Query 020472
Match_columns 326
No_of_seqs 115 out of 1168
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:39:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020472.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020472hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0181 HemC Porphobilinogen d 100.0 1.4E-90 3.1E-95 660.6 19.5 239 65-315 1-239 (307)
2 PLN02691 porphobilinogen deami 100.0 3.4E-89 7.4E-94 662.2 23.6 255 53-315 24-283 (351)
3 TIGR00212 hemC porphobilinogen 100.0 3.2E-89 6.9E-94 650.2 22.0 236 68-315 1-236 (292)
4 PRK00072 hemC porphobilinogen 100.0 8.6E-89 1.9E-93 648.0 22.9 239 65-315 2-240 (295)
5 cd00494 HMBS Hydroxymethylbila 100.0 1.8E-88 4E-93 645.0 22.7 236 68-315 1-236 (292)
6 PF01379 Porphobil_deam: Porph 100.0 5.3E-86 1.2E-90 605.3 19.7 213 67-284 1-215 (215)
7 PRK01066 porphobilinogen deami 100.0 1.3E-83 2.9E-88 593.8 22.0 215 63-287 13-227 (231)
8 KOG2892 Porphobilinogen deamin 100.0 4.2E-79 9E-84 574.7 12.8 243 62-316 2-248 (320)
9 PRK11063 metQ DL-methionine tr 97.7 0.00068 1.5E-08 64.4 12.6 184 66-288 31-252 (271)
10 TIGR00363 lipoprotein, YaeC fa 97.3 0.0052 1.1E-07 58.3 13.4 191 66-289 18-240 (258)
11 PRK11553 alkanesulfonate trans 96.2 0.09 1.9E-06 49.4 12.5 146 63-238 24-184 (314)
12 PRK09861 cytoplasmic membrane 95.8 0.21 4.4E-06 47.8 13.2 189 66-289 32-254 (272)
13 smart00062 PBPb Bacterial peri 95.5 0.19 4.1E-06 41.2 10.0 143 130-283 49-198 (219)
14 PRK10859 membrane-bound lytic 95.4 0.12 2.5E-06 52.7 10.5 150 64-239 41-204 (482)
15 PRK11260 cystine transporter s 95.4 0.16 3.6E-06 46.4 10.5 146 130-286 90-242 (266)
16 PF00497 SBP_bac_3: Bacterial 95.0 0.036 7.8E-07 47.2 4.6 141 131-284 49-203 (225)
17 cd00134 PBPb Bacterial peripla 94.7 0.27 5.9E-06 40.5 9.0 144 130-283 48-197 (218)
18 TIGR03427 ABC_peri_uca ABC tra 94.7 0.46 9.9E-06 46.5 11.9 144 67-241 3-164 (328)
19 PRK15007 putative ABC transpor 94.5 0.68 1.5E-05 41.2 11.7 148 131-286 71-223 (243)
20 TIGR01728 SsuA_fam ABC transpo 94.5 0.55 1.2E-05 42.2 11.1 109 131-244 41-162 (288)
21 TIGR01098 3A0109s03R phosphate 94.5 1.5 3.3E-05 39.3 13.9 153 64-243 30-207 (254)
22 TIGR01096 3A0103s03R lysine-ar 94.3 0.65 1.4E-05 41.3 11.1 147 131-285 74-231 (250)
23 PF14503 YhfZ_C: YhfZ C-termin 94.1 0.29 6.4E-06 46.5 8.8 145 134-286 57-210 (232)
24 PRK15010 ABC transporter lysin 94.1 1 2.2E-05 41.1 12.1 146 130-285 75-234 (260)
25 PF13379 NMT1_2: NMT1-like fam 93.4 0.65 1.4E-05 42.4 9.5 168 65-262 5-202 (252)
26 TIGR01729 taurine_ABC_bnd taur 93.0 0.2 4.3E-06 46.8 5.6 110 131-244 39-161 (300)
27 cd08437 PBP2_MleR The substrat 92.8 3.9 8.5E-05 33.6 12.6 140 67-238 1-153 (198)
28 TIGR02122 TRAP_TAXI TRAP trans 92.8 0.66 1.4E-05 43.0 8.8 145 65-237 29-197 (320)
29 PRK09959 hybrid sensory histid 92.4 0.86 1.9E-05 50.5 10.5 142 130-285 107-258 (1197)
30 PRK09959 hybrid sensory histid 92.3 1 2.2E-05 49.9 11.0 144 129-284 351-500 (1197)
31 COG0834 HisJ ABC-type amino ac 92.1 1.1 2.4E-05 39.9 9.1 108 131-243 88-202 (275)
32 PF03466 LysR_substrate: LysR 91.8 5.9 0.00013 32.7 12.5 139 65-235 5-155 (209)
33 cd08467 PBP2_SyrM The C-termin 90.7 1.2 2.5E-05 37.3 7.3 56 68-148 2-57 (200)
34 cd08466 PBP2_LeuO The C-termin 90.6 1.6 3.6E-05 35.8 8.0 57 67-148 1-57 (200)
35 cd08440 PBP2_LTTR_like_4 TThe 90.3 2 4.2E-05 34.6 8.1 133 67-231 1-145 (197)
36 cd05466 PBP2_LTTR_substrate Th 89.5 8.8 0.00019 30.2 13.9 135 67-234 1-148 (197)
37 cd08418 PBP2_TdcA The C-termin 89.5 10 0.00022 30.9 13.4 57 67-148 1-57 (201)
38 cd08438 PBP2_CidR The C-termin 89.2 2.1 4.6E-05 34.7 7.5 57 67-148 1-57 (197)
39 PRK11480 tauA taurine transpor 88.7 0.73 1.6E-05 43.9 5.1 108 131-242 63-181 (320)
40 PRK00489 hisG ATP phosphoribos 88.7 1.9 4E-05 41.1 7.9 102 130-237 54-159 (287)
41 TIGR02995 ectoine_ehuB ectoine 88.7 3.2 6.9E-05 38.3 9.2 145 131-284 83-240 (275)
42 cd08414 PBP2_LTTR_aromatics_li 88.5 1.8 3.9E-05 35.1 6.7 56 67-147 1-56 (197)
43 cd08456 PBP2_LysR The C-termin 88.0 3.3 7.2E-05 33.7 8.0 57 67-148 1-57 (196)
44 cd08453 PBP2_IlvR The C-termin 87.9 4.7 0.0001 33.2 8.8 68 67-160 1-68 (200)
45 TIGR03431 PhnD phosphonate ABC 87.6 9 0.0002 35.5 11.5 108 131-241 71-199 (288)
46 PF03180 Lipoprotein_9: NLPA l 87.5 2.2 4.7E-05 40.4 7.4 184 68-288 1-218 (237)
47 cd08419 PBP2_CbbR_RubisCO_like 87.2 3.6 7.7E-05 33.3 7.7 56 67-148 1-56 (197)
48 cd08439 PBP2_LrhA_like The C-t 87.1 2.7 5.8E-05 34.5 7.0 57 67-148 1-57 (185)
49 cd08420 PBP2_CysL_like C-termi 87.1 3.9 8.4E-05 33.0 7.8 57 67-148 1-57 (201)
50 COG0715 TauA ABC-type nitrate/ 86.9 2.6 5.6E-05 39.6 7.6 124 131-258 73-212 (335)
51 cd08446 PBP2_Chlorocatechol Th 86.8 4.9 0.00011 32.9 8.3 57 67-148 2-58 (198)
52 cd08447 PBP2_LTTR_aromatics_li 86.6 4.4 9.6E-05 33.0 7.9 137 67-239 1-154 (198)
53 cd08448 PBP2_LTTR_aromatics_li 86.4 5.1 0.00011 32.4 8.1 57 67-148 1-57 (197)
54 cd08425 PBP2_CynR The C-termin 86.4 16 0.00036 29.7 13.9 133 66-231 1-147 (197)
55 cd08433 PBP2_Nac The C-teminal 86.2 3.4 7.4E-05 33.8 7.1 58 67-149 1-58 (198)
56 cd08417 PBP2_Nitroaromatics_li 86.2 3.3 7.2E-05 33.9 7.0 58 67-149 1-58 (200)
57 cd08469 PBP2_PnbR The C-termin 86.1 4.8 0.0001 34.0 8.2 57 68-149 2-58 (221)
58 PRK11917 bifunctional adhesin/ 86.0 14 0.00031 34.1 11.8 140 134-286 95-242 (259)
59 cd08459 PBP2_DntR_NahR_LinR_li 86.0 18 0.00039 29.7 14.5 57 67-148 1-57 (201)
60 cd08465 PBP2_ToxR The C-termin 86.0 19 0.00041 30.0 12.9 56 67-147 1-56 (200)
61 cd08436 PBP2_LTTR_like_3 The C 86.0 4.5 9.7E-05 32.7 7.6 138 67-236 1-151 (194)
62 cd08464 PBP2_DntR_like_2 The C 85.9 3.2 6.9E-05 33.9 6.7 57 67-148 1-57 (200)
63 cd08441 PBP2_MetR The C-termin 85.6 4.3 9.4E-05 33.3 7.4 56 67-147 1-56 (198)
64 cd08435 PBP2_GbpR The C-termin 84.5 6 0.00013 32.1 7.7 132 67-231 1-148 (201)
65 cd08449 PBP2_XapR The C-termin 84.4 5.6 0.00012 32.3 7.5 58 67-149 1-58 (197)
66 PRK11151 DNA-binding transcrip 84.4 34 0.00075 31.6 17.5 192 65-295 90-298 (305)
67 PF09084 NMT1: NMT1/THI5 like; 84.3 0.96 2.1E-05 39.6 3.1 103 131-237 33-147 (216)
68 cd08486 PBP2_CbnR The C-termin 84.3 4.4 9.5E-05 33.9 7.0 133 67-231 2-148 (198)
69 cd08411 PBP2_OxyR The C-termin 83.3 24 0.00051 28.9 13.1 145 66-243 1-157 (200)
70 cd08461 PBP2_DntR_like_3 The C 83.2 5.8 0.00013 32.5 7.2 56 67-147 1-56 (198)
71 cd08421 PBP2_LTTR_like_1 The C 82.7 8.7 0.00019 31.3 8.0 134 68-234 2-148 (198)
72 cd08445 PBP2_BenM_CatM_CatR Th 82.2 9.6 0.00021 31.6 8.2 58 66-148 1-58 (203)
73 cd08427 PBP2_LTTR_like_2 The C 81.9 5.7 0.00012 32.2 6.6 55 68-147 2-56 (195)
74 cd08442 PBP2_YofA_SoxR_like Th 81.8 8.5 0.00019 31.1 7.6 56 67-147 1-56 (193)
75 cd08452 PBP2_AlsR The C-termin 81.6 9.7 0.00021 31.5 8.0 56 68-148 2-57 (197)
76 PRK11013 DNA-binding transcrip 81.6 11 0.00024 35.2 9.3 62 64-150 92-153 (309)
77 PRK09986 DNA-binding transcrip 81.5 26 0.00056 31.9 11.5 58 64-146 95-152 (294)
78 PRK11074 putative DNA-binding 81.4 8.1 0.00018 35.9 8.2 58 64-146 90-147 (300)
79 PRK15437 histidine ABC transpo 81.3 31 0.00067 31.4 11.8 101 131-238 76-184 (259)
80 CHL00180 rbcR LysR transcripti 81.2 16 0.00034 34.0 10.1 148 64-241 93-255 (305)
81 cd08431 PBP2_HupR The C-termin 81.2 4.7 0.0001 33.0 5.9 56 68-148 2-57 (195)
82 cd08450 PBP2_HcaR The C-termin 81.1 10 0.00022 30.8 7.9 135 68-235 2-150 (196)
83 PRK09508 leuO leucine transcri 81.0 8.5 0.00018 36.1 8.3 60 65-149 111-170 (314)
84 PRK10341 DNA-binding transcrip 80.7 29 0.00063 32.5 11.7 138 65-234 96-245 (312)
85 cd08485 PBP2_ClcR The C-termin 80.3 33 0.00071 28.5 11.9 136 67-234 2-151 (198)
86 PF02621 VitK2_biosynth: Menaq 79.9 6.6 0.00014 36.9 7.1 101 129-236 33-140 (251)
87 cd08416 PBP2_MdcR The C-termin 79.8 9.1 0.0002 31.2 7.2 57 67-148 1-57 (199)
88 cd08415 PBP2_LysR_opines_like 79.6 7.6 0.00017 31.5 6.6 57 67-148 1-57 (196)
89 cd08423 PBP2_LTTR_like_6 The C 79.5 18 0.00038 29.3 8.8 136 67-230 1-149 (200)
90 PRK09791 putative DNA-binding 77.4 16 0.00034 33.9 8.7 59 64-147 93-151 (302)
91 cd08462 PBP2_NodD The C-termin 77.1 14 0.0003 30.6 7.6 136 68-238 2-150 (200)
92 PF12974 Phosphonate-bd: ABC t 76.9 0.45 9.8E-06 43.0 -1.6 113 130-245 40-172 (243)
93 PRK09495 glnH glutamine ABC tr 76.7 19 0.00042 32.3 8.9 104 131-240 74-182 (247)
94 PRK12683 transcriptional regul 76.2 70 0.0015 30.1 14.7 146 64-242 91-249 (309)
95 cd08444 PBP2_Cbl The C-termina 76.2 43 0.00094 27.7 12.5 143 68-242 2-156 (198)
96 cd08457 PBP2_OccR The C-termin 75.7 11 0.00023 31.1 6.5 57 67-148 1-57 (196)
97 cd08429 PBP2_NhaR The C-termin 75.5 6.5 0.00014 33.6 5.3 41 196-237 16-56 (204)
98 TIGR02136 ptsS_2 phosphate bin 75.4 5.7 0.00012 37.5 5.3 57 64-146 34-90 (287)
99 cd08429 PBP2_NhaR The C-termin 75.4 11 0.00024 32.1 6.7 145 68-242 2-157 (204)
100 PRK10837 putative DNA-binding 74.9 66 0.0014 29.2 13.4 134 64-231 87-233 (290)
101 cd08413 PBP2_CysB_like The C-t 74.9 9.4 0.0002 31.7 6.0 141 67-239 1-153 (198)
102 cd08426 PBP2_LTTR_like_5 The C 74.7 44 0.00096 27.1 12.2 57 67-148 1-57 (199)
103 cd08412 PBP2_PAO1_like The C-t 74.7 7.4 0.00016 31.6 5.2 42 196-238 16-57 (198)
104 cd08467 PBP2_SyrM The C-termin 74.7 6.1 0.00013 32.9 4.8 49 188-237 1-56 (200)
105 cd08452 PBP2_AlsR The C-termin 74.4 7 0.00015 32.4 5.1 41 196-237 16-56 (197)
106 cd08449 PBP2_XapR The C-termin 74.4 7.4 0.00016 31.6 5.2 42 196-238 16-57 (197)
107 cd08463 PBP2_DntR_like_4 The C 73.8 17 0.00038 30.6 7.5 143 67-242 1-157 (203)
108 cd08460 PBP2_DntR_like_1 The C 73.5 17 0.00037 30.0 7.2 132 67-231 1-143 (200)
109 cd08458 PBP2_NocR The C-termin 72.1 54 0.0012 27.0 12.9 137 67-235 1-149 (196)
110 PRK11716 DNA-binding transcrip 71.9 33 0.00071 30.5 9.1 60 64-148 65-124 (269)
111 PRK12680 transcriptional regul 71.3 22 0.00047 34.1 8.3 61 64-149 91-151 (327)
112 cd08427 PBP2_LTTR_like_2 The C 71.0 8.7 0.00019 31.1 4.8 41 197-238 17-57 (195)
113 PF04069 OpuAC: Substrate bind 70.7 20 0.00044 33.0 7.7 188 66-287 1-227 (257)
114 cd08453 PBP2_IlvR The C-termin 70.4 11 0.00024 31.0 5.3 41 196-237 16-56 (200)
115 TIGR03870 ABC_MoxJ methanol ox 70.3 28 0.0006 31.7 8.4 68 219-286 152-226 (246)
116 cd08466 PBP2_LeuO The C-termin 70.2 11 0.00024 30.8 5.3 40 197-237 17-56 (200)
117 PRK10216 DNA-binding transcrip 70.0 97 0.0021 29.0 12.5 58 67-150 98-155 (319)
118 cd08451 PBP2_BudR The C-termin 70.0 57 0.0012 26.4 11.7 57 67-147 1-57 (199)
119 cd08458 PBP2_NocR The C-termin 70.0 12 0.00027 30.9 5.6 41 196-237 16-56 (196)
120 PRK10797 glutamate and asparta 69.9 35 0.00076 32.5 9.3 131 132-284 98-250 (302)
121 cd08465 PBP2_ToxR The C-termin 69.8 11 0.00024 31.4 5.3 40 197-237 17-56 (200)
122 cd08411 PBP2_OxyR The C-termin 68.8 12 0.00026 30.6 5.3 47 190-237 4-57 (200)
123 PRK12681 cysB transcriptional 68.5 1.1E+02 0.0024 29.1 14.3 175 64-277 91-279 (324)
124 cd08450 PBP2_HcaR The C-termin 67.9 12 0.00026 30.4 5.0 41 196-237 16-56 (196)
125 PRK12684 transcriptional regul 67.8 24 0.00051 33.2 7.6 59 64-147 91-149 (313)
126 PRK12679 cbl transcriptional r 66.7 1.2E+02 0.0025 28.6 12.7 60 64-148 91-150 (316)
127 cd08418 PBP2_TdcA The C-termin 66.4 15 0.00033 29.8 5.4 41 196-237 16-56 (201)
128 cd08430 PBP2_IlvY The C-termin 66.2 13 0.00029 30.1 5.0 56 68-148 2-57 (199)
129 cd08439 PBP2_LrhA_like The C-t 65.9 16 0.00034 29.9 5.4 40 197-237 17-56 (185)
130 cd08486 PBP2_CbnR The C-termin 65.7 13 0.00028 31.1 4.9 40 197-237 18-57 (198)
131 cd08442 PBP2_YofA_SoxR_like Th 65.3 14 0.00031 29.7 5.0 41 196-237 16-56 (193)
132 cd08431 PBP2_HupR The C-termin 65.2 10 0.00022 31.0 4.1 40 197-237 17-56 (195)
133 PRK15421 DNA-binding transcrip 64.9 36 0.00078 32.3 8.3 59 65-148 88-146 (317)
134 PRK12682 transcriptional regul 64.8 27 0.00059 32.5 7.4 175 64-275 91-277 (309)
135 cd08464 PBP2_DntR_like_2 The C 63.9 12 0.00026 30.5 4.3 41 197-238 17-57 (200)
136 cd08447 PBP2_LTTR_aromatics_li 63.9 17 0.00037 29.6 5.2 41 196-237 16-56 (198)
137 PRK11233 nitrogen assimilation 63.6 47 0.001 31.0 8.7 61 64-148 89-149 (305)
138 cd08413 PBP2_CysB_like The C-t 63.4 18 0.00038 30.1 5.3 41 196-237 16-56 (198)
139 cd08415 PBP2_LysR_opines_like 63.3 17 0.00037 29.4 5.1 43 196-239 16-58 (196)
140 cd05466 PBP2_LTTR_substrate Th 63.2 19 0.00042 28.3 5.3 42 197-239 17-58 (197)
141 cd08456 PBP2_LysR The C-termin 62.9 18 0.00039 29.4 5.2 41 196-237 16-56 (196)
142 cd08443 PBP2_CysB The C-termin 62.9 18 0.00038 30.2 5.2 41 196-237 16-56 (198)
143 cd08430 PBP2_IlvY The C-termin 62.6 19 0.00041 29.2 5.3 41 196-237 16-56 (199)
144 PRK11242 DNA-binding transcrip 60.7 1.3E+02 0.0029 27.3 13.2 135 65-231 90-237 (296)
145 TIGR02424 TF_pcaQ pca operon t 60.5 36 0.00078 31.3 7.2 60 63-147 90-149 (300)
146 cd08468 PBP2_Pa0477 The C-term 60.1 98 0.0021 25.6 14.8 57 67-148 1-57 (202)
147 PRK10094 DNA-binding transcrip 59.6 29 0.00064 32.6 6.6 59 64-146 90-148 (308)
148 cd08416 PBP2_MdcR The C-termin 59.3 20 0.00044 29.1 4.9 42 196-238 16-57 (199)
149 cd08434 PBP2_GltC_like The sub 59.3 90 0.002 24.9 14.7 57 67-148 1-57 (195)
150 cd08440 PBP2_LTTR_like_4 TThe 58.9 26 0.00055 28.1 5.3 41 197-238 17-57 (197)
151 cd08446 PBP2_Chlorocatechol Th 58.6 25 0.00054 28.7 5.3 40 197-237 18-57 (198)
152 cd08441 PBP2_MetR The C-termin 57.7 20 0.00043 29.4 4.6 41 196-237 16-56 (198)
153 cd08444 PBP2_Cbl The C-termina 57.2 27 0.00058 29.0 5.3 41 196-237 16-56 (198)
154 cd08438 PBP2_CidR The C-termin 56.9 25 0.00054 28.4 5.0 42 196-238 16-57 (197)
155 cd08445 PBP2_BenM_CatM_CatR Th 56.6 25 0.00053 29.1 5.0 39 197-236 18-56 (203)
156 cd08448 PBP2_LTTR_aromatics_li 55.8 24 0.00053 28.4 4.8 40 197-237 17-56 (197)
157 TIGR03414 ABC_choline_bnd chol 55.6 40 0.00087 32.3 6.9 189 66-288 8-233 (290)
158 PRK03601 transcriptional regul 55.5 71 0.0015 29.4 8.3 60 64-148 87-146 (275)
159 cd08443 PBP2_CysB The C-termin 55.1 1.2E+02 0.0026 25.1 10.8 135 68-233 2-148 (198)
160 cd08434 PBP2_GltC_like The sub 53.3 34 0.00074 27.4 5.2 41 197-238 17-57 (195)
161 cd08412 PBP2_PAO1_like The C-t 53.2 1.2E+02 0.0026 24.4 16.5 140 67-239 1-151 (198)
162 cd08432 PBP2_GcdR_TrpI_HvrB_Am 53.1 28 0.00061 28.1 4.7 135 67-239 1-148 (194)
163 cd08421 PBP2_LTTR_like_1 The C 52.8 24 0.00053 28.7 4.3 41 197-238 17-57 (198)
164 cd08451 PBP2_BudR The C-termin 51.1 34 0.00073 27.7 4.9 41 196-237 17-57 (199)
165 cd08433 PBP2_Nac The C-teminal 50.8 36 0.00078 27.7 5.1 40 197-237 17-56 (198)
166 cd08422 PBP2_CrgA_like The C-t 50.8 56 0.0012 26.2 6.1 54 67-148 2-55 (197)
167 cd08420 PBP2_CysL_like C-termi 50.8 38 0.00083 27.2 5.1 41 196-237 16-56 (201)
168 cd08423 PBP2_LTTR_like_6 The C 50.0 33 0.00072 27.7 4.7 42 196-238 16-57 (200)
169 PF03900 Porphobil_deamC: Porp 49.8 10 0.00022 29.2 1.5 16 300-315 2-17 (74)
170 TIGR03339 phn_lysR aminoethylp 49.3 70 0.0015 28.6 7.1 54 65-146 86-139 (279)
171 PRK11716 DNA-binding transcrip 49.1 38 0.00082 30.1 5.3 39 198-237 85-123 (269)
172 cd08436 PBP2_LTTR_like_3 The C 49.1 38 0.00082 27.2 4.9 42 196-238 16-57 (194)
173 cd08426 PBP2_LTTR_like_5 The C 47.4 33 0.00071 27.9 4.3 40 197-237 17-56 (199)
174 cd08414 PBP2_LTTR_aromatics_li 47.2 42 0.00092 27.0 4.9 41 196-237 16-56 (197)
175 cd08435 PBP2_GbpR The C-termin 47.0 38 0.00083 27.3 4.6 41 196-237 16-56 (201)
176 PRK13348 chromosome replicatio 46.1 2.4E+02 0.0052 25.8 12.2 59 63-147 87-145 (294)
177 PF03466 LysR_substrate: LysR 45.8 34 0.00075 28.1 4.2 43 197-240 23-65 (209)
178 PRK09906 DNA-binding transcrip 45.8 2.4E+02 0.0052 25.8 13.4 140 65-238 89-243 (296)
179 PRK15092 DNA-binding transcrip 45.7 2.7E+02 0.0059 26.4 14.8 60 63-147 96-155 (310)
180 cd08417 PBP2_Nitroaromatics_li 45.2 48 0.001 26.9 4.9 41 197-238 17-57 (200)
181 cd08457 PBP2_OccR The C-termin 44.7 36 0.00079 27.8 4.2 41 196-237 16-56 (196)
182 PRK11482 putative DNA-binding 44.1 1.1E+02 0.0023 29.1 7.8 132 64-231 115-259 (317)
183 PRK14498 putative molybdopteri 44.1 2.4E+02 0.0052 30.0 11.1 53 65-147 416-468 (633)
184 PRK04056 Maf-like protein; Rev 44.1 23 0.00051 32.2 3.2 23 190-212 3-25 (180)
185 cd08428 PBP2_IciA_ArgP The C-t 43.9 82 0.0018 25.7 6.2 138 67-238 1-151 (195)
186 cd08470 PBP2_CrgA_like_1 The C 43.8 60 0.0013 26.4 5.3 29 67-96 2-30 (197)
187 cd08459 PBP2_DntR_NahR_LinR_li 43.6 37 0.00081 27.8 4.1 41 197-238 17-57 (201)
188 PRK00078 Maf-like protein; Rev 43.5 24 0.00052 32.3 3.2 24 189-212 3-26 (192)
189 cd08461 PBP2_DntR_like_3 The C 43.2 33 0.00071 28.0 3.7 41 196-237 16-56 (198)
190 PRK11062 nhaR transcriptional 43.0 2.8E+02 0.006 25.7 13.2 141 64-234 91-240 (296)
191 cd08425 PBP2_CynR The C-termin 43.0 48 0.001 26.9 4.6 41 196-237 17-57 (197)
192 cd08460 PBP2_DntR_like_1 The C 42.6 47 0.001 27.4 4.6 39 197-237 17-55 (200)
193 PRK04694 Maf-like protein; Rev 42.5 26 0.00056 32.1 3.2 23 190-212 3-25 (190)
194 cd08474 PBP2_CrgA_like_5 The C 42.1 89 0.0019 25.5 6.1 54 66-147 3-56 (202)
195 TIGR03339 phn_lysR aminoethylp 42.0 55 0.0012 29.3 5.2 38 198-236 102-139 (279)
196 PRK12679 cbl transcriptional r 40.5 61 0.0013 30.5 5.5 42 196-238 109-150 (316)
197 TIGR02136 ptsS_2 phosphate bin 40.1 33 0.00071 32.4 3.6 47 190-237 39-91 (287)
198 cd08462 PBP2_NodD The C-termin 39.7 41 0.00089 27.8 3.8 38 198-237 18-55 (200)
199 cd08485 PBP2_ClcR The C-termin 38.7 59 0.0013 27.0 4.6 41 196-237 17-57 (198)
200 cd08437 PBP2_MleR The substrat 38.6 59 0.0013 26.5 4.5 42 196-238 16-57 (198)
201 PRK03601 transcriptional regul 38.5 62 0.0013 29.8 5.1 41 196-237 105-145 (275)
202 PRK00148 Maf-like protein; Rev 37.9 34 0.00073 31.5 3.2 24 189-212 3-26 (194)
203 cd08480 PBP2_CrgA_like_10 The 37.9 86 0.0019 25.8 5.4 53 67-147 2-54 (198)
204 cd08481 PBP2_GcdR_like The C-t 37.8 87 0.0019 25.2 5.4 53 67-147 1-53 (194)
205 cd08475 PBP2_CrgA_like_6 The C 37.5 1.6E+02 0.0035 23.7 6.9 29 67-96 2-30 (199)
206 PRK02478 Maf-like protein; Rev 37.0 35 0.00076 31.5 3.2 24 189-212 5-28 (199)
207 PRK14363 Maf-like protein; Pro 37.0 34 0.00075 31.8 3.2 24 189-212 3-26 (204)
208 TIGR00172 maf MAF protein. Thi 37.0 38 0.00083 30.9 3.4 33 187-222 3-35 (183)
209 cd08471 PBP2_CrgA_like_2 The C 36.9 1.4E+02 0.0031 24.1 6.6 53 67-147 2-54 (201)
210 PRK00032 Maf-like protein; Rev 36.7 36 0.00077 31.3 3.2 24 189-212 4-27 (190)
211 PRK00234 Maf-like protein; Rev 36.5 38 0.00081 31.1 3.3 24 189-212 4-27 (192)
212 PRK07377 hypothetical protein; 35.7 1.3E+02 0.0029 28.0 6.7 58 64-146 73-135 (184)
213 cd08419 PBP2_CbbR_RubisCO_like 34.7 62 0.0013 26.0 4.0 39 198-237 17-55 (197)
214 cd08468 PBP2_Pa0477 The C-term 34.4 58 0.0013 26.9 3.9 41 197-238 17-57 (202)
215 PRK14361 Maf-like protein; Pro 33.9 42 0.00092 30.7 3.2 23 190-212 2-24 (187)
216 PRK04425 Maf-like protein; Rev 33.9 43 0.00093 30.9 3.2 24 189-212 7-30 (196)
217 PRK01839 Maf-like protein; Rev 33.7 43 0.00092 31.2 3.2 35 188-225 11-45 (209)
218 PRK14368 Maf-like protein; Pro 33.6 43 0.00093 30.9 3.2 24 189-212 7-30 (193)
219 PRK00884 Maf-like protein; Rev 33.4 46 0.001 30.7 3.4 24 189-212 4-27 (194)
220 PRK14365 Maf-like protein; Pro 33.3 40 0.00086 31.1 2.9 24 189-212 4-28 (197)
221 cd00555 Maf Nucleotide binding 32.7 43 0.00092 30.3 3.0 31 190-223 2-32 (180)
222 PRK14362 Maf-like protein; Pro 32.6 48 0.001 30.9 3.3 25 188-212 13-37 (207)
223 PRK03635 chromosome replicatio 31.5 2.6E+02 0.0056 25.8 8.1 57 65-147 89-145 (294)
224 PF02545 Maf: Maf-like protein 31.3 32 0.0007 31.5 2.0 31 190-223 4-34 (195)
225 PRK14367 Maf-like protein; Pro 31.1 50 0.0011 30.6 3.2 24 189-212 4-27 (202)
226 cd08476 PBP2_CrgA_like_7 The C 31.0 1.4E+02 0.003 23.9 5.5 27 67-96 2-28 (197)
227 cd08472 PBP2_CrgA_like_3 The C 31.0 1.6E+02 0.0034 23.9 5.9 29 67-96 2-30 (202)
228 PRK09508 leuO leucine transcri 30.9 90 0.002 29.2 5.0 42 196-238 128-169 (314)
229 PRK10341 DNA-binding transcrip 30.9 1.1E+02 0.0023 28.7 5.4 41 197-238 114-154 (312)
230 cd08477 PBP2_CrgA_like_8 The C 30.4 1.5E+02 0.0033 23.9 5.7 29 67-96 2-30 (197)
231 PRK11119 proX glycine betaine 29.8 1.6E+02 0.0034 29.1 6.6 56 64-145 27-83 (331)
232 PRK10837 putative DNA-binding 29.3 1.1E+02 0.0024 27.7 5.1 41 196-237 105-145 (290)
233 cd08478 PBP2_CrgA The C-termin 29.1 44 0.00095 27.3 2.3 37 197-237 20-56 (199)
234 PRK00648 Maf-like protein; Rev 28.8 57 0.0012 29.9 3.1 24 189-212 5-28 (191)
235 TIGR00787 dctP tripartite ATP- 28.8 4.6E+02 0.01 24.1 11.4 65 180-250 129-194 (257)
236 PRK12683 transcriptional regul 28.6 1.2E+02 0.0025 28.6 5.3 39 197-236 110-148 (309)
237 PRK12684 transcriptional regul 28.4 1.2E+02 0.0026 28.5 5.3 40 197-237 110-149 (313)
238 cd08469 PBP2_PnbR The C-termin 28.2 86 0.0019 26.3 4.0 41 197-238 17-57 (221)
239 PRK02141 Maf-like protein; Rev 28.0 62 0.0013 30.2 3.3 25 188-212 10-34 (207)
240 TIGR03298 argP transcriptional 27.3 3.2E+02 0.0069 25.0 7.8 143 65-243 89-245 (292)
241 PRK14364 Maf-like protein; Pro 27.1 50 0.0011 30.1 2.4 30 191-223 1-30 (181)
242 cd08479 PBP2_CrgA_like_9 The C 27.0 90 0.0019 25.4 3.8 37 196-236 17-53 (198)
243 PRK14366 Maf-like protein; Pro 27.0 69 0.0015 29.6 3.3 24 189-212 7-31 (195)
244 PRK15421 DNA-binding transcrip 26.8 97 0.0021 29.4 4.5 41 196-237 105-145 (317)
245 cd00985 Maf_Ham1 Maf_Ham1. Maf 26.2 70 0.0015 26.5 3.0 23 190-212 2-25 (131)
246 PRK12682 transcriptional regul 26.0 1.2E+02 0.0025 28.3 4.8 40 197-237 110-149 (309)
247 PRK09906 DNA-binding transcrip 25.9 95 0.0021 28.4 4.1 41 197-238 107-147 (296)
248 PRK09791 putative DNA-binding 25.7 95 0.0021 28.7 4.1 40 197-237 112-151 (302)
249 TIGR02424 TF_pcaQ pca operon t 25.7 1.4E+02 0.003 27.4 5.2 40 196-236 109-148 (300)
250 COG4623 Predicted soluble lyti 24.8 1E+02 0.0022 32.3 4.4 150 64-244 21-190 (473)
251 COG3265 GntK Gluconate kinase 24.4 1E+02 0.0023 28.2 3.9 43 188-231 69-115 (161)
252 PRK10094 DNA-binding transcrip 24.3 1.3E+02 0.0028 28.2 4.8 39 197-236 110-148 (308)
253 PF04422 FrhB_FdhB_N: Coenzyme 23.6 67 0.0014 25.3 2.3 24 125-148 20-43 (82)
254 PRK01526 Maf-like protein; Rev 23.3 86 0.0019 29.2 3.3 24 189-212 10-34 (205)
255 PRK11074 putative DNA-binding 23.1 1.2E+02 0.0027 28.0 4.3 41 196-237 108-148 (300)
256 PRK11242 DNA-binding transcrip 22.7 1.3E+02 0.0027 27.5 4.2 40 197-237 108-147 (296)
257 COG0583 LysR Transcriptional r 22.6 5.5E+02 0.012 22.8 8.4 58 66-150 92-149 (297)
258 PRK11151 DNA-binding transcrip 22.5 1.5E+02 0.0033 27.3 4.8 40 198-238 109-148 (305)
259 cd08428 PBP2_IciA_ArgP The C-t 22.1 1.5E+02 0.0033 24.1 4.3 39 197-237 17-55 (195)
260 COG1732 OpuBC Periplasmic glyc 21.1 2.5E+02 0.0054 28.1 6.1 192 63-287 30-267 (300)
261 PRK12680 transcriptional regul 20.8 1.7E+02 0.0036 28.1 4.8 42 196-238 109-150 (327)
No 1
>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism]
Probab=100.00 E-value=1.4e-90 Score=660.56 Aligned_cols=239 Identities=50% Similarity=0.774 Sum_probs=231.2
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
+++||||||+|+||+|||++|+++|++.||++ +|||++|+|+||+++|+||+++||||+||||||+||++|+||+|
T Consensus 1 ~~~irIgTR~S~LAl~Qa~~V~~~L~~~~p~~----~~ei~~i~T~GD~i~d~pL~~iGgkGlFtkEle~all~g~~DiA 76 (307)
T COG0181 1 MMKLRIGTRGSKLALAQANEVIERLKAAYPDL----EVEIVTIKTKGDRILDKPLSKIGGKGLFTKELEQALLEGEIDIA 76 (307)
T ss_pred CCceEEecCCCHHHHHHHHHHHHHHHHhCCCc----eEEEEEEecccchhccchHHHcCCcEEEHHHHHHHHHcCCCCEE
Confidence 46899999999999999999999999999987 59999999999999999999999999999999999999999999
Q ss_pred EeeCCCCCCCCCCCceeeeecCCCCCcceeeccCccCcccCCCCCEEecCChHHHHHHHhhCCCCEEEeccCCCHHHHHh
Q 020472 145 VHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLR 224 (326)
Q Consensus 145 VHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~ 224 (326)
||||||||+++|+||.|+||++|+||||+||++++.+|.+||+|++|||||+||++||+++|||++|+ ++||||+|||+
T Consensus 77 VHSlKDvP~~~p~gL~laai~~R~dprDalVs~~~~~l~~LP~Ga~VGTSSlRR~aql~~~rPdl~i~-~lRGNVdTRL~ 155 (307)
T COG0181 77 VHSLKDVPTELPEGLVLAAIPEREDPRDALVSRDGYDLEELPEGAVVGTSSLRRQAQLKALRPDLKIE-PLRGNVDTRLR 155 (307)
T ss_pred EeecccCCccCCCCceEEEecCCCChhheEEECCCCchhhCCCCCccccchHHHHHHHHHhCCCCeEE-eccCcHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999998 99999999999
Q ss_pred hhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhhccccccccccccccchhHHH
Q 020472 225 KLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKL 304 (326)
Q Consensus 225 KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~~~~~~~~n~~~~~~~~c~~~ 304 (326)
||++|+|||||||+|||+|||+.++++++|+|++|+|||||||||||||++|+++.++|+.++ +.+ +..|+..
T Consensus 156 KL~~g~yDAIILA~AGL~RLgl~~~~~~~l~p~~~~PA~gQGal~ie~R~~d~~~~~ll~~i~-----~~~--t~~~v~a 228 (307)
T COG0181 156 KLDEGEYDAIILAAAGLKRLGLENRITEILDPEEFLPAPGQGALAIECRAGDEKVLELLAELN-----DED--TRICVTA 228 (307)
T ss_pred HhhcCCccHHHHHHHHHHhcCCcccceeecChhhcCCCCCCceEEEEEecCcHHHHHHHHhcc-----Cch--HHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999995 222 3789999
Q ss_pred HHHHHhhhchh
Q 020472 305 HFGFLNLVELR 315 (326)
Q Consensus 305 er~~l~~l~~~ 315 (326)
||.|++.|++|
T Consensus 229 ERa~l~~L~gg 239 (307)
T COG0181 229 ERAFLRELEGG 239 (307)
T ss_pred HHHHHHhhCCC
Confidence 99999999987
No 2
>PLN02691 porphobilinogen deaminase
Probab=100.00 E-value=3.4e-89 Score=662.22 Aligned_cols=255 Identities=74% Similarity=1.049 Sum_probs=241.4
Q ss_pred hhhhhccccc-----cCCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccc
Q 020472 53 GLVRASAAVE-----TKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGL 127 (326)
Q Consensus 53 ~~~~~~~~~~-----~~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGl 127 (326)
+.++|.+|++ +.+++||||||+|+||+|||++|+++|++.+|++.+++++||++|+|+||+++++||+++||||+
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~irIGTR~S~LAl~Qt~~V~~~L~~~~p~~~~~~~~eiv~i~T~GD~~~d~pL~~iGgkGl 103 (351)
T PLN02691 24 AVVRAAVAVEASSGKTDVAPIRIGTRGSPLALAQAYETRDLLKAAHPELAEEGALEIVIIKTTGDKILDQPLADIGGKGL 103 (351)
T ss_pred ceeeccccccccCcccCCceEEEEeCCcHHHHHHHHHHHHHHHHhCCCcCCCCCEEEEEEeecCCccccchHHHcCCceE
Confidence 3677888887 34578999999999999999999999999999885445699999999999999999999999999
Q ss_pred cHHHHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCccCcccCCCCCEEecCChHHHHHHHhhCC
Q 020472 128 FTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYP 207 (326)
Q Consensus 128 FtkELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTSS~RR~aQL~~~~P 207 (326)
||||||+||++|+||||||||||||+++|+||.|+||++|+||||+||++++++|++||+|++|||||+||++||+++||
T Consensus 104 Ftkele~aLl~g~iDiAVHSlKDlP~~l~~gl~i~Avl~RedprDvLv~~~~~~L~~Lp~ga~IGTSS~RR~aql~~~rP 183 (351)
T PLN02691 104 FTKEIDDALLSGRIDIAVHSMKDVPTYLPEGTILPCNLPREDVRDAFISLKAKSLAELPAGSVVGTASLRRQSQILHKYP 183 (351)
T ss_pred eHHHHHHHHHcCCCCEEEeccccCCCCCCCCcEEEEEcCCCCCceEEEECCCCChhHCCCCCEeccCcHHHHHHHHHHCC
Confidence 99999999999999999999999999999999999999999999999999989999999999999999999999999999
Q ss_pred CCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhhccc
Q 020472 208 SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQ 287 (326)
Q Consensus 208 dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~~~~ 287 (326)
|++|+ ++||||+|||+||++|+|||||||+|||+|||++++++++|++++|+||||||+||||||++|+++.++|+.++
T Consensus 184 dl~v~-~iRGNVdTRL~KL~~geyDaiILA~AGL~RLgl~~~i~~~l~~~~~~PA~gQGaLaVe~r~~d~~~~~ll~~in 262 (351)
T PLN02691 184 HLKVV-NFRGNVQTRLRKLQEGVVDATLLALAGLKRLDMTEHATSILSTDEMLPAVAQGAIGIACRTDDDKMLEYLASLN 262 (351)
T ss_pred CCEEE-eccCCHHHHHHHhcCCCCCeeehHHHHHHhCCCcccccEecchhhcCCccccceEEEEEecCCHHHHHHHHHCC
Confidence 99999 99999999999999999999999999999999999999999999999999999999999999999999999995
Q ss_pred cccccccccccchhHHHHHHHHhhhchh
Q 020472 288 ASILNTFNCSGKLCYKLHFGFLNLVELR 315 (326)
Q Consensus 288 ~~~~n~~~~~~~~c~~~er~~l~~l~~~ 315 (326)
+ . .+..|+..||+||+.|++|
T Consensus 263 d-----~--~T~~~~~aER~~L~~L~Gg 283 (351)
T PLN02691 263 H-----E--ETRLAVACERAFLAALDGS 283 (351)
T ss_pred C-----H--HHHHHHHHHHHHHHHhCCC
Confidence 2 2 2378899999999999988
No 3
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=100.00 E-value=3.2e-89 Score=650.22 Aligned_cols=236 Identities=50% Similarity=0.723 Sum_probs=228.2
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||||+|+||+|||++|+++|++.||++ ++|+++|+|+||+++++||+++||||+||||||+||++|+|||||||
T Consensus 1 i~IgTR~S~LAl~Qa~~V~~~L~~~~p~~----~~ei~~i~T~GD~~~~~~L~~iGgkGlFtkele~aLl~g~iDiAVHS 76 (292)
T TIGR00212 1 LRIGTRGSKLALAQANLVREQLKAVYPEL----DTEIVIIKTTGDKIQDKPLYDIGGKGLFTKELEQALLDGEIDLAVHS 76 (292)
T ss_pred CEEEcCCCHHHHHHHHHHHHHHHHhCCCc----eEEEEEEeeeCcccccCcHHHcCCceeeHHHHHHHHhcCCCCEEEec
Confidence 58999999999999999999999999987 59999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCceeeeecCCCCCcceeeccCccCcccCCCCCEEecCChHHHHHHHhhCCCCEEEeccCCCHHHHHhhhc
Q 020472 148 MKDVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLN 227 (326)
Q Consensus 148 lKDlPt~lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~ 227 (326)
|||||+++|+||+|+||++|+||||+||++++.++.+||+|++|||||+||++||+++|||++|+ ++||||+|||+||+
T Consensus 77 lKDlPt~lp~gl~i~av~~RedprD~lv~~~~~~l~~Lp~ga~VGTsS~RR~aql~~~rPdl~i~-~iRGNV~TRL~KL~ 155 (292)
T TIGR00212 77 LKDVPTVLPEGLEIAAVLKREDPRDVLVSRKYLSLDSLPQGAKVGTSSLRRKAQLKAIRPDLKIE-PLRGNIDTRLRKLD 155 (292)
T ss_pred cccCCCCCCCCcEEEEEecCCCCceEEEECCCCChhHCCCCCEeccCCHHHHHHHHHHCCCCEEE-ECcCCHHHHHHHhc
Confidence 99999999999999999999999999999988899999999999999999999999999999999 99999999999999
Q ss_pred cCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhhccccccccccccccchhHHHHHH
Q 020472 228 ERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKLHFG 307 (326)
Q Consensus 228 ~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~~~~~~~~n~~~~~~~~c~~~er~ 307 (326)
+|+|||||||+|||+|||+.++++++||+++|+||||||+||||||++|+++.++|+.++. . .+..|+..||.
