 58 (155)
T PF10777_consen 35 HPYLCLAMYAAYLAVAALMYYSPY 58 (155)
T ss_pred CcHHHHHHHHHHHHHHHHHHhcch
Confidence 456788888888888888887764
No 215
>COG0107 HisF Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]
Probab=20.78 E-value=1.2e+02 Score=29.39 Aligned_cols=47 Identities=19% Similarity=0.348 Sum_probs=37.3
Q ss_pred eEEEehHHHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHcCcccEEEe
Q 037841 78 SVTGFCIDVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFLGEFDAAVG 133 (561)
Q Consensus 78 ~~~G~~idl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~g~~D~~vg 133 (561)
.-.||++++++.+++..+. +. +..+. .|+-..+.+.+..+++|.+.+
T Consensus 182 tk~GyDl~l~~~v~~~v~i--Pv--IASGG-----aG~~ehf~eaf~~~~adAaLA 228 (256)
T COG0107 182 TKAGYDLELTRAVREAVNI--PV--IASGG-----AGKPEHFVEAFTEGKADAALA 228 (256)
T ss_pred cccCcCHHHHHHHHHhCCC--CE--EecCC-----CCcHHHHHHHHHhcCccHHHh
Confidence 5689999999999999874 33 23221 268899999999999999876
No 216
>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=20.65 E-value=8.4e+02 Score=24.24 Aligned_cols=39 Identities=21% Similarity=0.191 Sum_probs=26.9
Q ss_pred HHHHHHHHHCCCceeEEEEecCCCCCCCCCCHHHHHHHHHc----CcccEEEe
Q 037841 85 DVFKAVIQELPYAVAYDFVPYGQPDGTSSGSYNDLIYQVFL----GEFDAAVG 133 (561)
Q Consensus 85 dl~~~i~~~l~f~v~~~~v~~~~~~g~~ngs~~~li~~l~~----g~~D~~vg 133 (561)
.+++.+.++.|++ ++++.++ +-.+++..|.. ..+|++++
T Consensus 21 ~~~~~Fe~~~gi~--V~~~~~~--------s~~~l~~kl~~e~~~~~~DVv~~ 63 (309)
T TIGR01276 21 VVKKAFEADCNCE--LKLVALE--------DGVSLLNRLRLEGKNSKADVVLG 63 (309)
T ss_pred HHHHHHHHHHCCE--EEEEecC--------cHHHHHHHHHHcCCCCCCCEEEe
Confidence 5788898898875 4444432 34567878775 46999876
No 217
>COG4736 CcoQ Cbb3-type cytochrome oxidase, subunit 3 [Posttranslational modification, protein turnover, chaperones]
Probab=20.24 E-value=1.1e+02 Score=22.95 Aligned_cols=24 Identities=25% Similarity=0.443 Sum_probs=19.2
Q ss_pred hhHHHHHHHHHHHHHHHhhhhccc
Q 037841 180 DLWVTSGCFFIFIGFVVWALEHRV 203 (561)
Q Consensus 180 ~vW~~~~~~~i~~~~v~~~l~~~~ 203 (561)
..|.++.+++++++.+.|.+....
T Consensus 11 ~a~~t~~~~l~fiavi~~ayr~~~ 34 (60)
T COG4736 11 DAWGTIAFTLFFIAVIYFAYRPGK 34 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccc
Confidence 468888888899999988886543
Done!