T Consensus 156 ~g~~DaiiLA~AGL~RLgl~~~i~~~l~~~~~~PA~gQGalaIe~r~~d~~~~~ll~~l~d-----~--~t~~~~~aER~ 228 (292)
T TIGR00212 156 EGEYDAIILAEAGLKRLGLEDVITEVLDPEVMLPAPGQGAIAVECRKDDTEIKEILKEINH-----P--PTRVEATAERA 228 (292)
T ss_pred CCCCCEeehHhhHHHhCCCccccccccChhhcCCccccceEEEEEecCCHHHHHHHHHcCC-----H--HHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999852 2 23789999999
Q ss_pred HHhhhchh
Q 020472 308 FLNLVELR 315 (326)
Q Consensus 308 ~l~~l~~~ 315 (326)
||+.|++|
T Consensus 229 ~l~~L~gg 236 (292)
T TIGR00212 229 FLKELGGG 236 (292)
T ss_pred HHHHhCCC
Confidence 99999987
No 4
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=100.00 E-value=8.6e-89 Score=648.03 Aligned_cols=239 Identities=50% Similarity=0.758 Sum_probs=230.6
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
+++||||||+|+||++||++|+++|++.+|++ ++|+++|+|+||+++++||+++||||+||||||+||++|+||||
T Consensus 2 ~~~irIGtR~S~LAl~Qt~~V~~~L~~~~p~~----~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiA 77 (295)
T PRK00072 2 MRKIRIGTRGSKLALWQAEWVKDRLKAAHPGL----EVELVPIKTKGDKILDVPLAKIGGKGLFVKELEEALLEGEIDIA 77 (295)
T ss_pred CccEEEEeCCCHHHHHHHHHHHHHHHHHCCCC----eEEEEEeeccCcccccccHHHcCCcceeHHHHHHHHHcCCCCEE
Confidence 56799999999999999999999999999987 59999999999999999999999999999999999999999999
Q ss_pred EeeCCCCCCCCCCCceeeeecCCCCCcceeeccCccCcccCCCCCEEecCChHHHHHHHhhCCCCEEEeccCCCHHHHHh
Q 020472 145 VHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLR 224 (326)
Q Consensus 145 VHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~ 224 (326)
||||||||+++|+||.|+||++|+||||+||++++.++.+||+|++|||||+||++||+++|||++|+ ++||||+|||+
T Consensus 78 VHSlKDlP~~l~~gl~i~avl~R~dprDvlv~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~~Pdl~~~-~iRGNV~TRL~ 156 (295)
T PRK00072 78 VHSLKDVPTELPEGLVLAAIPEREDPRDALVSRDYKSLDDLPEGAVVGTSSLRRQAQLLALRPDLEIK-PLRGNVDTRLR 156 (295)
T ss_pred EeccCcCCCCCCCCcEEEEEecCCCCceEEEECCCCChhHCCCCCEEecCcHHHHHHHHHHCcCCEEE-ECccCHHHHHH
Confidence 99999999999999999999999999999999988999999999999999999999999999999999 99999999999
Q ss_pred hhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhhccccccccccccccchhHHH
Q 020472 225 KLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKL 304 (326)
Q Consensus 225 KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~~~~~~~~n~~~~~~~~c~~~ 304 (326)
||++|+|||||||+|||+|||+.++++++|++++|+||||||+||||||++|+++.++|+.+++ . .+..|+..
T Consensus 157 KL~~g~~DaivLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGaiave~r~~d~~~~~~l~~i~d-----~--~t~~~~~a 229 (295)
T PRK00072 157 KLDEGEYDAIILAAAGLKRLGLEDRITEYLDPEEMLPAPGQGALGIECRADDEEILELLAPLNH-----E--ETRLRVTA 229 (295)
T ss_pred HhhCCCCCEeehHhhHHHHcCCccccceecChhhcCCcccccceeeeeecCCHHHHHHHHHcCC-----H--HHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999962 2 23789999
Q ss_pred HHHHHhhhchh
Q 020472 305 HFGFLNLVELR 315 (326)
Q Consensus 305 er~~l~~l~~~ 315 (326)
||+||+.|++|
T Consensus 230 ER~~L~~L~gg 240 (295)
T PRK00072 230 ERAFLRALEGG 240 (295)
T ss_pred HHHHHHHhCCC
Confidence 99999999987
No 5
>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=100.00 E-value=1.8e-88 Score=645.00 Aligned_cols=236 Identities=53% Similarity=0.783 Sum_probs=228.2
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
||||||+|+||+|||++|+++|++.+|++ ++|+++|+|+||+++++||+++||||+||||||+||++|+|||||||
T Consensus 1 irIgtR~S~LAl~Qa~~V~~~L~~~~p~~----~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVHS 76 (292)
T cd00494 1 IRIGTRKSKLALIQTNKVIEKLKELCPGI----EVEIVIIKTTGDKILDKPLAKIGGKGLFTKELEEALLNGEIDLAVHS 76 (292)
T ss_pred CEEEcCCCHHHHHHHHHHHHHHHHhCCCC----eEEEEEEEecCcccccccHHHcCCcceeHHHHHHHHHcCCCCEEEec
Confidence 68999999999999999999999999987 59999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCceeeeecCCCCCcceeeccCccCcccCCCCCEEecCChHHHHHHHhhCCCCEEEeccCCCHHHHHhhhc
Q 020472 148 MKDVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLN 227 (326)
Q Consensus 148 lKDlPt~lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~ 227 (326)
|||||+++|+||.|+||++|+||||+||++++.++.+||+|++|||||+||++||+++|||++|+ ++||||+|||+||+
T Consensus 77 lKDlP~~lp~gl~i~av~~RedprDvlv~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~rpdl~~~-~iRGNV~TRL~KL~ 155 (292)
T cd00494 77 LKDVPTELPEGLVLGAIPKREDPRDALVSRNGSSLEDLPAGSVVGTSSLRRQAQLKRKRPDLKFE-PLRGNVDTRLRKLD 155 (292)
T ss_pred cccCCCCCCCCcEEEEEecCCCCceEEEECCCCChhHCCCCCEEecCCHHHHHHHHHHCCCCEEE-EcCCCHHHHHHHhc
Confidence 99999999999999999999999999999988899999999999999999999999999999999 99999999999999
Q ss_pred cCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhhccccccccccccccchhHHHHHH
Q 020472 228 ERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKLHFG 307 (326)
Q Consensus 228 ~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~~~~~~~~n~~~~~~~~c~~~er~ 307 (326)
+|+|||||||+|||+|||+.++++++|++++|+||||||+||||||++|+++.++|+.+++ . .+..|+..||.
T Consensus 156 ~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~i~d-----~--~t~~~~~aER~ 228 (292)
T cd00494 156 EGEYDAIILAAAGLKRLGLEDRITQYLSPEVMLPAVGQGALAIECRKGDEELLALLKPLNH-----E--ETALCVLAERA 228 (292)
T ss_pred CCCCCEeehHhhHHHHcCCcccCccccCccccCCccccceEEEEEecCCHHHHHHHHHCCC-----H--HHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999962 2 23789999999
Q ss_pred HHhhhchh
Q 020472 308 FLNLVELR 315 (326)
Q Consensus 308 ~l~~l~~~ 315 (326)
||+.|++|
T Consensus 229 ~L~~L~gg 236 (292)
T cd00494 229 FLRELEGG 236 (292)
T ss_pred HHHHhCCC
Confidence 99999998
No 6
>PF01379 Porphobil_deam: Porphobilinogen deaminase, dipyromethane cofactor binding domain; InterPro: IPR022417 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the N-terminal domains 1 and 2 of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this domain consists of a duplication of two similar intertwined domains with three layers of (a/b/a) each. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A 3EQ1_B 3ECR_A.
Probab=100.00 E-value=5.3e-86 Score=605.29 Aligned_cols=213 Identities=52% Similarity=0.833 Sum_probs=167.8
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+||||||+|+||++||++|+++|++.||++ +||+++|+|+||++++.||+++||||+||||||+||++|+||||||
T Consensus 1 ~irIGtR~S~LAl~Qa~~V~~~L~~~~P~~----~~ei~~i~T~GD~~~~~~L~~~ggkg~Ftkele~aLl~g~iDiAVH 76 (215)
T PF01379_consen 1 KIRIGTRGSKLALAQAEMVIDRLKKAFPDL----EFEIVTIKTTGDRDLDRPLSKIGGKGLFTKELEEALLDGEIDIAVH 76 (215)
T ss_dssp -EEEEEESSHHHHHHHHHHHHHHHHHSTTS----EEEEEEE--CCHH--------TT--HCCCHHHHHHHHTTS-SEEEE
T ss_pred CEEEEeCCCHHHHHHHHHHHHHHHHhCCCc----eEEEEEccCCCCcccccchhhcCCccHHHHHHHHHHHcCCccEEEe
Confidence 589999999999999999999999999997 5999999999999999999999999999999999999999999999
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeec--cCccCcccCCCCCEEecCChHHHHHHHhhCCCCEEEeccCCCHHHHHh
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFIS--LSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLR 224 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~--~~~~~l~dLp~ga~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~ 224 (326)
||||||+++|+||.|+||++|+||||+||+ ++++++++||+|++|||||+||++||+++|||++|+ ++||||+|||+
T Consensus 77 SlKDlP~~l~~gl~iaav~~R~dprD~Lv~~~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~~pdl~~~-~iRGNv~TRL~ 155 (215)
T PF01379_consen 77 SLKDLPTELPEGLVIAAVLKREDPRDVLVSRGRDGKSLEDLPKGARIGTSSLRRRAQLKRLRPDLEVV-PIRGNVDTRLR 155 (215)
T ss_dssp EGGGS-SS--TTEEEEEE-------EEEEE-GCTTSSCCCS-TT-EEE---HHHHHHHHHH-TTSEEE----S-HHHHHH
T ss_pred ccccCCCCCCCCceEeccCCCCCCccEEEEecCCCCChHHCccccccCCCCHHHHHHHHHhccCCeEE-EecCCHHHHHH
Confidence 999999999999999999999999999999 567899999999999999999999999999999999 99999999999
Q ss_pred hhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhh
Q 020472 225 KLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTT 284 (326)
Q Consensus 225 KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~ 284 (326)
||++|+|||||||+|||+|||++++++++|++++|+|||||||||||||++|+++.++|+
T Consensus 156 KL~~g~~daiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~llK 215 (215)
T PF01379_consen 156 KLDEGEYDAIILAAAGLKRLGLEDRISEILDPEEMLPAPGQGALAVECRKDDEEIIELLK 215 (215)
T ss_dssp HHHCTS-SEEEEEHHHHHHCT-GGGESEEE-TTTS-B-TTTT-EEEEEETT-HHHHHHH-
T ss_pred HhcccCCCEEEhhhChhhhccccceeeeecCchhcCCCCCCeEEEEEEecCcHHHHHHhC
Confidence 999999999999999999999999999999999999999999999999999999999885
No 7
>PRK01066 porphobilinogen deaminase; Provisional
Probab=100.00 E-value=1.3e-83 Score=593.84 Aligned_cols=215 Identities=29% Similarity=0.379 Sum_probs=208.7
Q ss_pred cCCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCc
Q 020472 63 TKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQID 142 (326)
Q Consensus 63 ~~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iD 142 (326)
..+++||||||+|+||+|||++|.+.|++.+|++ ++||++|+|+||++++.||+++||||+||||||+||++|+||
T Consensus 13 ~~~~~irIgTR~S~LAl~Qa~~v~~~L~~~~p~~----~~ei~~i~T~GD~~~~~~L~~iGgkGlFtkele~aLl~g~iD 88 (231)
T PRK01066 13 LGKRPLRIASRQSSLAVAQVHECLRLLRSFFPKL----WFQISTTTTQGDLDQKTPLHLVENTGFFTDDVDFLVLSGQCD 88 (231)
T ss_pred CCCceEEEEeCCCHHHHHHHHHHHHHHHHhCCCC----cEEEEEEeccCcccccccHHHcCCceeeHHHHHHHHHcCCCC
Confidence 4567899999999999999999999999999987 599999999999999999999999999999999999999999
Q ss_pred EEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCccCcccCCCCCEEecCChHHHHHHHhhCCCCEEEeccCCCHHHH
Q 020472 143 IAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTR 222 (326)
Q Consensus 143 iAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TR 222 (326)
||||||||||+ |+||.|+||++|+||||+||++++.++.+||+|++|||||+||++||+++|||++|+ ++||||+||
T Consensus 89 iAVHSlKDlPt--~~gl~l~av~~RedprDvLv~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~rPdl~v~-~iRGNV~TR 165 (231)
T PRK01066 89 LAIHSAKDLPE--PPKLTVVAITAGLDPRDLLVYAEKYLSQPLPRRPRIGSSSLRREELLKLLFPSGIIL-DIRGTIEER 165 (231)
T ss_pred EEEecCCcCCC--CCCCEEEEEcCCCCCceEEEECCCCchhhCCCCCEEeCChHHHHHHHHHHCCCCEEE-eCcCCHHHH
Confidence 99999999999 999999999999999999999988899999999999999999999999999999999 999999999
Q ss_pred HhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhhccc
Q 020472 223 LRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQ 287 (326)
Q Consensus 223 L~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~~~~ 287 (326)
|+||++|+|||||||+|||+|||+.++++++|++++ |||||+||||||++|+++.++|+.++
T Consensus 166 L~KL~~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~~---A~gQGalaie~R~~d~~~~~ll~~i~ 227 (231)
T PRK01066 166 LKLLEEKKYDAIVVAKAAVLRLGLRLPYTKELPPPY---HPLQGRLAITASKHIRSWKGLFLPLG 227 (231)
T ss_pred HHHhcCCCCCchhhHHHHHHhcCCcccceeECCCCC---CCCCCeEEEEEecCCHHHHHHHHHhc
Confidence 999999999999999999999999999999999984 99999999999999999999999986
No 8
>KOG2892 consensus Porphobilinogen deaminase [Coenzyme transport and metabolism]
Probab=100.00 E-value=4.2e-79 Score=574.67 Aligned_cols=243 Identities=53% Similarity=0.817 Sum_probs=232.1
Q ss_pred ccCCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCC
Q 020472 62 ETKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQI 141 (326)
Q Consensus 62 ~~~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~i 141 (326)
+...+.||||||+|+||++|+++|+..|+++||++ +|+|..++|+||+++++||++||+|++||||||++|.+|++
T Consensus 2 ~~~~~~irIGtRKSkLAvIQs~~v~~~Lek~YP~l----~f~I~t~~T~GDkIl~k~L~~ig~KsLfTkELE~aL~~~~~ 77 (320)
T KOG2892|consen 2 SPRTAVIRIGTRKSKLAVIQSYHVREKLEKKYPEL----AFEIITMSTTGDKILSKPLAKIGGKSLFTKELEDALINGHV 77 (320)
T ss_pred CCcceEEEecCcccchhhhhHHHHHHHHHhhCCCc----eeEEEEecccchHHhhchHhhhcccchhHHHHHHHHhcCCc
Confidence 45678899999999999999999999999999998 59999999999999999999999999999999999999999
Q ss_pred cEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC---ccCcccCCCCCEEecCChHHHHHHHhhCCCCEEEeccCCC
Q 020472 142 DIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS---AASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGN 218 (326)
Q Consensus 142 DiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~---~~~l~dLp~ga~IGTSS~RR~aQL~~~~Pdl~v~~~iRGN 218 (326)
||+|||||||||.+|+|+.|+|++||+||+|+||++. |+++.|||+|++|||||+||+|||++.||+++|+ .+|||
T Consensus 78 divVHSLKDlPT~LP~G~~ig~i~kRedp~DalV~~~~s~~kTladLP~GsVVGTSSlRR~Aql~RkyPHL~f~-~~rgn 156 (320)
T KOG2892|consen 78 DIVVHSLKDLPTYLPEGMIIGCILKREDPRDALVFLTYSAYKTLADLPAGSVVGTSSLRRKAQILRKYPHLHVE-SIRGN 156 (320)
T ss_pred cEEEEecccccccCCCCcEeccccCCCCccceEEEecccccccHhhCCCCceechHHHhHHHHHHhhCCceEEE-EecCh
Confidence 9999999999999999999999999999999999976 7899999999999999999999999999999998 89999
Q ss_pred HHHHHhhhccCC-ccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhhccccccccccccc
Q 020472 219 VQTRLRKLNERV-VQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCS 297 (326)
Q Consensus 219 V~TRL~KL~~ge-~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~~~~~~~~n~~~~~ 297 (326)
++|||+||+.+. |.|||||.|||.|+||.+++.++|.|++|+||+||||++||||.||+.+..++..++ +.|
T Consensus 157 ~~trl~kld~~~~~~~iilA~agl~rmg~~~ri~qil~p~~~~~avgqgalgie~r~~d~~m~~~l~~l~-----~~~-- 229 (320)
T KOG2892|consen 157 LQTRLSKLDGGKPFQAIILALAGLKRMGWTNRIAQILHPDEMLYAVGQGALGIECRADDDKMLTYLASLN-----DLN-- 229 (320)
T ss_pred HHHHHHhhcCCCcchhHHHHHHHHHHhhhHhHHHHhcChHHHHHHhccceeEEEEecChHHHHHHHHHhc-----ChH--
Confidence 999999999997 999999999999999999999999999999999999999999999999999999884 222
Q ss_pred cchhHHHHHHHHhhhchhH
Q 020472 298 GKLCYKLHFGFLNLVELRR 316 (326)
Q Consensus 298 ~~~c~~~er~~l~~l~~~~ 316 (326)
+..|+..||.||++|+||=
T Consensus 230 t~~~~~~eraflrtl~Ggc 248 (320)
T KOG2892|consen 230 TTLRILAERAFLRTLEGGC 248 (320)
T ss_pred HHHHHHHHHHHHHhhCCCc
Confidence 2788999999999999983
No 9
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=97.67 E-value=0.00068 Score=64.42 Aligned_cols=184 Identities=18% Similarity=0.180 Sum_probs=111.1
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
++|+||+-.+.=+. .++.+.+.|++.. ++++|++.+... .+.-+||.+|++|+..
T Consensus 31 ~~I~IG~~~~~~~~-~~~~~~~~l~~~~-----G~~Vel~~f~~~-------------------~~~~~ALa~GdID~~~ 85 (271)
T PRK11063 31 NHIKVGVIVGAEQQ-VAEVAQKVAKEKY-----GLDVELVTFNDY-------------------VLPNEALSKGDIDANA 85 (271)
T ss_pred CcEEEEeCCCChHH-HHHHHHHHHHHhc-----CCeEEEEEecCc-------------------HHHHHHHHcCCcceec
Confidence 35999998655443 4777888887653 235788777532 2466899999999965
Q ss_pred eeCCCC-C-CCCCCCceeeeecCCCCCcceee------ccCccCcccCCCCCEEecCC-h---HHHHHHHhh--------
Q 020472 146 HSMKDV-P-TYLPEKTILPCNLQREDVRDAFI------SLSAASLAELPAGSIVGTAS-L---RRKSQILHR-------- 205 (326)
Q Consensus 146 HSlKDl-P-t~lp~gL~iaAv~kReDprD~LV------~~~~~~l~dLp~ga~IGTSS-~---RR~aQL~~~-------- 205 (326)
....+. . .....|..+..+- ..++ +.+.++++|||+|++|++.+ + =|.-.+++.
T Consensus 86 ~qh~~~l~~~~~~~g~~l~~~~------~~~vvp~~~ys~~i~si~DL~~Gk~IAip~d~~n~~r~L~lL~~~Gli~l~~ 159 (271)
T PRK11063 86 FQHKPYLDQQIKDRGYKLVAVG------NTFVYPIAGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVGLIKLKD 159 (271)
T ss_pred ccCHHHHHHHHHHcCCcEEEEe------EEEEEEeeccccCCCCHHHhcCCCEEEecCCCccHHHHHHHHHHCCCEEecC
Confidence 322211 0 0001233222221 1233 23567899999999999886 2 344333332
Q ss_pred -------------CC-CCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCc-cceeeecCCCCCCCcccceeee
Q 020472 206 -------------YP-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTE-NVTNILSVDDMLPAVAQGAIGI 270 (326)
Q Consensus 206 -------------~P-dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~-~i~~~L~~~~~lPA~GQGaLAV 270 (326)
+| +++++ ++. -..=-+-|++|+.||.++..-=....|++. .-.-+++..+. +++..+
T Consensus 160 ~~~~~~t~~di~~n~~~v~~v-~~~--~~~~~~al~~g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~~~-----~~~~~~ 231 (271)
T PRK11063 160 GVGLLPTVLDIVENPKNLKIV-ELE--APQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKDS-----PYVNLI 231 (271)
T ss_pred CCCCCCCHHHHhcCCCCCEEE-ECc--HHHHHHhcccccccEEEEChHHHHHcCCCCCCCeeEECCCCC-----CeEEEE
Confidence 23 58888 665 344446678999999999877777777654 22234444332 456666
Q ss_pred EeecC---chhHHhhhhcccc
Q 020472 271 ACRSN---DEKMVPFTTHSQA 288 (326)
Q Consensus 271 e~R~d---D~~~~~lL~~~~~ 288 (326)
.+|++ ++++..+++.+++
T Consensus 232 ~v~~~~~~~~~~~~l~~a~~s 252 (271)
T PRK11063 232 VAREDNKDAENVKKFVQAYQS 252 (271)
T ss_pred EECCcccCCHHHHHHHHHHcC
Confidence 67654 4466777776654
No 10
>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=97.31 E-value=0.0052 Score=58.28 Aligned_cols=191 Identities=15% Similarity=0.087 Sum_probs=109.3
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
++|+||+-...- ..+-+.+.+.+.+.. ++++|++.+..- -+..+||.+|+||+..
T Consensus 18 ~~l~vG~~~~~~-~~~~~~~~~~~~~~~-----G~~Ve~~~f~d~-------------------~~~~~Al~~G~ID~~~ 72 (258)
T TIGR00363 18 LHIKVGVISGAE-QQVAEVAAKVAKEKY-----GLDVELVEFNDY-------------------ALPNEAVSKGDLDANA 72 (258)
T ss_pred CcEEEEeCCCCh-HHHHHHHHHHHHHhc-----CCEEEEEEeCCc-------------------HHHHHHHHcCCCCeEe
Confidence 469999986544 234445555554432 235888877531 2567999999999986
Q ss_pred eeCCCCCC--CCCCCceeeeecCCCCCcceeeccCccCcccCCCCCEEecC----ChHHHHHHHhh--------------
Q 020472 146 HSMKDVPT--YLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTA----SLRRKSQILHR-------------- 205 (326)
Q Consensus 146 HSlKDlPt--~lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTS----S~RR~aQL~~~-------------- 205 (326)
....+.=. .-..|+.+.++..=.-..=.+.+.++++++|||+|++|+.+ ..=|.-.++..
T Consensus 73 ~q~~~~l~~~~~~~g~~lv~v~~~~~~p~~~ys~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~ 152 (258)
T TIGR00363 73 FQHKPYLDQDAKAKGYKLVAVGNTFVYPLAGYSKKIKNVNELQDGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLP 152 (258)
T ss_pred cCCHHHHHHHHHhCCCcEEEEeeeEEecccccCcCCCCHHHcCCCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcC
Confidence 43222100 01234444444310000002235677899999999999865 22444444443
Q ss_pred --------CCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCcc-ceeeecCCCCCCCcccceeeeEeecC-
Q 020472 206 --------YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTEN-VTNILSVDDMLPAVAQGAIGIACRSN- 275 (326)
Q Consensus 206 --------~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~-i~~~L~~~~~lPA~GQGaLAVe~R~d- 275 (326)
.-|++++ ++-- .+=.+-|.+|+.||.++..-=+...|+... -.-+++... -+|+-.+.+|.+
T Consensus 153 t~~DI~~n~~~v~~v-el~~--~~~~~al~~g~vDaa~v~~~~~~~agl~~~~~~i~~e~~~-----~~~~n~l~~r~~~ 224 (258)
T TIGR00363 153 TVLDIVENPKKLNIT-ELET--SQLPRALDDPKVDLAVINTTYAGQVGLNPQDDGVFVEDKD-----SPYVNIIVSREDN 224 (258)
T ss_pred ChhhhhcCCCCCEEE-EcCH--HHHHHHhhcccccEEEEChHHHHHcCCCcCcCceeecCCC-----CCeeEEEEEcCCc
Confidence 4458888 5552 333467889999999986554554544321 112233322 146666777765
Q ss_pred --chhHHhhhhccccc
Q 020472 276 --DEKMVPFTTHSQAS 289 (326)
Q Consensus 276 --D~~~~~lL~~~~~~ 289 (326)
++.+.++++.+++.
T Consensus 225 ~~~~~~~~lv~~~~s~ 240 (258)
T TIGR00363 225 KDAENVKDFIQSYQSE 240 (258)
T ss_pred cCCHHHHHHHHHHcCH
Confidence 34677888777643
No 11
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=96.21 E-value=0.09 Score=49.39 Aligned_cols=146 Identities=16% Similarity=0.150 Sum_probs=84.7
Q ss_pred cCCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCc
Q 020472 63 TKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQID 142 (326)
Q Consensus 63 ~~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iD 142 (326)
....+||||.=.+.... ..-.....+++.+|++ +++++...+ | .++.++|.+|++|
T Consensus 24 ~~~~~lrIg~~~~~~~~-~l~~~~~~~~~~~p~v----~ie~~~~~~-~------------------~~~~~aL~~G~iD 79 (314)
T PRK11553 24 SSPEALRIGYQKGSIGL-VLAKSHQLLEKRFPQT----KISWVEFPA-G------------------PQMLEALNVGSID 79 (314)
T ss_pred CCCCeEEEEeCCCchHH-HHHHhhCHHHHhCCCC----eeEEEECCC-c------------------HHHHHHHHcCCCC
Confidence 34578999998775543 2233344667778875 366655421 2 2577999999999
Q ss_pred EEEeeCCCCCCCC--CCCceeeeec--CCCCCcceeeccCc---cCcccCCCCCEEecCC---hHH-HHH-HHhhC---C
Q 020472 143 IAVHSMKDVPTYL--PEKTILPCNL--QREDVRDAFISLSA---ASLAELPAGSIVGTAS---LRR-KSQ-ILHRY---P 207 (326)
Q Consensus 143 iAVHSlKDlPt~l--p~gL~iaAv~--kReDprD~LV~~~~---~~l~dLp~ga~IGTSS---~RR-~aQ-L~~~~---P 207 (326)
+++-. +.|... ..|+.+..+. ...+...++|.+++ .+++|| .|.+||++. .+. -.+ ++... .
T Consensus 80 ia~~~--~~~~~~~~~~g~~~~~v~~~~~~~~~~~lvv~~~s~i~s~~dL-~Gk~I~~~~gs~~~~~l~~~l~~~g~~~~ 156 (314)
T PRK11553 80 LGSTG--DIPPIFAQAAGADLVYVGVEPPKPKAEVILVAENSPIKTVADL-KGHKVAFQKGSSSHNLLLRALRKAGLKFT 156 (314)
T ss_pred EEccC--CHHHHHHHhCCCCEEEEEEecCCCcceEEEEeCCCCCCCHHHh-CCCEEeecCCCcHHHHHHHHHHHcCCCHH
Confidence 99854 443321 3455444432 22233346666533 467777 466777642 222 122 22221 1
Q ss_pred CCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 208 SLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 208 dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+++++ ..+...-..-|.+|++||+++..
T Consensus 157 dv~~v---~~~~~~~~~al~~G~vDa~~~~e 184 (314)
T PRK11553 157 DIQPT---YLTPADARAAFQQGNVDAWAIWD 184 (314)
T ss_pred HeEEE---ecChHHHHHHHHcCCCCEEEEcC
Confidence 33333 44666778889999999998754
No 12
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=95.84 E-value=0.21 Score=47.83 Aligned_cols=189 Identities=14% Similarity=0.131 Sum_probs=103.3
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
++|+||.-.+.-. ...+.+.+.+++.. + +++|++.+ .+ - -...+||.+|+||+.+
T Consensus 32 ~tLkVG~~~~~~~-~~~e~a~~~~k~~~-G----~~Velv~f--sd-~----------------~~~n~AL~~G~ID~n~ 86 (272)
T PRK09861 32 KHIKVGVINGAEQ-DVAEVAKKVAKEKY-G----LDVELVGF--SG-S----------------LLPNDATNHGELDANV 86 (272)
T ss_pred CcEEEEEcCCchH-HHHHHHHHHHHHcC-C----CeEEEEec--Cc-h----------------hhHHHHHHcCCcceeh
Confidence 4699999876554 45556666665422 2 24666633 11 1 1356899999999976
Q ss_pred eeCCCCCCC----CCCCceeeeecCCCCCcceeeccCccCcccCCCCCEEecCC----hHHHHHHHhhC-----------
Q 020472 146 HSMKDVPTY----LPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTAS----LRRKSQILHRY----------- 206 (326)
Q Consensus 146 HSlKDlPt~----lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTSS----~RR~aQL~~~~----------- 206 (326)
-. +.|-. -.-|..+.++..---....+-+.+.++++|||+|++|.-+. .=|.-.|+..-
T Consensus 87 ~q--h~~yl~~~~~~~g~~lv~~~~~~~~P~~~Ys~~iksl~DL~~Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~ 164 (272)
T PRK09861 87 FQ--HRPFLEQDNQAHGYKLVAVGNTFVFPMAGYSKKIKTVAQIKEGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGL 164 (272)
T ss_pred hh--hHHHHHHHHHhcCCCeEEEeEEEEEeeeccccCCCCHHHcCCCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCC
Confidence 21 11100 01233333331100000112245678999999999999874 22555544442
Q ss_pred -----------CCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccce-eeecCCCCCCCcccceeeeEeec
Q 020472 207 -----------PSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVT-NILSVDDMLPAVAQGAIGIACRS 274 (326)
Q Consensus 207 -----------Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~-~~L~~~~~lPA~GQGaLAVe~R~ 274 (326)
.+++++ ++- -.+=.+-|++|..|+.++..-=...-|+...-. -+++.. +. +++..+.+|+
T Consensus 165 ~~t~~di~~np~~l~~v-e~~--~~q~~~al~dg~vD~a~i~~~~~~~ag~~~~~~~l~~e~~---~~--~~~n~~~~r~ 236 (272)
T PRK09861 165 LPTALDITDNPRHLQIM-ELE--GAQLPRVLDDPKVDVAIISTTYIQQTGLSPVHDSVFIEDK---NS--PYVNILVARE 236 (272)
T ss_pred CCCHhHHhcCCCCCEEE-EcC--HHHhHhhccCcccCEEEEchhHHHHcCCCcccceeEEcCC---CC--CeEEEEEEcC
Confidence 357777 554 344556688999999988433222334332111 122221 12 4566666675
Q ss_pred C---chhHHhhhhccccc
Q 020472 275 N---DEKMVPFTTHSQAS 289 (326)
Q Consensus 275 d---D~~~~~lL~~~~~~ 289 (326)
+ ++.+.++++.+|+.
T Consensus 237 ~~~~~~~~~~lv~~~~s~ 254 (272)
T PRK09861 237 DNKNAENVKEFLQSYQSP 254 (272)
T ss_pred CccCCHHHHHHHHHHcCH
Confidence 4 45778888877753
No 13
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=95.45 E-value=0.19 Score=41.19 Aligned_cols=143 Identities=16% Similarity=0.212 Sum_probs=77.8
Q ss_pred HHHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc---cCcccCCCCCEEecCChH-HHHHHHhh
Q 020472 130 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTASLR-RKSQILHR 205 (326)
Q Consensus 130 kELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~---~~l~dLp~ga~IGTSS~R-R~aQL~~~ 205 (326)
.++.++|.+|++|+++-+.-.-|.. ...+......- ....+++.+++ .+++|| +|-+||+..-- -...+...
T Consensus 49 ~~~~~~l~~g~~D~~~~~~~~~~~~-~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~dL-~g~~i~~~~g~~~~~~~~~~ 124 (219)
T smart00062 49 DNLLTALKSGKIDVVAAGMTITPER-AKQVDFSDPYY--KSGQVILVRKDSPIKSLEDL-KGKKVAVVAGTTGEELLKKL 124 (219)
T ss_pred HHHHHHHHCCcccEEeccccCCHHH-Hhheeecccee--eceeEEEEecCCCCCChHHh-CCCEEEEecCccHHHHHHHh
Confidence 4678999999999999765321111 11111111110 11134444332 467777 57778775321 22334445
Q ss_pred CCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCC---CccceeeecCCCCCCCcccceeeeEeecCchhHHhh
Q 020472 206 YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSM---TENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPF 282 (326)
Q Consensus 206 ~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl---~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~l 282 (326)
.++.+++ .. ++...-+..|.+|++|++++...-+..+-. ...+ .++.+ . -..+.-+.+.++++++++.+.
T Consensus 125 ~~~~~~~-~~-~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~~~-~~~~~-~---~~~~~~~~~~~~~~~~~~~~~ 197 (219)
T smart00062 125 YPEAKIV-SY-DSQAEALAALKAGRADAAVADAPALAALVKQHGLPEL-KIVGD-P---LDTPEGYAFAVRKGDPELLDK 197 (219)
T ss_pred CCCceEE-Ec-CCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCCce-eeccC-C---CCCCcceEEEEECCCHHHHHH
Confidence 6788887 44 567888999999999999997774333211 1111 11211 1 111155667777777654444
Q ss_pred h
Q 020472 283 T 283 (326)
Q Consensus 283 L 283 (326)
+
T Consensus 198 ~ 198 (219)
T smart00062 198 I 198 (219)
T ss_pred H
Confidence 3
No 14
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=95.43 E-value=0.12 Score=52.68 Aligned_cols=150 Identities=16% Similarity=0.199 Sum_probs=84.3
Q ss_pred CCceEEEEeCCCHHHHHH-----HHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHc
Q 020472 64 KVAIIRIGTRGSPLALAQ-----AHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALIN 138 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQ-----a~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~ 138 (326)
..++|+|||..++..-.. .....+.+++....+. .+++++...+ ..++-.+|.+
T Consensus 41 ~~g~LrVg~~~~P~~~~~~~~~~~G~~~DLl~~ia~~LG--v~~e~v~~~~-------------------~~~ll~aL~~ 99 (482)
T PRK10859 41 ERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLG--VKLEIKVRDN-------------------ISQLFDALDK 99 (482)
T ss_pred hCCEEEEEEecCCCeeEecCCCcccHHHHHHHHHHHHhC--CcEEEEecCC-------------------HHHHHHHHhC
Confidence 457899999988765321 2233333333222221 2355542211 2467799999
Q ss_pred CCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc----cCcccCCCCCEEe----cCChHHHHHHHhhCCCCE
Q 020472 139 SQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA----ASLAELPAGSIVG----TASLRRKSQILHRYPSLK 210 (326)
Q Consensus 139 g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~----~~l~dLp~ga~IG----TSS~RR~aQL~~~~Pdl~ 210 (326)
|++||++-.+-.-|.. .+.+..... =-...-++|.+++ .+++|| .|.+|| |+..-.-..+...+|++.
T Consensus 100 G~iDi~~~~lt~T~eR-~~~~~FS~P--y~~~~~~lv~r~~~~~i~~l~dL-~Gk~I~V~~gS~~~~~L~~l~~~~p~i~ 175 (482)
T PRK10859 100 GKADLAAAGLTYTPER-LKQFRFGPP--YYSVSQQLVYRKGQPRPRSLGDL-KGGTLTVAAGSSHVETLQELKKKYPELS 175 (482)
T ss_pred CCCCEEeccCcCChhh-hccCcccCC--ceeeeEEEEEeCCCCCCCCHHHh-CCCeEEEECCCcHHHHHHHHHHhCCCce
Confidence 9999987766333321 122221110 0012234444322 345666 355554 444333444556789988
Q ss_pred EEecc-CCCHHHHHhhhccCCccEEeeehh
Q 020472 211 VMENF-RGNVQTRLRKLNERVVQATLLALA 239 (326)
Q Consensus 211 v~~~i-RGNV~TRL~KL~~ge~DAIILA~A 239 (326)
++ .. -.+.+.-++.|.+|++|++|.-..
T Consensus 176 ~~-~~~~~s~~e~l~aL~~G~iDa~v~d~~ 204 (482)
T PRK10859 176 WE-ESDDKDSEELLEQVAEGKIDYTIADSV 204 (482)
T ss_pred EE-ecCCCCHHHHHHHHHCCCCCEEEECcH
Confidence 76 33 368999999999999999998544
No 15
>PRK11260 cystine transporter subunit; Provisional
Probab=95.41 E-value=0.16 Score=46.40 Aligned_cols=146 Identities=14% Similarity=0.145 Sum_probs=79.9
Q ss_pred HHHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC-----ccCcccCCCCCEEecC--ChHHHHHH
Q 020472 130 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS-----AASLAELPAGSIVGTA--SLRRKSQI 202 (326)
Q Consensus 130 kELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~-----~~~l~dLp~ga~IGTS--S~RR~aQL 202 (326)
+++.++|.+|++|+++-++-.-|. ..+.+.+....-+ ...+++.++ ..++++| .|-+||+. +.- ...+
T Consensus 90 ~~~~~~l~~G~~D~~~~~~~~~~~-r~~~~~fs~p~~~--~~~~~~~~~~~~~~~~~~~dL-~g~~Igv~~G~~~-~~~l 164 (266)
T PRK11260 90 DGMLASLDSKRIDVVINQVTISDE-RKKKYDFSTPYTV--SGIQALVKKGNEGTIKTAADL-KGKKVGVGLGTNY-EQWL 164 (266)
T ss_pred HHHHHHHhcCCCCEEEeccccCHH-HHhccccCCceee--cceEEEEEcCCcCCCCCHHHc-CCCEEEEecCCcH-HHHH
Confidence 468899999999999865422222 1222222211111 112344332 1345666 56677752 222 4556
Q ss_pred HhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhh
Q 020472 203 LHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPF 282 (326)
Q Consensus 203 ~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~l 282 (326)
+..+|+.++. .... .++-++.|.+|++|++|....-+..+--.......+....+ ... -+++.++++++++.+.
T Consensus 165 ~~~~~~~~i~-~~~~-~~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~--~~~--~~~~~v~~~~~~l~~~ 238 (266)
T PRK11260 165 RQNVQGVDVR-TYDD-DPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVAGEAF--SRQ--ESGVALRKGNPDLLKA 238 (266)
T ss_pred HHhCCCCceE-ecCC-HHHHHHHHHcCCCCEEEechHHHHHHHHhCCCcceecCCcc--ccC--ceEEEEeCCCHHHHHH
Confidence 7789999887 6665 46678999999999999855432322111000001111111 222 2555668888877777
Q ss_pred hhcc
Q 020472 283 TTHS 286 (326)
Q Consensus 283 L~~~ 286 (326)
+++.
T Consensus 239 ln~~ 242 (266)
T PRK11260 239 VNQA 242 (266)
T ss_pred HHHH
Confidence 6543
No 16
>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=95.02 E-value=0.036 Score=47.15 Aligned_cols=141 Identities=16% Similarity=0.250 Sum_probs=85.7
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc-----c---CcccCCCCCEEecCChHHHH-H
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-----A---SLAELPAGSIVGTASLRRKS-Q 201 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-----~---~l~dLp~ga~IGTSS~RR~a-Q 201 (326)
++.++|.+|++|+++-.+-.-|.. .+.+.... +=-....+++.+++ . ++.+| .|.+||+..-.... .
T Consensus 49 ~~~~~l~~g~~D~~~~~~~~~~~r-~~~~~~s~--p~~~~~~~~~~~~~~~~~~~~~~~~~dl-~~~~i~~~~g~~~~~~ 124 (225)
T PF00497_consen 49 RLLEMLENGKADIIIGGLSITPER-AKKFDFSD--PYYSSPYVLVVRKGDAPPIKTIKSLDDL-KGKRIGVVRGSSYADY 124 (225)
T ss_dssp GHHHHHHTTSSSEEESSEB-BHHH-HTTEEEES--ESEEEEEEEEEETTSTCSTSSHSSGGGG-TTSEEEEETTSHHHHH
T ss_pred cccccccccccccccccccccccc-cccccccc--cccchhheeeeccccccccccccchhhh-cCcccccccchhHHHH
Confidence 466789999999998544332221 22333221 11111344444422 1 34477 67788876654443 6
Q ss_pred HHhhCC-CCEEEeccCCCHHHHHhhhccCCccEEeeehhhhc----ccCCCccceeeecCCCCCCCcccceeeeEeecCc
Q 020472 202 ILHRYP-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLK----RLSMTENVTNILSVDDMLPAVAQGAIGIACRSND 276 (326)
Q Consensus 202 L~~~~P-dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~----RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD 276 (326)
+...+| +.+++ .. .|.+.-++.|.+|++|++|....-+. +.+...... . .+...+.-+++-.+.++
T Consensus 125 l~~~~~~~~~~~-~~-~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~--~-----~~~~~~~~~~~~~~~~~ 195 (225)
T PF00497_consen 125 LKQQYPSNINIV-EV-DSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVV--I-----PPPISPSPVYFAVRKKN 195 (225)
T ss_dssp HHHHTHHTSEEE-EE-SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEE--E-----EEEEEEEEEEEEEETTT
T ss_pred hhhhccchhhhc-cc-ccHHHHHHHHhcCCeeeeeccchhhhhhhhhcccccccc--c-----ccccccceeEEeecccc
Confidence 777776 89988 54 69999999999999999999776543 333332211 1 33455555666677888
Q ss_pred hhHHhhhh
Q 020472 277 EKMVPFTT 284 (326)
Q Consensus 277 ~~~~~lL~ 284 (326)
+.+.+.++
T Consensus 196 ~~l~~~~n 203 (225)
T PF00497_consen 196 PELLEIFN 203 (225)
T ss_dssp HHHHHHHH
T ss_pred cHHHHHHH
Confidence 87766554
No 17
>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=94.75 E-value=0.27 Score=40.51 Aligned_cols=144 Identities=14% Similarity=0.203 Sum_probs=78.4
Q ss_pred HHHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc---cCcccCCCCCEEecCC-hHHHHHHHhh
Q 020472 130 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTAS-LRRKSQILHR 205 (326)
Q Consensus 130 kELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~---~~l~dLp~ga~IGTSS-~RR~aQL~~~ 205 (326)
.++.++|.+|++|+++-..-..+.. .+.+.+.. +-..++ -+++.+++ .+++|| .|.+||+.+ .-=...+...
T Consensus 48 ~~~~~~l~~g~~D~~~~~~~~~~~~-~~~~~~~~-~~~~~~-~~~~~~~~~~~~~~~dl-~g~~i~~~~~~~~~~~~~~~ 123 (218)
T cd00134 48 DGLITALKSGKVDLIAAGMTITPER-AKQVDFSD-PYYKSG-QVILVKKGSPIKSVKDL-KGKKVAVQKGSTAEKYLKKA 123 (218)
T ss_pred HHHHHHHhcCCcCEEeecCcCCHHH-HhhccCcc-cceecc-EEEEEECCCCCCChHHh-CCCEEEEEcCchHHHHHHHh
Confidence 4688999999999998776222211 11111111 111111 13333322 245666 466777641 1112345556
Q ss_pred CCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCC--ccceeeecCCCCCCCcccceeeeEeecCchhHHhhh
Q 020472 206 YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMT--ENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFT 283 (326)
Q Consensus 206 ~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~--~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL 283 (326)
++..+++ ... +.+.-+..|.+|.+|+++........+--. ..+ .+++.. ...-...+++..+.+++++...+
T Consensus 124 ~~~~~~~-~~~-~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l-~~~~~~---~~~~~~~~~~~~~~~~~~l~~~~ 197 (218)
T cd00134 124 LPEAKVV-SYD-DNAEALAALENGRADAVIVDEIALAALLKKHPPEL-KIVGPS---IDLEPLGFGVAVGKDNKELLDAV 197 (218)
T ss_pred CCcccEE-EeC-CHHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCc-EEeccc---cCCCccceEEEEcCCCHHHHHHH
Confidence 6667776 554 488999999999999999977655443211 222 222221 12344566777777665444433
No 18
>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=94.70 E-value=0.46 Score=46.52 Aligned_cols=144 Identities=15% Similarity=0.078 Sum_probs=90.6
Q ss_pred eEEEEeCCC----HHHHHHHHHH-HHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCC
Q 020472 67 IIRIGTRGS----PLALAQAHET-RNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQI 141 (326)
Q Consensus 67 ~IrIGTR~S----~LAlaQa~~V-~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~i 141 (326)
+||||.-.+ ++.++|.+-. .+.|++.. .++|++.+.+. ...+ +||.+|++
T Consensus 3 ~~~i~~~~w~G~~p~~lA~~~G~fe~~l~~~G------l~Ve~~~f~~~------------------~~~l-~Al~aG~i 57 (328)
T TIGR03427 3 KFKVCWSIYAGWMPWGYAAQQGIVDKWADKYG------ITIEVVQINDY------------------VESI-NQYTAGKF 57 (328)
T ss_pred ceEEEecCCccHHHHHHHHHcCchhhhHHHcC------CeEEEEECCCh------------------HHHH-HHHHcCCC
Confidence 577877765 4555555443 34555432 24777766431 1234 68999999
Q ss_pred cEEEeeCCCCCCC---CCCC--ceeeeecCCCCCcceeeccCccCcccCCCCCEEecC--ChHHH---HHHHhh--C-CC
Q 020472 142 DIAVHSMKDVPTY---LPEK--TILPCNLQREDVRDAFISLSAASLAELPAGSIVGTA--SLRRK---SQILHR--Y-PS 208 (326)
Q Consensus 142 DiAVHSlKDlPt~---lp~g--L~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTS--S~RR~---aQL~~~--~-Pd 208 (326)
|++.- =|.|.. ...| +.+.++....+..|++|.++.+++.|| +|-+||+. |..-- ..|+.. - .|
T Consensus 58 D~~~~--g~~~~~~~~~a~g~~~~iv~v~~~~~g~~~ivv~~i~svaDL-KGKkIav~~gs~~~~ll~~aL~~aGL~~~D 134 (328)
T TIGR03427 58 DGCTM--TNMDALTIPAAGGVDTTALIVGDFSNGNDGIVLKGGKSLADL-KGQKVNLVELSVSHYLLARALESVGLSEKD 134 (328)
T ss_pred CEEee--cCHHHHHHHHhCCCCeEEEEEEccCCCceEEEECCCCCHHHc-CCCEEeccCCChHHHHHHHHHHHcCCCHHH
Confidence 99853 444322 1344 346666666777899998888889999 78899872 33321 112221 1 46
Q ss_pred CEEEeccCCCHHHHHhhhccCCccEEeeehhhh
Q 020472 209 LKVMENFRGNVQTRLRKLNERVVQATLLALAGL 241 (326)
Q Consensus 209 l~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL 241 (326)
++++ ++. ...-..-|.+|+.||.++..--+
T Consensus 135 V~~v-~~~--~~d~~aAl~~G~VDAa~~~eP~~ 164 (328)
T TIGR03427 135 VKVV-NTS--DADIVAAFITKDVTAVVTWNPQL 164 (328)
T ss_pred eEEE-eCC--hHHHHHHHhcCCCcEEEEcCchH
Confidence 8888 774 46678889999999998844433
No 19
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=94.51 E-value=0.68 Score=41.16 Aligned_cols=148 Identities=14% Similarity=0.183 Sum_probs=78.5
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC--ccCcccCCCCCEEecC--ChHHHHHHHhhC
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS--AASLAELPAGSIVGTA--SLRRKSQILHRY 206 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~--~~~l~dLp~ga~IGTS--S~RR~aQL~~~~ 206 (326)
++.++|.+|++|+++=++---| +..+.+...... -+..-+++.++ ..++++| .|-+||.- +.- ...+...+
T Consensus 71 ~~~~~l~~g~~D~~~~~~~~~~-~r~~~~~fs~p~--~~~~~~~v~~~~~~~~~~dL-~g~~Igv~~g~~~-~~~l~~~~ 145 (243)
T PRK15007 71 SLIPSLKFRRVEAVMAGMDITP-EREKQVLFTTPY--YDNSALFVGQQGKYTSVDQL-KGKKVGVQNGTTH-QKFIMDKH 145 (243)
T ss_pred HHhHHHhCCCcCEEEEcCccCH-HHhcccceecCc--cccceEEEEeCCCCCCHHHh-CCCeEEEecCcHH-HHHHHHhC
Confidence 5778999999998754331111 112222222111 11123444432 2356666 46677652 111 23456678
Q ss_pred CCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhccc-CCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhhc
Q 020472 207 PSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRL-SMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTH 285 (326)
Q Consensus 207 Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RL-gl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~~ 285 (326)
|.++++ .. .|.+..+..|..|++|+++.-..-+... .....+ ..+......+.....-+++-++.+++++.+.++.
T Consensus 146 ~~~~~~-~~-~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ln~ 222 (243)
T PRK15007 146 PEITTV-PY-DSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNPKL-AAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNT 222 (243)
T ss_pred CCCeEE-Ec-CCHHHHHHHHHcCCCCEEEeCHHHHHHHHhcCCCc-eeecCcccccccCCcceEEEEeCCCHHHHHHHHH
Confidence 999987 54 6889999999999999999765432211 111111 1111110011112233677788888877766653
Q ss_pred c
Q 020472 286 S 286 (326)
Q Consensus 286 ~ 286 (326)
.
T Consensus 223 ~ 223 (243)
T PRK15007 223 A 223 (243)
T ss_pred H
Confidence 3
No 20
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=94.50 E-value=0.55 Score=42.20 Aligned_cols=109 Identities=12% Similarity=-0.007 Sum_probs=59.3
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCC--CCCceeeeecCCCCCcceeeccC---ccCcccCCCCCEEecC---Ch-HHHHH
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYL--PEKTILPCNLQREDVRDAFISLS---AASLAELPAGSIVGTA---SL-RRKSQ 201 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~l--p~gL~iaAv~kReDprD~LV~~~---~~~l~dLp~ga~IGTS---S~-RR~aQ 201 (326)
++-++|.+|++|+++-+.=..-... ...+.+.+.....+ ...++.+. .++++|| .|.+||+. +. .-..+
T Consensus 41 ~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~-~~~~v~~~~~~i~s~~dL-~Gk~i~~~~~~~~~~~~~~ 118 (288)
T TIGR01728 41 PALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSDNK-ATAIVVIKGSPIRTVADL-KGKRIAVPKGGSGHDLLLR 118 (288)
T ss_pred HHHHHHhcCCccccccCCcHHHHHHhcCCCEEEEEEecCCC-ceEEEECCCCCCCCHHHc-CCCEEEecCCccHHHHHHH
Confidence 4568999999999864321111111 23466655554332 34455443 2466777 57788752 22 22222
Q ss_pred HHhhC---C-CCEEEeccCCCHHHHHhhhccCCccEEeeehhhhccc
Q 020472 202 ILHRY---P-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRL 244 (326)
Q Consensus 202 L~~~~---P-dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RL 244 (326)
+.... + +.+++ . .+...-+.-|.+|+.|++++..--...+
T Consensus 119 ~l~~~G~~~~~v~~~-~--~~~~~~~~al~~g~vda~~~~~p~~~~~ 162 (288)
T TIGR01728 119 ALLKAGLSGDDVTIL-Y--LGPSDARAAFAAGQVDAWAIWEPWGSAL 162 (288)
T ss_pred HHHHcCCCccceeEE-e--cCcHHHHHHHHCCCCCEEEeccchHhHH
Confidence 22211 1 23333 2 3456678889999999999975443333
No 21
>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=94.49 E-value=1.5 Score=39.33 Aligned_cols=153 Identities=14% Similarity=0.132 Sum_probs=82.2
Q ss_pred CCceEEEEeCC--CHHHHHHH-HHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCC
Q 020472 64 KVAIIRIGTRG--SPLALAQA-HETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQ 140 (326)
Q Consensus 64 ~~~~IrIGTR~--S~LAlaQa-~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~ 140 (326)
...+|+||+-. ++....+. ..+.+.|.+.. ++ +++++.. +| -.++.++|.+|+
T Consensus 30 ~~~~l~vg~~~~~~~~~~~~~~~~l~~~l~~~~-g~----~v~~~~~---~~----------------~~~~~~~l~~g~ 85 (254)
T TIGR01098 30 VPKELNFGILPGENASNLTRRWEPLADYLEKKL-GI----KVQLFVA---TD----------------YSAVIEAMRFGR 85 (254)
T ss_pred CCCceEEEECCCCCHHHHHHHHHHHHHHHHHHh-CC----cEEEEeC---CC----------------HHHHHHHHHcCC
Confidence 34679999765 44444442 34555555432 22 3555432 11 135678999999
Q ss_pred CcEEEeeCCCCCCC-CCCC-ceeee-ecCCCC--Cc-ceeeccCc---cCcccCCCCCEEecCChH-----H--HHHHHh
Q 020472 141 IDIAVHSMKDVPTY-LPEK-TILPC-NLQRED--VR-DAFISLSA---ASLAELPAGSIVGTASLR-----R--KSQILH 204 (326)
Q Consensus 141 iDiAVHSlKDlPt~-lp~g-L~iaA-v~kReD--pr-D~LV~~~~---~~l~dLp~ga~IGTSS~R-----R--~aQL~~ 204 (326)
+|+++.+.=..+.. ...+ ..+.. +..... .. -+||.+++ ++++|| .|.+||+.... - ...++.
T Consensus 86 ~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~~i~~~~dL-~gk~I~~~~~~s~~~~~~~~~~l~~ 164 (254)
T TIGR01098 86 VDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADSPIKSLKDL-KGKTFAFGDPASTSGYLVPRYQLKK 164 (254)
T ss_pred ccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCCCCCChHHh-cCCEEEeeCCCCccchHhHHHHHHH
Confidence 99999765333311 1112 11111 111110 11 14555432 467788 48888864321 1 122343
Q ss_pred hCC------CCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcc
Q 020472 205 RYP------SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKR 243 (326)
Q Consensus 205 ~~P------dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~R 243 (326)
.+. +.+++ .-++.++-+..|.+|+.||.+.....+..
T Consensus 165 ~~~~~~~~~~~~i~--~~~~~~~~~~al~~G~~Da~~~~~~~~~~ 207 (254)
T TIGR01098 165 EGGLDADGFFSEVV--FSGSHDASALAVANGKVDAATNNSSAIGR 207 (254)
T ss_pred hcCCChHHhhhhee--ecCchHHHHHHHHcCCCCeEEecHHHHHH
Confidence 332 24554 33567888999999999999987765443
No 22
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=94.33 E-value=0.65 Score=41.27 Aligned_cols=147 Identities=12% Similarity=0.170 Sum_probs=80.6
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc----cCcccCCCCCEEecCChHH-HHHHHhh
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA----ASLAELPAGSIVGTASLRR-KSQILHR 205 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~----~~l~dLp~ga~IGTSS~RR-~aQL~~~ 205 (326)
++..+|.+|++|+++-++-. ..+..+.+.+....-. ....++.+.. .++++| +|.+||+-+--= ...+...
T Consensus 74 ~~~~~l~~G~~D~~~~~~~~-~~~r~~~~~~s~p~~~--~~~~~~~~~~~~~~~~~~dl-~g~~i~~~~g~~~~~~l~~~ 149 (250)
T TIGR01096 74 GLIPSLKAKKVDAIMATMSI-TPKRQKQIDFSDPYYA--TGQGFVVKKGSDLAKTLEDL-DGKTVGVQSGTTHEQYLKDY 149 (250)
T ss_pred HHHHHHhCCCcCEEEecCcc-CHHHhhccccccchhc--CCeEEEEECCCCcCCChHHc-CCCEEEEecCchHHHHHHHh
Confidence 56688999999999764421 1112223322221111 1233443322 245666 477887532111 3456667
Q ss_pred CC-CCEEEeccCCCHHHHHhhhccCCccEEeeehhhh----cccCCCccceeeecCCCCCCCcccce-eeeEeecCchhH
Q 020472 206 YP-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGL----KRLSMTENVTNILSVDDMLPAVAQGA-IGIACRSNDEKM 279 (326)
Q Consensus 206 ~P-dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL----~RLgl~~~i~~~L~~~~~lPA~GQGa-LAVe~R~dD~~~ 279 (326)
+| +++++ ... +.+.-+..|.+|++|++|.-..-+ .+.+..+.+. ++++ .+.+.+-+|. +++.+++++.++
T Consensus 150 ~~~~~~~~-~~~-s~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~~~~~~l~-~~~~-~~~~~~~~~~~~~~~~~~~~~~l 225 (250)
T TIGR01096 150 FKPGVDIV-EYD-SYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFK-FVGP-SVTDEKYFGDGYGIGLRKGDTEL 225 (250)
T ss_pred ccCCcEEE-EcC-CHHHHHHHHHcCCCCEEEeCHHHHHHHHHhCCCCCceE-Eecc-ccccccccCCceEEEEeCCCHHH
Confidence 77 88888 665 567889999999999999965543 3333322221 2221 1111111222 677788888777
Q ss_pred Hhhhhc
Q 020472 280 VPFTTH 285 (326)
Q Consensus 280 ~~lL~~ 285 (326)
...+++
T Consensus 226 ~~~ln~ 231 (250)
T TIGR01096 226 KAAFNK 231 (250)
T ss_pred HHHHHH
Confidence 666653
No 23
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=94.10 E-value=0.29 Score=46.46 Aligned_cols=145 Identities=17% Similarity=0.173 Sum_probs=75.6
Q ss_pred HHHHcCCCcEEEee---CCCCCCCCCCCceeeeecCCCC--CcceeeccCccCcccCCCCCEEec--CChHHHHHHHhhC
Q 020472 134 EALINSQIDIAVHS---MKDVPTYLPEKTILPCNLQRED--VRDAFISLSAASLAELPAGSIVGT--ASLRRKSQILHRY 206 (326)
Q Consensus 134 ~ALl~g~iDiAVHS---lKDlPt~lp~gL~iaAv~kReD--prD~LV~~~~~~l~dLp~ga~IGT--SS~RR~aQL~~~~ 206 (326)
++|.+|..|+||-| ++---.+ .+++.|+.-+--.. ...+||.+++. -....+|.+||- +|+=...--+..+
T Consensus 57 e~l~~g~yDfaVvS~lAA~~~i~~-~~~l~i~~~fG~~sYvs~Hvli~~~~~-~~~i~dGmRVGiD~~S~Dq~~LT~~~~ 134 (232)
T PF14503_consen 57 EALKNGRYDFAVVSKLAAEHYIEE-GEDLEIVLEFGPGSYVSEHVLIFRDGE-KKEIEDGMRVGIDPSSIDQKILTEAEF 134 (232)
T ss_dssp HHHHTTS-SEEEEEHHHHCCCCCC--SSEEEEEE--TTSSS--EEEEEETT--GGG-----EEEE-TT-HHHHHHHHHHH
T ss_pred HHHHhCCcceEeehHHHHHHHHhh-ccCeEEEEeeCCCCcccceEEEEecCC-ccceeeeeEeecCCCCccHHHHHHHHh
Confidence 79999999999988 3433333 56777765442222 23467776643 345667999995 4444444444445
Q ss_pred CC--CEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhh
Q 020472 207 PS--LKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTT 284 (326)
Q Consensus 207 Pd--l~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~ 284 (326)
++ ++++ ++++ ..=+..|.+|+.||.|+=...++.-...-. ...++...+.-..++.+ |.+|++|+.+..+|+
T Consensus 135 ~gk~Ve~V-ei~Y--~q~~~~l~~g~IDA~IWN~d~i~~~~~~l~-~~~l~~~~~~~~~seAV--ivi~~~~~~i~~ll~ 208 (232)
T PF14503_consen 135 EGKNVEFV-EIPY--NQLLELLRSGEIDAAIWNYDEIEDKNFGLK-YVPLKDDPMSKDASEAV--IVIRKDNEPIKALLR 208 (232)
T ss_dssp TTS--EEE-E--H--HHHHHHHHHTS--EEEEE--HHCCHHCTEE-EEE--SSCHHHHTT-EE--EEEETT-HHHHHHHH
T ss_pred CCCceEEE-EecH--HHHHHHHHCCCccEEEECCcccccccCCee-EEeCCchHHHHhcCeeE--EEEeCCCHHHHHHHH
Confidence 54 5577 6664 477888999999999998774444332211 12333333323344443 578999999999998
Q ss_pred cc
Q 020472 285 HS 286 (326)
Q Consensus 285 ~~ 286 (326)
..
T Consensus 209 ~~ 210 (232)
T PF14503_consen 209 KL 210 (232)
T ss_dssp HH
T ss_pred Hh
Confidence 43
No 24
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=94.09 E-value=1 Score=41.05 Aligned_cols=146 Identities=15% Similarity=0.206 Sum_probs=71.8
Q ss_pred HHHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc----cCcccCCCCCEEec---CChHHHHHH
Q 020472 130 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA----ASLAELPAGSIVGT---ASLRRKSQI 202 (326)
Q Consensus 130 kELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~----~~l~dLp~ga~IGT---SS~RR~aQL 202 (326)
+++-+++..|++|+++=++---|. .-+.+......-. + .-+++.+++ .++++| .|-+||+ ++.- ..+
T Consensus 75 ~~~~~~l~~g~~Di~~~~~~~t~e-R~~~~~fs~p~~~-~-~~~~~~~~~~~~~~~~~dl-~g~~Igv~~gs~~~--~~~ 148 (260)
T PRK15010 75 DALIPSLKAKKIDAIISSLSITDK-RQQEIAFSDKLYA-A-DSRLIAAKGSPIQPTLDSL-KGKHVGVLQGSTQE--AYA 148 (260)
T ss_pred HHHHHHHHCCCCCEEEecCcCCHH-HHhhcccccceEe-c-cEEEEEECCCCCCCChhHc-CCCEEEEecCchHH--HHH
Confidence 467788999999998754321111 0111111110001 1 123333222 146677 4667766 3221 122
Q ss_pred Hh--hCCCCEEEeccCCCHHHHHhhhccCCccEEeeehh----hhcccCCCccceeeecCCC-CCCCcccceeeeEeecC
Q 020472 203 LH--RYPSLKVMENFRGNVQTRLRKLNERVVQATLLALA----GLKRLSMTENVTNILSVDD-MLPAVAQGAIGIACRSN 275 (326)
Q Consensus 203 ~~--~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~A----GL~RLgl~~~i~~~L~~~~-~lPA~GQGaLAVe~R~d 275 (326)
.. ..++++++ .. .+.+.-+++|..|++|++|.-.. ++..-.....+ .+.++.. ..+-.+++ +++-++.+
T Consensus 149 ~~~~~~~~~~~~-~~-~~~~~~~~~l~~griDa~i~d~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~a~~~~ 224 (260)
T PRK15010 149 NETWRSKGVDVV-AY-ANQDLVYSDLAAGRLDAALQDEVAASEGFLKQPAGKDF-AFAGPSVKDKKYFGDG-TGVGLRKD 224 (260)
T ss_pred HHhcccCCceEE-ec-CCHHHHHHHHHcCCccEEEeCcHHHHHHHHhCCCCCce-EEecCccccccccCCc-eEEEEeCC
Confidence 22 23456776 54 57888999999999999987422 22222111222 1222111 11222233 55666778
Q ss_pred chhHHhhhhc
Q 020472 276 DEKMVPFTTH 285 (326)
Q Consensus 276 D~~~~~lL~~ 285 (326)
++++.+.++.
T Consensus 225 ~~~L~~~ln~ 234 (260)
T PRK15010 225 DAELTAAFNK 234 (260)
T ss_pred CHHHHHHHHH
Confidence 8777666653
No 25
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=93.37 E-value=0.65 Score=42.40 Aligned_cols=168 Identities=16% Similarity=0.131 Sum_probs=92.2
Q ss_pred CceEEEEeCCCHHHHHHHHHH-HHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 65 VAIIRIGTRGSPLALAQAHET-RNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V-~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+||||.=.+.-....--.. ...+++++ + +++++...+. .++-+||++|++|+
T Consensus 5 ~~~l~ig~~~~~~~~p~~~a~~~g~f~~~G--~----~ve~~~~~~g-------------------~~~~~al~~G~iD~ 59 (252)
T PF13379_consen 5 PTTLRIGYLPGPDYAPLYVAQEKGLFEKEG--L----DVEWVQFASG-------------------ADILEALAAGEIDI 59 (252)
T ss_dssp ESEEEEEETSSGGGHHHHHHHHTTHHHHTT--S----CEEEEEESSH-------------------HHHHHHHHCTSSSE
T ss_pred CcEEEEEeecchHHHHHHHHHHcChHHHcC--C----EEEEEEcCCH-------------------HHHHHHHHcCCCCE
Confidence 467999998877555441111 12344432 3 4677666442 25669999999999
Q ss_pred EEeeCCCCCCCCC-------CCceeeeecCCCCCcceeecc------CccCcccC----C--CCCEEecC---ChHHH--
Q 020472 144 AVHSMKDVPTYLP-------EKTILPCNLQREDVRDAFISL------SAASLAEL----P--AGSIVGTA---SLRRK-- 199 (326)
Q Consensus 144 AVHSlKDlPt~lp-------~gL~iaAv~kReDprD~LV~~------~~~~l~dL----p--~ga~IGTS---S~RR~-- 199 (326)
+.= .=.++.... ..+.+.+-.. .+...+++.. +.++++|| . +|.+||++ |.-.-
T Consensus 60 a~~-~~~~~~~~~~g~~~~~~~~~~~~~~~-~~g~~lvv~~~~~~~~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l 137 (252)
T PF13379_consen 60 AFV-LAPALIAIAKGAGGPDVDIVVLAGLS-QNGNALVVRNDLKDASDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLL 137 (252)
T ss_dssp EEE-CTHHHHHHHTTTTT----EEEEEECS-BSSEEEEECGGGTTCSTTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHH
T ss_pred EEe-chHHHHHHHcCCCCcccceEEeeccC-CCceEEEEcCccccCCCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHH
Confidence 976 433222222 2344443333 3444555542 34567776 1 68899985 33322
Q ss_pred ---HHHHhhCC--CCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCC
Q 020472 200 ---SQILHRYP--SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPA 262 (326)
Q Consensus 200 ---aQL~~~~P--dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA 262 (326)
.+-.-+.| |++++ ++.. ...+.-|.+|+.||.++..--..++--...-..+++..++.|.
T Consensus 138 ~~~l~~~Gl~~~~dv~~~-~~~~--~~~~~al~~g~iDa~~~~eP~~~~~~~~g~g~~v~~~~~~~~~ 202 (252)
T PF13379_consen 138 RYLLKKAGLDPKDDVTLV-NVPP--PEMVAALRAGEIDAAVLWEPFASQAEAKGIGKIVADSGDVWGN 202 (252)
T ss_dssp HHHHHHTT--TTTSSEEE-E--G--HHHHHHHHTTS-SEEEEETTHHHHHHHTTS-EEEEEHHHCSTT
T ss_pred HHHHHhCCCCcccceEEE-ecCH--HHHHHHHhCCCcCEEEecCCHHHHHHhccCCeEEEEeccccCC
Confidence 11112345 78998 7765 8999999999999999966554443211111234555555443
No 26
>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=92.97 E-value=0.2 Score=46.77 Aligned_cols=110 Identities=15% Similarity=0.166 Sum_probs=66.9
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCCCc--eeeeecCCCCCcceeeccCc---cCcccCCCCCEEecC---C-hHHH-H
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPEKT--ILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTA---S-LRRK-S 200 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~gL--~iaAv~kReDprD~LV~~~~---~~l~dLp~ga~IGTS---S-~RR~-a 200 (326)
++-++|..|++|+++.+.--+-.....|. .+.++.......+.||.++. ++++|| +|-+||+. + -.-- .
T Consensus 39 ~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~~~~~lv~~~~s~I~s~~DL-kGK~Igv~~~s~~~~~l~~ 117 (300)
T TIGR01729 39 DISTALASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIGKSEALVAREGSGIEKPEDL-KGKNVAVPFVSTTHYSLLA 117 (300)
T ss_pred HHHHHHHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCCccceEEecCCCCCCChhHc-CCCEEEeCCCCcHHHHHHH
Confidence 56799999999999864221101122333 44555555556678887654 467788 68888862 2 1111 1
Q ss_pred HHHhhC--C-CCEEEeccCCCHHHHHhhhccCCccEEeeehhhhccc
Q 020472 201 QILHRY--P-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRL 244 (326)
Q Consensus 201 QL~~~~--P-dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RL 244 (326)
.|.+.. | +++++ ..+-...+.-|.+|+.||+++......++
T Consensus 118 ~L~~~Gl~~~dv~~v---~~~~~~~~~al~~G~vDa~~~~~p~~~~~ 161 (300)
T TIGR01729 118 ALKHWKTDPREVNIL---NLKPPQIVAAWQRGDIDAAYVWPPALSEL 161 (300)
T ss_pred HHHHcCCChhheEEE---ecCcHHHHHHHHcCCcCEEEEecHHHHHH
Confidence 233222 2 34444 44567788899999999999976654443
No 27
>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=92.79 E-value=3.9 Score=33.59 Aligned_cols=140 Identities=11% Similarity=0.037 Sum_probs=73.2
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+=.+. +..-.-.+...+++.||++. +++... + +.++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~-~~~~l~~~l~~~~~~~P~v~----i~~~~~----~----------------~~~~~~~l~~g~~Dl~i~ 55 (198)
T cd08437 1 KLRFGLPPII-GNYYFPKLAKDLIKTGLMIQ----IDTYEG----G----------------SAELLEQLLQGDLDIALL 55 (198)
T ss_pred CeEEeeChHH-HHHHhHHHHHHHHHhCCceE----EEEEEc----C----------------HHHHHHHHHcCCCCEEEe
Confidence 4788885553 33344556677888899752 444321 1 357889999999999996
Q ss_pred eCCCCCCCCCCCceee--------eecCCCCCcceeeccCccCcccCCCCCEEecCC---hHHHH-HHH-hhCCCCEEEe
Q 020472 147 SMKDVPTYLPEKTILP--------CNLQREDVRDAFISLSAASLAELPAGSIVGTAS---LRRKS-QIL-HRYPSLKVME 213 (326)
Q Consensus 147 SlKDlPt~lp~gL~ia--------Av~kReDprD~LV~~~~~~l~dLp~ga~IGTSS---~RR~a-QL~-~~~Pdl~v~~ 213 (326)
...+. ..++++... .+..+..|. -.++..+++||..-..|..++ .|+.. ++. ......++.
T Consensus 56 ~~~~~--~~~~~l~~~~l~~~~~~~~~~~~hpl---~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~- 129 (198)
T cd08437 56 GSLTP--LENSALHSKIIKTQHFMIIVSKDHPL---AKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIV- 129 (198)
T ss_pred cCCCC--CCcccceEEEeecceEEEEecCCCcc---cccCcccHHHHcCCCeEEecccchHHHHHHHHHHHcCCCccEE-
Confidence 43221 113344322 222222221 011122455665444554432 23321 111 222233444
Q ss_pred ccCCCHHHHHhhhccCCccEEeeeh
Q 020472 214 NFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 214 ~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
-.-.|+.+-++-+.+|.. ..+++.
T Consensus 130 ~~~~~~~~~~~~v~~g~g-i~~~p~ 153 (198)
T cd08437 130 YRTNDIHILKSMVRENVG-IGFLTD 153 (198)
T ss_pred EEeCcHHHHHHHHHcCCc-EEEEEh
Confidence 345789999998888854 334443
No 28
>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=92.77 E-value=0.66 Score=43.02 Aligned_cols=145 Identities=16% Similarity=0.145 Sum_probs=78.4
Q ss_pred CceEEEEeCCCHHH-HHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 65 VAIIRIGTRGSPLA-LAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 65 ~~~IrIGTR~S~LA-laQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
.++|+|||-.+.-. ..-+..+.+.+.+.+|++ ++..+.+.|. .++-++|.+|++|+
T Consensus 29 ~~~l~Ig~~~~~~~~~~~~~~la~~~~~~~~~i------~v~~~~~~~~-----------------~~~~~~l~~G~~D~ 85 (320)
T TIGR02122 29 PTFVTIGTGGTGGVYYPIGGAIAQLINKKSGKL------RVRVQSTGGS-----------------VENVNLLEAGEADL 85 (320)
T ss_pred CceEEEEeCCCCCChHHHHHHHHHHHhccCCCe------eEEEEeCcch-----------------HHHHHHHhCCCCcE
Confidence 46799999766544 233466777777777653 3444443332 24557899999999
Q ss_pred EEeeCCCC--------CC---CCCCCceeeeecCCCCCcceeeccC---ccCcccCCCCCEEec----CChHHH-HHHHh
Q 020472 144 AVHSMKDV--------PT---YLPEKTILPCNLQREDVRDAFISLS---AASLAELPAGSIVGT----ASLRRK-SQILH 204 (326)
Q Consensus 144 AVHSlKDl--------Pt---~lp~gL~iaAv~kReDprD~LV~~~---~~~l~dLp~ga~IGT----SS~RR~-aQL~~ 204 (326)
++.+.-.. +. ..++.+...+.+-++ + -+++.++ .++++||. |-+|+. ++.++. .++..
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~-~-~~lvv~~d~~i~sl~dL~-gk~v~~~~~~s~~~~~~~~~l~ 162 (320)
T TIGR02122 86 AIVQSDVAYYAYEGDGEFEFEGPVEKLRALASLYPE-Y-IQIVVRKDSGIKTVADLK-GKRVAVGAPGSGTELNARAVLK 162 (320)
T ss_pred EEEcchhHHHHhcCcCccccCCCCccHHhHHHhccc-c-EEEEEECCCCCCcHHHcC-CCEEecCCCCcchHHHHHHHHH
Confidence 98763211 00 112344422222222 2 1244432 24677774 444432 334433 23333
Q ss_pred hC---CC-CEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 205 RY---PS-LKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 205 ~~---Pd-l~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.+ |+ ++.+ ... +....+..|.+|++|+++..
T Consensus 163 ~~G~~~~~~~~v-~~~-~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 163 AAGLTYDDVKKV-EYL-GYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred HcCCCHHHccch-hcC-CHHHHHHHHHCCCccEEEEe
Confidence 22 11 2223 333 45678899999999999976
No 29
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=92.43 E-value=0.86 Score=50.51 Aligned_cols=142 Identities=11% Similarity=0.076 Sum_probs=77.6
Q ss_pred HHHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC---ccCcccCCCCCEEec---CChHHHHHHH
Q 020472 130 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS---AASLAELPAGSIVGT---ASLRRKSQIL 203 (326)
Q Consensus 130 kELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~---~~~l~dLp~ga~IGT---SS~RR~aQL~ 203 (326)
.++-++|.+|+||++...+-.-|.. .+.+.... +=-...-++|.+. ..++.++ .|.+||. ++. ...++
T Consensus 107 ~~~l~~l~~g~iDl~~~~~~~~~~r-~~~~~fs~--py~~~~~~~v~~~~~~~~~~~~l-~~~~i~~~~g~~~--~~~~~ 180 (1197)
T PRK09959 107 QKAMDALEEGEVDIVLSHLVASPPL-NDDIAATK--PLIITFPALVTTLHDSMRPLTSS-KPVNIARVANYPP--DEVIH 180 (1197)
T ss_pred HHHHHHHHcCCCcEecCcccccccc-ccchhcCC--CccCCCceEEEeCCCCCCCcccc-cCeEEEEeCCCCC--HHHHH
Confidence 4788999999999987654332211 11111110 0000011122211 1234444 4455543 222 56788
Q ss_pred hhCCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhccc----CCCccceeeecCCCCCCCcccceeeeEeecCchhH
Q 020472 204 HRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRL----SMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKM 279 (326)
Q Consensus 204 ~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RL----gl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~ 279 (326)
..+|+.+++ ... |.+.-+..|.+|+.||+|...+-+.-+ +... + .+... .+.+-+. ..+..|++++.+
T Consensus 181 ~~~p~~~i~-~~~-s~~~al~av~~G~~Da~i~~~~~~~~~i~~~~~~~-l-~~~~~---~~~~~~~-~~~~~~~~~~~L 252 (1197)
T PRK09959 181 QSFPKATII-SFT-NLYQALASVSAGQNDYFIGSNIITSSMISRYFTHS-L-NVVKY---YNSPRQY-NFFLTRKESVIL 252 (1197)
T ss_pred HhCCCCEEE-eCC-CHHHHHHHHHcCCCCEEEccHHHHHHHHhcccccc-e-EEEee---ccCCCCc-eeEEEcCCcHHH
Confidence 899999998 555 899999999999999999865533322 1111 1 01111 1111122 345668888888
Q ss_pred Hhhhhc
Q 020472 280 VPFTTH 285 (326)
Q Consensus 280 ~~lL~~ 285 (326)
.++|+.
T Consensus 253 ~~~lnk 258 (1197)
T PRK09959 253 NEVLNR 258 (1197)
T ss_pred HHHHHH
Confidence 777653
No 30
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=92.34 E-value=1 Score=49.90 Aligned_cols=144 Identities=15% Similarity=0.172 Sum_probs=78.8
Q ss_pred HHHHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc-cCcccCCCCCEEecCChH-HHHHHHhhC
Q 020472 129 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-ASLAELPAGSIVGTASLR-RKSQILHRY 206 (326)
Q Consensus 129 tkELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-~~l~dLp~ga~IGTSS~R-R~aQL~~~~ 206 (326)
-.+...+|.+|++|+..-... -|.. .+.+...- +==.. .-++|.++. ....++..|.+||...-- -...++..+
T Consensus 351 ~~~~~~~l~~g~~D~i~~~~~-t~~r-~~~~~fs~-py~~~-~~~~v~~~~~~~~~~~~~g~~vav~~g~~~~~~~~~~~ 426 (1197)
T PRK09959 351 NIHAGTQLNPGGWDIIPGAIY-SEDR-ENNVLFAE-AFITT-PYVFVMQKAPDSEQTLKKGMKVAIPYYYELHSQLKEMY 426 (1197)
T ss_pred HHHHHHHHHCCCceEeecccC-Cccc-cccceecc-ccccC-CEEEEEecCCCCccccccCCEEEEeCCcchHHHHHHHC
Confidence 446677899999998654432 2211 11111100 00001 112333322 123344467777653221 135677889
Q ss_pred CCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhc----ccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhh
Q 020472 207 PSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLK----RLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPF 282 (326)
Q Consensus 207 Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~----RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~l 282 (326)
|+++++ .. .|.+.-|..|.+|+.||.|....-.. +.+... ...... |....--+++-+|++|+.+.++
T Consensus 427 p~~~~~-~~-~~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~~-l~~~~~-----~~~~~~~~~~av~k~~~~L~~~ 498 (1197)
T PRK09959 427 PEVEWI-KV-DNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNE-LYHFLI-----PGVPNASLSFAFPRGEPELKDI 498 (1197)
T ss_pred CCcEEE-Ec-CCHHHHHHHHHcCCCCEEehhhHHHHHHHHhccccc-ceeeec-----CCCCchheEEeeCCCCHHHHHH
Confidence 999998 44 68999999999999999997443322 222211 111111 1111123577789999988877
Q ss_pred hh
Q 020472 283 TT 284 (326)
Q Consensus 283 L~ 284 (326)
++
T Consensus 499 ln 500 (1197)
T PRK09959 499 IN 500 (1197)
T ss_pred HH
Confidence 75
No 31
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=92.09 E-value=1.1 Score=39.91 Aligned_cols=108 Identities=19% Similarity=0.194 Sum_probs=70.0
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC----ccCcccCCC---CCEEecCChHHHHHHH
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS----AASLAELPA---GSIVGTASLRRKSQIL 203 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~----~~~l~dLp~---ga~IGTSS~RR~aQL~ 203 (326)
.+-.+|..|++|+++.++=-.| +..+.+.. ..+--....-+++... .++++||.. |...||+ .+-..-..
T Consensus 88 ~~~~~l~~g~~D~~~~~~~~t~-er~~~~~f-s~py~~~~~~~~~~~~~~~~~~~~~DL~gk~v~v~~gt~-~~~~~~~~ 164 (275)
T COG0834 88 GLIPALKAGKVDIIIAGMTITP-ERKKKVDF-SDPYYYSGQVLLVKKDSDIGIKSLEDLKGKKVGVQLGTT-DEAEEKAK 164 (275)
T ss_pred hhhHHHhcCCcCEEEeccccCH-HHhccccc-cccccccCeEEEEECCCCcCcCCHHHhCCCEEEEEcCcc-hhHHHHHh
Confidence 4668999999999999955445 43344443 3332333333344211 124667753 4455666 45556666
Q ss_pred hhCCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcc
Q 020472 204 HRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKR 243 (326)
Q Consensus 204 ~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~R 243 (326)
...+..+++ ....+ ..-+..|.+|..||++.-..-+..
T Consensus 165 ~~~~~~~~~-~~~~~-~~~~~al~~Gr~Da~~~d~~~~~~ 202 (275)
T COG0834 165 KPGPNAKIV-AYDSN-AEALLALKNGRADAVVSDSAVLAG 202 (275)
T ss_pred hccCCceEE-eeCCH-HHHHHHHHcCCccEEEcchHhhhh
Confidence 667888888 66655 788999999999999987776655
No 32
>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=91.78 E-value=5.9 Score=32.74 Aligned_cols=139 Identities=17% Similarity=0.095 Sum_probs=82.0
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.++|+||+-.+.. ..-.-.+...+++.+|++. +++.... ..++.++|.+|++|++
T Consensus 5 ~~~l~Ig~~~~~~-~~~l~~~l~~~~~~~P~i~----i~~~~~~--------------------~~~~~~~l~~g~~Dl~ 59 (209)
T PF03466_consen 5 RGTLRIGASPSFA-SSLLPPLLAEFRERHPNIR----IEIREGD--------------------SDELIEALRSGELDLA 59 (209)
T ss_dssp EEEEEEEEEHHHH-HHTHHHHHHHHHHHSTTEE----EEEEEES--------------------HHHHHHHHHTTSSSEE
T ss_pred ceEEEEEEEhHHH-HHHHHHHHHHHHHHCCCcE----EEEEecc--------------------chhhhHHHhcccccEE
Confidence 4679999986544 3345556777888899752 4443321 2578899999999999
Q ss_pred EeeCCCCCCCCCCCceeeeecCCCCCcceeeccC-------ccCcccCCCCCEEecC---ChHHHH-H-HHhhCCCCEEE
Q 020472 145 VHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS-------AASLAELPAGSIVGTA---SLRRKS-Q-ILHRYPSLKVM 212 (326)
Q Consensus 145 VHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~-------~~~l~dLp~ga~IGTS---S~RR~a-Q-L~~~~Pdl~v~ 212 (326)
+..... .++++....+. .++-=+++.++ ..++++|..-..|..+ ..+... + +.......++.
T Consensus 60 i~~~~~----~~~~~~~~~l~--~~~~~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 133 (209)
T PF03466_consen 60 ITFGPP----PPPGLESEPLG--EEPLVLVVSPDHPLAQKKPITLEDLADYPLILLSPGSPYRDQLDRWLREHGFSPNIV 133 (209)
T ss_dssp EESSSS----SSTTEEEEEEE--EEEEEEEEETTSGGGTTSSSSGGGGTTSEEEEESTTTSHHHHHHHHHHHTTEEEEEE
T ss_pred EEEeec----ccccccccccc--ceeeeeeeeccccccccccchhhhhhhcccccccccccccccccccccccccccccc
Confidence 998877 45665443332 22222222222 2356677555555522 233321 1 23333334444
Q ss_pred eccCCCHHHHHhhhccCCccEEe
Q 020472 213 ENFRGNVQTRLRKLNERVVQATL 235 (326)
Q Consensus 213 ~~iRGNV~TRL~KL~~ge~DAII 235 (326)
-.=.|+++-+.-+.+|..=+++
T Consensus 134 -~~~~~~~~~~~~v~~g~gi~~~ 155 (209)
T PF03466_consen 134 -IEVDSFESILSLVASGDGIAIL 155 (209)
T ss_dssp -EEESSHHHHHHHHHTTSEBEEE
T ss_pred -ccccchhhhccccccccceeec
Confidence 4457999999999888654443
No 33
>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=90.69 E-value=1.2 Score=37.27 Aligned_cols=56 Identities=18% Similarity=0.226 Sum_probs=39.2
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
++||+=.+ ++....-.+...+++.||++. +++.... +.++.+.|.+|++|++++.
T Consensus 2 ~~I~~~~~-~~~~~l~~~l~~~~~~~P~i~----l~~~~~~--------------------~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08467 2 FTLAMPDY-AEVALLPRLAPRLRERAPGLD----LRLCPIG--------------------DDLAERGLEQGTIDLAVGR 56 (200)
T ss_pred eEEEechh-hHHHHHHHHHHHHHhhCCCCE----EEEecCC--------------------cccHHHHhhCCCcCEEEec
Confidence 67888444 455566677788888899862 4443221 2468899999999999985
Q ss_pred C
Q 020472 148 M 148 (326)
Q Consensus 148 l 148 (326)
.
T Consensus 57 ~ 57 (200)
T cd08467 57 F 57 (200)
T ss_pred C
Confidence 3
No 34
>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=90.57 E-value=1.6 Score=35.78 Aligned_cols=57 Identities=12% Similarity=0.166 Sum_probs=38.4
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+-.+... .---.+...+++.||++. +++..- . +.++.+.|.+|++|++++
T Consensus 1 ~~~Ig~~~~~~~-~~l~~~l~~f~~~~P~v~----l~~~~~----~----------------~~~~~~~l~~g~~Dl~i~ 55 (200)
T cd08466 1 TFNIAANETLDL-LLLPRLLARLKQLAPNIS----LRESPS----S----------------EEDLFEDLRLQEVDLVID 55 (200)
T ss_pred CEEEEechHHHH-HHHHHHHHHHHHHCCCCE----EEEecC----c----------------hHhHHHHHHcCCccEEEe
Confidence 478999666533 333455666677799863 544321 1 246889999999999998
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (200)
T cd08466 56 YV 57 (200)
T ss_pred cc
Confidence 53
No 35
>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=90.35 E-value=2 Score=34.64 Aligned_cols=133 Identities=14% Similarity=0.127 Sum_probs=70.4
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+ ++..-.-.+...+++.+|++. +++.... +.++.+.|.+|++|+++-
T Consensus 1 ~l~Ig~~~~-~~~~~l~~~l~~~~~~~p~v~----i~i~~~~--------------------~~~~~~~l~~g~~D~~i~ 55 (197)
T cd08440 1 RVRVAALPS-LAATLLPPVLAAFRRRHPGIR----VRLRDVS--------------------AEQVIEAVRSGEVDFGIG 55 (197)
T ss_pred CeEEEeccc-hhhhHHHHHHHHHHHhCCCcE----EEEEeCC--------------------hHHHHHHHHcCCccEEEE
Confidence 478998666 444445667778888899752 4443211 247889999999999997
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEec---CChHHH-HHH-HhhCCCCEEEec
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGT---ASLRRK-SQI-LHRYPSLKVMEN 214 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGT---SS~RR~-aQL-~~~~Pdl~v~~~ 214 (326)
...+ .++++....+. .++.-+++.++. .++++|..-..|.. ++.++. .+. .......++. -
T Consensus 56 ~~~~----~~~~~~~~~l~--~~~~~~~~~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 128 (197)
T cd08440 56 SEPE----ADPDLEFEPLL--RDPFVLVCPKDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPA-Y 128 (197)
T ss_pred eCCC----CCCCeeEEEee--cccEEEEecCCCCcccCCccCHHHHccCCEEecCCCccHHHHHHHHHHHcCCCcceE-E
Confidence 5432 23455433222 222222222221 23444443333332 123332 222 2222222333 2
Q ss_pred cCCCHHHHHhhhccCCc
Q 020472 215 FRGNVQTRLRKLNERVV 231 (326)
Q Consensus 215 iRGNV~TRL~KL~~ge~ 231 (326)
.-.|+.+-+.-+.+|..
T Consensus 129 ~~~~~~~~~~~v~~g~g 145 (197)
T cd08440 129 EVSHMSTALGMVAAGLG 145 (197)
T ss_pred EeccHHHHHHHHHcCCe
Confidence 33688888888888743
No 36
>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=89.55 E-value=8.8 Score=30.24 Aligned_cols=135 Identities=13% Similarity=0.052 Sum_probs=71.2
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+. +..--......+.+.+|++. +++.... ..++.+.|.+|++|+++.
T Consensus 1 ~l~I~~~~~~-~~~~l~~~i~~~~~~~p~i~----i~~~~~~--------------------~~~~~~~l~~g~~D~~i~ 55 (197)
T cd05466 1 TLRIGASPSI-AAYLLPPLLAAFRQRYPGVE----LSLVEGG--------------------SSELLEALLEGELDLAIV 55 (197)
T ss_pred CeEEEechhh-HHHHhHHHHHHHHHHCCCCE----EEEEECC--------------------hHHHHHHHHcCCceEEEE
Confidence 4789996553 33344445566777899752 5443221 246889999999999998
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeeccCc--------cCcccCCCCCEEecCChH---HH--HHHHhhCCCCEEEe
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISLSA--------ASLAELPAGSIVGTASLR---RK--SQILHRYPSLKVME 213 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~--------~~l~dLp~ga~IGTSS~R---R~--aQL~~~~Pdl~v~~ 213 (326)
.... .++++....+. + ++ -++++.++ .++++|..-..|...... .. ..+.....+.+..
T Consensus 56 ~~~~----~~~~~~~~~l~-~-~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~- 127 (197)
T cd05466 56 ALPV----DDPGLESEPLF-E-EP-LVLVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIA- 127 (197)
T ss_pred cCCC----CCCcceEeeee-c-cc-eEEEecCCCCcccCcEecHHHHcCCCEEEecCCchHHHHHHHHHHHcCCCceEE-
Confidence 6543 23344322221 1 11 22222211 134444333344433221 11 1233444444444
Q ss_pred ccCCCHHHHHhhhccCCccEE
Q 020472 214 NFRGNVQTRLRKLNERVVQAT 234 (326)
Q Consensus 214 ~iRGNV~TRL~KL~~ge~DAI 234 (326)
-.-.++.+-+.-+.+|..=++
T Consensus 128 ~~~~~~~~~~~~~~~~~g~~~ 148 (197)
T cd05466 128 LEVDSLEAIKALVAAGLGIAL 148 (197)
T ss_pred EEeccHHHHHHHHHhCCCEEE
Confidence 345688888888888874333
No 37
>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=89.48 E-value=10 Score=30.86 Aligned_cols=57 Identities=18% Similarity=0.272 Sum_probs=40.5
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+ ++..-.-.+...+++.+|++. +++.... ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~-~~~~~l~~~l~~~~~~~P~i~----l~i~~~~--------------------~~~~~~~l~~g~~Dl~i~ 55 (201)
T cd08418 1 KVSIGVSSL-IAHTLMPAVINRFKEQFPDVQ----ISIYEGQ--------------------LSSLLPELRDGRLDFAIG 55 (201)
T ss_pred CEEEEechH-HHHhhhHHHHHHHHHHCCCce----EEEEeCc--------------------HHHHHHHHHcCCCcEEEE
Confidence 478998665 444455567778888899863 5554321 347889999999999998
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (201)
T cd08418 56 TL 57 (201)
T ss_pred ec
Confidence 64
No 38
>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=89.20 E-value=2.1 Score=34.66 Aligned_cols=57 Identities=12% Similarity=0.291 Sum_probs=38.7
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+... ...-.+...+.+.+|++. +++ ... + ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~~-~~l~~~l~~~~~~~p~v~----i~i--~~~--~----------------~~~~~~~L~~~~~Dl~i~ 55 (197)
T cd08438 1 HLRLGLPPLGGS-LLFAPLLAAFRQRYPNIE----LEL--VEY--G----------------GKKVEQAVLNGELDVGIT 55 (197)
T ss_pred CeEEEecchhhh-hhcHHHHHHHHHHCcCeE----EEE--EEc--C----------------cHHHHHHHHcCCCCEEEE
Confidence 378888665443 345556677788899752 444 321 1 257889999999999997
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (197)
T cd08438 56 VL 57 (197)
T ss_pred ec
Confidence 64
No 39
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=88.74 E-value=0.73 Score=43.92 Aligned_cols=108 Identities=8% Similarity=0.091 Sum_probs=64.6
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCC--CceeeeecCCCCCcceeeccC-ccCcccCCCCCEEecCC---hHH--HHHH
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPE--KTILPCNLQREDVRDAFISLS-AASLAELPAGSIVGTAS---LRR--KSQI 202 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~--gL~iaAv~kReDprD~LV~~~-~~~l~dLp~ga~IGTSS---~RR--~aQL 202 (326)
++-++|.+|++|+++-+.-.+....-. ++.+.++.......+.+|.++ -+++.|| +|-+||+.. ... ...|
T Consensus 63 ~~~~al~~G~~D~a~~~~~~~~~a~~~g~~~~~v~~~~~~~~~~~lv~~~~I~s~~DL-kGK~Iav~~~s~~~~~l~~~L 141 (320)
T PRK11480 63 SIVRALASGDVQIGNLGSSPLAVAASQQVPIEVFLLASKLGNSEALVVKKTISKPEDL-IGKRIAVPFISTTHYSLLAAL 141 (320)
T ss_pred HHHHHHHCCCCCEECcCchHHHHHHHCCCCeEEEEeeccCCcceEEEecCCCCChHHc-CCCEEecCCCCchHHHHHHHH
Confidence 467999999999996543211111112 244545555555556777754 3578888 699999732 211 1123
Q ss_pred Hhh--C-CCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhc
Q 020472 203 LHR--Y-PSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLK 242 (326)
Q Consensus 203 ~~~--~-Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~ 242 (326)
+.. - .|++++ ++. -..-..-|.+|+.||+++..-...
T Consensus 142 ~~~Gl~~~dv~~v-~~~--~~~~~~Al~~G~VDAa~~~~p~~~ 181 (320)
T PRK11480 142 KHWGIKPGQVEIV-NLQ--PPAIIAAWQRGDIDGAYVWAPAVN 181 (320)
T ss_pred HHcCCCHhheEEE-ECC--cHHHHHHHHcCCcCEEEEcchHHH
Confidence 322 1 355655 443 566778899999999987654433
No 40
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=88.74 E-value=1.9 Score=41.12 Aligned_cols=102 Identities=13% Similarity=0.107 Sum_probs=59.9
Q ss_pred HHHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC---ccCcccCCCCCEEecCChHHHHHH-Hhh
Q 020472 130 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS---AASLAELPAGSIVGTASLRRKSQI-LHR 205 (326)
Q Consensus 130 kELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~---~~~l~dLp~ga~IGTSS~RR~aQL-~~~ 205 (326)
.++-.+|.+|++|+++=.+ |...+............-...+-+++.++ .++++|| +|.+|||+...-..+. ...
T Consensus 54 ~~i~~~L~sG~vDlgi~g~-~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~~i~sl~DL-~Gk~ia~~~~~~~~~~l~~~ 131 (287)
T PRK00489 54 DDIPGYVADGVVDLGITGE-DLLEESGADVEELLDLGFGKCRLVLAVPEDSDWQGVEDL-AGKRIATSYPNLTRRYLAEK 131 (287)
T ss_pred HHHHHHHHcCCCCEEEcch-HHHHHCCCCceEeeeccCCceEEEEEEECCCCCCChHHh-CCCEEEEcCcHHHHHHHHHc
Confidence 5788999999999998663 22111111111111111112223344332 2457777 5889999766543332 233
Q ss_pred CCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 206 YPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 206 ~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.-+.+++ ..-|+++. -+..|..||++--
T Consensus 132 gi~~~iv-~~~gs~ea---a~~~G~aDaivd~ 159 (287)
T PRK00489 132 GIDAEVV-ELSGAVEV---APRLGLADAIVDV 159 (287)
T ss_pred CCceEEE-ECCCchhh---hhcCCcccEEEee
Confidence 3357777 88899997 4566999999763
No 41
>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=88.72 E-value=3.2 Score=38.32 Aligned_cols=145 Identities=12% Similarity=0.084 Sum_probs=72.6
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc-----cCcccCC--CCCEEecCChHH-HHHH
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-----ASLAELP--AGSIVGTASLRR-KSQI 202 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-----~~l~dLp--~ga~IGTSS~RR-~aQL 202 (326)
++..+|.+|++|++...+-.-|... +.+.... +-. .....++.++. .++++|. +|.+||...--= ..++
T Consensus 83 ~~~~~l~~G~~Di~~~~~~~t~eR~-~~~~fs~-py~-~~~~~~~~~~~~~~~i~~~~dl~~~~g~~Igv~~g~~~~~~l 159 (275)
T TIGR02995 83 ALIPGLQAGRFDAIAAGLFIKPERC-KQVAFTQ-PIL-CDAEALLVKKGNPKGLKSYKDIAKNPDAKIAAPGGGTEEKLA 159 (275)
T ss_pred HHHHHHHCCCcCEEeecccCCHHHH-hcccccc-cee-ecceeEEEECCCCCCCCCHHHhccCCCceEEEeCCcHHHHHH
Confidence 4668899999999876542222111 1111100 000 00112222221 2455554 266666432111 2344
Q ss_pred Hhh-CCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcc----cCCCccceeeecCCCCCCCcccceeeeEeecCch
Q 020472 203 LHR-YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKR----LSMTENVTNILSVDDMLPAVAQGAIGIACRSNDE 277 (326)
Q Consensus 203 ~~~-~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~R----Lgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~ 277 (326)
+.. +|..+++ ... +.++-++.|.+|++|++|.-..-+.. .+.. .+. ...+ +.+.+-+.-.++-.+.+++
T Consensus 160 ~~~~~~~~~i~-~~~-~~~~~i~~L~~grvDa~i~d~~~~~~~~~~~~~~-~~~-~~~~--~~~~~~~~~~~~~~~~~~~ 233 (275)
T TIGR02995 160 REAGVKREQII-VVP-DGQSGLKMVQDGRADAYSLTVLTINDLASKAGDP-NVE-VLAP--FKDAPVRYYGGAAFRPEDK 233 (275)
T ss_pred HHcCCChhhEE-EeC-CHHHHHHHHHcCCCCEEecChHHHHHHHHhCCCC-Cce-eecC--ccCCccccceeEEECCCCH
Confidence 443 4766776 454 68899999999999999986553332 2321 221 1111 1122222223455677777
Q ss_pred hHHhhhh
Q 020472 278 KMVPFTT 284 (326)
Q Consensus 278 ~~~~lL~ 284 (326)
++.+.++
T Consensus 234 ~l~~~~n 240 (275)
T TIGR02995 234 ELRDAFN 240 (275)
T ss_pred HHHHHHH
Confidence 7766665
No 42
>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=88.54 E-value=1.8 Score=35.08 Aligned_cols=56 Identities=23% Similarity=0.277 Sum_probs=38.2
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+-.+. +....-.+...+++.+|++. +++.. + + ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~-~~~~l~~~l~~~~~~~p~i~----i~i~~--~--~----------------~~~~~~~l~~~~~Dl~i~ 55 (197)
T cd08414 1 RLRIGFVGSA-LYGLLPRLLRRFRARYPDVE----LELRE--M--T----------------TAEQLEALRAGRLDVGFV 55 (197)
T ss_pred CEEEEeeHHH-HHHHHHHHHHHHHHHCCCcE----EEEec--C--C----------------hHHHHHHHHcCCccEEEE
Confidence 4788885544 44455666777778899752 44322 1 1 257889999999999996
Q ss_pred e
Q 020472 147 S 147 (326)
Q Consensus 147 S 147 (326)
.
T Consensus 56 ~ 56 (197)
T cd08414 56 R 56 (197)
T ss_pred c
Confidence 4
No 43
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=88.02 E-value=3.3 Score=33.72 Aligned_cols=57 Identities=19% Similarity=0.251 Sum_probs=38.1
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+.- ..=.-.+...+++.+|++. +++... + ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~-~~~l~~~l~~~~~~~P~i~----~~i~~~----~----------------~~~~~~~l~~g~~Dl~i~ 55 (196)
T cd08456 1 ELRIAVLPALS-QSFLPRAIKAFLQRHPDVT----ISIHTR----D----------------SPTVEQWLSAQQCDLGLV 55 (196)
T ss_pred CeEEEecHHHH-HhhHHHHHHHHHHHCCCcE----EEEEeC----C----------------HHHHHHHHHcCCccEEEE
Confidence 37888855543 3334566777788899752 444321 1 246889999999999997
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (196)
T cd08456 56 ST 57 (196)
T ss_pred ec
Confidence 54
No 44
>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=87.87 E-value=4.7 Score=33.17 Aligned_cols=68 Identities=13% Similarity=0.110 Sum_probs=43.6
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.||||+-.+.- ..-.-.+...+.+.+|++. +++.... +.++.++|.+|++|+++.
T Consensus 1 ~l~ig~~~~~~-~~~l~~~l~~~~~~~P~i~----l~i~~~~--------------------~~~~~~~l~~g~~D~~i~ 55 (200)
T cd08453 1 RLSLAFVSTAD-YSVLPELVRRFREAYPDVE----LQLREAT--------------------SDVQLEALLAGEIDAGIV 55 (200)
T ss_pred CEEEEEechHH-hHHHHHHHHHHHHhCCCce----EEEEeCC--------------------HHHHHHHHHcCCCCEEEE
Confidence 37888877653 3345557777888899862 5443211 356889999999999997
Q ss_pred eCCCCCCCCCCCce
Q 020472 147 SMKDVPTYLPEKTI 160 (326)
Q Consensus 147 SlKDlPt~lp~gL~ 160 (326)
.. +.+...++++.
T Consensus 56 ~~-~~~~~~~~~~~ 68 (200)
T cd08453 56 IP-PPGASAPPALA 68 (200)
T ss_pred ec-CcccCCCccee
Confidence 53 22222345553
No 45
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=87.60 E-value=9 Score=35.52 Aligned_cols=108 Identities=17% Similarity=0.154 Sum_probs=58.2
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCC--CCCCCceeeeecCCCC---Cc-ceeeccC---ccCcccCCCCCEEecC---Ch--
Q 020472 131 EIDEALINSQIDIAVHSMKDVPT--YLPEKTILPCNLQRED---VR-DAFISLS---AASLAELPAGSIVGTA---SL-- 196 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt--~lp~gL~iaAv~kReD---pr-D~LV~~~---~~~l~dLp~ga~IGTS---S~-- 196 (326)
++-++|.+|++|+++-+.=++.. +...+..+ .+..+.+ +. -++|.++ .++++|| +|.+||+. |.
T Consensus 71 ~~~~al~~g~~D~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~y~~~lvv~~ds~i~sl~DL-~Gk~v~~~~~~s~~~ 148 (288)
T TIGR03431 71 GVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAF-AIEVNADGSTGYYSVLIVKKDSPIKSLEDL-KGKTFGFVDPNSTSG 148 (288)
T ss_pred HHHHHHHcCCccEEEEChHHHHHHHHhcCCeEE-EEeccCCCCCceEEEEEEeCCCCCCcHHHh-CCCEEEeeCCCcchh
Confidence 46689999999999865321111 11222111 1111111 11 2455443 2467888 58888853 21
Q ss_pred H--HHHHHHhhC-CC----CEEEeccCCCHHHHHhhhccCCccEEeeehhhh
Q 020472 197 R--RKSQILHRY-PS----LKVMENFRGNVQTRLRKLNERVVQATLLALAGL 241 (326)
Q Consensus 197 R--R~aQL~~~~-Pd----l~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL 241 (326)
- +...+.... .+ +..+ ..-|+....+.-|.+|+.||.++...-+
T Consensus 149 ~~~~~~~l~~~~g~~~~~~~~~v-~~~~~~~~~~~al~~G~vDa~~~~~~~~ 199 (288)
T TIGR03431 149 FLVPSYYLFKKNGIKPKEYFKKV-TFSGSHEAAILAVANGTVDAATTNDENL 199 (288)
T ss_pred hHHHHHHHHHhcCCChHHhHHhh-eecCchHHHHHHHHcCCCCeEeccHHHH
Confidence 1 122232221 11 1223 3446888899999999999999866543
No 46
>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=87.51 E-value=2.2 Score=40.41 Aligned_cols=184 Identities=20% Similarity=0.159 Sum_probs=102.6
Q ss_pred EEEEeCCCHHHH-HHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 68 IRIGTRGSPLAL-AQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 68 IrIGTR~S~LAl-aQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
|+||+...+-+. ++ .|.+.+++.+ + ++|++.+. |- .+..+||.+|+||+-+.
T Consensus 1 ikIG~~~~~~~~i~~--~v~~~~~~~G--i----~vevv~f~---D~----------------~~~N~AL~~G~iDaN~f 53 (237)
T PF03180_consen 1 IKIGVTPGPDAEILE--AVKEKLKKKG--I----DVEVVEFS---DY----------------VQPNEALADGEIDANFF 53 (237)
T ss_dssp EEEEEETTCHHHHHH--HHHHHHHHTT--E----EEEEEEES---ST----------------THHHHHHHTTSSSEEEE
T ss_pred CEEEEeCCCHHHHHH--HHHHHHHhcC--C----eEEEEEec---ch----------------hhcChHHHCCCcceecc
Confidence 689999766553 44 8888888865 3 47777763 32 25789999999999875
Q ss_pred eCC----CCCCCCCCCceeeeecCCCCCcceeeccCccCcccCCCCCEEecCC----hHHHHHHHhhCC-----------
Q 020472 147 SMK----DVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTAS----LRRKSQILHRYP----------- 207 (326)
Q Consensus 147 SlK----DlPt~lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTSS----~RR~aQL~~~~P----------- 207 (326)
--+ .--.+ .|..+.++-+---..=.|-|+++++++++|+|++|+=+. .=|.-.++...-
T Consensus 54 Qh~~yl~~~n~~--~~~~L~~v~~~~~~p~glYS~k~~sl~~lp~Ga~VaIpnD~sN~~RaL~lLq~aGLI~Lk~~~~~~ 131 (237)
T PF03180_consen 54 QHIPYLEQFNKE--NGYNLVPVGPTYIEPMGLYSKKYKSLDDLPDGATVAIPNDPSNQARALKLLQEAGLITLKDGVGLT 131 (237)
T ss_dssp EEHHHHHHHHHH--HT--EEEEEEEEE---EEEESSSSSGGGS-TTEEEEEESSHHHHHHHHHHHHHTTSEEE-TT-GCC
T ss_pred CCHHHHHHHHHH--CCCcEEEecceeEEeEEEeecccCchhhcCCCCEEEEeCCccchhHHHHHHHhCCeEEEcCCCCCc
Confidence 321 11111 344444444322222335568889999999999999654 345555555322
Q ss_pred -----------CCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeec--
Q 020472 208 -----------SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRS-- 274 (326)
Q Consensus 208 -----------dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~-- 274 (326)
+++|+ ++-.. +=-+-|+ ++|+.|+.-.=...-|+...-.-++..+. ..-.=+..+.+|+
T Consensus 132 ~t~~DI~~Npk~l~~~-evd~~--~l~~~l~--dvD~avi~~~~a~~agl~~~~~~~~~e~~---~~~~y~n~lv~r~~~ 203 (237)
T PF03180_consen 132 ATVDDITENPKNLKFK-EVDAA--QLPRALD--DVDAAVINGNYALDAGLDPKKDLLFEEPD---ADKPYANVLVVREDD 203 (237)
T ss_dssp -SGGGEEEETTSEEEE-EE-GG--GHHHHTT--TSSEEEE-HHHHHHTT--CCCHSSEE-SS---SSCGGEEEEEEEGGG
T ss_pred cChhhhhhcccCceEE-EecHh--hHHhhcc--cCCEEEecHhHHHHcCcCcccceeeeecc---cCcceeEEEEEECCc
Confidence 34444 33211 1112233 49999986555566666543222232222 2345566667766
Q ss_pred -CchhHHhhhhcccc
Q 020472 275 -NDEKMVPFTTHSQA 288 (326)
Q Consensus 275 -dD~~~~~lL~~~~~ 288 (326)
||+++..+.+.+++
T Consensus 204 ~d~~~ik~l~ea~~s 218 (237)
T PF03180_consen 204 KDDPWIKKLVEAYQS 218 (237)
T ss_dssp TTCHHHHHHHHHHTS
T ss_pred cCCHHHHHHHHHHCC
Confidence 66677777776664
No 47
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=87.24 E-value=3.6 Score=33.34 Aligned_cols=56 Identities=20% Similarity=0.295 Sum_probs=38.8
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+= + ++..-.-.+...+++.+|++. +++.. ++ ..++.+.|.+|++|+|+.
T Consensus 1 ~l~Ig~~-~-~~~~~l~~~l~~~~~~~P~i~----l~i~~----~~----------------~~~~~~~l~~g~~Dl~i~ 54 (197)
T cd08419 1 RLRLAVV-S-TAKYFAPRLLGAFCRRHPGVE----VSLRV----GN----------------REQVLERLADNEDDLAIM 54 (197)
T ss_pred CEEEEEe-c-hhHhHhhHHHHHHHHHCCCce----EEEEE----CC----------------HHHHHHHHhcCCccEEEe
Confidence 4789985 4 344445667777888899762 44432 11 257889999999999997
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
+.
T Consensus 55 ~~ 56 (197)
T cd08419 55 GR 56 (197)
T ss_pred cC
Confidence 64
No 48
>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=87.13 E-value=2.7 Score=34.49 Aligned_cols=57 Identities=25% Similarity=0.337 Sum_probs=39.2
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+-.+....+-. .+...+++.+|++. +++.... +.++.+.|.+|++|+|+.
T Consensus 1 ~l~i~~~~~~~~~~l~-~~l~~~~~~~P~v~----i~~~~~~--------------------~~~~~~~l~~~~~Dl~i~ 55 (185)
T cd08439 1 TLRIGCPDDYADTILP-FLLNRFASVYPRLA----IEVVCKR--------------------TPRLMEMLERGEVDLALI 55 (185)
T ss_pred CeEEEcchhHhHHHHH-HHHHHHHHHCCCeE----EEEEECC--------------------hHHHHHHHHCCCCcEEEE
Confidence 4788888776655544 44566677899762 4443211 357889999999999997
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (185)
T cd08439 56 TH 57 (185)
T ss_pred ec
Confidence 53
No 49
>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=87.06 E-value=3.9 Score=33.01 Aligned_cols=57 Identities=23% Similarity=0.352 Sum_probs=39.3
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+.. ..-...+...+.+.+|++. +++.. ++ +.++.++|.+|++|+++.
T Consensus 1 ~l~i~~~~~~~-~~~l~~~l~~~~~~~P~~~----l~~~~----~~----------------~~~~~~~l~~g~~D~~i~ 55 (201)
T cd08420 1 TLRIGASTTIG-EYLLPRLLARFRKRYPEVR----VSLTI----GN----------------TEEIAERVLDGEIDLGLV 55 (201)
T ss_pred CeEEeeccchh-hhhhHHHHHHHHHHCCCce----EEEEe----CC----------------cHHHHHHHHCCCccEEEe
Confidence 47888877743 3445566677778899752 44432 11 246889999999999998
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (201)
T cd08420 56 EG 57 (201)
T ss_pred cC
Confidence 64
No 50
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=86.93 E-value=2.6 Score=39.63 Aligned_cols=124 Identities=19% Similarity=0.136 Sum_probs=81.9
Q ss_pred HHHHHHHcCCCcEEEeeCCCCC--CCCCC--CceeeeecCCCCCcceeeccCc---cCcccCCCCCEEecCChHH-HHHH
Q 020472 131 EIDEALINSQIDIAVHSMKDVP--TYLPE--KTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTASLRR-KSQI 202 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlP--t~lp~--gL~iaAv~kReDprD~LV~~~~---~~l~dLp~ga~IGTSS~RR-~aQL 202 (326)
+.-++|..|.+|+++...-+.| ..... .+.+++...+.....+++.++. +++.|| +|-+||..-.-- ...+
T Consensus 73 ~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~~va~~~~~~~~~~i~~~~~~~i~~~adl-kGk~vg~~~~~~~~~~~ 151 (335)
T COG0715 73 PVLEALAAGALDFAVYYTGDTPLIAAGAAGAPVKVVAALVQNGNGIALLVLKDSGIKSVADL-KGKKVGVPFGGSTSDFL 151 (335)
T ss_pred HHHHHHhcCCcCccccccCchHHHHhhccCCCeEEeeecccCCceeEEEeccCCCcccccCC-CCceEEEeCCCchHHHH
Confidence 4679999999999999888888 44444 4888888888875566665543 346888 899999877654 3222
Q ss_pred Hhh--------CCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCC
Q 020472 203 LHR--------YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDD 258 (326)
Q Consensus 203 ~~~--------~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~ 258 (326)
..+ ..|.+++ ++..+ .-...|..|..||.+...--..++-........++..+
T Consensus 152 l~~~L~~~Gl~~~dv~~v-~~~~~--~~~~al~~g~vda~~~~ep~~~~~~~~~~~~~~~~~~~ 212 (335)
T COG0715 152 LRYALAKAGLDPDDVELV-NLPPA--DAVAALAAGQVDAFVVWEPWNAAAEGEGGGRVLLDGAD 212 (335)
T ss_pred HHHHHHHcCCCcccceEE-eeCcH--HHHHHHhcCCcceEEecCCchhhhhccCCeEEEEcchh
Confidence 221 2445555 55544 67778899999998776665555544333323344433
No 51
>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=86.84 E-value=4.9 Score=32.89 Aligned_cols=57 Identities=19% Similarity=0.279 Sum_probs=38.0
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.|+||.=.+. +..---.+.+.+++.||++. +++. + |+ ..++.+.|.+|++|+++.
T Consensus 2 ~l~ig~~~~~-~~~~l~~~i~~~~~~~P~v~----l~i~---~-~~----------------~~~~~~~l~~~~~Dl~i~ 56 (198)
T cd08446 2 ELDVGYFGSA-ILDTVPRLLRAFLTARPDVT----VSLH---N-MT----------------KDEQIEALRAGRIHIGFG 56 (198)
T ss_pred eEEEEechHH-HHHHHHHHHHHHHHHCCCeE----EEEe---e-CC----------------HHHHHHHHHCCCccEEEE
Confidence 5888884444 33334566677788899752 4332 1 22 246889999999999996
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 57 ~~ 58 (198)
T cd08446 57 RF 58 (198)
T ss_pred ec
Confidence 43
No 52
>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=86.63 E-value=4.4 Score=33.05 Aligned_cols=137 Identities=15% Similarity=0.103 Sum_probs=73.5
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.++||+-.+ ++....-.+...+++.+|++. +++... . ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~-~~~~~l~~~l~~~~~~~P~i~----v~~~~~----~----------------~~~~~~~l~~g~~D~~i~ 55 (198)
T cd08447 1 SLRIGFTAA-SAYSFLPRLLAAARAALPDVD----LVLREM----V----------------TTDQIEALESGRIDLGLL 55 (198)
T ss_pred CEEEEEehH-HHHHHHHHHHHHHHHHCCCeE----EEEEeC----C----------------HHHHHHHHHcCCceEEEe
Confidence 378888665 455556667788888899752 444221 1 357889999999999998
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeecc-C-------ccCcccCCCCCEEecC--C---hHHH-HH-HHhh--CCCC
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISL-S-------AASLAELPAGSIVGTA--S---LRRK-SQ-ILHR--YPSL 209 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~-~-------~~~l~dLp~ga~IGTS--S---~RR~-aQ-L~~~--~Pdl 209 (326)
.... .++++..-.+. + ++. ++++. + ..++++|.+-..|... + .|+. .+ +... .|+.
T Consensus 56 ~~~~----~~~~~~~~~l~-~-~~~-~~v~~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 128 (198)
T cd08447 56 RPPF----ARPGLETRPLV-R-EPL-VAAVPAGHPLAGAERLTLEDLDGQPFIMYSPTEARYFHDLVVRLFASAGVQPRY 128 (198)
T ss_pred cCCC----CCCCeeEEEee-c-Cce-EEEecCCCchhhcCcccHHHhCCCeEEEeCCCCCchHHHHHHHHHHHcCCCCCc
Confidence 6322 13444332222 2 211 23322 1 1234566555555532 1 1221 12 2222 2333
Q ss_pred EEEeccCCCHHHHHhhhccCCccEEeeehh
Q 020472 210 KVMENFRGNVQTRLRKLNERVVQATLLALA 239 (326)
Q Consensus 210 ~v~~~iRGNV~TRL~KL~~ge~DAIILA~A 239 (326)
.+ .-.|+++-++-+.+|..=+ +++..
T Consensus 129 ~~---~~~~~~~~~~~v~~g~gi~-~~p~~ 154 (198)
T cd08447 129 VQ---YLSQIHTMLALVRAGLGVA-LVPAS 154 (198)
T ss_pred ee---ecCCHHHHHHHHHcCCCeE-EhhHH
Confidence 22 2368899988888886422 44443
No 53
>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=86.43 E-value=5.1 Score=32.45 Aligned_cols=57 Identities=23% Similarity=0.268 Sum_probs=38.0
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||.=.+....+ .-.+...+++.+|++. ++++... ..++.+.|.+|++|+++.
T Consensus 1 ~l~i~~~~~~~~~~-l~~~l~~~~~~~P~i~----i~i~~~~--------------------~~~~~~~l~~~~~Di~i~ 55 (197)
T cd08448 1 RLRIGFVGSMLYRG-LPRILRAFRAEYPGIE----VALHEMS--------------------SAEQIEALLRGELDLGFV 55 (197)
T ss_pred CeEEEEchhHHHHH-HHHHHHHHHHHCCCCe----EEEEeCC--------------------HHHHHHHHHcCCcceEEE
Confidence 36788865544443 3445666777799863 5553221 357889999999999997
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (197)
T cd08448 56 HS 57 (197)
T ss_pred eC
Confidence 54
No 54
>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=86.40 E-value=16 Score=29.73 Aligned_cols=133 Identities=11% Similarity=0.116 Sum_probs=71.9
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
+.|+||+=.+.... ..-.+...+.+.+|++. +++.... ..++.+.|.+|++|+|+
T Consensus 1 g~l~Ig~~~~~~~~-~l~~~l~~~~~~~P~v~----i~i~~~~--------------------~~~~~~~l~~g~~Dl~i 55 (197)
T cd08425 1 GSLRLAMTPTFTAY-LIGPLIDRFHARYPGIA----LSLREMP--------------------QERIEAALADDRLDLGI 55 (197)
T ss_pred CeEEEEechhhhhh-hhHHHHHHHHHHCCCcE----EEEEECc--------------------HHHHHHHHHcCCccEEE
Confidence 36899997664433 44556666677899762 5543321 24688999999999999
Q ss_pred eeCCCCCCCCCCCceeeeecCCCCCcceeec-cCc--------cCcccCCCCCEEecCC---hHH--HHHHHhhCCCCEE
Q 020472 146 HSMKDVPTYLPEKTILPCNLQREDVRDAFIS-LSA--------ASLAELPAGSIVGTAS---LRR--KSQILHRYPSLKV 211 (326)
Q Consensus 146 HSlKDlPt~lp~gL~iaAv~kReDprD~LV~-~~~--------~~l~dLp~ga~IGTSS---~RR--~aQL~~~~Pdl~v 211 (326)
..... .++++....+.+ ++ -++|+ ++. .+++||..-..|...+ .|+ ...+.......++
T Consensus 56 ~~~~~----~~~~~~~~~l~~--~~-~~~v~~~~~pl~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 128 (197)
T cd08425 56 AFAPV----RSPDIDAQPLFD--ER-LALVVGATHPLAQRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRI 128 (197)
T ss_pred EecCC----CCCCcEEEEecc--cc-EEEEecCCCchhHhcccCCHHHHhcCCcEecCCCccHHHHHHHHHHHcCCCeee
Confidence 75422 134554333222 11 23332 211 2445555544444322 332 1223332222233
Q ss_pred EeccCCCHHHHHhhhccCCc
Q 020472 212 MENFRGNVQTRLRKLNERVV 231 (326)
Q Consensus 212 ~~~iRGNV~TRL~KL~~ge~ 231 (326)
. -.-.|+++-+.-+.+|..
T Consensus 129 ~-~~~~~~~~~~~~v~~g~g 147 (197)
T cd08425 129 A-IEANSISAVLEVVRRGRL 147 (197)
T ss_pred E-EeeCcHHHHHHHHhcCCc
Confidence 3 223688999988888864
No 55
>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=86.20 E-value=3.4 Score=33.83 Aligned_cols=58 Identities=22% Similarity=0.214 Sum_probs=40.4
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.|+||+=.+ ++....-.+...+++.+|++. +++.. ++ ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~-~~~~~l~~~l~~~~~~~P~i~----i~~~~----~~----------------~~~~~~~l~~~~~D~~i~ 55 (198)
T cd08433 1 RVSVGLPPS-AASVLAVPLLRAVRRRYPGIR----LRIVE----GL----------------SGHLLEWLLNGRLDLALL 55 (198)
T ss_pred CeEEEechh-hhhhcchHHHHHHHHHCCCcE----EEEEe----cC----------------cHHHHHHHhCCCCcEEEE
Confidence 378888665 555555666778888899762 44432 11 247889999999999998
Q ss_pred eCC
Q 020472 147 SMK 149 (326)
Q Consensus 147 SlK 149 (326)
...
T Consensus 56 ~~~ 58 (198)
T cd08433 56 YGP 58 (198)
T ss_pred eCC
Confidence 653
No 56
>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=86.16 E-value=3.3 Score=33.85 Aligned_cols=58 Identities=24% Similarity=0.296 Sum_probs=39.7
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||.=.|.... -...+...+++.||++. +++.. ++ ..++.+.|.+|++|+|++
T Consensus 1 ~l~Ig~~~~~~~~-~~~~~i~~~~~~~P~i~----l~~~~----~~----------------~~~~~~~l~~g~~D~~i~ 55 (200)
T cd08417 1 TFRIAASDYLEAL-LLPPLLARLRQEAPGVR----LRFVP----LD----------------RDDLEEALESGEIDLAIG 55 (200)
T ss_pred CeEEeccHHHHHH-HHHHHHHHHHhhCCCeE----EEecc----CC----------------HHHHHHHHHcCCCCEEEe
Confidence 3788877765543 34556677778899752 44421 11 247899999999999998
Q ss_pred eCC
Q 020472 147 SMK 149 (326)
Q Consensus 147 SlK 149 (326)
...
T Consensus 56 ~~~ 58 (200)
T cd08417 56 VFP 58 (200)
T ss_pred ecc
Confidence 654
No 57
>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=86.12 E-value=4.8 Score=33.99 Aligned_cols=57 Identities=14% Similarity=0.183 Sum_probs=39.7
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||+-.+. +..-.-.+...+++.||++. +++... + ..++.+.|.+|++|+++..
T Consensus 2 ~~Ig~~~~~-~~~~l~~~l~~f~~~~P~v~----l~i~~~----~----------------~~~~~~~l~~g~~Di~i~~ 56 (221)
T cd08469 2 FVIAANDYV-TAVLLPALVRRLETEAPGID----LRIRPV----T----------------RLDLAEQLDLGRIDLVIGI 56 (221)
T ss_pred EEEEEChHH-HHHHHHHHHHHHHHHCCCcE----EEEeeC----C----------------hhhHHHHHHCCCccEEEec
Confidence 788985554 44456677788888899752 444321 1 2468899999999999975
Q ss_pred CC
Q 020472 148 MK 149 (326)
Q Consensus 148 lK 149 (326)
..
T Consensus 57 ~~ 58 (221)
T cd08469 57 FE 58 (221)
T ss_pred CC
Confidence 43
No 58
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=86.00 E-value=14 Score=34.08 Aligned_cols=140 Identities=17% Similarity=0.221 Sum_probs=70.1
Q ss_pred HHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC---ccCcccCCCCCEEecC--C-hHH--HHHHHhh
Q 020472 134 EALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS---AASLAELPAGSIVGTA--S-LRR--KSQILHR 205 (326)
Q Consensus 134 ~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~---~~~l~dLp~ga~IGTS--S-~RR--~aQL~~~ 205 (326)
.+|.+|++|+++.++..=|.. .+.+.... +=-.-.-+++.++ ..++++| .|.+||+. | ... ..+++..
T Consensus 95 ~~l~~g~~D~~~~~~~~t~eR-~~~~~fs~--py~~~~~~lvv~~~~~~~s~~dL-~g~~V~v~~gs~~~~~l~~~~~~~ 170 (259)
T PRK11917 95 PLLDNGSVDAVIATFTITPER-KRIYNFSE--PYYQDAIGLLVLKEKNYKSLADM-KGANIGVAQAATTKKAIGEAAKKI 170 (259)
T ss_pred HHHHCCCccEEEecccCChhh-hheeeecc--CceeeceEEEEECCCCCCCHHHh-CCCeEEEecCCcHHHHHHHhhHhc
Confidence 578899999999987543321 11111110 0000011222221 2356777 46666651 2 111 1223334
Q ss_pred CCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCchhHHhhhhc
Q 020472 206 YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTH 285 (326)
Q Consensus 206 ~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~~~~~lL~~ 285 (326)
.++.+++ .. .+...-++.|.+|++||++.-..-+..+ ..+. ...++ +.+.+. -+++..+++|+++.+.++.
T Consensus 171 ~~~~~~~-~~-~~~~~~~~~l~~GrvDa~~~d~~~~~~~-~~~~-~~~~~-~~~~~~----~~~~a~~k~~~~l~~~ln~ 241 (259)
T PRK11917 171 GIDVKFS-EF-PDYPSIKAALDAKRVDAFSVDKSILLGY-VDDK-SEILP-DSFEPQ----SYGIVTKKDDPAFAKYVDD 241 (259)
T ss_pred CCceeEE-ec-CCHHHHHHHHHcCCCcEEEecHHHHHHh-hhcC-CeecC-CcCCCC----ceEEEEeCCCHHHHHHHHH
Confidence 4556665 33 3567778999999999998764322211 1111 11221 122221 1356678998877776654
Q ss_pred c
Q 020472 286 S 286 (326)
Q Consensus 286 ~ 286 (326)
.
T Consensus 242 ~ 242 (259)
T PRK11917 242 F 242 (259)
T ss_pred H
Confidence 4
No 59
>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=85.96 E-value=18 Score=29.72 Aligned_cols=57 Identities=23% Similarity=0.297 Sum_probs=40.5
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+-.+ ++..-.-.+...+++.||++. ++++.-. +.++.+.|.+|++|+++.
T Consensus 1 ~l~I~~~~~-~~~~~l~~~l~~~~~~~P~v~----v~i~~~~--------------------~~~~~~~l~~g~~D~~i~ 55 (201)
T cd08459 1 TFRIAMSDI-GEMYFLPRLLAALREVAPGVR----IETVRLP--------------------VDELEEALESGEIDLAIG 55 (201)
T ss_pred CeEEEeChH-HHHHHHHHHHHHHHHHCCCCe----EEEEecC--------------------ccCHHHHhhCCCceEEEE
Confidence 478999644 555556678888889999862 5553221 135778999999999998
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (201)
T cd08459 56 YL 57 (201)
T ss_pred cC
Confidence 64
No 60
>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=85.96 E-value=19 Score=30.02 Aligned_cols=56 Identities=13% Similarity=0.183 Sum_probs=39.7
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+-.+.. ....-.+...+++.||++. +++.. ++ ..++-+.|.+|++|+++-
T Consensus 1 ~l~Ig~~~~~~-~~~l~~~l~~f~~~~P~i~----l~i~~----~~----------------~~~~~~~L~~g~~Dl~i~ 55 (200)
T cd08465 1 VFRLAMSDYGA-RLVLPALMRQLRAEAPGID----LAVSQ----AS----------------REAMLAQVADGEIDLALG 55 (200)
T ss_pred CEEEEechhhH-HHhhhHHHHHHHHHCCCcE----EEEec----CC----------------hHhHHHHHHCCCccEEEe
Confidence 47888887654 4455567788888899863 44432 11 257889999999999995
Q ss_pred e
Q 020472 147 S 147 (326)
Q Consensus 147 S 147 (326)
.
T Consensus 56 ~ 56 (200)
T cd08465 56 V 56 (200)
T ss_pred c
Confidence 3
No 61
>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=85.95 E-value=4.5 Score=32.68 Aligned_cols=138 Identities=17% Similarity=0.128 Sum_probs=72.0
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+=.+.. ..-.-.+.+.+.+.+|++. +++..-. +.++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~-~~~l~~~l~~~~~~~P~v~----i~i~~~~--------------------~~~~~~~l~~~~~Dl~i~ 55 (194)
T cd08436 1 RLAIGTITSLA-AVDLPELLARFHRRHPGVD----IRLRQAG--------------------SDDLLAAVREGRLDLAFV 55 (194)
T ss_pred CEEEEeehHHH-HHHHHHHHHHHHHHCCCcE----EEEecCC--------------------HHHHHHHHHcCCccEEEE
Confidence 37888876643 3334556677788899762 4443211 357889999999999997
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeec-cC-------ccCcccCCCCCEEec---CChHHH-HHH-HhhCCCCEEEe
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFIS-LS-------AASLAELPAGSIVGT---ASLRRK-SQI-LHRYPSLKVME 213 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~-~~-------~~~l~dLp~ga~IGT---SS~RR~-aQL-~~~~Pdl~v~~ 213 (326)
...+ ..++++..--+.+ ++ -+++. ++ ..++++|-.-..|.. ++.|+. .+. .......++.
T Consensus 56 ~~~~---~~~~~~~~~~l~~--~~-~~~~~~~~~~l~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~- 128 (194)
T cd08436 56 GLPE---RRPPGLASRELAR--EP-LVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVA- 128 (194)
T ss_pred ecCC---CCCCCcEEEEeec--ce-EEEEecCCCcccCCCccCHHHHhCCCeEEecCcccHHHHHHHHHHHcCCCCceE-
Confidence 6543 2244543322211 11 22222 11 113444433333332 223433 222 2222222332
Q ss_pred ccCCCHHHHHhhhccCCccEEee
Q 020472 214 NFRGNVQTRLRKLNERVVQATLL 236 (326)
Q Consensus 214 ~iRGNV~TRL~KL~~ge~DAIIL 236 (326)
-.=.|..+-++-+.+|..=|++-
T Consensus 129 ~~~~~~~~~~~~v~~g~gi~~~p 151 (194)
T cd08436 129 FEVSDVDLLLDLVARGLGVALLP 151 (194)
T ss_pred EEeccHHHHHHHHHcCCceEEec
Confidence 22368888888888886544443
No 62
>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=85.88 E-value=3.2 Score=33.95 Aligned_cols=57 Identities=21% Similarity=0.214 Sum_probs=38.6
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+.-.. -.-.+...+++.||++. +++.. ++ ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~~~-~l~~~l~~~~~~~P~v~----l~i~~----~~----------------~~~~~~~l~~g~~D~~i~ 55 (200)
T cd08464 1 TFRIGLSDDVESW-LAPPLLAALRAEAPGVR----LVFRQ----VD----------------PFNVGDMLDRGEIDLAIG 55 (200)
T ss_pred CEEEEechHHHHH-HHHHHHHHHHHHCCCcE----EEEec----CC----------------cccHHHHHhcCcccEEEe
Confidence 4788887765543 35556667778899862 54432 11 135778999999999998
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (200)
T cd08464 56 VF 57 (200)
T ss_pred cC
Confidence 54
No 63
>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=85.61 E-value=4.3 Score=33.33 Aligned_cols=56 Identities=13% Similarity=0.119 Sum_probs=38.8
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.|+||+-.+.-..+ .-.+...+.+.||++. +++.... ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~~~~-~~~~l~~~~~~~P~i~----i~i~~~~--------------------~~~~~~~l~~g~~Dl~i~ 55 (198)
T cd08441 1 RLRIAVECHSCFDW-LMPVLDQFRERWPDVE----LDLSSGF--------------------HFDPLPALLRGELDLVIT 55 (198)
T ss_pred CEEEEeeccchhhh-hHHHHHHHHHhCCCeE----EEEEeCC--------------------chhHHHHHHcCCceEEEe
Confidence 37899877665443 3346678888899752 4443221 247889999999999997
Q ss_pred e
Q 020472 147 S 147 (326)
Q Consensus 147 S 147 (326)
.
T Consensus 56 ~ 56 (198)
T cd08441 56 S 56 (198)
T ss_pred c
Confidence 4
No 64
>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=84.49 E-value=6 Score=32.14 Aligned_cols=132 Identities=20% Similarity=0.241 Sum_probs=70.7
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.|. +..-.-.+...+++.+|++. +++.. ++ ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~-~~~~l~~~l~~~~~~~P~v~----i~i~~----~~----------------~~~~~~~l~~~~~Dl~i~ 55 (201)
T cd08435 1 TVRVGAVPAA-APVLLPPAIARLLARHPRLT----VRVVE----GT----------------SDELLEGLRAGELDLAIG 55 (201)
T ss_pred CeEEEechHH-HHHHHHHHHHHHHHHCCCeE----EEEEe----CC----------------HHHHHHHHHcCCccEEEE
Confidence 4788887764 44445566677788899752 44421 11 357889999999999997
Q ss_pred eCCCCCCCC-CCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEecC---ChHHH-HH-HHhhC---CCCE
Q 020472 147 SMKDVPTYL-PEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA---SLRRK-SQ-ILHRY---PSLK 210 (326)
Q Consensus 147 SlKDlPt~l-p~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGTS---S~RR~-aQ-L~~~~---Pdl~ 210 (326)
... ..+ ++++...- -..++--+++++++ .+++||-.-..|... ..++. .+ +.... |+..
T Consensus 56 ~~~---~~~~~~~~~~~~--l~~~~~~~~~~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 (201)
T cd08435 56 RLA---DDEQPPDLASEE--LADEPLVVVARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNV 130 (201)
T ss_pred ecC---cccCCCCcEEEE--cccCcEEEEEeCCCcCcccCCcCHHHHhcCCEEecCCCCcHHHHHHHHHHHcCCCCCCce
Confidence 532 211 34543322 22233333333321 234444333344332 23332 12 22111 3332
Q ss_pred EEeccCCCHHHHHhhhccCCc
Q 020472 211 VMENFRGNVQTRLRKLNERVV 231 (326)
Q Consensus 211 v~~~iRGNV~TRL~KL~~ge~ 231 (326)
+ .-+|+.+-++-+.+|..
T Consensus 131 ~---~~~~~~~~~~~v~~g~g 148 (201)
T cd08435 131 V---ETASISALLALLARSDM 148 (201)
T ss_pred E---EEccHHHHHHHHhcCCe
Confidence 2 34788998888888853
No 65
>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=84.37 E-value=5.6 Score=32.32 Aligned_cols=58 Identities=17% Similarity=0.259 Sum_probs=39.3
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+.-..+ .-.+...+++.+|++. +++... . ..++.+.|.+|++|+++.
T Consensus 1 ~l~ig~~~~~~~~~-l~~~l~~~~~~~P~i~----i~~~~~----~----------------~~~~~~~l~~~~~Dl~i~ 55 (197)
T cd08449 1 HLNIGMVGSVLWGG-LGPALRRFKRQYPNVT----VRFHEL----S----------------PEAQKAALLSKRIDLGFV 55 (197)
T ss_pred CeEEEEechHhhhh-HHHHHHHHHHHCCCeE----EEEEEC----C----------------HHHHHHHHhCCCccEEEe
Confidence 47888877766554 4445567778899752 444321 1 357889999999999996
Q ss_pred eCC
Q 020472 147 SMK 149 (326)
Q Consensus 147 SlK 149 (326)
...
T Consensus 56 ~~~ 58 (197)
T cd08449 56 RFA 58 (197)
T ss_pred ccc
Confidence 543
No 66
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=84.36 E-value=34 Score=31.63 Aligned_cols=192 Identities=14% Similarity=0.115 Sum_probs=101.2
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.+.|+||+-.|....+-...+.+ +.+.+|++. +++.... ..++.++|.+|++|++
T Consensus 90 ~g~l~i~~~~~~~~~~~~~~l~~-~~~~~P~v~----i~~~~~~--------------------~~~~~~~l~~g~~Dl~ 144 (305)
T PRK11151 90 SGPLHIGLIPTVGPYLLPHIIPM-LHQTFPKLE----MYLHEAQ--------------------THQLLAQLDSGKLDCA 144 (305)
T ss_pred CceEEEEecchhHHHHHHHHHHH-HHHHCCCcE----EEEEeCC--------------------HHHHHHHHHcCCccEE
Confidence 46899999999876666654444 666788752 4332211 2478899999999999
Q ss_pred EeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEecCC---hHHHH--HHHhh--CCCCE
Q 020472 145 VHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTAS---LRRKS--QILHR--YPSLK 210 (326)
Q Consensus 145 VHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGTSS---~RR~a--QL~~~--~Pdl~ 210 (326)
|... +.+ .+++.. ..-..++--+++.+.+ .++++|..-..|++.. .|+.. .+... .|...
T Consensus 145 i~~~-~~~---~~~l~~--~~l~~~~~~~~~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 (305)
T PRK11151 145 ILAL-VKE---SEAFIE--VPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTH 218 (305)
T ss_pred EEec-CCC---CCCeEE--EEeccCcEEEEecCCCCcccCCccCHHHhcCCCeEeecCCccHHHHHHHHHHHCCCCCCce
Confidence 9763 222 234432 2222233333333221 2456666666777643 44321 22222 34433
Q ss_pred EEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCch---hHHhhhhccc
Q 020472 211 VMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDE---KMVPFTTHSQ 287 (326)
Q Consensus 211 v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~---~~~~lL~~~~ 287 (326)
+. =.+..+-++-+.+|..=+ +++............+ ..+++..-.| ...+.+.++.+.. ....+++.+.
T Consensus 219 ~~---~~~~~~~~~~v~~g~gi~-ilp~~~~~~~~~~~~l-~~~~~~~~~~---~~~~~l~~~~~~~~~~~~~~~~~~~~ 290 (305)
T PRK11151 219 FR---ATSLETLRNMVAAGSGIT-LLPALAVPNERKRDGV-CYLPCIKPEP---RRTIGLVYRPGSPLRSRYEQLAEAIR 290 (305)
T ss_pred EE---eccHHHHHHHHHcCCCEE-EeeHHhhhhhcccCCE-EEEECcCCcc---ceEEEEEEcCCCcchHHHHHHHHHHH
Confidence 32 367888877777776533 4444333222111222 2344332222 3457777766543 3445555555
Q ss_pred cccccccc
Q 020472 288 ASILNTFN 295 (326)
Q Consensus 288 ~~~~n~~~ 295 (326)
....+.|+
T Consensus 291 ~~~~~~~~ 298 (305)
T PRK11151 291 ARMDGHFD 298 (305)
T ss_pred HHhcccHH
Confidence 44555553
No 67
>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=84.33 E-value=0.96 Score=39.59 Aligned_cols=103 Identities=18% Similarity=0.165 Sum_probs=60.1
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCCCc--eeeeecCCCCCcceeeccC--ccCcccCCCCCEEecCChHHH-----HH
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPEKT--ILPCNLQREDVRDAFISLS--AASLAELPAGSIVGTASLRRK-----SQ 201 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~gL--~iaAv~kReDprD~LV~~~--~~~l~dLp~ga~IGTSS~RR~-----aQ 201 (326)
+..++|.+|++|+++=..=-+......|. .+++..-...+..+++.++ -+++.|| +|-+||.+.---. +.
T Consensus 33 ~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DL-kGK~i~v~~~s~~~~~~~~~ 111 (216)
T PF09084_consen 33 DVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADL-KGKKIGVSRGSSSEYFLRAL 111 (216)
T ss_dssp HHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGG-TTSEEEESTTSHHHHHHHHH
T ss_pred HHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHh-CCCEEEEecCcchhHHHHHH
Confidence 56799999999999876644443334444 3333222233444343322 3567888 6999998882111 12
Q ss_pred HHhh---CCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 202 ILHR---YPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 202 L~~~---~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
|+.. ..+++++ ++. -......|.+|+.||+++-
T Consensus 112 l~~~g~~~~~v~~v-~~~--~~~~~~al~~g~vDa~~~~ 147 (216)
T PF09084_consen 112 LKKNGIDPDDVKIV-NLG--PPELAQALLSGQVDAAILW 147 (216)
T ss_dssp HHHTTT-GGGSEEE-ES---HHHHHHHHHTTSSSEEEEE
T ss_pred HHHhccccccceee-eee--hhhhhhhhhcCCCCEEEEc
Confidence 2222 2456666 453 3444458999999999943
No 68
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=84.26 E-value=4.4 Score=33.93 Aligned_cols=133 Identities=12% Similarity=0.060 Sum_probs=72.1
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+.... .--.+...+++.||++. +++... .+.++.+.|.+|++|+|+-
T Consensus 2 ~l~Ig~~~~~~~~-~l~~~l~~f~~~~P~v~----i~i~~~--------------------~~~~l~~~l~~g~~D~~~~ 56 (198)
T cd08486 2 ELSVAYFGTPIYR-SLPLLLRAFLTSTPTAT----VSLTHM--------------------TKDEQVEGLLAGTIHVGFS 56 (198)
T ss_pred eEEEEEechhhHH-HHHHHHHHHHHhCCCeE----EEEEEC--------------------CHHHHHHHHHcCCceEEEe
Confidence 5889987776432 23345566677799762 444321 1468999999999999995
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeeccC-------ccCcccCCCCCEEecC-----ChHHHHH--HHhhCCCCEEE
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISLS-------AASLAELPAGSIVGTA-----SLRRKSQ--ILHRYPSLKVM 212 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~~-------~~~l~dLp~ga~IGTS-----S~RR~aQ--L~~~~Pdl~v~ 212 (326)
.- | ..++++....+.+ ++-=++++++ ..++++|.+-..|+.+ +.|+... +.......++.
T Consensus 57 ~~---~-~~~~~~~~~~l~~--~~~~lv~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 (198)
T cd08486 57 RF---F-PRHPGIEIVNIAQ--EDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIA 130 (198)
T ss_pred cC---C-CCCCceEEEEEee--ccEEEEecCCCccccCCcccHHHHcCCCeEeecCCcCchHHHHHHHHHHHcCCCcceE
Confidence 32 1 1245554333222 2222233321 1245667665566543 2344322 12222233333
Q ss_pred eccCCCHHHHHhhhccCCc
Q 020472 213 ENFRGNVQTRLRKLNERVV 231 (326)
Q Consensus 213 ~~iRGNV~TRL~KL~~ge~ 231 (326)
-.=.++++=+.-+..|.-
T Consensus 131 -~~~~~~~~~~~~v~~g~G 148 (198)
T cd08486 131 -RVVEDATAALALTMAGAA 148 (198)
T ss_pred -EEeccHHHHHHHHHcCce
Confidence 223678888887777743
No 69
>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=83.27 E-value=24 Score=28.89 Aligned_cols=145 Identities=12% Similarity=0.001 Sum_probs=74.3
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
++|+||+=.+.... -.-.+...+++.+|++. +++..- . ..++.+.|.+|++|+++
T Consensus 1 g~l~I~~~~~~~~~-~l~~~l~~~~~~~P~i~----i~i~~~----~----------------~~~~~~~l~~~~~Dl~i 55 (200)
T cd08411 1 GPLRLGVIPTIAPY-LLPRLLPALRQAYPKLR----LYLRED----Q----------------TERLLEKLRSGELDAAL 55 (200)
T ss_pred CeEEEEecHHHHhh-hhHHHHHHHHHHCCCcE----EEEEeC----c----------------HHHHHHHHHcCCccEEE
Confidence 36899997665443 34455667778899752 444321 1 24788999999999999
Q ss_pred eeCCCCCCCCCCCceeeeecCCCCCcceeeccC-------ccCcccCCCCCEEecC---ChHHH-H-HHHhhCCCCEEEe
Q 020472 146 HSMKDVPTYLPEKTILPCNLQREDVRDAFISLS-------AASLAELPAGSIVGTA---SLRRK-S-QILHRYPSLKVME 213 (326)
Q Consensus 146 HSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~-------~~~l~dLp~ga~IGTS---S~RR~-a-QL~~~~Pdl~v~~ 213 (326)
.....- ++++..--+ .+++.-++++++ ..++++|..-..|..+ +.|+. . .+.......++.
T Consensus 56 ~~~~~~----~~~~~~~~l--~~~~~~~v~~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~- 128 (200)
T cd08411 56 LALPVD----EPGLEEEPL--FDEPFLLAVPKDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTD- 128 (200)
T ss_pred EeccCC----CCCceEEEe--eccceEEEecCCCCccccCccCHHHHcCCceEecCCCCcHHHHHHHHHHHcCCCcceE-
Confidence 753221 233322211 122222222221 1234455444444422 23332 1 222222222332
Q ss_pred ccCCCHHHHHhhhccCCccEEeeehhhhcc
Q 020472 214 NFRGNVQTRLRKLNERVVQATLLALAGLKR 243 (326)
Q Consensus 214 ~iRGNV~TRL~KL~~ge~DAIILA~AGL~R 243 (326)
-.-.|..+-+.-+.+|.. -.+++....+.
T Consensus 129 ~~~~~~~~~~~~v~~g~g-i~~~p~~~~~~ 157 (200)
T cd08411 129 FEATSLETLRQMVAAGLG-ITLLPELAVPS 157 (200)
T ss_pred EEeccHHHHHHHHHcCCC-EEEeCHHHhcc
Confidence 223688888888888853 33555554444
No 70
>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=83.22 E-value=5.8 Score=32.46 Aligned_cols=56 Identities=13% Similarity=0.202 Sum_probs=36.9
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+-.+....+ .-.+...+++.||++. +++... . ..++.+.|.+|++|+++.
T Consensus 1 ~l~I~~~~~~~~~~-l~~~l~~f~~~~P~v~----i~i~~~----~----------------~~~~~~~l~~~~~Di~i~ 55 (198)
T cd08461 1 TLVIAATDYAQKAI-LPPLLAALRQEAPGVR----VAIRDL----E----------------SDNLEAQLERGEVDLALT 55 (198)
T ss_pred CEEEEechHHHHHH-hHHHHHHHHHHCCCcE----EEEeeC----C----------------cccHHHHHhcCCCcEEEe
Confidence 47889866554433 4455667778899762 444321 1 135788999999999996
Q ss_pred e
Q 020472 147 S 147 (326)
Q Consensus 147 S 147 (326)
.
T Consensus 56 ~ 56 (198)
T cd08461 56 T 56 (198)
T ss_pred c
Confidence 4
No 71
>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=82.65 E-value=8.7 Score=31.30 Aligned_cols=134 Identities=13% Similarity=0.081 Sum_probs=70.1
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||+-.+.-..+ --.+...+++.+|++. +++.... ..++.+.|.+|++|+++..
T Consensus 2 l~I~~~~~~~~~~-l~~~l~~~~~~~P~i~----i~~~~~~--------------------~~~~~~~l~~~~~D~~i~~ 56 (198)
T cd08421 2 VRLLANTSAIVEF-LPEDLASFLAAHPDVR----IDLEERL--------------------SADIVRAVAEGRADLGIVA 56 (198)
T ss_pred EEEEeccchhhhh-hHHHHHHHHHHCCCce----EEEEecC--------------------cHHHHHHHhcCCceEEEEe
Confidence 7888876665544 3456777778899762 4443211 2478899999999999975
Q ss_pred CCCCCCCCCCCceeeeecCCCCCcceeec-cCc-------cCcccCCCCCEEecC---ChHHH-HHH-HhhCCCCEEEec
Q 020472 148 MKDVPTYLPEKTILPCNLQREDVRDAFIS-LSA-------ASLAELPAGSIVGTA---SLRRK-SQI-LHRYPSLKVMEN 214 (326)
Q Consensus 148 lKDlPt~lp~gL~iaAv~kReDprD~LV~-~~~-------~~l~dLp~ga~IGTS---S~RR~-aQL-~~~~Pdl~v~~~ 214 (326)
... .++++..-.+. .++ -++++ ++. .++++|-.-..|..+ +.|+. .+. ....-..++. -
T Consensus 57 ~~~----~~~~~~~~~l~--~~~-~~~v~~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 128 (198)
T cd08421 57 GNV----DAAGLETRPYR--TDR-LVVVVPRDHPLAGRASVAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLR-V 128 (198)
T ss_pred cCC----CCCCcEEEEee--cCc-EEEEeCCCCCccccCCCCHHHhcCCceEeecCCcchHHHHHHHHHHcCCCceEE-E
Confidence 433 23455433222 122 22332 221 234444433344422 23321 111 2222223333 2
Q ss_pred cCCCHHHHHhhhccCCccEE
Q 020472 215 FRGNVQTRLRKLNERVVQAT 234 (326)
Q Consensus 215 iRGNV~TRL~KL~~ge~DAI 234 (326)
.=.|+++=+.-+.+|..=|+
T Consensus 129 ~~~~~~~~~~~v~~g~gia~ 148 (198)
T cd08421 129 QVSSFDAVCRMVAAGLGIGI 148 (198)
T ss_pred EECCHHHHHHHHHcCCCeEE
Confidence 23678888888888765333
No 72
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=82.19 E-value=9.6 Score=31.60 Aligned_cols=58 Identities=22% Similarity=0.280 Sum_probs=39.0
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
+.++||+-.+... ...-.+...+.+.||++. +++... .+.++.+.|.+|++|+++
T Consensus 1 ~~l~Ig~~~~~~~-~~l~~~l~~~~~~~P~i~----l~i~~~--------------------~~~~~~~~l~~~~~Dl~i 55 (203)
T cd08445 1 RTFSIGFVPSTLY-GLLPELIRRFRQAAPDVE----IELIEM--------------------TTVQQIEALKEGRIDVGF 55 (203)
T ss_pred CeEEEEEehHHHH-hHHHHHHHHHHHHCCCeE----EEEEeC--------------------ChHHHHHHHHcCCCcEEE
Confidence 4688998775543 344455666777899752 444321 135788999999999999
Q ss_pred eeC
Q 020472 146 HSM 148 (326)
Q Consensus 146 HSl 148 (326)
...
T Consensus 56 ~~~ 58 (203)
T cd08445 56 GRL 58 (203)
T ss_pred ecC
Confidence 643
No 73
>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=81.87 E-value=5.7 Score=32.18 Aligned_cols=55 Identities=24% Similarity=0.344 Sum_probs=37.4
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
++||+-.+....+ .-.+...+.+.+|++. +++.. |+ ..++.+.|.+|++|+++..
T Consensus 2 l~Ig~~~~~~~~~-l~~~l~~~~~~~P~i~----l~~~~----~~----------------~~~~~~~l~~g~~Dl~i~~ 56 (195)
T cd08427 2 LRLGAIATVLTGL-LPRALARLRRRHPDLE----VHIVP----GL----------------SAELLARVDAGELDAAIVV 56 (195)
T ss_pred EEEEeeHHHHHHH-hHHHHHHHHHHCCCce----EEEEe----CC----------------cHHHHHHHHCCCCCEEEEc
Confidence 7888877765443 3446667778899752 44322 11 2478899999999999974
No 74
>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=81.76 E-value=8.5 Score=31.10 Aligned_cols=56 Identities=18% Similarity=0.267 Sum_probs=37.9
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+=.+.-..+ --.+...+.+.+|++. +++.. |+ ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~~~~-l~~~l~~~~~~~P~i~----l~i~~----~~----------------~~~~~~~l~~g~~Dl~i~ 55 (193)
T cd08442 1 PLRLGSMETTAAVR-LPPLLAAYHARYPKVD----LSLST----GT----------------TGALIQAVLEGRLDGAFV 55 (193)
T ss_pred CeEEeccccchhhh-hHHHHHHHHHHCCCce----EEEEe----CC----------------cHHHHHHHHCCCccEEEE
Confidence 47888877654444 3456667777899762 44432 21 247889999999999996
Q ss_pred e
Q 020472 147 S 147 (326)
Q Consensus 147 S 147 (326)
.
T Consensus 56 ~ 56 (193)
T cd08442 56 A 56 (193)
T ss_pred e
Confidence 5
No 75
>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=81.65 E-value=9.7 Score=31.51 Aligned_cols=56 Identities=16% Similarity=0.227 Sum_probs=37.2
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||+-.+.-. .-.-.+...+++.||++. +++... .+.++.+.|.+|++|+++..
T Consensus 2 l~ig~~~~~~~-~~l~~~l~~~~~~~P~v~----i~i~~~--------------------~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08452 2 LVIGFVGAAIY-EFLPPIVREYRKKFPSVK----VELREL--------------------SSPDQVEELLKGRIDIGFLH 56 (197)
T ss_pred EEEEEeHHHHH-hHHHHHHHHHHHHCCCcE----EEEEec--------------------ChHHHHHHHHCCCccEEEee
Confidence 67777654333 333456666788899752 444321 13578999999999999975
Q ss_pred C
Q 020472 148 M 148 (326)
Q Consensus 148 l 148 (326)
.
T Consensus 57 ~ 57 (197)
T cd08452 57 P 57 (197)
T ss_pred C
Confidence 4
No 76
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=81.56 E-value=11 Score=35.18 Aligned_cols=62 Identities=13% Similarity=0.143 Sum_probs=42.5
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||.-.+. +..-.-.+...+.+.+|++. +++.... ..++.+.|.+|++|+
T Consensus 92 ~~g~l~I~~~~~~-~~~~l~~~l~~~~~~~P~v~----i~i~~~~--------------------~~~~~~~l~~~~~Dl 146 (309)
T PRK11013 92 RQGQLSIACLPVF-SQSLLPGLCQPFLARYPDVS----LNIVPQE--------------------SPLLEEWLSAQRHDL 146 (309)
T ss_pred CCCcEEEEEcHHH-HHhhHHHHHHHHHHHCCCCe----EEEEeCC--------------------HHHHHHHHHcCCCCE
Confidence 4568999977653 33334556777788899752 5443321 136889999999999
Q ss_pred EEeeCCC
Q 020472 144 AVHSMKD 150 (326)
Q Consensus 144 AVHSlKD 150 (326)
+++...+
T Consensus 147 ~i~~~~~ 153 (309)
T PRK11013 147 GLTETLH 153 (309)
T ss_pred EEEcCCC
Confidence 9997543
No 77
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=81.54 E-value=26 Score=31.94 Aligned_cols=58 Identities=16% Similarity=0.236 Sum_probs=39.2
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||.-.|... ...-.+.+.+.+.+|++. ++++.. + ..++.+.|.+|++|+
T Consensus 95 ~~~~l~I~~~~~~~~-~~l~~~l~~f~~~~p~i~----l~i~~~----~----------------~~~~~~~l~~g~~D~ 149 (294)
T PRK09986 95 EAGRIEIGIVGTALW-GRLRPAMRHFLKENPNVE----WLLREL----S----------------PSMQMAALERRELDA 149 (294)
T ss_pred CcceEEEEEehHHhH-HHHHHHHHHHHHhCCCeE----EEEEeC----C----------------HHHHHHHHHcCCCCE
Confidence 357899998777543 233445677788899752 433311 1 246889999999999
Q ss_pred EEe
Q 020472 144 AVH 146 (326)
Q Consensus 144 AVH 146 (326)
++-
T Consensus 150 ~i~ 152 (294)
T PRK09986 150 GIW 152 (294)
T ss_pred EEe
Confidence 995
No 78
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=81.45 E-value=8.1 Score=35.88 Aligned_cols=58 Identities=12% Similarity=0.083 Sum_probs=39.8
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+.... ..-.+...+++.||++. +.+.. |+ ..++.+.|.+|++|+
T Consensus 90 ~~g~l~Ig~~~~~~~~-~l~~~l~~~~~~~p~i~----i~i~~----~~----------------~~~~~~~l~~g~~Dl 144 (300)
T PRK11074 90 WRGQLSIAVDNIVRPD-RTRQLIVDFYRHFDDVE----LIIRQ----EV----------------FNGVWDALADGRVDI 144 (300)
T ss_pred CCceEEEEEcCccchh-HHHHHHHHHHHhCCCce----EEEEe----hh----------------hhHHHHHHHCCCCCE
Confidence 4678999997666543 44456666677899752 33321 22 246788999999999
Q ss_pred EEe
Q 020472 144 AVH 146 (326)
Q Consensus 144 AVH 146 (326)
+|=
T Consensus 145 ~i~ 147 (300)
T PRK11074 145 AIG 147 (300)
T ss_pred EEe
Confidence 994
No 79
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=81.28 E-value=31 Score=31.39 Aligned_cols=101 Identities=10% Similarity=0.141 Sum_probs=51.7
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC---ccCcccCCCCCEEec---CChHHHHHHHh
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS---AASLAELPAGSIVGT---ASLRRKSQILH 204 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~---~~~l~dLp~ga~IGT---SS~RR~aQL~~ 204 (326)
.+-+++.+|++|+++-.+-.-|.. ...+.... +-=.++..+++-++ ..+++|| .|.+||. ++.. ..+..
T Consensus 76 ~~~~~l~~g~~D~~~~~~~~t~eR-~~~~~fs~-p~~~~~~~~~~~~~~~~~~~~~dl-~g~~Igv~~g~~~~--~~~~~ 150 (259)
T PRK15437 76 ALIPSLKAKKIDAIMSSLSITEKR-QQEIAFTD-KLYAADSRLVVAKNSDIQPTVESL-KGKRVGVLQGTTQE--TFGNE 150 (259)
T ss_pred HHHHHHHCCCCCEEEecCCCCHHH-hhhccccc-hhhcCceEEEEECCCCCCCChHHh-CCCEEEEecCcHHH--HHHHh
Confidence 456889999999998755322211 11111110 00011111122111 0245666 5667765 2211 12222
Q ss_pred hC--CCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 205 RY--PSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 205 ~~--Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
.. ++++++ ..- +.+.=+++|..|++|+++...
T Consensus 151 ~~~~~~~~~~-~~~-~~~~~i~~L~~grvD~~v~~~ 184 (259)
T PRK15437 151 HWAPKGIEIV-SYQ-GQDNIYSDLTAGRIDAAFQDE 184 (259)
T ss_pred hccccCceEE-ecC-CHHHHHHHHHcCCccEEEech
Confidence 22 356666 433 556778999999999998754
No 80
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=81.19 E-value=16 Score=34.02 Aligned_cols=148 Identities=18% Similarity=0.203 Sum_probs=77.9
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..++|+||+=.|.-. +-.-.+...+.+.||++. +++... + ..++.+.|.+|++|+
T Consensus 93 ~~g~l~ig~~~~~~~-~~~~~~l~~~~~~~P~v~----i~~~~~----~----------------~~~~~~~l~~g~~Dl 147 (305)
T CHL00180 93 QRGTLIIGASQTTGT-YLMPRLIGLFRQRYPQIN----VQLQVH----S----------------TRRIAWNVANGQIDI 147 (305)
T ss_pred cCceEEEEEcCcchH-hHHHHHHHHHHHHCCCce----EEEEeC----C----------------HHHHHHHHHcCCccE
Confidence 457899999877653 444455566777899752 444211 1 246888999999999
Q ss_pred EEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEecC---ChHHH-HHHHhh---CC-C
Q 020472 144 AVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA---SLRRK-SQILHR---YP-S 208 (326)
Q Consensus 144 AVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGTS---S~RR~-aQL~~~---~P-d 208 (326)
++.. .+.|...++++..-.+. .++.-+++.+++ .++.||..-..|..+ ..|+. .++... .| +
T Consensus 148 ~i~~-~~~~~~~~~~~~~~~l~--~~~~~~v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (305)
T CHL00180 148 AIVG-GEVPTELKKILEITPYV--EDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKR 224 (305)
T ss_pred EEEc-CccCcccccceeEEEec--cCcEEEEECCCCccccCCccCHHHHccCCceEecCCCcHHHHHHHHHHHcCCCccc
Confidence 9974 34444344555332222 122223332221 134455433334332 23432 222222 22 2
Q ss_pred CEEEeccCCCHHHHHhhhccCCccEEeeehhhh
Q 020472 209 LKVMENFRGNVQTRLRKLNERVVQATLLALAGL 241 (326)
Q Consensus 209 l~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL 241 (326)
+++. -.-+|+++=+.-+.+|.. ..+++..-.
T Consensus 225 ~~~~-~~~~~~~~~~~~v~~g~g-~~~lp~~~~ 255 (305)
T CHL00180 225 FKIE-MELNSIEAIKNAVQSGLG-AAFVSVSAI 255 (305)
T ss_pred ceEE-EEeCCHHHHHHHHHcCCc-EEEeEhHHH
Confidence 3333 335788888888877744 344444433
No 81
>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=81.19 E-value=4.7 Score=33.00 Aligned_cols=56 Identities=14% Similarity=0.118 Sum_probs=38.1
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||+-.+. +....-.+...+++.||++. +++.... ..++.++|.+|++|+++..
T Consensus 2 l~Ig~~~~~-~~~~l~~~l~~~~~~~P~v~----i~i~~~~--------------------~~~~~~~l~~g~~D~~i~~ 56 (195)
T cd08431 2 LRIAIDTVL-PLQPLYPLIAEFYQLNKATR----IRLSEEV--------------------LGGTWDALASGRADLVIGA 56 (195)
T ss_pred EEEEEcccc-ChHHHHHHHHHHHHHCCCCc----eEEEEec--------------------cchHHHHHhCCCCCEEEEe
Confidence 678865544 33345567777888899863 6654321 1357789999999999975
Q ss_pred C
Q 020472 148 M 148 (326)
Q Consensus 148 l 148 (326)
.
T Consensus 57 ~ 57 (195)
T cd08431 57 T 57 (195)
T ss_pred c
Confidence 4
No 82
>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=81.07 E-value=10 Score=30.81 Aligned_cols=135 Identities=14% Similarity=0.153 Sum_probs=69.2
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
++||+=.|.... -.-.+...+++.||++. +++.... ..++.+.|.+|++|+++..
T Consensus 2 l~Ig~~~~~~~~-~l~~~l~~~~~~~P~i~----l~i~~~~--------------------~~~~~~~l~~~~~Dl~i~~ 56 (196)
T cd08450 2 LTIGFLPGAEVQ-WLPEVLPILREEHPDLD----VELSSLF--------------------SPQLAEALMRGKLDVAFMR 56 (196)
T ss_pred EEEEEehhhhhh-hHHHHHHHHHhhCCCcE----EEEEecC--------------------hHHHHHHHhcCCccEEEEe
Confidence 678887775443 34455567778899752 4443211 2468899999999999964
Q ss_pred CCCCCCCCCCCceeeeecCCCCCcceeec-cC-------ccCcccCCCCCEEecCCh----HHH-HH-HHhhCCCCEEEe
Q 020472 148 MKDVPTYLPEKTILPCNLQREDVRDAFIS-LS-------AASLAELPAGSIVGTASL----RRK-SQ-ILHRYPSLKVME 213 (326)
Q Consensus 148 lKDlPt~lp~gL~iaAv~kReDprD~LV~-~~-------~~~l~dLp~ga~IGTSS~----RR~-aQ-L~~~~Pdl~v~~ 213 (326)
. |.. ++++....+. ++ + -++++ ++ ..+++||..-..|..+.. +.. .+ +.......++.
T Consensus 57 ~---~~~-~~~~~~~~l~-~~-~-~~~~~~~~~pl~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~- 128 (196)
T cd08450 57 P---EIQ-SDGIDYQLLL-KE-P-LIVVLPADHRLAGREKIPPQDLAGENFISPAPTAPVLQQVIENYAAQHNIQPNII- 128 (196)
T ss_pred C---CCC-CCCcEEEEEE-cc-c-eEEEecCCCCcccCceECHHHhCCCCeEeecCCCchHHHHHHHHHHHCCCCcEee-
Confidence 2 211 3455443322 11 1 22332 21 123455655555554321 221 11 22222222333
Q ss_pred ccCCCHHHHHhhhccCCccEEe
Q 020472 214 NFRGNVQTRLRKLNERVVQATL 235 (326)
Q Consensus 214 ~iRGNV~TRL~KL~~ge~DAII 235 (326)
..-.|+.+=+.-+..|..=+++
T Consensus 129 ~~~~~~~~~~~~v~~g~gi~~~ 150 (196)
T cd08450 129 QEADNLLSAMSLVASTLGCALL 150 (196)
T ss_pred eeechHHHHHHHHhcCCcEEEe
Confidence 2234677777777777654443
No 83
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=80.99 E-value=8.5 Score=36.07 Aligned_cols=60 Identities=8% Similarity=0.197 Sum_probs=41.4
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.++|+||+-.+ ++....-.+...+++.||++. +++.. |+ +.++.+.|.+|++|++
T Consensus 111 ~~~i~i~~~~~-~~~~~l~~~l~~f~~~~P~i~----l~i~~----~~----------------~~~~~~~l~~g~~Di~ 165 (314)
T PRK09508 111 ERVFNLCICSP-LDIRLTSQIYNRIEQIAPNIH----VVFKS----SL----------------NQNIEHQLRYQETEFV 165 (314)
T ss_pred ccEEEEEechh-HHHHHHHHHHHHHHHhCCCcE----EEEEe----Cc----------------chhHHHHHhcCCccEE
Confidence 35799998655 344445566778888899862 44432 11 2468899999999999
Q ss_pred EeeCC
Q 020472 145 VHSMK 149 (326)
Q Consensus 145 VHSlK 149 (326)
|....
T Consensus 166 i~~~~ 170 (314)
T PRK09508 166 ISYEE 170 (314)
T ss_pred EecCC
Confidence 98653
No 84
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=80.71 E-value=29 Score=32.46 Aligned_cols=138 Identities=12% Similarity=0.051 Sum_probs=73.6
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.++|+||+=.+. +..-.-.+...+++.+|++. +++.... +.++.++|.+|++|+|
T Consensus 96 ~~~l~ig~~~~~-~~~~l~~~l~~~~~~~p~v~----i~~~~~~--------------------~~~~~~~l~~g~~Dl~ 150 (312)
T PRK10341 96 VVDVSFGFPSLI-GFTFMSDMINKFKEVFPKAQ----VSMYEAQ--------------------LSSFLPAIRDGRLDFA 150 (312)
T ss_pred ceEEEEEechHH-hHhhHHHHHHHHHHhCCCCE----EEEEeCC--------------------HHHHHHHHHcCCCcEE
Confidence 467999996554 33334456667777899752 4443321 3578999999999999
Q ss_pred EeeCCCCCCCCCCCceeeeecCCCCCcceeeccC-----ccCcccCCCCCEEecC---ChHHH-HH-HHhh--CCCCEEE
Q 020472 145 VHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS-----AASLAELPAGSIVGTA---SLRRK-SQ-ILHR--YPSLKVM 212 (326)
Q Consensus 145 VHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~-----~~~l~dLp~ga~IGTS---S~RR~-aQ-L~~~--~Pdl~v~ 212 (326)
+....+- ..++++..-.+.+ ++--+++.++ ..+++||-.-..|..+ +.++. .+ +... .|+..+
T Consensus 151 i~~~~~~--~~~~~l~~~~l~~--~~~~lv~~~~~pl~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~- 225 (312)
T PRK10341 151 IGTLSNE--MKLQDLHVEPLFE--SEFVLVASKSRTCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIV- 225 (312)
T ss_pred EecCCcc--cccCCeeEEEEec--ccEEEEEcCCCchhccCCHHHHhCCCeEccCCCCcHHHHHHHHHHHcCcCCCceE-
Confidence 9764321 1234444332222 2222222221 1234555444455432 23333 12 2222 233332
Q ss_pred eccCCCHHHHHhhhccCCccEE
Q 020472 213 ENFRGNVQTRLRKLNERVVQAT 234 (326)
Q Consensus 213 ~~iRGNV~TRL~KL~~ge~DAI 234 (326)
.-.|+.+=+.-+.+|.+=++
T Consensus 226 --~~~~~~~~~~~v~~g~gi~~ 245 (312)
T PRK10341 226 --KTDSVVTIYNLVLNADFLTV 245 (312)
T ss_pred --EecCHHHHHHHHHhCCcEEE
Confidence 23578888888888865333
No 85
>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=80.27 E-value=33 Score=28.54 Aligned_cols=136 Identities=14% Similarity=0.080 Sum_probs=71.0
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.|+||+=.+....+=. .+...+++.||++. +++.. . ...++.++|.+|++|+++.
T Consensus 2 ~l~ig~~~~~~~~~l~-~~l~~~~~~~P~i~----l~~~~--~------------------~~~~~~~~l~~~~~D~~i~ 56 (198)
T cd08485 2 ELRVAYFGTVVLHTLP-LLLRQLLSVAPSAT----VSLTQ--M------------------SKNRQIEALDAGTIDIGFG 56 (198)
T ss_pred eEEEEEeccchhHHHH-HHHHHHHHhCCCcE----EEEEE--C------------------CHHHHHHHHHcCCccEEEe
Confidence 5888887776554423 35566677899862 44432 1 1357889999999999996
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEecC-----ChHHH-HH-HHhhCCCCEEE
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA-----SLRRK-SQ-ILHRYPSLKVM 212 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGTS-----S~RR~-aQ-L~~~~Pdl~v~ 212 (326)
... | .++++....+.+ ++.-+++.++. .++++|..-..|..+ +.++. .+ +....-..++.
T Consensus 57 ~~~--~--~~~~l~~~~l~~--~~~~~~~~~~~~~~~~~~v~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 (198)
T cd08485 57 RFY--P--YQEGVVVRNVTN--ERLFLGAQKSRARSFGEQVHCSALRNEPLILFPREGRPSFADEVIGVFKNARVEPKVV 130 (198)
T ss_pred cCC--C--CCCCeEEEEeec--cceEEEeCCCCccccCCCcCHHHHhcCCeEecCCCCCccHHHHHHHHHHHcCCCcceE
Confidence 431 1 245655433332 22122222211 234444333344321 23433 12 22222223333
Q ss_pred eccCCCHHHHHhhhccCCccEE
Q 020472 213 ENFRGNVQTRLRKLNERVVQAT 234 (326)
Q Consensus 213 ~~iRGNV~TRL~KL~~ge~DAI 234 (326)
..-++..+-+.-+..|..=|+
T Consensus 131 -~~~~~~~~~~~~v~~g~gi~~ 151 (198)
T cd08485 131 -AIVEDVNAAMALALAGVGVTI 151 (198)
T ss_pred -EEcCcHHHHHHHHHcCCceEE
Confidence 223688888888888854333
No 86
>PF02621 VitK2_biosynth: Menaquinone biosynthesis; InterPro: IPR003773 This entry describes proteins of unknown function, which appear to be putative periplasmic binding proteins.; PDB: 3A3U_A 2CZL_A 1ZBM_A 2NXO_C 2I6E_E.
Probab=79.95 E-value=6.6 Score=36.86 Aligned_cols=101 Identities=16% Similarity=0.223 Sum_probs=64.2
Q ss_pred HHHHHHHHHcCCCcEEEeeCCCCCCCCCCCceee--eecCCCCCcceeeccCccCcccCCCCCEEecCChHHHHHH--Hh
Q 020472 129 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILP--CNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQI--LH 204 (326)
Q Consensus 129 tkELe~ALl~g~iDiAVHSlKDlPt~lp~gL~ia--Av~kReDprD~LV~~~~~~l~dLp~ga~IGTSS~RR~aQL--~~ 204 (326)
..+|-++|++|++|++.-|+=.-+....+-..+. ++.-+..+.-+++..+ ..++++. |.+|..++.-+.+.+ +-
T Consensus 33 P~~Ln~~l~~g~~Dv~~iSs~~y~~~~~~y~ilp~~~i~s~g~v~Sv~l~s~-~p~~~l~-~~~ial~~~S~TS~~Llri 110 (251)
T PF02621_consen 33 PSELNQMLLEGELDVALISSIEYARNADDYLILPDLSISSDGPVYSVLLFSK-VPIEELD-GKKIALTGESTTSVALLRI 110 (251)
T ss_dssp HHHHHHHHHTTS-SEEEEEHHHHCTCTTTEEEESCECEEECCSSSSEEEEES-S-CCC-T-TSEEEESTTTSHHHHHHHH
T ss_pred HHHHHHHHHcCCCCEEEcCHHHHHHhhhhheecCCcEEEEcCCccceEEEEC-CChHHcC-CCeEEcCCCCHHHHHHHHH
Confidence 3689999999999999999877666444444444 5666888888887653 3466664 458877776665433 33
Q ss_pred hCCCC---EEEeccCCCHHHHHhhhccCCccEEee
Q 020472 205 RYPSL---KVMENFRGNVQTRLRKLNERVVQATLL 236 (326)
Q Consensus 205 ~~Pdl---~v~~~iRGNV~TRL~KL~~ge~DAIIL 236 (326)
++++. +++ +....+..-+ .+|. ||.++
T Consensus 111 ll~~~~~p~~~-~~~~~~~~~~---~~~~-da~Ll 140 (251)
T PF02621_consen 111 LLEEFYKPEYV-PMPDDIPPAM---LAGA-DAALL 140 (251)
T ss_dssp HHCCTT--EEE-EE-CGHHHHH---HTTS-SEEEE
T ss_pred HHHhcccccee-ecCchhhHHh---hcCC-CEEEE
Confidence 34444 777 6666665533 3555 77766
No 87
>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=79.84 E-value=9.1 Score=31.23 Aligned_cols=57 Identities=19% Similarity=0.221 Sum_probs=37.6
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.|+||+-.|.-..+ --.+...+++.+|++. +++ ... + ..++.+.|.+|++|+++.
T Consensus 1 ~l~ig~~~~~~~~~-l~~~l~~~~~~~P~i~----l~i--~~~--~----------------~~~~~~~l~~~~~Dl~i~ 55 (199)
T cd08416 1 RLRLGSLYSLTVNT-VPRIIMGLKLRRPELD----IEL--TLG--S----------------NKDLLKKLKDGELDAILV 55 (199)
T ss_pred CEEEEechHHHHhh-hHHHHHHHHHhCCCeE----EEE--EEc--C----------------cHHHHHHHhCCCCCEEEE
Confidence 37888866654443 3445566777799752 443 321 1 246889999999999998
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (199)
T cd08416 56 AT 57 (199)
T ss_pred ec
Confidence 64
No 88
>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=79.58 E-value=7.6 Score=31.48 Aligned_cols=57 Identities=19% Similarity=0.324 Sum_probs=37.7
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+.-..+ .-.+...+++.+|++. +++... + ..++.+.|.+|++|+|+.
T Consensus 1 ~l~Ig~~~~~~~~~-l~~~l~~~~~~~P~i~----l~i~~~----~----------------~~~~~~~l~~~~~Dl~i~ 55 (196)
T cd08415 1 TLRIAALPALALSL-LPRAIARFRARHPDVR----ISLHTL----S----------------SSTVVEAVLSGQADLGLA 55 (196)
T ss_pred CeEEEecccccccc-cHHHHHHHHHHCCCcE----EEEEec----c----------------hHHHHHHHHcCCccEEEE
Confidence 36788776654332 3345677778899752 444322 1 247889999999999997
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (196)
T cd08415 56 SL 57 (196)
T ss_pred eC
Confidence 53
No 89
>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=79.50 E-value=18 Score=29.31 Aligned_cols=136 Identities=18% Similarity=0.122 Sum_probs=68.0
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+-.+.-..+- -.+...+.+.+|++. +++... + ..++.+.|.+|++|+++.
T Consensus 1 ~l~I~~~~~~~~~~l-~~~l~~~~~~~P~i~----i~~~~~----~----------------~~~~~~~l~~~~~Dl~i~ 55 (200)
T cd08423 1 TLRVGAFPTAAAALL-PPALAALRARHPGLE----VRLREA----E----------------PPESLDALRAGELDLAVV 55 (200)
T ss_pred CEEEEehhHHHHHhh-hHHHHHHHHhCCCCe----EEEEeC----C----------------HHHHHHHHhcCCccEEEE
Confidence 367888776544443 445555777789752 444321 1 246889999999999996
Q ss_pred eC-CCCCCCCCCCceeeeecCCCCCcceeeccC-------ccCcccCCCCCEEecCC---hHHH-HHH-HhhCCCCEEEe
Q 020472 147 SM-KDVPTYLPEKTILPCNLQREDVRDAFISLS-------AASLAELPAGSIVGTAS---LRRK-SQI-LHRYPSLKVME 213 (326)
Q Consensus 147 Sl-KDlPt~lp~gL~iaAv~kReDprD~LV~~~-------~~~l~dLp~ga~IGTSS---~RR~-aQL-~~~~Pdl~v~~ 213 (326)
.. .+.|...++++...-+. . ++--++++++ ..++++|..-..|..+. .+.. .+. .......++.
T Consensus 56 ~~~~~~~~~~~~~~~~~~l~-~-~~~~~~~~~~~p~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~- 132 (200)
T cd08423 56 FDYPVTPPPDDPGLTRVPLL-D-DPLDLVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIA- 132 (200)
T ss_pred eccccccCCCCCCcEEEEec-c-CcEEEEecCCCCccccCCCCHHHhcCCceEEecCCchHHHHHHHHHHHcCCCCCee-
Confidence 43 22222234555432221 1 1111222221 12345554433444322 2221 222 2222222333
Q ss_pred ccCCCHHHHHhhhccCC
Q 020472 214 NFRGNVQTRLRKLNERV 230 (326)
Q Consensus 214 ~iRGNV~TRL~KL~~ge 230 (326)
-.=.|+.+-++-+.+|.
T Consensus 133 ~~~~~~~~~~~~v~~g~ 149 (200)
T cd08423 133 HEADDYATVLALVAAGL 149 (200)
T ss_pred eeeccHHHHHHHHHcCC
Confidence 23467888888888875
No 90
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=77.36 E-value=16 Score=33.87 Aligned_cols=59 Identities=19% Similarity=0.317 Sum_probs=43.6
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+. +......+...+.+.+|++. +++.. ++ +.++.++|.+|++|+
T Consensus 93 ~~g~l~I~~~~~~-~~~~l~~~l~~~~~~~p~i~----~~~~~----~~----------------~~~~~~~l~~g~~Di 147 (302)
T PRK09791 93 LAGQINIGMGASI-ARSLMPAVISRFHQQHPQVK----VRIME----GQ----------------LVSMINELRQGELDF 147 (302)
T ss_pred cceEEEEEechHH-HHhhhHHHHHHHHHHCCCeE----EEEEe----CC----------------hHHHHHHHHCCCccE
Confidence 4578999998775 45566667778889999762 44431 11 357899999999999
Q ss_pred EEee
Q 020472 144 AVHS 147 (326)
Q Consensus 144 AVHS 147 (326)
++..
T Consensus 148 ~i~~ 151 (302)
T PRK09791 148 TINT 151 (302)
T ss_pred EEEe
Confidence 9974
No 91
>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=77.05 E-value=14 Score=30.65 Aligned_cols=136 Identities=9% Similarity=-0.023 Sum_probs=70.4
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||+-.+. +..-.-.+...+++.+|++. ++++. +. . ++.+.|.+|++|+|+..
T Consensus 2 l~I~~~~~~-~~~~l~~~i~~~~~~~P~i~----l~i~~----~~----------------~-~~~~~l~~g~~D~~i~~ 55 (200)
T cd08462 2 FRIIASDYV-ITVLLPPVIERVAREAPGVR----FELLP----PD----------------D-QPHELLERGEVDLLIAP 55 (200)
T ss_pred EEEEecHHh-HHHHHHHHHHHHHHHCCCCE----EEEec----CC----------------h-hHHHHHhcCCeeEEEec
Confidence 678885554 33445567777888899762 44421 10 2 58899999999999974
Q ss_pred CCCCCCCCCCCceeeeecCCCCCcceee-ccC------ccCcccCCCCCEEe--c-CChHHH--HH-HHhhCCCCEEEec
Q 020472 148 MKDVPTYLPEKTILPCNLQREDVRDAFI-SLS------AASLAELPAGSIVG--T-ASLRRK--SQ-ILHRYPSLKVMEN 214 (326)
Q Consensus 148 lKDlPt~lp~gL~iaAv~kReDprD~LV-~~~------~~~l~dLp~ga~IG--T-SS~RR~--aQ-L~~~~Pdl~v~~~ 214 (326)
.... ++++...-+.+ ++ -++| .++ ..++++|..-..|. . +..++. .+ +.......++. -
T Consensus 56 ~~~~----~~~~~~~~l~~--~~-~~~v~~~~hpl~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 127 (200)
T cd08462 56 ERFM----SDGHPSEPLFE--EE-FVCVVWADNPLVGGELTAEQYFSAGHVVVRFGRNRRPSFEDWFLNEYGLKRRVE-V 127 (200)
T ss_pred CCCC----CCCceeeeeec--cc-eEEEEcCCCCccCCCCCHHHHhhCCCEEEecCCCCCccHHHHHHHHcCCcceEE-E
Confidence 3211 23443322221 22 2233 222 12344444333332 1 122221 22 23333334443 2
Q ss_pred cCCCHHHHHhhhccCCccEEeeeh
Q 020472 215 FRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 215 iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
--.|+++-+.-+.+|.. -.+++.
T Consensus 128 ~~~~~~~~~~~v~~g~g-iailp~ 150 (200)
T cd08462 128 VTPSFSSIPPLLVGTNR-IATLHR 150 (200)
T ss_pred EeChHHHHHHHHHcCch-hhhhHH
Confidence 34789999998888853 334443
No 92
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=76.91 E-value=0.45 Score=43.03 Aligned_cols=113 Identities=20% Similarity=0.193 Sum_probs=68.7
Q ss_pred HHHHHHHHcCCCcEEEeeCCCCCCCC-CCCceeeeecCC----CCCcceeeccCc---cCcccCCCCCEEecCChH----
Q 020472 130 KEIDEALINSQIDIAVHSMKDVPTYL-PEKTILPCNLQR----EDVRDAFISLSA---ASLAELPAGSIVGTASLR---- 197 (326)
Q Consensus 130 kELe~ALl~g~iDiAVHSlKDlPt~l-p~gL~iaAv~kR----eDprD~LV~~~~---~~l~dLp~ga~IGTSS~R---- 197 (326)
.|+.+++.+|++|+++=+.-...... ..|....+...+ ..-+-++|.+.. .+++|| +|.+||..+.-
T Consensus 40 ~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds~i~~l~dL-~Gk~v~~~~~~s~sg 118 (243)
T PF12974_consen 40 AEFIEALRSGEIDLAFMGPLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADSPITSLADL-KGKRVAFPDPSSTSG 118 (243)
T ss_dssp HHHHHHHHTTS-SEEE--HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTSS--SHHHH-GGSEEEEE-TT-TTT
T ss_pred HHHHHHHHcCCccEEEECcHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCCCCCChhhc-CCCEEEEecCCccHH
Confidence 58889999999999976532222111 235665565554 223335555543 357787 78888876555
Q ss_pred ---HHHHH-HhhC--C--CCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccC
Q 020472 198 ---RKSQI-LHRY--P--SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLS 245 (326)
Q Consensus 198 ---R~aQL-~~~~--P--dl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLg 245 (326)
-...| +..- | ++..+ .-||-+.=+.-|.+|++|+.++....++++-
T Consensus 119 ~l~~~~~L~~~~Gl~~~~~~~~~--~~~~~~~~~~~l~~G~~Da~~~~~~~~~~~~ 172 (243)
T PF12974_consen 119 YLIPRYELLREAGLDPGDDFKQV--FVGSHDAVLEALLNGKADAAAIPSDAFERLE 172 (243)
T ss_dssp THHHHHHTCCCCT--HHHHSSEE--EEE-HHHHHHHHHTTSSSEEEEEHHHHHHHH
T ss_pred HHHHHHHHHHHcCCChhHceeEE--EeCCHHHHHHHHHcCCccEEEEechhHHHHH
Confidence 22333 1211 1 13343 4578899999999999999999888877774
No 93
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=76.73 E-value=19 Score=32.31 Aligned_cols=104 Identities=14% Similarity=0.100 Sum_probs=58.1
Q ss_pred HHHHHHHcCCCcEEEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC----ccCcccCCCCCEEecCC-hHHHHHHHhh
Q 020472 131 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS----AASLAELPAGSIVGTAS-LRRKSQILHR 205 (326)
Q Consensus 131 ELe~ALl~g~iDiAVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~----~~~l~dLp~ga~IGTSS-~RR~aQL~~~ 205 (326)
++-++|.+|++|+++=.+.--|.. .+.+.... +-.. ...+++.++ ..+++|| .|.+||... .=-...+...
T Consensus 74 ~~~~~l~~G~vDi~~~~~~~t~~R-~~~~~fs~-p~~~-~~~~~~~~~~~~~~~~~~dL-~g~~I~v~~g~~~~~~l~~~ 149 (247)
T PRK09495 74 GIIPALQTKNVDLALAGITITDER-KKAIDFSD-GYYK-SGLLVMVKANNNDIKSVKDL-DGKVVAVKSGTGSVDYAKAN 149 (247)
T ss_pred HHHHHHhCCCcCEEEecCccCHHH-Hhhccccc-hhee-cceEEEEECCCCCCCChHHh-CCCEEEEecCchHHHHHHhc
Confidence 456889999999986544211111 11111100 0001 112223221 2355666 466665321 1124566677
Q ss_pred CCCCEEEeccCCCHHHHHhhhccCCccEEeeehhh
Q 020472 206 YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAG 240 (326)
Q Consensus 206 ~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AG 240 (326)
+|+.+++ ... |.++-+..|.+|++|+++.-..-
T Consensus 150 ~~~~~i~-~~~-~~~~~~~~L~~grvDa~i~~~~~ 182 (247)
T PRK09495 150 IKTKDLR-QFP-NIDNAYLELGTGRADAVLHDTPN 182 (247)
T ss_pred CCCCceE-EcC-CHHHHHHHHHcCceeEEEeChHH
Confidence 8888887 544 88888999999999999975443
No 94
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=76.21 E-value=70 Score=30.09 Aligned_cols=146 Identities=10% Similarity=0.059 Sum_probs=78.5
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+.. ..-.-.+...+++.||++. +++... + ..++.+.|.+|++|+
T Consensus 91 ~~g~l~Ig~~~~~~-~~~l~~~i~~f~~~~P~i~----l~~~~~----~----------------~~~~~~~L~~~~~D~ 145 (309)
T PRK12683 91 DSGHLTVATTHTQA-RYALPKVVRQFKEVFPKVH----LALRQG----S----------------PQEIAEMLLNGEADI 145 (309)
T ss_pred CCceEEEEeccchH-HHHHHHHHHHHHHHCCCce----EEEEeC----C----------------HHHHHHHHHcCCccE
Confidence 35789999966643 3344456678888899762 444221 1 357889999999999
Q ss_pred EEeeCCCCCCCCCCCceeeeecCCCCCcceeecc-C-------ccCcccCCCCCEEecC---ChHHH-HHHH-hhCCCCE
Q 020472 144 AVHSMKDVPTYLPEKTILPCNLQREDVRDAFISL-S-------AASLAELPAGSIVGTA---SLRRK-SQIL-HRYPSLK 210 (326)
Q Consensus 144 AVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~-~-------~~~l~dLp~ga~IGTS---S~RR~-aQL~-~~~Pdl~ 210 (326)
++-... . ..++++....+.. ++- ++|+. + ..++++|..-..|..+ +.|+. .++. ......+
T Consensus 146 ~i~~~~-~--~~~~~l~~~~l~~--~~~-~~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 219 (309)
T PRK12683 146 GIATEA-L--DREPDLVSFPYYS--WHH-VVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPD 219 (309)
T ss_pred EEecCC-C--CCCCCceEEEccc--CeE-EEEecCCCCcccCCccCHHHHhcCCeEeccCCCcHHHHHHHHHHHCCCCce
Confidence 995321 1 1134443322221 222 23322 1 1345666666666643 23442 2222 2222333
Q ss_pred EEeccCCCHHHHHhhhccCCccEEeeehhhhc
Q 020472 211 VMENFRGNVQTRLRKLNERVVQATLLALAGLK 242 (326)
Q Consensus 211 v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~ 242 (326)
+. .-=.|+++-+.-+..|..=+ +++.....
T Consensus 220 ~~-~~~~~~~~~~~~v~~g~Gi~-~lp~~~~~ 249 (309)
T PRK12683 220 IV-LTALDADVIKTYVELGMGVG-IVAAMAYD 249 (309)
T ss_pred eE-EEeccHHHHHHHHHhCCCeE-Eeehhhcc
Confidence 33 23458888888888776433 34444433
No 95
>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=76.16 E-value=43 Score=27.71 Aligned_cols=143 Identities=9% Similarity=0.036 Sum_probs=73.6
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||+=.+... .-.-.+...+++.||++. +++... + +.++.+.|.+|++|+++..
T Consensus 2 l~ig~~~~~~~-~~l~~~l~~~~~~~P~v~----l~i~~~----~----------------~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08444 2 LTIATTHTQAR-YALPWVVQAFKEQFPNVH----LVLHQG----S----------------PEEIASMLANGQADIGIAT 56 (198)
T ss_pred eEEeecchhhh-hhhhHHHHHHHHHCCCeE----EEEEeC----C----------------HHHHHHHHHCCCccEEEec
Confidence 67888776633 335556677778899752 444321 1 3578899999999999974
Q ss_pred CCCCCCCCCCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEecC---ChHHH-HHH-HhhCCCCEEEecc
Q 020472 148 MKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA---SLRRK-SQI-LHRYPSLKVMENF 215 (326)
Q Consensus 148 lKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGTS---S~RR~-aQL-~~~~Pdl~v~~~i 215 (326)
.. . ..++++...-+. .++..+++++.. .++++|-.-..|..+ +.|+. .+. ....-..++. ..
T Consensus 57 ~~-~--~~~~~~~~~~l~--~~~~~~~~~~~hpl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 130 (198)
T cd08444 57 EA-L--ENHPELVSFPYY--DWHHHIIVPVGHPLESITPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIV-LS 130 (198)
T ss_pred cc-c--CCCcCcEEeecc--ccceeEEecCCCccccCCCcCHHHHhCCCEEEecCCCchHHHHHHHHHHcCCCCceE-EE
Confidence 21 1 113444322221 222233333221 133444333444432 33332 112 2222222333 23
Q ss_pred CCCHHHHHhhhccCCccEEeeehhhhc
Q 020472 216 RGNVQTRLRKLNERVVQATLLALAGLK 242 (326)
Q Consensus 216 RGNV~TRL~KL~~ge~DAIILA~AGL~ 242 (326)
-.|+++=++-+.+|.. -.+++.....
T Consensus 131 ~~~~~~~~~~v~~g~G-i~~lp~~~~~ 156 (198)
T cd08444 131 ALDADVIKTYVGLGMG-IGIVAEMAFE 156 (198)
T ss_pred eCCHHHHHHHHHcCCc-EEeccHHHHh
Confidence 4788888888888743 3445544333
No 96
>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=75.74 E-value=11 Score=31.05 Aligned_cols=57 Identities=14% Similarity=0.210 Sum_probs=37.0
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||.-.+.-..+-. .+...+.+.+|++. +++.. +. +.++.+.|.+|++|+++.
T Consensus 1 ~l~I~~~~~~~~~~l~-~~l~~~~~~~P~i~----l~~~~--~~------------------~~~~~~~l~~~~~Dl~i~ 55 (196)
T cd08457 1 TLRIAAMPALANGFLP-RFLAAFLRLRPNLH----LSLMG--LS------------------SSQVLEAVASGRADLGIA 55 (196)
T ss_pred CEEEEeehhHhccccH-HHHHHHHHHCCCeE----EEEEe--cC------------------cHHHHHHHHcCCccEEEe
Confidence 3678886665444434 34555667799752 44432 21 246889999999999998
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (196)
T cd08457 56 DG 57 (196)
T ss_pred cc
Confidence 64
No 97
>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=75.51 E-value=6.5 Score=33.57 Aligned_cols=41 Identities=12% Similarity=0.158 Sum_probs=36.7
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++..++++..||++++. -..|+-.+-++.|.+|++|..|..
T Consensus 16 ~~~l~~f~~~~P~v~l~-i~~~~~~~~~~~L~~~~~D~~i~~ 56 (204)
T cd08429 16 YRLLEPAMDLHEPIRLV-CREGKLEQLLADLALHRLDMVLAD 56 (204)
T ss_pred HHHHHHHHHhCCCcEEE-EEeCCHHHHHHHHHcCCccEEEec
Confidence 57788889999999998 889999999999999999998753
No 98
>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=75.43 E-value=5.7 Score=37.52 Aligned_cols=57 Identities=21% Similarity=0.247 Sum_probs=42.8
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
...+||||+=.| .+-+ ...+.+.+++.||++. +++..- .+.|+.++|.+|++|+
T Consensus 34 ~~~~lrig~s~s-~~~~-lp~~l~~f~~~~P~i~----v~i~~~--------------------~s~~l~~~L~~G~iDl 87 (287)
T TIGR02136 34 GSSTITIDGSTT-VAPL-AEAAAEEFQKIHPGVS----VTVQGA--------------------GSGTGIKALINGTVDI 87 (287)
T ss_pred ccceEEEeccch-HHHH-HHHHHHHHHhhCCCce----EEEccC--------------------CchHHHHHHHcCCCch
Confidence 456899999998 4554 8888999999999752 433221 1357889999999999
Q ss_pred EEe
Q 020472 144 AVH 146 (326)
Q Consensus 144 AVH 146 (326)
++=
T Consensus 88 ai~ 90 (287)
T TIGR02136 88 GNS 90 (287)
T ss_pred hhc
Confidence 884
No 99
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=75.40 E-value=11 Score=32.13 Aligned_cols=145 Identities=13% Similarity=0.001 Sum_probs=72.5
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||+=.|.. ..-.-.+.+.+.+.||++. ++++. . .+.++.+.|.+|++|+|+..
T Consensus 2 l~ig~~~~~~-~~~l~~~l~~f~~~~P~v~----l~i~~--~------------------~~~~~~~~L~~~~~D~~i~~ 56 (204)
T cd08429 2 FRVGVADAVP-KSIAYRLLEPAMDLHEPIR----LVCRE--G------------------KLEQLLADLALHRLDMVLAD 56 (204)
T ss_pred eeEEcchhhh-HHHHHHHHHHHHHhCCCcE----EEEEe--C------------------CHHHHHHHHHcCCccEEEec
Confidence 6788776664 3444556666777799752 44332 1 13578899999999999964
Q ss_pred CCCCCCCCCCCceeeeecCCCCCcceeec-----c-CccCcccCCCCCEEec---CChHH-HHHH-HhhCCCCEEEeccC
Q 020472 148 MKDVPTYLPEKTILPCNLQREDVRDAFIS-----L-SAASLAELPAGSIVGT---ASLRR-KSQI-LHRYPSLKVMENFR 216 (326)
Q Consensus 148 lKDlPt~lp~gL~iaAv~kReDprD~LV~-----~-~~~~l~dLp~ga~IGT---SS~RR-~aQL-~~~~Pdl~v~~~iR 216 (326)
... +..+..++... .-..++.-+.+. + +..++.||..-..|.. ++.|+ -.++ .......++. .--
T Consensus 57 ~~~-~~~~~~~~~~~--~l~~~~~~~~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~-~~~ 132 (204)
T cd08429 57 RPM-PSSLDVKGYSH--RLGECGVSFFAAPPLAKRLEKPFPASLDEAPLLLPGEDSALRRKLLQWFERQGLRPQIV-GEF 132 (204)
T ss_pred CCC-ccccchheeec--cccccceEEEecCCcccccccCCHhHhccCCeeecCCCCcHHHHHHHHHHHcCCCcceE-EEe
Confidence 421 11111121110 111111111111 0 1123455554445442 22332 2222 2222223333 334
Q ss_pred CCHHHHHhhhccCCccEEeeehhhhc
Q 020472 217 GNVQTRLRKLNERVVQATLLALAGLK 242 (326)
Q Consensus 217 GNV~TRL~KL~~ge~DAIILA~AGL~ 242 (326)
.|+++-++-+.+|. .-.++....+.
T Consensus 133 ~~~~~~~~~v~~G~-Gv~~lp~~~~~ 157 (204)
T cd08429 133 DDSALMKAFGQAGA-GIFAAPTVIAD 157 (204)
T ss_pred CCHHHHHHHHHcCC-CeEeccHHHHH
Confidence 78999988888774 44566655443
No 100
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=74.94 E-value=66 Score=29.22 Aligned_cols=134 Identities=13% Similarity=0.119 Sum_probs=72.1
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.|....+=...+ ..+++.||++. +++... ...++.+.|.+|++|+
T Consensus 87 ~~g~l~i~~~~~~~~~~~~~~l-~~~~~~~P~i~----i~v~~~--------------------~~~~~~~~l~~g~~Di 141 (290)
T PRK10837 87 DNGALRIYASSTIGNYILPAMI-ARYRRDYPQLP----LELSVG--------------------NSQDVINAVLDFRVDI 141 (290)
T ss_pred hCCeEEEEecchhHhhhhHHHH-HHHHHHCCCce----EEEEEC--------------------CHHHHHHHHHhCCceE
Confidence 3578999999887765544444 56777799762 444321 1357889999999999
Q ss_pred EEeeCCCCCCCCCCCce--------eeeecCCCCCcceeeccCccCcccCCCCCEEecC---ChHHH--HHHHhhCCCCE
Q 020472 144 AVHSMKDVPTYLPEKTI--------LPCNLQREDVRDAFISLSAASLAELPAGSIVGTA---SLRRK--SQILHRYPSLK 210 (326)
Q Consensus 144 AVHSlKDlPt~lp~gL~--------iaAv~kReDprD~LV~~~~~~l~dLp~ga~IGTS---S~RR~--aQL~~~~Pdl~ 210 (326)
++.....- ++++. +..+..++.|.. ....++++|..-..|... ..|.. ..+....+..+
T Consensus 142 ~i~~~~~~----~~~~~~~~l~~~~~~lv~~~~hpl~----~~~i~~~~L~~~~~i~~~~~~~~~~~l~~~~~~~~~~~~ 213 (290)
T PRK10837 142 GLIEGPCH----SPELISEPWLEDELVVFAAPDSPLA----RGPVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFE 213 (290)
T ss_pred EEecCCCC----CCceeEEEeecceEEEEEcCCChhh----cCCCCHHHHhcCCeEEecCCCcHHHHHHHHHHHcCCCCc
Confidence 99753211 22332 222223333211 111234555444444432 22331 11222233444
Q ss_pred EEeccCCCHHHHHhhhccCCc
Q 020472 211 VMENFRGNVQTRLRKLNERVV 231 (326)
Q Consensus 211 v~~~iRGNV~TRL~KL~~ge~ 231 (326)
+. -.-.|+++-++-+..|..
T Consensus 214 ~~-~~~~~~~~~~~~v~~g~g 233 (290)
T PRK10837 214 LA-MELGNSEAIKHAVRHGLG 233 (290)
T ss_pred eE-EEeCCHHHHHHHHHhCCc
Confidence 43 223688888888887743
No 101
>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=74.90 E-value=9.4 Score=31.72 Aligned_cols=141 Identities=9% Similarity=-0.002 Sum_probs=69.9
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.|+||+-.+.-.. -.-.+...+.+.||++. +++... + ..++.++|.+|++|+++.
T Consensus 1 ~l~ig~~~~~~~~-~l~~~l~~~~~~~P~i~----v~~~~~----~----------------~~~~~~~l~~g~~D~~i~ 55 (198)
T cd08413 1 QLTIATTHTQARY-VLPPVIAAFRKRYPKVK----LSLHQG----T----------------PSQIAEMVLKGEADIAIA 55 (198)
T ss_pred CeEEeecchhhhh-hccHHHHHHHHhCCceE----EEEEeC----C----------------HHHHHHHHHcCCCCEEEE
Confidence 3678877654332 23345567778899752 444321 1 257889999999999996
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEecC---ChHHH-HH-HHhhCCCCEEEec
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA---SLRRK-SQ-ILHRYPSLKVMEN 214 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGTS---S~RR~-aQ-L~~~~Pdl~v~~~ 214 (326)
.... ..++++....+ ..++--+++++++ .++++|-+-..|..+ +.++. .+ +.......++. -
T Consensus 56 ~~~~---~~~~~~~~~~l--~~~~~~~v~~~~hpl~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 129 (198)
T cd08413 56 TEAL---DDHPDLVTLPC--YRWNHCVIVPPGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIV-L 129 (198)
T ss_pred ccCC---CCCCCcEEEEe--eeeeEEEEecCCCcccccCCCCHHHHhcCCEEECCCCccHHHHHHHHHHHcCCCcceE-E
Confidence 4311 11344433222 2233333333322 234444333344432 12221 12 22222222333 2
Q ss_pred cCCCHHHHHhhhccCCccEEeeehh
Q 020472 215 FRGNVQTRLRKLNERVVQATLLALA 239 (326)
Q Consensus 215 iRGNV~TRL~KL~~ge~DAIILA~A 239 (326)
.-.++.+=+.-+.+|..=| +++..
T Consensus 130 ~~~~~~~~~~~v~~g~Gi~-~lp~~ 153 (198)
T cd08413 130 TALDADVIKTYVRLGLGVG-IIAEM 153 (198)
T ss_pred EeCCHHHHHHHHHhCCCEE-Ecccc
Confidence 2367888887777776433 33443
No 102
>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=74.74 E-value=44 Score=27.13 Aligned_cols=57 Identities=16% Similarity=0.152 Sum_probs=37.4
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+=.+.... =--.+...+++.+|++. +++ ... + ..++.+.|.+|++|+++.
T Consensus 1 ~l~I~~~~~~~~~-~l~~~l~~~~~~~P~i~----l~i--~~~--~----------------~~~~~~~l~~~~~D~~i~ 55 (199)
T cd08426 1 RVRVATGEGLAAE-LLPSLIARFRQRYPGVF----FTV--DVA--S----------------TADVLEAVLSGEADIGLA 55 (199)
T ss_pred CeEEEecHHHHHH-HHHHHHHHHHHhCCCeE----EEE--EeC--C----------------cHHHHHHHHCCCccEEEe
Confidence 3678885544332 24556777788899752 443 211 1 257889999999999997
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (199)
T cd08426 56 FS 57 (199)
T ss_pred cC
Confidence 53
No 103
>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=74.74 E-value=7.4 Score=31.61 Aligned_cols=42 Identities=17% Similarity=0.130 Sum_probs=35.9
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+..-.+++..+|++++. -..++-+.-++.|.+|++|..|...
T Consensus 16 ~~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~~~~D~~i~~~ 57 (198)
T cd08412 16 PGLLRRFREAYPGVEVR-VVEGNQEELEEGLRSGELDLALTYD 57 (198)
T ss_pred HHHHHHHHHHCCCcEEE-EEECCHHHHHHHHHcCCCcEEEEcC
Confidence 35678889999999997 7788888889999999999988743
No 104
>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=74.69 E-value=6.1 Score=32.93 Aligned_cols=49 Identities=14% Similarity=0.121 Sum_probs=38.9
Q ss_pred CCEEecCC-------hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 188 GSIVGTAS-------LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 188 ga~IGTSS-------~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
|-+||+++ ++-..+++..+|++++. -.-++-++-+.+|.+|++|..|..
T Consensus 1 ~~~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~-~~~~~~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08467 1 GFTLAMPDYAEVALLPRLAPRLRERAPGLDLR-LCPIGDDLAERGLEQGTIDLAVGR 56 (200)
T ss_pred CeEEEechhhHHHHHHHHHHHHHhhCCCCEEE-EecCCcccHHHHhhCCCcCEEEec
Confidence 45677654 35568888999999997 777777788899999999998853
No 105
>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=74.41 E-value=7 Score=32.38 Aligned_cols=41 Identities=15% Similarity=0.139 Sum_probs=35.1
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.....+++..||++++. -..|+-..-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~v~i~-i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08452 16 PPIVREYRKKFPSVKVE-LRELSSPDQVEELLKGRIDIGFLH 56 (197)
T ss_pred HHHHHHHHHHCCCcEEE-EEecChHHHHHHHHCCCccEEEee
Confidence 46678888999999997 777888889999999999988863
No 106
>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=74.38 E-value=7.4 Score=31.58 Aligned_cols=42 Identities=10% Similarity=0.126 Sum_probs=36.2
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
++...+++..+|++++. -..++-++.+..|.+|++|..|...
T Consensus 16 ~~~l~~~~~~~P~i~i~-~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08449 16 GPALRRFKRQYPNVTVR-FHELSPEAQKAALLSKRIDLGFVRF 57 (197)
T ss_pred HHHHHHHHHHCCCeEEE-EEECCHHHHHHHHhCCCccEEEecc
Confidence 46678889999999997 7788999999999999999988643
No 107
>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=73.82 E-value=17 Score=30.61 Aligned_cols=143 Identities=13% Similarity=0.059 Sum_probs=74.9
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+.... ..-.+...+++.||++. +++....+ ..++.+.|.+|++|+++-
T Consensus 1 ~~~Ig~~~~~~~~-~~~~~l~~~~~~~P~~~----v~~~~~~~-------------------~~~l~~~L~~g~lDl~i~ 56 (203)
T cd08463 1 TFRIAAPDYLNAL-FLPELVARFRREAPGAR----LEIHPLGP-------------------DFDYERALASGELDLVIG 56 (203)
T ss_pred CEEEEechhhHHH-HhHHHHHHHHHHCCCCE----EEEEeCCc-------------------chhHHHHHhcCCeeEEEe
Confidence 4788987766554 45567777888899863 55532111 246889999999999996
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeecc-Cc-------cCcccCCCCCEEec--C--ChHHH--HHHHhhCCCCEEE
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISL-SA-------ASLAELPAGSIVGT--A--SLRRK--SQILHRYPSLKVM 212 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~-~~-------~~l~dLp~ga~IGT--S--S~RR~--aQL~~~~Pdl~v~ 212 (326)
.. |. .++++....+.. ++ -+++.. +. .++++|.+-..|.. + ..|.. ..+.......++.
T Consensus 57 ~~---~~-~~~~l~~~~l~~--~~-~~lv~~~~h~l~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129 (203)
T cd08463 57 NW---PE-PPEHLHLSPLFS--DE-IVCLMRADHPLARRGLMTLDDYLEAPHLAPTPYSVGQRGVIDSHLARLGLKRNIV 129 (203)
T ss_pred cc---cc-CCCCcEEeEeec--Cc-eEEEEeCCCCcccCCCCCHHHHhhCCcEEEEcCCCCCCchHHHHHHHcCCCceEE
Confidence 42 21 234454433322 22 223322 11 13445544444432 1 22221 2233333333443
Q ss_pred eccCCCHHHHHhhhccCCccEEeeehhhhc
Q 020472 213 ENFRGNVQTRLRKLNERVVQATLLALAGLK 242 (326)
Q Consensus 213 ~~iRGNV~TRL~KL~~ge~DAIILA~AGL~ 242 (326)
---.|+.|=++-+..|..-+ +++...+.
T Consensus 130 -~~~~~~~~i~~~v~~~~~i~-~~p~~~~~ 157 (203)
T cd08463 130 -VTVPYFGLAPYMLAQSDLVF-TTGRHFAE 157 (203)
T ss_pred -EEeChHHHHHHHHhCCCeeE-ecHHHHHH
Confidence 33468888777777773333 35544433
No 108
>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=73.46 E-value=17 Score=30.00 Aligned_cols=132 Identities=11% Similarity=0.046 Sum_probs=67.6
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+-.+.-..+ --.+...+++.||++. +++..- + . ++.+.|.+|++|+++.
T Consensus 1 ~~~i~~~~~~~~~~-l~~~l~~~~~~~P~v~----v~l~~~-~-------------------~-~~~~~l~~g~~D~~i~ 54 (200)
T cd08460 1 TFTIRANDGFVAAF-GPALLAAVAAEAPGVR----LRFVPE-S-------------------D-KDVDALREGRIDLEIG 54 (200)
T ss_pred CEEEEechhHHHHH-HHHHHHHHHHHCCCCE----EEEecC-c-------------------h-hHHHHHHCCCccEEEe
Confidence 47888866654444 4455667777899763 544211 1 2 4668999999999998
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeeccCc------cCcccCCCCCEEec---CChHHH-HH-HHhhCCCCEEEecc
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISLSA------ASLAELPAGSIVGT---ASLRRK-SQ-ILHRYPSLKVMENF 215 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~------~~l~dLp~ga~IGT---SS~RR~-aQ-L~~~~Pdl~v~~~i 215 (326)
.... .++++.. .+-.+++--+++.+++ .+++||..-..|.. ++.|+. .+ +.......++. -.
T Consensus 55 ~~~~----~~~~~~~--~~l~~~~~~~v~~~~hpl~~~~~~l~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 127 (200)
T cd08460 55 VLGP----TGPEIRV--QTLFRDRFVGVVRAGHPLARGPITPERYAAAPHVSVSRRGRLHGPIDDALAALGLTRRVV-AV 127 (200)
T ss_pred cCCC----CCcchhe--eeeeccceEEEEeCCCCCCCCCCCHHHHhcCCCEEEecCCCCcchHHHHHHhcCCceeEE-EE
Confidence 5422 1233322 2222333222222221 23455544344432 223332 22 22222223333 23
Q ss_pred CCCHHHHHhhhccCCc
Q 020472 216 RGNVQTRLRKLNERVV 231 (326)
Q Consensus 216 RGNV~TRL~KL~~ge~ 231 (326)
=+|+++=+.-+..|..
T Consensus 128 ~~~~~~~~~~v~~g~g 143 (200)
T cd08460 128 VPTFAAALFLARGSDL 143 (200)
T ss_pred cCcHHHHHHHHhcCCH
Confidence 4788888888887754
No 109
>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=72.06 E-value=54 Score=26.97 Aligned_cols=137 Identities=7% Similarity=-0.011 Sum_probs=71.2
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
++|||+=.|... .-.-.+...+++.+|++. +++.. ++ +.++.++|.+|++|+++-
T Consensus 1 ~l~ig~~~~~~~-~~l~~~l~~f~~~~P~v~----i~~~~----~~----------------~~~~~~~l~~g~~Dl~i~ 55 (196)
T cd08458 1 SLRVACYTAPAL-SFMSGVIQTFIADRPDVS----VYLDT----VP----------------SQTVLELVSLQHYDLGIS 55 (196)
T ss_pred CeEEEEcchhhh-hhhHHHHHHHHHHCCCcE----EEEec----cC----------------hHHHHHHHHcCCCCEEEE
Confidence 478888777444 344455666677899752 44421 11 357889999999999996
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEecCC---hHHH-HH-HHhhCCCCEEEec
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTAS---LRRK-SQ-ILHRYPSLKVMEN 214 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGTSS---~RR~-aQ-L~~~~Pdl~v~~~ 214 (326)
... . .++++..--+. +++.-+++.+++ .+++||..-..|..++ .|.. .+ +.......++. -
T Consensus 56 ~~~-~---~~~~~~~~~l~--~~~~~~v~~~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 128 (196)
T cd08458 56 ILA-G---DYPGLTTEPVP--SFRAVCLLPPGHRLEDKETVHATDLEGESLICLSPVSLLRMQTDAALDSCGVHCNRR-I 128 (196)
T ss_pred ecc-C---CCCCceEEEec--cCceEEEecCCCccccCCccCHHHhCCCccEEecCCCcHHHHHHHHHHHcCCCcceE-E
Confidence 532 1 13455433222 222222222211 2345565444554332 2221 22 22322233333 2
Q ss_pred cCCCHHHHHhhhccCCccEEe
Q 020472 215 FRGNVQTRLRKLNERVVQATL 235 (326)
Q Consensus 215 iRGNV~TRL~KL~~ge~DAII 235 (326)
--+|+.+=+.-+.+|..=|++
T Consensus 129 ~~~~~~~~~~~v~~g~Gia~l 149 (196)
T cd08458 129 ESSLALNLCDLVSRGMGVGIV 149 (196)
T ss_pred EeccHHHHHHHHHcCCcEEEE
Confidence 236788777777777544433
No 110
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=71.86 E-value=33 Score=30.52 Aligned_cols=60 Identities=13% Similarity=0.158 Sum_probs=40.7
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+.... -.-.+...+.+.||++. +++ +.. + +.++.+.|.+|++|+
T Consensus 65 ~~~~l~I~~~~~~~~~-~~~~~l~~~~~~~p~i~----l~i--~~~--~----------------~~~~~~~l~~~~~D~ 119 (269)
T PRK11716 65 LSGELSLFCSVTAAYS-HLPPILDRFRAEHPLVE----IKL--TTG--D----------------AADAVEKVQSGEADL 119 (269)
T ss_pred cCceEEEEecchHHHH-HHHHHHHHHHHHCCCeE----EEE--EEC--C----------------HHHHHHHHHCCCccE
Confidence 4567999987655433 24456666777899752 333 221 1 357889999999999
Q ss_pred EEeeC
Q 020472 144 AVHSM 148 (326)
Q Consensus 144 AVHSl 148 (326)
++...
T Consensus 120 ~i~~~ 124 (269)
T PRK11716 120 AIAAK 124 (269)
T ss_pred EEEec
Confidence 99764
No 111
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=71.35 E-value=22 Score=34.06 Aligned_cols=61 Identities=11% Similarity=0.135 Sum_probs=42.9
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.||||+-.|....+ .-.+...+.+.||++. +++.... +.++.++|.+|++|+
T Consensus 91 ~~g~lrIg~~~~~~~~~-l~~~l~~f~~~~P~v~----i~l~~~~--------------------~~~~~~~l~~g~~Dl 145 (327)
T PRK12680 91 SQGQLTLTTTHTQARFV-LPPAVAQIKQAYPQVS----VHLQQAA--------------------ESAALDLLGQGDADI 145 (327)
T ss_pred CceEEEEEecchhHHHh-hHHHHHHHHHHCCCcE----EEEEeCC--------------------hHHHHHHHHCCCCcE
Confidence 35789999998865443 4445566777899752 4442221 357889999999999
Q ss_pred EEeeCC
Q 020472 144 AVHSMK 149 (326)
Q Consensus 144 AVHSlK 149 (326)
+|....
T Consensus 146 ~i~~~~ 151 (327)
T PRK12680 146 AIVSTA 151 (327)
T ss_pred EEEecC
Confidence 998754
No 112
>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=71.01 E-value=8.7 Score=31.10 Aligned_cols=41 Identities=20% Similarity=0.286 Sum_probs=34.8
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
.--.++...+|++++. -..|+-++-++.|.+|++|-.|...
T Consensus 17 ~~l~~~~~~~P~i~l~-~~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (195)
T cd08427 17 RALARLRRRHPDLEVH-IVPGLSAELLARVDAGELDAAIVVE 57 (195)
T ss_pred HHHHHHHHHCCCceEE-EEeCCcHHHHHHHHCCCCCEEEEcC
Confidence 4457888899999997 7778888889999999999988754
No 113
>PF04069 OpuAC: Substrate binding domain of ABC-type glycine betaine transport system; InterPro: IPR007210 This domain is a part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. It is often found in integral membrane proteins or proteins predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis []. OpuBC is closely related and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine []. L-carnitine is important for osmoregulation in Listeria monocytogenes. This domain is found also in proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA).; GO: 0005215 transporter activity, 0005488 binding, 0006810 transport; PDB: 3R6U_A 3TMG_C 3MAM_A 1SW5_C 1SW4_B 1SW1_A 1SW2_A 3O66_A 1R9Q_A 1R9L_A ....
Probab=70.68 E-value=20 Score=33.02 Aligned_cols=188 Identities=16% Similarity=0.115 Sum_probs=105.7
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
++|+||+-++.=+.+.|+.+...|++.+ . .++++...+ +..+.++|.+|+||+.+
T Consensus 1 k~I~ig~~~w~~~~~~a~i~~~~Le~~G--~----~v~~~~~~~-------------------~~~~~~al~~G~iD~~~ 55 (257)
T PF04069_consen 1 KPIVIGSKNWTESQILAEIYAQLLEAAG--Y----VVEVVNLGS-------------------TPVIFAALASGDIDIYP 55 (257)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHHHHHTT--E----EEEEEEESS-------------------HHHHHHHHHTTSSSEEE
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHCC--C----eEEEecCCc-------------------hHHHHHHHHCCCCeEEh
Confidence 4799999999999999999999999863 2 244444422 13477899999999998
Q ss_pred -eeCCCCC----CCCCCCceee--eecCCCCCcceeecc-------CccCcccCC----------CCCEEecC----ChH
Q 020472 146 -HSMKDVP----TYLPEKTILP--CNLQREDVRDAFISL-------SAASLAELP----------AGSIVGTA----SLR 197 (326)
Q Consensus 146 -HSlKDlP----t~lp~gL~ia--Av~kReDprD~LV~~-------~~~~l~dLp----------~ga~IGTS----S~R 197 (326)
=-+.... ..++++..+. ....- .....++.+ .-++++||. .+-.+|.. +-+
T Consensus 56 ~~w~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~g~~Vp~~~ae~~~i~si~dL~~~~~~~~~~~~~~~~~~~~g~~~~~ 134 (257)
T PF04069_consen 56 EEWTPTTYEAYKKALEEKLGVVWLGPLGA-GNTYGWAVPKYVAEKPGIKSISDLAKPAEDLEFGGKGEFYGRPDGWGCTT 134 (257)
T ss_dssp EEEETTTHHHHHHHHHHHHEEEEEEEEEE-EEEEEEEEEHHHHHHHT-SBGGGGGTCGGGCEEEETTEEECSSTTHHHHH
T ss_pred hhcCchhHHHHHHhhhhcCccccCCcccc-CCEEEEEEecccccccCcccHHHHhhcccccccCCCCceeeCCCCcchhh
Confidence 3333322 1233334443 22232 233334432 224667773 23345543 123
Q ss_pred HHHHHHhhC-CCCEEEeccCCCHH----HHHhhhccCCccEEeee--hhhhcccCCCccceeeecCCCCCCCcccceeee
Q 020472 198 RKSQILHRY-PSLKVMENFRGNVQ----TRLRKLNERVVQATLLA--LAGLKRLSMTENVTNILSVDDMLPAVAQGAIGI 270 (326)
Q Consensus 198 R~aQL~~~~-Pdl~v~~~iRGNV~----TRL~KL~~ge~DAIILA--~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAV 270 (326)
...++...| =+ .+. .+.|+.. ..-+.+.+|+.+.+.+= -.-+...++ ...=||..+.|++.+ +..
T Consensus 135 ~~~~~~~~ygl~-~~~-~~~~s~~~~~~~~~~A~~~~~~~v~~~w~p~~~~~~~~l----~~L~D~~~~~~~~~~--~~~ 206 (257)
T PF04069_consen 135 FNEQLLKAYGLD-NFE-LFPGSEAAMDAALYAAYKRGEPIVFYAWSPDWMIAKYDL----VVLEDPKGFFPPAYN--VVP 206 (257)
T ss_dssp HHHHHHHHCTCT-TSE-EESSEHHHHHHHHHHHHHTTSSSEEEEETSSTHHHHSTE----EE-BTTTCTSSSSEE--EEE
T ss_pred HHHHHHHhcCCC-cce-ecccccchhHHHHHHHHHcCCCEEEEEecCChhhccCCe----EEeecCCCCCCCCCE--EEE
Confidence 333444444 22 554 5556654 55666788998877652 122333322 122266666666544 444
Q ss_pred Eeec----CchhHHhhhhccc
Q 020472 271 ACRS----NDEKMVPFTTHSQ 287 (326)
Q Consensus 271 e~R~----dD~~~~~lL~~~~ 287 (326)
.+|+ +.+++.++|+.+.
T Consensus 207 ~~r~~~~~~~P~~~~~l~~~~ 227 (257)
T PF04069_consen 207 VVRKGFAEDHPEAAEFLNRFS 227 (257)
T ss_dssp EEEHHHHHHSHHHHHHHHCTT
T ss_pred EecHHHHhhChHHHHHHHhcC
Confidence 5553 4566888888774
No 114
>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=70.38 E-value=11 Score=30.97 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=34.4
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++-.+++...+|++++. -..++-.+-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08453 16 PELVRRFREAYPDVELQ-LREATSDVQLEALLAGEIDAGIVI 56 (200)
T ss_pred HHHHHHHHHhCCCceEE-EEeCCHHHHHHHHHcCCCCEEEEe
Confidence 35678888899999997 777888888999999999987764
No 115
>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=70.27 E-value=28 Score=31.72 Aligned_cols=68 Identities=9% Similarity=0.048 Sum_probs=35.3
Q ss_pred HHHHHhhhccCCccEEeeeh-hhhcccCC-CccceeeecCCCCC-----CCcccceeeeEeecCchhHHhhhhcc
Q 020472 219 VQTRLRKLNERVVQATLLAL-AGLKRLSM-TENVTNILSVDDML-----PAVAQGAIGIACRSNDEKMVPFTTHS 286 (326)
Q Consensus 219 V~TRL~KL~~ge~DAIILA~-AGL~RLgl-~~~i~~~L~~~~~l-----PA~GQGaLAVe~R~dD~~~~~lL~~~ 286 (326)
..+-++.|.+|..||++.-. .....+.- ...+......+... +.+.+--+++-++++|+++.+.++..
T Consensus 152 ~~~~~~aL~~GrvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~a 226 (246)
T TIGR03870 152 PRKLVSEVATGKADLAVAFAPEVARYVKASPEPLRMTVIPDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAA 226 (246)
T ss_pred HHHHHHHHHcCCCCEEEeeHHhHHHHHHhCCCCceEEeccccccccCCCCcceeeEEEEEEccCCHHHHHHHHHH
Confidence 46789999999999998842 22222211 11111000001000 00112125788899998777766543
No 116
>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=70.16 E-value=11 Score=30.81 Aligned_cols=40 Identities=10% Similarity=0.101 Sum_probs=33.6
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+--.+++..||++++. -.-|+-++-+..|.+|++|..|..
T Consensus 17 ~~l~~f~~~~P~v~l~-~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (200)
T cd08466 17 RLLARLKQLAPNISLR-ESPSSEEDLFEDLRLQEVDLVIDY 56 (200)
T ss_pred HHHHHHHHHCCCCEEE-EecCchHhHHHHHHcCCccEEEec
Confidence 4457888899999997 777888888999999999988763
No 117
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=70.02 E-value=97 Score=29.05 Aligned_cols=58 Identities=10% Similarity=0.188 Sum_probs=41.4
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.|+||+=.+. +....-.+...+++.||++. +++.. ++. ++.++|++|++|+++.
T Consensus 98 ~l~I~~~~~~-~~~~~~~~l~~f~~~~P~v~----v~i~~----~~~-----------------~~~~~l~~g~~D~~i~ 151 (319)
T PRK10216 98 KFELAAESPL-MMIMLNALSKRIYQRYPQAT----IKLRN----WDY-----------------DSLDAITRGEVDIGFT 151 (319)
T ss_pred EEEEEecchh-HHHHHHHHHHHHHHHCCCCE----EEEEe----CCc-----------------chHHHHhcCCccEEEe
Confidence 7999998775 55677778888888999863 55432 110 2358899999999998
Q ss_pred eCCC
Q 020472 147 SMKD 150 (326)
Q Consensus 147 SlKD 150 (326)
....
T Consensus 152 ~~~~ 155 (319)
T PRK10216 152 GRES 155 (319)
T ss_pred cCCC
Confidence 6433
No 118
>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=70.01 E-value=57 Score=26.37 Aligned_cols=57 Identities=19% Similarity=0.232 Sum_probs=36.9
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+....+-.-.+.+.+++.+|++. +++..- + ..++.+.|.+|++|+++-
T Consensus 1 ~l~Ig~~~~~~~~~~l~~~l~~~~~~~P~i~----l~i~~~----~----------------~~~~~~~l~~g~~Dl~i~ 56 (199)
T cd08451 1 RLRVGFTSSAAFHPLVPGLIRRFREAYPDVE----LTLEEA----N----------------TAELLEALREGRLDAAFV 56 (199)
T ss_pred CeeEEeeeeeeeecccHHHHHHHHHHCCCcE----EEEecC----C----------------hHHHHHHHHCCCccEEEE
Confidence 3678875443322344556677888899752 444321 1 246889999999999994
Q ss_pred e
Q 020472 147 S 147 (326)
Q Consensus 147 S 147 (326)
.
T Consensus 57 ~ 57 (199)
T cd08451 57 R 57 (199)
T ss_pred e
Confidence 3
No 119
>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=69.96 E-value=12 Score=30.87 Aligned_cols=41 Identities=12% Similarity=-0.026 Sum_probs=35.5
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++.-+.+++.+|++++. -..+|-++-.+.|.+|++|..|..
T Consensus 16 ~~~l~~f~~~~P~v~i~-~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08458 16 SGVIQTFIADRPDVSVY-LDTVPSQTVLELVSLQHYDLGISI 56 (196)
T ss_pred HHHHHHHHHHCCCcEEE-EeccChHHHHHHHHcCCCCEEEEe
Confidence 46678888899999997 778898889999999999998864
No 120
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=69.90 E-value=35 Score=32.52 Aligned_cols=131 Identities=21% Similarity=0.222 Sum_probs=70.7
Q ss_pred HHHHHHcCCCcEEEeeCCCCCCC----------CCCCceeeeecCCCCCcceeeccCccCcccCCCCCEE----ecCChH
Q 020472 132 IDEALINSQIDIAVHSMKDVPTY----------LPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIV----GTASLR 197 (326)
Q Consensus 132 Le~ALl~g~iDiAVHSlKDlPt~----------lp~gL~iaAv~kReDprD~LV~~~~~~l~dLp~ga~I----GTSS~R 197 (326)
+..+|.+|++|++.-++---|.. ...+..+ .-|.+. + ..+++|| .|-+| ||.+..
T Consensus 98 ~i~~L~~G~~Di~~~~~~~t~eR~~~~~fS~Py~~~~~~l---v~r~~~-~------i~sl~dL-~Gk~V~v~~gs~~~~ 166 (302)
T PRK10797 98 RIPLLQNGTFDFECGSTTNNLERQKQAAFSDTIFVVGTRL---LTKKGG-D------IKDFADL-KGKAVVVTSGTTSEV 166 (302)
T ss_pred HHHHHHCCCccEEecCCccCcchhhcceecccEeeccEEE---EEECCC-C------CCChHHc-CCCEEEEeCCCcHHH
Confidence 45899999999988765333221 1222222 122221 1 1356677 34444 344333
Q ss_pred HHHHHHhh----CCCCEEEeccCCCHHHHHhhhccCCccEEeeehh---hh-cccCCCccceeeecCCCCCCCcccceee
Q 020472 198 RKSQILHR----YPSLKVMENFRGNVQTRLRKLNERVVQATLLALA---GL-KRLSMTENVTNILSVDDMLPAVAQGAIG 269 (326)
Q Consensus 198 R~aQL~~~----~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~A---GL-~RLgl~~~i~~~L~~~~~lPA~GQGaLA 269 (326)
.++.+ .|..+++ . --+.++-++.|.+|++||+|.-.. +. ..-+-.+.+ ..+. +. ......+
T Consensus 167 ---~l~~~~~~~~~~~~i~-~-~~~~~~~l~~L~~GrvDa~i~d~~~~~~~~~~~~~~~~l-~i~~-~~----~~~~~~~ 235 (302)
T PRK10797 167 ---LLNKLNEEQKMNMRII-S-AKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNW-EIVG-KP----QSQEAYG 235 (302)
T ss_pred ---HHHHHhhhcCCceEEE-E-eCCHHHHHHHHHcCCceEEEccHHHHHHHHHcCCCCcce-EECC-cc----CCcCcee
Confidence 23332 3456776 3 457889999999999999987432 32 211111111 2222 11 1234567
Q ss_pred eEeecCchhHHhhhh
Q 020472 270 IACRSNDEKMVPFTT 284 (326)
Q Consensus 270 Ve~R~dD~~~~~lL~ 284 (326)
+-.|++++++.+.++
T Consensus 236 ~a~~k~~~~L~~~in 250 (302)
T PRK10797 236 CMLRKDDPQFKKLMD 250 (302)
T ss_pred EEEeCCCHHHHHHHH
Confidence 778888887666554
No 121
>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=69.80 E-value=11 Score=31.45 Aligned_cols=40 Identities=10% Similarity=0.123 Sum_probs=34.2
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.--+.+++.||++++. -.-++-++-++.|.+|++|..|..
T Consensus 17 ~~l~~f~~~~P~i~l~-i~~~~~~~~~~~L~~g~~Dl~i~~ 56 (200)
T cd08465 17 ALMRQLRAEAPGIDLA-VSQASREAMLAQVADGEIDLALGV 56 (200)
T ss_pred HHHHHHHHHCCCcEEE-EecCChHhHHHHHHCCCccEEEec
Confidence 4457778889999997 777888999999999999998864
No 122
>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=68.78 E-value=12 Score=30.60 Aligned_cols=47 Identities=26% Similarity=0.345 Sum_probs=38.1
Q ss_pred EEecCC-------hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 190 IVGTAS-------LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 190 ~IGTSS-------~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+||++. ++-.++++..+|++++. -.-+|-+.-++.|.+|++|-.|..
T Consensus 4 ~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~-i~~~~~~~~~~~l~~~~~Dl~i~~ 57 (200)
T cd08411 4 RLGVIPTIAPYLLPRLLPALRQAYPKLRLY-LREDQTERLLEKLRSGELDAALLA 57 (200)
T ss_pred EEEecHHHHhhhhHHHHHHHHHHCCCcEEE-EEeCcHHHHHHHHHcCCccEEEEe
Confidence 567664 35578888999999997 667888888999999999988753
No 123
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=68.47 E-value=1.1e+02 Score=29.12 Aligned_cols=175 Identities=11% Similarity=0.101 Sum_probs=87.4
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+. +..-.-.+...+.+.||++. +++.. . + ..++.+.|.+|++|+
T Consensus 91 ~~g~l~Ig~~~~~-~~~~l~~~l~~f~~~~P~i~----i~i~~--~--~----------------~~~~~~~L~~g~iDl 145 (324)
T PRK12681 91 DKGSLYIATTHTQ-ARYALPPVIKGFIERYPRVS----LHMHQ--G--S----------------PTQIAEAAAKGNADF 145 (324)
T ss_pred CCCeEEEEechhH-HHHhhHHHHHHHHHHCCCcE----EEEEe--C--C----------------HHHHHHHHHcCCCCE
Confidence 4568999996644 34444556666677899752 44422 1 1 257889999999999
Q ss_pred EEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEecC---ChHHHH-HH-Hh--hCCCC
Q 020472 144 AVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA---SLRRKS-QI-LH--RYPSL 209 (326)
Q Consensus 144 AVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGTS---S~RR~a-QL-~~--~~Pdl 209 (326)
++... |...++++....+ -.++.-+++.+++ .++++|-.-..|..+ ..|..- ++ .. ..|..
T Consensus 146 ~i~~~---~~~~~~~l~~~~l--~~~~~~~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (324)
T PRK12681 146 AIATE---ALHLYDDLIMLPC--YHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRI 220 (324)
T ss_pred EEecC---cccCCCCeEEEEe--ccceeEEEeCCCChhhcCCCcCHHHHhCCCeEeccCCCchHHHHHHHHHHcCCCCce
Confidence 99742 2222344432221 1222223333221 123444443455542 233321 11 11 23333
Q ss_pred EEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecCch
Q 020472 210 KVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDE 277 (326)
Q Consensus 210 ~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~dD~ 277 (326)
.+ .-.|+++-+.-+..|.. ..+++..-.... ....+ ..++.+... . .--+.+..|++..
T Consensus 221 ~~---~~~s~~~~~~~v~~g~G-i~~lp~~~~~~~-~~~~l-~~~~~~~~~-~--~~~~~l~~~~~~~ 279 (324)
T PRK12681 221 VF---TATDADVIKTYVRLGLG-VGVIASMAVDPV-ADPDL-VAIDASHLF-S--HSTTKIGFRRGTF 279 (324)
T ss_pred EE---EeCCHHHHHHHHHhCCC-EEEeehhhcccc-cCCce-EEeecCCCC-C--ceEEEEEEECCch
Confidence 32 23688888888887754 334454333332 11222 223333321 2 2247778887753
No 124
>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=67.95 E-value=12 Score=30.41 Aligned_cols=41 Identities=10% Similarity=-0.040 Sum_probs=34.4
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++..+.+++.+|++++. -.-++-.+=++.|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (196)
T cd08450 16 PEVLPILREEHPDLDVE-LSSLFSPQLAEALMRGKLDVAFMR 56 (196)
T ss_pred HHHHHHHHhhCCCcEEE-EEecChHHHHHHHhcCCccEEEEe
Confidence 45668888999999997 777788888899999999998853
No 125
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=67.83 E-value=24 Score=33.24 Aligned_cols=59 Identities=19% Similarity=0.310 Sum_probs=40.0
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+-.+....+ .-.+...+.+.+|++. +++.. ++ ..++.+.|.+|++|+
T Consensus 91 ~~g~l~Ig~~~~~~~~~-l~~~l~~~~~~~p~i~----l~~~~----~~----------------~~~~~~~L~~g~~D~ 145 (313)
T PRK12684 91 DQGNLTIATTHTQARYA-LPAAIKEFKKRYPKVR----LSILQ----GS----------------PTQIAEMVLHGQADL 145 (313)
T ss_pred CCCeEEEEechHHHHHH-hHHHHHHHHHHCCCce----EEEEe----CC----------------hHHHHHHHHCCCcCE
Confidence 45789999965555443 4455666777889752 44321 11 357889999999999
Q ss_pred EEee
Q 020472 144 AVHS 147 (326)
Q Consensus 144 AVHS 147 (326)
++-.
T Consensus 146 ~i~~ 149 (313)
T PRK12684 146 AIAT 149 (313)
T ss_pred EEee
Confidence 9954
No 126
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=66.70 E-value=1.2e+02 Score=28.64 Aligned_cols=60 Identities=22% Similarity=0.371 Sum_probs=40.1
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+....+=.. +.+.+.+.+|++. +++.. |+ ..++.++|.+|++|+
T Consensus 91 ~~g~lrIg~~~~~~~~~l~~-~l~~f~~~~P~i~----l~l~~----~~----------------~~~~~~~L~~g~~Dl 145 (316)
T PRK12679 91 TSGVLTIATTHTQARYSLPE-VIKAFRELFPEVR----LELIQ----GT----------------PQEIATLLQNGEADI 145 (316)
T ss_pred cCceEEEEechHhhhcchHH-HHHHHHHHCCCeE----EEEec----CC----------------HHHHHHHHHcCCCCE
Confidence 35789999966555444444 4556667789752 43321 11 346889999999999
Q ss_pred EEeeC
Q 020472 144 AVHSM 148 (326)
Q Consensus 144 AVHSl 148 (326)
+|+.-
T Consensus 146 ~i~~~ 150 (316)
T PRK12679 146 GIASE 150 (316)
T ss_pred EEecc
Confidence 99854
No 127
>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=66.42 E-value=15 Score=29.80 Aligned_cols=41 Identities=10% Similarity=0.278 Sum_probs=35.1
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++-.++++..+|++++. -.-++-++-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (201)
T cd08418 16 PAVINRFKEQFPDVQIS-IYEGQLSSLLPELRDGRLDFAIGT 56 (201)
T ss_pred HHHHHHHHHHCCCceEE-EEeCcHHHHHHHHHcCCCcEEEEe
Confidence 35578899999999997 667788888999999999999864
No 128
>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=66.24 E-value=13 Score=30.14 Aligned_cols=56 Identities=14% Similarity=0.159 Sum_probs=35.7
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||+=.+.-..+-.. +...+.+.+|++. +++... ...++.+.|.+|++|+++..
T Consensus 2 l~ig~~~~~~~~~l~~-~l~~~~~~~P~v~----l~~~~~--------------------~~~~~~~~l~~g~~Dl~i~~ 56 (199)
T cd08430 2 LSLYCSVTASYSFLPP-ILERFRAQHPQVE----IKLHTG--------------------DPADAIDKVLNGEADIAIAA 56 (199)
T ss_pred eEEEeccccceeeccH-HHHHHHHHCCCce----EEEEeC--------------------CHHHHHHHHHCCCCCEEEEe
Confidence 5677665544333333 4466667789752 444321 13578899999999999976
Q ss_pred C
Q 020472 148 M 148 (326)
Q Consensus 148 l 148 (326)
.
T Consensus 57 ~ 57 (199)
T cd08430 57 R 57 (199)
T ss_pred c
Confidence 3
No 129
>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=65.90 E-value=16 Score=29.92 Aligned_cols=40 Identities=15% Similarity=0.169 Sum_probs=33.0
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.-.++++..+|++++. -.-++-++-+..|.+|++|..|.-
T Consensus 17 ~~l~~~~~~~P~v~i~-~~~~~~~~~~~~l~~~~~Dl~i~~ 56 (185)
T cd08439 17 FLLNRFASVYPRLAIE-VVCKRTPRLMEMLERGEVDLALIT 56 (185)
T ss_pred HHHHHHHHHCCCeEEE-EEECChHHHHHHHHCCCCcEEEEe
Confidence 5568888999999997 666777788899999999987763
No 130
>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=65.67 E-value=13 Score=31.08 Aligned_cols=40 Identities=10% Similarity=0.022 Sum_probs=34.4
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+-.+.++..+|++++. -..++-..=++.|.+|++|..+..
T Consensus 18 ~~l~~f~~~~P~v~i~-i~~~~~~~l~~~l~~g~~D~~~~~ 57 (198)
T cd08486 18 LLLRAFLTSTPTATVS-LTHMTKDEQVEGLLAGTIHVGFSR 57 (198)
T ss_pred HHHHHHHHhCCCeEEE-EEECCHHHHHHHHHcCCceEEEec
Confidence 4557788889999997 677888999999999999999864
No 131
>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=65.31 E-value=14 Score=29.75 Aligned_cols=41 Identities=15% Similarity=0.203 Sum_probs=34.0
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++-.++++..+|++++. -.-|+-++-++.|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (193)
T cd08442 16 PPLLAAYHARYPKVDLS-LSTGTTGALIQAVLEGRLDGAFVA 56 (193)
T ss_pred HHHHHHHHHHCCCceEE-EEeCCcHHHHHHHHCCCccEEEEe
Confidence 35568888999999997 666787888899999999998864
No 132
>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=65.17 E-value=10 Score=31.02 Aligned_cols=40 Identities=5% Similarity=-0.075 Sum_probs=32.3
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
...+.++..+|++++. -.-++.+.-++.|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~v~i~-i~~~~~~~~~~~l~~g~~D~~i~~ 56 (195)
T cd08431 17 PLIAEFYQLNKATRIR-LSEEVLGGTWDALASGRADLVIGA 56 (195)
T ss_pred HHHHHHHHHCCCCceE-EEEeccchHHHHHhCCCCCEEEEe
Confidence 5567888899999987 555666677889999999998874
No 133
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=64.91 E-value=36 Score=32.26 Aligned_cols=59 Identities=14% Similarity=0.099 Sum_probs=40.6
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.++|+||.=.+.... -...+...+++.||++. +++... + +.++.+.|.+|++|++
T Consensus 88 ~g~l~Ig~~~~~~~~-~l~~~l~~~~~~~P~i~----l~~~~~----~----------------~~~~~~~L~~g~~Dl~ 142 (317)
T PRK15421 88 QTRLRIAIECHSCIQ-WLTPALENFHKNWPQVE----MDFKSG----V----------------TFDPQPALQQGELDLV 142 (317)
T ss_pred ceeEEEEecccchHH-HHHHHHHHHHHHCCCce----EEEEeC----c----------------cHHHHHHHHCCCcCEE
Confidence 467999986654433 23556677788899763 554321 1 2478899999999999
Q ss_pred EeeC
Q 020472 145 VHSM 148 (326)
Q Consensus 145 VHSl 148 (326)
++.-
T Consensus 143 i~~~ 146 (317)
T PRK15421 143 MTSD 146 (317)
T ss_pred EecC
Confidence 9753
No 134
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=64.78 E-value=27 Score=32.54 Aligned_cols=175 Identities=9% Similarity=0.043 Sum_probs=87.6
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+. +.+---.+...+.+.+|++. +++... + +.++.+.|.+|++|+
T Consensus 91 ~~g~l~Ig~~~~~-~~~~l~~~l~~~~~~~P~i~----i~i~~~----~----------------~~~~~~~l~~g~~D~ 145 (309)
T PRK12682 91 DSGTLTIATTHTQ-ARYVLPRVVAAFRKRYPKVN----LSLHQG----S----------------PDEIARMVISGEADI 145 (309)
T ss_pred CCCeEEEeeCchH-HHHHHHHHHHHHHHhCCCeE----EEEecC----C----------------HHHHHHHHHcCCccE
Confidence 3467999998775 44555566778888899752 443221 1 246788999999999
Q ss_pred EEeeCCCCCCCCCCCceeeeecCCCCCcceeeccC-------ccCcccCCCCCEEecCC---hHHH-HHHH-hhCCCCEE
Q 020472 144 AVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS-------AASLAELPAGSIVGTAS---LRRK-SQIL-HRYPSLKV 211 (326)
Q Consensus 144 AVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~-------~~~l~dLp~ga~IGTSS---~RR~-aQL~-~~~Pdl~v 211 (326)
++-.. +.+ .++++....+. .++..+++.++ ..++++|..-..|.++. .|+. .++. ...-+.++
T Consensus 146 ~i~~~-~~~--~~~~l~~~~l~--~~~~~~~~~~~~pl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~ 220 (309)
T PRK12682 146 GIATE-SLA--DDPDLATLPCY--DWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDI 220 (309)
T ss_pred EEecC-ccc--CCCcceEEEee--eeeEEEEecCCCccccCCCcCHHHHhcCCceeeCCCccHHHHHHHHHHHcCCCCcE
Confidence 99642 211 13344322211 12222222221 12345554445566532 3332 2222 22223333
Q ss_pred EeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccceeeecCCCCCCCcccceeeeEeecC
Q 020472 212 MENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSN 275 (326)
Q Consensus 212 ~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i~~~L~~~~~lPA~GQGaLAVe~R~d 275 (326)
. ..=.++.+=+.-+.+|.. -.+++..-...+ -...+. .++..+..| ..-+.+..+++
T Consensus 221 ~-~~~~~~~~~~~~v~~g~G-i~~lp~~~~~~~-~~~~l~-~~~~~~~~~---~~~~~l~~~~~ 277 (309)
T PRK12682 221 V-LEAIDSDVIKTYVRLGLG-VGIVAEMAYRPD-RDGDLV-ALPAGHLFG---PNTAWVALKRG 277 (309)
T ss_pred E-EEeCCHHHHHHHHHhCCc-eEEehhhhhhhc-cCCcEE-EeeCCCCCc---ceeEEEeeecC
Confidence 3 223478887777777744 334444433332 122232 233333222 33456666654
No 135
>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=63.94 E-value=12 Score=30.54 Aligned_cols=41 Identities=5% Similarity=-0.003 Sum_probs=33.6
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+-...++..||++++. -.-++-++-++.|.+|++|..|...
T Consensus 17 ~~l~~~~~~~P~v~l~-i~~~~~~~~~~~l~~g~~D~~i~~~ 57 (200)
T cd08464 17 PLLAALRAEAPGVRLV-FRQVDPFNVGDMLDRGEIDLAIGVF 57 (200)
T ss_pred HHHHHHHHHCCCcEEE-EecCCcccHHHHHhcCcccEEEecC
Confidence 4457888899999997 6667777788999999999998643
No 136
>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=63.85 E-value=17 Score=29.59 Aligned_cols=41 Identities=12% Similarity=0.103 Sum_probs=34.9
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++-..+++..+|++++. -..++-++-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~v~-~~~~~~~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08447 16 PRLLAAARAALPDVDLV-LREMVTTDQIEALESGRIDLGLLR 56 (198)
T ss_pred HHHHHHHHHHCCCeEEE-EEeCCHHHHHHHHHcCCceEEEec
Confidence 35567888899999997 667888999999999999988864
No 137
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=63.65 E-value=47 Score=30.96 Aligned_cols=61 Identities=20% Similarity=0.237 Sum_probs=40.5
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+.....-.-.+...+.+.||++. +++ ... + ..++.+.|.+|++|+
T Consensus 89 ~~g~l~I~~~~~~~~~~~~~~~l~~~~~~~p~i~----l~~--~~~--~----------------~~~~~~~l~~g~~Di 144 (305)
T PRK11233 89 LSGQVSIGLAPGTAASSLTMPLLQAVRAEFPGIV----LYL--HEN--S----------------GATLNEKLMNGQLDM 144 (305)
T ss_pred cCceEEEEcccchhhHHHHHHHHHHHHHHCCCcE----EEE--EEC--C----------------cHHHHHHHHCCCCCE
Confidence 3568999987765543333346778888899752 333 211 1 136788999999999
Q ss_pred EEeeC
Q 020472 144 AVHSM 148 (326)
Q Consensus 144 AVHSl 148 (326)
++-..
T Consensus 145 ~i~~~ 149 (305)
T PRK11233 145 AVIYE 149 (305)
T ss_pred EEEcC
Confidence 99653
No 138
>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=63.38 E-value=18 Score=30.07 Aligned_cols=41 Identities=12% Similarity=0.148 Sum_probs=34.7
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++..+++...+|++++. -.-++-.+-++.|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~v~-~~~~~~~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08413 16 PPVIAAFRKRYPKVKLS-LHQGTPSQIAEMVLKGEADIAIAT 56 (198)
T ss_pred cHHHHHHHHhCCceEEE-EEeCCHHHHHHHHHcCCCCEEEEc
Confidence 46678899999999997 777888888899999999988764
No 139
>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=63.32 E-value=17 Score=29.39 Aligned_cols=43 Identities=14% Similarity=0.120 Sum_probs=35.7
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeehh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALA 239 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~A 239 (326)
+..-..++..+|++++. -.-++-++-.+.|.+|++|..|....
T Consensus 16 ~~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (196)
T cd08415 16 PRAIARFRARHPDVRIS-LHTLSSSTVVEAVLSGQADLGLASLP 58 (196)
T ss_pred HHHHHHHHHHCCCcEEE-EEecchHHHHHHHHcCCccEEEEeCC
Confidence 35667788889999998 77788888889999999999997543
No 140
>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=63.16 E-value=19 Score=28.27 Aligned_cols=42 Identities=21% Similarity=0.320 Sum_probs=32.6
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeehh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALA 239 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~A 239 (326)
....++...+|++++. -..++-+.-+..|.+|++|..|.-..
T Consensus 17 ~~i~~~~~~~p~i~i~-~~~~~~~~~~~~l~~g~~D~~i~~~~ 58 (197)
T cd05466 17 PLLAAFRQRYPGVELS-LVEGGSSELLEALLEGELDLAIVALP 58 (197)
T ss_pred HHHHHHHHHCCCCEEE-EEECChHHHHHHHHcCCceEEEEcCC
Confidence 4456777889999987 66666667788899999999886543
No 141
>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=62.94 E-value=18 Score=29.39 Aligned_cols=41 Identities=17% Similarity=0.189 Sum_probs=34.7
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++.-.+++..+|++++. -..++-.+-++.|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~~~-i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08456 16 PRAIKAFLQRHPDVTIS-IHTRDSPTVEQWLSAQQCDLGLVS 56 (196)
T ss_pred HHHHHHHHHHCCCcEEE-EEeCCHHHHHHHHHcCCccEEEEe
Confidence 36678889999999998 777887777888999999998864
No 142
>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=62.92 E-value=18 Score=30.16 Aligned_cols=41 Identities=12% Similarity=0.233 Sum_probs=35.2
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++--.++...+|++++. -.-++-++-+..|.+|++|-.|..
T Consensus 16 ~~~l~~f~~~~P~~~i~-i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08443 16 PPVIKGFIERYPRVSLQ-MHQGSPTQIAEMVSKGLVDFAIAT 56 (198)
T ss_pred cHHHHHHHHHCCCeEEE-EEeCCHHHHHHHHHCCCccEEEEe
Confidence 45567888899999998 777899999999999999998864
No 143
>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=62.56 E-value=19 Score=29.19 Aligned_cols=41 Identities=10% Similarity=0.116 Sum_probs=34.2
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.+..+++...+|++++. -.-++-+.=+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~v~l~-~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (199)
T cd08430 16 PPILERFRAQHPQVEIK-LHTGDPADAIDKVLNGEADIAIAA 56 (199)
T ss_pred cHHHHHHHHHCCCceEE-EEeCCHHHHHHHHHCCCCCEEEEe
Confidence 47789999999999997 555777777888999999998864
No 144
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=60.69 E-value=1.3e+02 Score=27.31 Aligned_cols=135 Identities=11% Similarity=0.088 Sum_probs=72.6
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.++|+||+-.+.... ....+...+...+|++. +++.... ..++.++|.+|++|+|
T Consensus 90 ~~~i~I~~~~~~~~~-~l~~~l~~~~~~~p~~~----i~~~~~~--------------------~~~~~~~l~~g~~Dl~ 144 (296)
T PRK11242 90 RGSLRLAMTPTFTAY-LIGPLIDAFHARYPGIT----LTIREMS--------------------QERIEALLADDELDVG 144 (296)
T ss_pred eeEEEEEeccchhhh-hhHHHHHHHHHHCCCCE----EEEEeCC--------------------HHHHHHHHHCCCCcEE
Confidence 467999998776444 44556666677789763 4443221 2578899999999999
Q ss_pred EeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc--------cCcccCCCCCEEecCC---hHH-HH-HHHhhCCCCEE
Q 020472 145 VHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA--------ASLAELPAGSIVGTAS---LRR-KS-QILHRYPSLKV 211 (326)
Q Consensus 145 VHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~--------~~l~dLp~ga~IGTSS---~RR-~a-QL~~~~Pdl~v 211 (326)
+=.... .++++..-.+. +++--+++.+++ .++++|-.-..|.... .+. -. .+.......++
T Consensus 145 i~~~~~----~~~~l~~~~l~--~~~~~~~~~~~~pl~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 218 (296)
T PRK11242 145 IAFAPV----HSPEIEAQPLF--TETLALVVGRHHPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRV 218 (296)
T ss_pred EEecCC----CCcceeEEEee--eccEEEEEcCCCcccccCCCcCHHHHhCCCcEeeCCCccHHHHHHHHHHHcCCCccE
Confidence 954321 23454432222 232222222221 1223333333343322 222 12 23333333343
Q ss_pred EeccCCCHHHHHhhhccCCc
Q 020472 212 MENFRGNVQTRLRKLNERVV 231 (326)
Q Consensus 212 ~~~iRGNV~TRL~KL~~ge~ 231 (326)
. -.=.|+++-++-+.+|..
T Consensus 219 ~-~~~~~~~~~~~~v~~g~g 237 (296)
T PRK11242 219 A-IEANSISAVLEIVRRGRL 237 (296)
T ss_pred E-EEeccHHHHHHHHHhCCe
Confidence 3 334689999998888875
No 145
>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=60.50 E-value=36 Score=31.28 Aligned_cols=60 Identities=18% Similarity=0.228 Sum_probs=41.3
Q ss_pred cCCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCc
Q 020472 63 TKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQID 142 (326)
Q Consensus 63 ~~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iD 142 (326)
...+.|+||+=.+.. ....-.+...+.+.+|++. +++.... ..++.++|.+|++|
T Consensus 90 ~~~~~l~I~~~~~~~-~~~~~~~l~~~~~~~P~~~----i~~~~~~--------------------~~~~~~~l~~g~~D 144 (300)
T TIGR02424 90 GEGPTVRIGALPTVA-ARLMPEVVKRFLARAPRLR----VRIMTGP--------------------NAYLLDQLRVGALD 144 (300)
T ss_pred CCCceEEEecccHHH-HhhhHHHHHHHHHhCCCcE----EEEEeCc--------------------hHHHHHHHHCCCCC
Confidence 346789999876543 3345566777888899763 4443221 24688999999999
Q ss_pred EEEee
Q 020472 143 IAVHS 147 (326)
Q Consensus 143 iAVHS 147 (326)
+++-.
T Consensus 145 ~~i~~ 149 (300)
T TIGR02424 145 LVVGR 149 (300)
T ss_pred EEEEe
Confidence 99954
No 146
>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=60.09 E-value=98 Score=25.57 Aligned_cols=57 Identities=25% Similarity=0.276 Sum_probs=40.4
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||.=.+. +..-.-.+...+++.+|++. ++++... ..++.+.|.+|++|+++.
T Consensus 1 ~~~Ig~~~~~-~~~~l~~~l~~~~~~~P~v~----i~~~~~~--------------------~~~~~~~l~~g~~Dl~i~ 55 (202)
T cd08468 1 RFRFAVTDYT-ALAVMPRLMARLEELAPSVR----LNLVHAE--------------------QKLPLDALLAGEIDFALG 55 (202)
T ss_pred CEEEEechHH-HHHHhHHHHHHHHhhCCCCE----EEEEECC--------------------hHhHHHHHHCCCccEEEe
Confidence 3678876554 34456677888888999762 5554321 357889999999999998
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (202)
T cd08468 56 YS 57 (202)
T ss_pred cc
Confidence 54
No 147
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=59.59 E-value=29 Score=32.58 Aligned_cols=59 Identities=10% Similarity=-0.035 Sum_probs=38.2
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..++|+||+-....+...--.+...+++.||++. +++..-. ..++.++|.+|++|+
T Consensus 90 ~~g~l~Ig~~~~~~~~~~l~~~l~~~~~~~P~i~----l~l~~~~--------------------~~~~~~~l~~g~~D~ 145 (308)
T PRK10094 90 VERQVNIVINNLLYNPQAVAQLLAWLNERYPFTQ----FHISRQI--------------------YMGVWDSLLYEGFSL 145 (308)
T ss_pred CCccEEEEecccccCHHHHHHHHHHHHHhCCCcE----EEEEeeh--------------------hhhHHHHHhCCCccE
Confidence 3568999985432222223356777888899862 4442211 246778999999999
Q ss_pred EEe
Q 020472 144 AVH 146 (326)
Q Consensus 144 AVH 146 (326)
++=
T Consensus 146 ~i~ 148 (308)
T PRK10094 146 AIG 148 (308)
T ss_pred EEe
Confidence 884
No 148
>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=59.30 E-value=20 Score=29.12 Aligned_cols=42 Identities=26% Similarity=0.269 Sum_probs=33.7
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
.+-.++++..+|++++. -.-++-.+-+..|.+|++|..|.-.
T Consensus 16 ~~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (199)
T cd08416 16 PRIIMGLKLRRPELDIE-LTLGSNKDLLKKLKDGELDAILVAT 57 (199)
T ss_pred HHHHHHHHHhCCCeEEE-EEEcCcHHHHHHHhCCCCCEEEEec
Confidence 35678899999999997 5556666668889999999998743
No 149
>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=59.28 E-value=90 Score=24.91 Aligned_cols=57 Identities=19% Similarity=0.217 Sum_probs=38.0
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+.-..+ -..+...+++.||++. +++.. + + ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~~~~-l~~~l~~~~~~~P~i~----i~i~~--~-~-----------------~~~~~~~l~~~~~Dl~i~ 55 (195)
T cd08434 1 TVRLGFLHSLGTSL-VPDLIRAFRKEYPNVT----FELHQ--G-S-----------------TDELLDDLKNGELDLALC 55 (195)
T ss_pred CeEEEecchhhhhh-hHHHHHHHHHhCCCeE----EEEec--C-c-----------------HHHHHHHHHcCCccEEEE
Confidence 37888877655443 4446677777899752 44432 1 1 246889999999999996
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 56 ~~ 57 (195)
T cd08434 56 SP 57 (195)
T ss_pred cc
Confidence 53
No 150
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=58.85 E-value=26 Score=28.10 Aligned_cols=41 Identities=10% Similarity=0.033 Sum_probs=33.1
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+-...++..+|++++. -..++-+.-...|.+|++|..|...
T Consensus 17 ~~l~~~~~~~p~v~i~-i~~~~~~~~~~~l~~g~~D~~i~~~ 57 (197)
T cd08440 17 PVLAAFRRRHPGIRVR-LRDVSAEQVIEAVRSGEVDFGIGSE 57 (197)
T ss_pred HHHHHHHHhCCCcEEE-EEeCChHHHHHHHHcCCccEEEEeC
Confidence 4567788889999997 6667777788899999999888653
No 151
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=58.56 E-value=25 Score=28.67 Aligned_cols=40 Identities=13% Similarity=0.107 Sum_probs=33.7
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+-.+.++..+|++++. -.-|+-++-...|.+|++|-.|..
T Consensus 18 ~~i~~~~~~~P~v~l~-i~~~~~~~~~~~l~~~~~Dl~i~~ 57 (198)
T cd08446 18 RLLRAFLTARPDVTVS-LHNMTKDEQIEALRAGRIHIGFGR 57 (198)
T ss_pred HHHHHHHHHCCCeEEE-EeeCCHHHHHHHHHCCCccEEEEe
Confidence 4467888899999997 677888888899999999998864
No 152
>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=57.67 E-value=20 Score=29.38 Aligned_cols=41 Identities=15% Similarity=0.134 Sum_probs=33.8
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+.-.++++..+|++++. -..++-.+-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~i~-i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08441 16 MPVLDQFRERWPDVELD-LSSGFHFDPLPALLRGELDLVITS 56 (198)
T ss_pred HHHHHHHHHhCCCeEEE-EEeCCchhHHHHHHcCCceEEEec
Confidence 35568889999999997 666777778899999999998864
No 153
>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=57.19 E-value=27 Score=28.98 Aligned_cols=41 Identities=7% Similarity=0.136 Sum_probs=33.9
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++--.+++..+|++++. -.-|+-+.-++.|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~P~v~l~-i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08444 16 PWVVQAFKEQFPNVHLV-LHQGSPEEIASMLANGQADIGIAT 56 (198)
T ss_pred hHHHHHHHHHCCCeEEE-EEeCCHHHHHHHHHCCCccEEEec
Confidence 45567888899999997 777887888899999999998763
No 154
>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=56.88 E-value=25 Score=28.36 Aligned_cols=42 Identities=10% Similarity=0.097 Sum_probs=35.0
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
++-...+.+.+|++++. -.-+|-++-++.|.+|++|-.|...
T Consensus 16 ~~~l~~~~~~~p~v~i~-i~~~~~~~~~~~L~~~~~Dl~i~~~ 57 (197)
T cd08438 16 APLLAAFRQRYPNIELE-LVEYGGKKVEQAVLNGELDVGITVL 57 (197)
T ss_pred HHHHHHHHHHCcCeEEE-EEEcCcHHHHHHHHcCCCCEEEEec
Confidence 35667888899999998 6678888888999999999988643
No 155
>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=56.55 E-value=25 Score=29.14 Aligned_cols=39 Identities=8% Similarity=0.096 Sum_probs=33.3
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 236 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIIL 236 (326)
.-.+++...+|++++. -.-++-+.-+..|.+|++|..|.
T Consensus 18 ~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~~~~Dl~i~ 56 (203)
T cd08445 18 ELIRRFRQAAPDVEIE-LIEMTTVQQIEALKEGRIDVGFG 56 (203)
T ss_pred HHHHHHHHHCCCeEEE-EEeCChHHHHHHHHcCCCcEEEe
Confidence 4457778889999997 77788899999999999999885
No 156
>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=55.76 E-value=24 Score=28.41 Aligned_cols=40 Identities=13% Similarity=0.171 Sum_probs=34.4
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
..-++++..+|++++. -.-|+-..-.+.|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~i~i~-i~~~~~~~~~~~l~~~~~Di~i~~ 56 (197)
T cd08448 17 RILRAFRAEYPGIEVA-LHEMSSAEQIEALLRGELDLGFVH 56 (197)
T ss_pred HHHHHHHHHCCCCeEE-EEeCCHHHHHHHHHcCCcceEEEe
Confidence 5568888899999997 777888888999999999998863
No 157
>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=55.62 E-value=40 Score=32.33 Aligned_cols=189 Identities=14% Similarity=0.095 Sum_probs=98.2
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
++|+||.-+..=+.++++.+...|++.+ ++++++.. |. .-+.++|.+|+||+.+
T Consensus 8 ~~I~ig~~~w~~~~~~~~i~~~iLE~~G------y~Ve~~~~----~~----------------~~~~~al~~GdiD~~~ 61 (290)
T TIGR03414 8 KTVRFADVGWTDITATTALASVLLEGLG------YQPKVTLL----SV----------------PVTYAGLKDGDLDVFL 61 (290)
T ss_pred CeEEEeeCCcchHHHHHHHHHHHHHHcC------CcceeEEc----cH----------------HHHHHHHHcCCceEec
Confidence 5699999999999999999999999643 24665322 21 2367899999999987
Q ss_pred eeCCCCCCC------C-CC-CceeeeecCCCCCcceeeccC------ccCcccCCC------CCEEecC---ChHHH--H
Q 020472 146 HSMKDVPTY------L-PE-KTILPCNLQREDVRDAFISLS------AASLAELPA------GSIVGTA---SLRRK--S 200 (326)
Q Consensus 146 HSlKDlPt~------l-p~-gL~iaAv~kReDprD~LV~~~------~~~l~dLp~------ga~IGTS---S~RR~--a 200 (326)
=.. +|.. . .+ ++....... .+-+..|..++ -++++||.+ |..+|.. ...+. .
T Consensus 62 e~W--~p~~~~~~~~~~~~~~l~~lg~~~-~~~~~g~~Vp~y~ae~~i~sisDL~~~a~~f~g~~~g~~~g~~~~~~~~~ 138 (290)
T TIGR03414 62 GNW--MPAMEPDIKPYLESGSVEVLGPNL-EGAKYTLAVPTYVADAGLKSFADIAKFKDKLDGKIYGIEPGNDGNRLIQK 138 (290)
T ss_pred ccc--CCcCHHHHHhhccCCeEEEecccC-CCceEEEEEChhhhhcCCCCHHHHhhHHHhcCCEEEcccCChhHHHHHHH
Confidence 443 3321 1 11 344433222 22233344332 234566642 4445543 22222 2
Q ss_pred HHHhhCCCCE-EEeccCCCHHHHH----hhhccCCccEEee-e-hhhhcccCCCccceeeecCCCCC-CCcccceeeeEe
Q 020472 201 QILHRYPSLK-VMENFRGNVQTRL----RKLNERVVQATLL-A-LAGLKRLSMTENVTNILSVDDML-PAVAQGAIGIAC 272 (326)
Q Consensus 201 QL~~~~Pdl~-v~~~iRGNV~TRL----~KL~~ge~DAIIL-A-~AGL~RLgl~~~i~~~L~~~~~l-PA~GQGaLAVe~ 272 (326)
++++..=+|. +. .++|+-..=+ +.+.+|+.+.+-. . -.-+..+++. ..=++..+. |.-.-+-+-+.+
T Consensus 139 ~~~~~~ygL~~~~-~~~~s~~a~~a~~~~A~~~~e~~v~~~w~P~w~~~~~dl~----~LeD~~~~~g~~~~~~~i~~v~ 213 (290)
T TIGR03414 139 MIDKNAFGLGGFK-LVESSEAGMLAQVARAVKRKEWVVFLGWEPHPMNTNFKMT----YLTGGDDYFGPNYGGATVYTNT 213 (290)
T ss_pred HHhhccCCCCCce-EeecCHHHHHHHHHHHHHCCCCEEEEEecCchhhhcccee----ECCCCccccCCCCCCCeEEEEe
Confidence 3442111222 43 5556554443 5567788765522 1 1112233221 111223333 321223444555
Q ss_pred ec----CchhHHhhhhcccc
Q 020472 273 RS----NDEKMVPFTTHSQA 288 (326)
Q Consensus 273 R~----dD~~~~~lL~~~~~ 288 (326)
|+ +.+++.++|+.++-
T Consensus 214 ~~~~~~~~P~~~~~L~~~~~ 233 (290)
T TIGR03414 214 RKGYAAECPNVGKLLTNLTF 233 (290)
T ss_pred ccchHHHChHHHHHHHhCCc
Confidence 54 45788999988753
No 158
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=55.50 E-value=71 Score=29.37 Aligned_cols=60 Identities=15% Similarity=0.187 Sum_probs=40.5
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+.-. .=.-.+...+.+.||++. ++++.-. ..++.+.|.+|++|+
T Consensus 87 ~~~~l~Ig~~~~~~~-~~l~~~l~~f~~~~P~v~----v~~~~~~--------------------~~~~~~~l~~g~~Dl 141 (275)
T PRK03601 87 QHNELSIGASASLWE-CMLTPWLGRLYQNQEALQ----FEARIAQ--------------------RQSLVKQLHERQLDL 141 (275)
T ss_pred cCceEEEeccHHHHH-HHHHHHHHHHHHhCCCcE----EEEEECC--------------------hHHHHHHHHcCCCCE
Confidence 346899998765432 233445667778899762 4443221 247889999999999
Q ss_pred EEeeC
Q 020472 144 AVHSM 148 (326)
Q Consensus 144 AVHSl 148 (326)
|+...
T Consensus 142 ~i~~~ 146 (275)
T PRK03601 142 LITTE 146 (275)
T ss_pred EEEcC
Confidence 99853
No 159
>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=55.07 E-value=1.2e+02 Score=25.08 Aligned_cols=135 Identities=11% Similarity=0.008 Sum_probs=67.7
Q ss_pred EEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEee
Q 020472 68 IRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHS 147 (326)
Q Consensus 68 IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVHS 147 (326)
|+||+=.+.-..+ .-.+...+.+.+|++. +++... + ..++.+.|.+|++|+++-.
T Consensus 2 l~Ig~~~~~~~~~-l~~~l~~f~~~~P~~~----i~i~~~----~----------------~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08443 2 LYVATTHTQARYV-LPPVIKGFIERYPRVS----LQMHQG----S----------------PTQIAEMVSKGLVDFAIAT 56 (198)
T ss_pred EEEeeccceeeeE-CcHHHHHHHHHCCCeE----EEEEeC----C----------------HHHHHHHHHCCCccEEEEe
Confidence 5677766654333 2334556677799752 444221 1 2578899999999999964
Q ss_pred CCCCCCCCCCCceeeeecCCCCCcceeeccCc-------cCcccCCCCCEEecCC---hHHHH-HH-HhhCCCCEEEecc
Q 020472 148 MKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTAS---LRRKS-QI-LHRYPSLKVMENF 215 (326)
Q Consensus 148 lKDlPt~lp~gL~iaAv~kReDprD~LV~~~~-------~~l~dLp~ga~IGTSS---~RR~a-QL-~~~~Pdl~v~~~i 215 (326)
.. ...++++....+ ..++.-+++++++ .++++|..-..|..+. .|+.. ++ .+.....++. -.
T Consensus 57 ~~---~~~~~~~~~~~l--~~~~~~~v~~~~hpl~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 130 (198)
T cd08443 57 EA---LHDYDDLITLPC--YHWNRCVVVKRDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIV-LT 130 (198)
T ss_pred cc---ccccCCceEeee--eeceEEEEEcCCCccccCCCCCHHHHhcCCEEEecCCccHHHHHHHHHHHcCCCceEE-EE
Confidence 32 111233332211 1222222222211 2345555555565432 33321 22 2222233333 22
Q ss_pred CCCHHHHHhhhccCCccE
Q 020472 216 RGNVQTRLRKLNERVVQA 233 (326)
Q Consensus 216 RGNV~TRL~KL~~ge~DA 233 (326)
=.++++-++-+.+|.-=|
T Consensus 131 ~~~~~~~~~~v~~g~Gia 148 (198)
T cd08443 131 ATDADVIKTYVRLGLGVG 148 (198)
T ss_pred ECCHHHHHHHHHcCCcEE
Confidence 368888888888775433
No 160
>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=53.32 E-value=34 Score=27.41 Aligned_cols=41 Identities=15% Similarity=0.213 Sum_probs=33.2
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+...++...+|++++. -.-++-+.-++.|.+|++|..|...
T Consensus 17 ~~l~~~~~~~P~i~i~-i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (195)
T cd08434 17 DLIRAFRKEYPNVTFE-LHQGSTDELLDDLKNGELDLALCSP 57 (195)
T ss_pred HHHHHHHHhCCCeEEE-EecCcHHHHHHHHHcCCccEEEEcc
Confidence 5567888899999997 6667777778899999999888643
No 161
>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=53.17 E-value=1.2e+02 Score=24.45 Aligned_cols=140 Identities=16% Similarity=0.174 Sum_probs=71.5
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+....+ .-.+...+++.+|++. +++.. ++ ..++.+.|.+|++|+++.
T Consensus 1 ~l~I~~~~~~~~~~-l~~~l~~~~~~~P~i~----l~i~~----~~----------------~~~~~~~l~~~~~D~~i~ 55 (198)
T cd08412 1 TLRIGCFSTLAPYY-LPGLLRRFREAYPGVE----VRVVE----GN----------------QEELEEGLRSGELDLALT 55 (198)
T ss_pred CEEEecccccchhh-hHHHHHHHHHHCCCcE----EEEEE----CC----------------HHHHHHHHHcCCCcEEEE
Confidence 36788876665443 4456667777899762 44432 11 357889999999999997
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeeccC-------ccCcccCCCCCEEecC--ChHHH-HH-HHhhCCCCEEEecc
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISLS-------AASLAELPAGSIVGTA--SLRRK-SQ-ILHRYPSLKVMENF 215 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~~-------~~~l~dLp~ga~IGTS--S~RR~-aQ-L~~~~Pdl~v~~~i 215 (326)
...+. ++++..-.+ ..++.-+++.++ ..++++|..-..|... +.++. .+ +....-..++. -.
T Consensus 56 ~~~~~----~~~~~~~~l--~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 128 (198)
T cd08412 56 YDLDL----PEDIAFEPL--ARLPPYVWLPADHPLAGKDEVSLADLAAEPLILLDLPHSREYFLSLFAAAGLTPRIA-YR 128 (198)
T ss_pred cCCCC----Ccccceeee--eccceEEEecCCCCCCCCCcCCHHHHcCCcEEecCchhHHHHHHHHHHHcCCCccEE-EE
Confidence 54432 344432111 111111222211 1234555443444432 12222 12 22222223333 22
Q ss_pred CCCHHHHHhhhccCCccEEeeehh
Q 020472 216 RGNVQTRLRKLNERVVQATLLALA 239 (326)
Q Consensus 216 RGNV~TRL~KL~~ge~DAIILA~A 239 (326)
=++.++-++-+.+|..= .+++.-
T Consensus 129 ~~~~~~~~~~v~~g~gi-~~~p~~ 151 (198)
T cd08412 129 TSSFEAVRSLVANGLGY-SLLNDR 151 (198)
T ss_pred eCcHHHHHHHHHcCCCE-EEeecc
Confidence 47888888888887542 344443
No 162
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=53.13 E-value=28 Score=28.09 Aligned_cols=135 Identities=13% Similarity=0.032 Sum_probs=67.3
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+++||+=.|.....=... ...+.+.+|++. +++.. ++ .+ +.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~~~~l~~~-l~~~~~~~P~v~----i~~~~----~~------------------~~-~~l~~g~~D~~i~ 52 (194)
T cd08432 1 VLTVSVTPSFAARWLIPR-LARFQARHPDID----LRLST----SD------------------RL-VDFAREGIDLAIR 52 (194)
T ss_pred CEEEEccHHHHHHHHHHH-hHHHHHHCCCeE----EEEEe----cC------------------Cc-cccccccccEEEE
Confidence 478998887765443334 477788899752 44431 11 12 3578999999997
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeecc------CccCcccCCCCCEEecCChHH-HHHHHh------hCCCCEEEe
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISL------SAASLAELPAGSIVGTASLRR-KSQILH------RYPSLKVME 213 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~------~~~~l~dLp~ga~IGTSS~RR-~aQL~~------~~Pdl~v~~ 213 (326)
....- ++++....+ ..++.-+++.+ +..++++|-+-..|..+.... ...+.. ..|+..+
T Consensus 53 ~~~~~----~~~~~~~~l--~~~~~~~v~~~~~~~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-- 124 (194)
T cd08432 53 YGDGD----WPGLEAERL--MDEELVPVCSPALLAGLPLLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGP-- 124 (194)
T ss_pred ecCCC----CCCcceEEc--cCCcEEEecCHHHHHhcCCCCHHHhhcCceEEecCcccccHHHHhcCCeeccccCCeE--
Confidence 54321 234432211 11222222221 223466665544555433221 111211 1133332
Q ss_pred ccCCCHHHHHhhhccCCccEEeeehh
Q 020472 214 NFRGNVQTRLRKLNERVVQATLLALA 239 (326)
Q Consensus 214 ~iRGNV~TRL~KL~~ge~DAIILA~A 239 (326)
.-.|+.+-+.-+.+|.. ..+++..
T Consensus 125 -~~~~~~~~~~~v~~g~g-i~~lp~~ 148 (194)
T cd08432 125 -RFDDSSLALQAAVAGLG-VALAPRA 148 (194)
T ss_pred -EECCHHHHHHHHHhCCC-eEEeeHH
Confidence 23688888887877754 3344443
No 163
>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=52.83 E-value=24 Score=28.65 Aligned_cols=41 Identities=12% Similarity=0.074 Sum_probs=34.4
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+...+++..+|++++. -.-++-..-+++|.+|++|..|...
T Consensus 17 ~~l~~~~~~~P~i~i~-~~~~~~~~~~~~l~~~~~D~~i~~~ 57 (198)
T cd08421 17 EDLASFLAAHPDVRID-LEERLSADIVRAVAEGRADLGIVAG 57 (198)
T ss_pred HHHHHHHHHCCCceEE-EEecCcHHHHHHHhcCCceEEEEec
Confidence 5678888999999997 6667778888999999999988744
No 164
>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=51.09 E-value=34 Score=27.75 Aligned_cols=41 Identities=17% Similarity=0.209 Sum_probs=34.8
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++-.+.++..+|++++. -.-++-+.-+..|.+|++|..|..
T Consensus 17 ~~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~g~~Dl~i~~ 57 (199)
T cd08451 17 PGLIRRFREAYPDVELT-LEEANTAELLEALREGRLDAAFVR 57 (199)
T ss_pred HHHHHHHHHHCCCcEEE-EecCChHHHHHHHHCCCccEEEEe
Confidence 45578889999999997 777788888899999999998864
No 165
>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=50.82 E-value=36 Score=27.73 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=32.1
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+..++++..+|++++. -.-++-..=++.|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~i~i~-~~~~~~~~~~~~l~~~~~D~~i~~ 56 (198)
T cd08433 17 PLLRAVRRRYPGIRLR-IVEGLSGHLLEWLLNGRLDLALLY 56 (198)
T ss_pred HHHHHHHHHCCCcEEE-EEecCcHHHHHHHhCCCCcEEEEe
Confidence 5678899999999987 544666666788899999998864
No 166
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=50.76 E-value=56 Score=26.20 Aligned_cols=54 Identities=20% Similarity=0.277 Sum_probs=34.4
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+...- -.-.+...+++.||++. +++. + ++ +++ .+++|++|+|+-
T Consensus 2 ~l~Ig~~~~~~~~-~l~~~l~~~~~~~P~v~----i~i~---~-~~------------------~~~-~l~~~~~D~~i~ 53 (197)
T cd08422 2 RLRISAPVSFGRL-HLAPLLAEFLARYPDVR----LELV---L-SD------------------RLV-DLVEEGFDLAIR 53 (197)
T ss_pred eEEEEecHHHHHH-HHHHHHHHHHHhCCceE----EEEe---c-Cc------------------ccc-chhhcCccEEEE
Confidence 6889987776443 34456777888899752 4443 1 11 122 356789999996
Q ss_pred eC
Q 020472 147 SM 148 (326)
Q Consensus 147 Sl 148 (326)
..
T Consensus 54 ~~ 55 (197)
T cd08422 54 IG 55 (197)
T ss_pred eC
Confidence 53
No 167
>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=50.75 E-value=38 Score=27.16 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=32.3
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.+-..+++..+|++++. -.-++-..-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~~~l~-~~~~~~~~~~~~l~~g~~D~~i~~ 56 (201)
T cd08420 16 PRLLARFRKRYPEVRVS-LTIGNTEEIAERVLDGEIDLGLVE 56 (201)
T ss_pred HHHHHHHHHHCCCceEE-EEeCCcHHHHHHHHCCCccEEEec
Confidence 35567888899999987 556777777788899999988764
No 168
>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=50.02 E-value=33 Score=27.70 Aligned_cols=42 Identities=14% Similarity=0.078 Sum_probs=35.6
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
.+...+++..+|++++. -..++-+.-+..|.+|++|..|...
T Consensus 16 ~~~l~~~~~~~P~i~i~-~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (200)
T cd08423 16 PPALAALRARHPGLEVR-LREAEPPESLDALRAGELDLAVVFD 57 (200)
T ss_pred hHHHHHHHHhCCCCeEE-EEeCCHHHHHHHHhcCCccEEEEec
Confidence 46678889999999998 7788888889999999999877643
No 169
>PF03900 Porphobil_deamC: Porphobilinogen deaminase, C-terminal domain; InterPro: IPR022418 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the C-terminal domain of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this alpha/beta domain consists of alpha-beta(3)-alpha in two layers []. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 3EQ1_B 3ECR_A 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A.
Probab=49.85 E-value=10 Score=29.20 Aligned_cols=16 Identities=13% Similarity=0.023 Sum_probs=13.0
Q ss_pred hhHHHHHHHHhhhchh
Q 020472 300 LCYKLHFGFLNLVELR 315 (326)
Q Consensus 300 ~c~~~er~~l~~l~~~ 315 (326)
+|+..||.||..|++|
T Consensus 2 ~~v~aER~fl~~l~gg 17 (74)
T PF03900_consen 2 IEVEAERAFLKELGGG 17 (74)
T ss_dssp HHHHHHHHHHHHCT--
T ss_pred hhHHHHHHHHHHhCCC
Confidence 5889999999999987
No 170
>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=49.25 E-value=70 Score=28.64 Aligned_cols=54 Identities=19% Similarity=0.294 Sum_probs=35.2
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.++|+||+=.+ .+-. .+...+.+.||++. +++..- + ..++.+.|.+|++|+|
T Consensus 86 ~~~l~ig~~~~---~~~~-~~l~~~~~~~p~v~----l~i~~~----~----------------~~~~~~~l~~g~~Dl~ 137 (279)
T TIGR03339 86 EGSLRIAATAP---YYVL-DLVARFRQRYPGIE----VSVRIG----N----------------SQEVLQALQSYRVDVA 137 (279)
T ss_pred ceEEEEeCchH---HHHH-HHHHHHHHHCCCcE----EEEEEC----C----------------HHHHHHHHHcCCCcEE
Confidence 47899998532 1222 34456667799752 444321 1 2478899999999999
Q ss_pred Ee
Q 020472 145 VH 146 (326)
Q Consensus 145 VH 146 (326)
+-
T Consensus 138 i~ 139 (279)
T TIGR03339 138 VS 139 (279)
T ss_pred EE
Confidence 95
No 171
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=49.15 E-value=38 Score=30.11 Aligned_cols=39 Identities=10% Similarity=0.140 Sum_probs=33.3
Q ss_pred HHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 198 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 198 R~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
--.++...||++++. -..++.+.-+..|.+|++|..|.-
T Consensus 85 ~l~~~~~~~p~i~l~-i~~~~~~~~~~~l~~~~~D~~i~~ 123 (269)
T PRK11716 85 ILDRFRAEHPLVEIK-LTTGDAADAVEKVQSGEADLAIAA 123 (269)
T ss_pred HHHHHHHHCCCeEEE-EEECCHHHHHHHHHCCCccEEEEe
Confidence 357788889999997 777998999999999999988864
No 172
>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=49.12 E-value=38 Score=27.20 Aligned_cols=42 Identities=12% Similarity=0.163 Sum_probs=34.7
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
++...++...+|++++. -.-++-+.-+..|.+|++|-.|...
T Consensus 16 ~~~l~~~~~~~P~v~i~-i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (194)
T cd08436 16 PELLARFHRRHPGVDIR-LRQAGSDDLLAAVREGRLDLAFVGL 57 (194)
T ss_pred HHHHHHHHHHCCCcEEE-EecCCHHHHHHHHHcCCccEEEEec
Confidence 34568888999999998 6667778888999999999988753
No 173
>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=47.43 E-value=33 Score=27.91 Aligned_cols=40 Identities=13% Similarity=0.059 Sum_probs=33.9
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+--.+++..+|++++. -.-++-+.-+..|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~~~~D~~i~~ 56 (199)
T cd08426 17 SLIARFRQRYPGVFFT-VDVASTADVLEAVLSGEADIGLAF 56 (199)
T ss_pred HHHHHHHHhCCCeEEE-EEeCCcHHHHHHHHCCCccEEEec
Confidence 4467888899999998 667888888999999999998864
No 174
>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=47.15 E-value=42 Score=27.00 Aligned_cols=41 Identities=15% Similarity=0.192 Sum_probs=34.8
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+..-.+++..+|++++. -..++-+.-+..|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~p~i~i~-i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08414 16 PRLLRRFRARYPDVELE-LREMTTAEQLEALRAGRLDVGFVR 56 (197)
T ss_pred HHHHHHHHHHCCCcEEE-EecCChHHHHHHHHcCCccEEEEc
Confidence 35567888899999998 777888889999999999998864
No 175
>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=47.04 E-value=38 Score=27.35 Aligned_cols=41 Identities=20% Similarity=0.213 Sum_probs=34.5
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++..+.++..+|++++. -.-++-++-+..|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~P~v~i~-i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (201)
T cd08435 16 PPAIARLLARHPRLTVR-VVEGTSDELLEGLRAGELDLAIGR 56 (201)
T ss_pred HHHHHHHHHHCCCeEEE-EEeCCHHHHHHHHHcCCccEEEEe
Confidence 46678889999999997 666888888889999999988864
No 176
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=46.10 E-value=2.4e+02 Score=25.85 Aligned_cols=59 Identities=12% Similarity=0.120 Sum_probs=37.4
Q ss_pred cCCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCc
Q 020472 63 TKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQID 142 (326)
Q Consensus 63 ~~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iD 142 (326)
...++|+||+-.+.++.+-...+.+.+++ |++ .+++.. ++ ..++.+.|.+|++|
T Consensus 87 ~~~g~l~I~~~~~~~~~~~~~~l~~~~~~--~~i----~i~~~~----~~----------------~~~~~~~L~~~~~d 140 (294)
T PRK13348 87 GSPPTLAIAVNADSLATWFLPALAAVLAG--ERI----LLELIV----DD----------------QDHTFALLERGEVV 140 (294)
T ss_pred CCceEEEEEecchhHHHHHHHHHHHHHhC--CCe----EEEEEE----cc----------------hHHHHHHHhcCCeE
Confidence 34578999998766665555544444432 543 233321 22 24788999999999
Q ss_pred EEEee
Q 020472 143 IAVHS 147 (326)
Q Consensus 143 iAVHS 147 (326)
++|..
T Consensus 141 ~~i~~ 145 (294)
T PRK13348 141 GCVST 145 (294)
T ss_pred EEEec
Confidence 99964
No 177
>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=45.84 E-value=34 Score=28.12 Aligned_cols=43 Identities=9% Similarity=0.120 Sum_probs=37.1
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeehhh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAG 240 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AG 240 (326)
.-..+++..+|++++. -.-++-++-++.|.+|++|..|.....
T Consensus 23 ~~l~~~~~~~P~i~i~-~~~~~~~~~~~~l~~g~~Dl~i~~~~~ 65 (209)
T PF03466_consen 23 PLLAEFRERHPNIRIE-IREGDSDELIEALRSGELDLAITFGPP 65 (209)
T ss_dssp HHHHHHHHHSTTEEEE-EEEESHHHHHHHHHTTSSSEEEESSSS
T ss_pred HHHHHHHHHCCCcEEE-EEeccchhhhHHHhcccccEEEEEeec
Confidence 4567888899999998 777899999999999999999886665
No 178
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=45.75 E-value=2.4e+02 Score=25.79 Aligned_cols=140 Identities=13% Similarity=0.124 Sum_probs=74.9
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.+.++||+-.+....+ ...+...+.+.+|++. +.+.... ..++.+.|.+|++|++
T Consensus 89 ~~~l~Ig~~~~~~~~~-l~~~~~~~~~~~p~v~----i~~~~~~--------------------~~~~~~~l~~~~~D~~ 143 (296)
T PRK09906 89 DRQLTIGFVPSAEVNL-LPKVLPMFRLRHPDTL----IELVSLI--------------------TTQQEEKLRRGELDVG 143 (296)
T ss_pred CCcEEEEEecchhhhH-HHHHHHHHHHHCCCeE----EEEEeCC--------------------cHHHHHHHHcCCeeEE
Confidence 3459999998875443 4455566777889752 3332221 2468899999999999
Q ss_pred EeeCCCCCCCCCCCceeeeecCCCCCcceeecc-C-------ccCcccCCCCCEEecCC-----hHHH-HH-HHhhCCCC
Q 020472 145 VHSMKDVPTYLPEKTILPCNLQREDVRDAFISL-S-------AASLAELPAGSIVGTAS-----LRRK-SQ-ILHRYPSL 209 (326)
Q Consensus 145 VHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~-~-------~~~l~dLp~ga~IGTSS-----~RR~-aQ-L~~~~Pdl 209 (326)
+.... . .++++....+.+ + +-++|++ + ..++++|..-..|..+. .+.. .+ +....-..
T Consensus 144 i~~~~---~-~~~~l~~~~l~~--~-~~~~v~~~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 216 (296)
T PRK09906 144 FMRHP---V-YSDEIDYLELLD--E-PLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHNSQP 216 (296)
T ss_pred EecCC---C-CCCCceEEEEec--c-cEEEEecCCCccccCCCcCHHHHcCCCEEeccCCCCchHHHHHHHHHHHcCCCc
Confidence 98553 2 234444322211 1 1223322 1 12345565555665432 2322 22 33322223
Q ss_pred EEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 210 KVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 210 ~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
++. -.-.|+.+-+.-+.+|.. -.+++.
T Consensus 217 ~~~-~~~~~~~~~~~~v~~g~g-~~~~p~ 243 (296)
T PRK09906 217 NIV-QVATNILVTMNLVGMGLG-CTIIPG 243 (296)
T ss_pred ceE-EEeccHHHHHHHHHcCCc-EEEeeH
Confidence 333 234678888888888854 333444
No 179
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=45.69 E-value=2.7e+02 Score=26.37 Aligned_cols=60 Identities=20% Similarity=0.280 Sum_probs=42.2
Q ss_pred cCCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCc
Q 020472 63 TKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQID 142 (326)
Q Consensus 63 ~~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iD 142 (326)
...++|+||+=.+. +....-.+...+++.||++. +++..- . ..++.++|.+|++|
T Consensus 96 ~~~g~l~Ig~~~~~-~~~~l~~~l~~f~~~~P~i~----i~l~~~---~-----------------~~~~~~~l~~g~~D 150 (310)
T PRK15092 96 NLQGVLTIGASDDT-ADTILPFLLNRVSSVYPKLA----LDVRVK---R-----------------NAFMMEMLESQEVD 150 (310)
T ss_pred CceeEEEEeCChHH-HHHHHHHHHHHHHHHCCCcE----EEEEEC---C-----------------cHHHHHHHhCCCee
Confidence 34578999998764 54455567778888999762 444211 1 24688999999999
Q ss_pred EEEee
Q 020472 143 IAVHS 147 (326)
Q Consensus 143 iAVHS 147 (326)
+++..
T Consensus 151 i~i~~ 155 (310)
T PRK15092 151 LAVTT 155 (310)
T ss_pred EEEEe
Confidence 99975
No 180
>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=45.16 E-value=48 Score=26.94 Aligned_cols=41 Identities=5% Similarity=0.034 Sum_probs=33.9
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+-..+++..+|++++. -.-++-+.-++.|.+|++|..|...
T Consensus 17 ~~i~~~~~~~P~i~l~-~~~~~~~~~~~~l~~g~~D~~i~~~ 57 (200)
T cd08417 17 PLLARLRQEAPGVRLR-FVPLDRDDLEEALESGEIDLAIGVF 57 (200)
T ss_pred HHHHHHHhhCCCeEEE-eccCCHHHHHHHHHcCCCCEEEeec
Confidence 4467888899999997 6667777788899999999998754
No 181
>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=44.67 E-value=36 Score=27.84 Aligned_cols=41 Identities=12% Similarity=0.060 Sum_probs=34.4
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.+..+++...+|++++. -.-++.++-+..|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~P~i~l~-~~~~~~~~~~~~l~~~~~Dl~i~~ 56 (196)
T cd08457 16 PRFLAAFLRLRPNLHLS-LMGLSSSQVLEAVASGRADLGIAD 56 (196)
T ss_pred HHHHHHHHHHCCCeEEE-EEecCcHHHHHHHHcCCccEEEec
Confidence 46778899999999997 666777888888999999988864
No 182
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=44.15 E-value=1.1e+02 Score=29.11 Aligned_cols=132 Identities=15% Similarity=0.092 Sum_probs=72.6
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+....+ .-.+...+.+.||++ ++.... ..++.+.|.+|++|+
T Consensus 115 ~~~~l~Ig~~~~~~~~~-l~~~l~~f~~~~P~i------~i~~~~--------------------~~~~~~~l~~g~~Dl 167 (317)
T PRK11482 115 KQRTITIATTPSVGALV-MPVIYQAIKTHYPQL------LLRNIP--------------------ISDAENQLSQFQTDL 167 (317)
T ss_pred CCceEEEEecHHHHHHH-HHHHHHHHHHHCCCC------EEEEec--------------------chhHHHHHHCCCcCE
Confidence 34689999998886654 556667777889974 332111 135779999999999
Q ss_pred EEeeCCCCCCCCCCCceeeeecCCCCCcceeeccCc------cCcccCCCC--CEEec-----CChHHHHHHHhhCCCCE
Q 020472 144 AVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA------ASLAELPAG--SIVGT-----ASLRRKSQILHRYPSLK 210 (326)
Q Consensus 144 AVHSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~------~~l~dLp~g--a~IGT-----SS~RR~aQL~~~~Pdl~ 210 (326)
++..... .++++..-. -..++--+++.++. .+++||-.- ..+.+ ++.|+. +...++..+
T Consensus 168 ~i~~~~~----~~~~~~~~~--l~~~~~~lv~~~~hpl~~~~~~~~dL~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 239 (317)
T PRK11482 168 IIDTHSC----SNRTIQHHV--LFTDNVVLVCRQGHPLLSLEDDEETLDNAEHTLLLPEGQNFSGLRQR--LQEMFPDRQ 239 (317)
T ss_pred EEeccCC----CCCceEEEE--EecCcEEEEEeCCCCccCCCCCHHHHhhCCCEEEecCCCCcchHHHH--HHHhCCCce
Confidence 9965432 234544322 22333333333221 234454321 22322 234433 344455555
Q ss_pred EEeccCCCHHHHHhhhccCCc
Q 020472 211 VMENFRGNVQTRLRKLNERVV 231 (326)
Q Consensus 211 v~~~iRGNV~TRL~KL~~ge~ 231 (326)
+. ---.|+.+=+.-+.+|..
T Consensus 240 ~~-~~~~~~~~~~~~v~~g~g 259 (317)
T PRK11482 240 IS-FSSYNILTIAALIASSDM 259 (317)
T ss_pred EE-EEcCcHHHHHHHHHcCCe
Confidence 44 334677777776766643
No 183
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=44.08 E-value=2.4e+02 Score=29.97 Aligned_cols=53 Identities=17% Similarity=-0.021 Sum_probs=34.2
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.++++||+-.+.-.-+=++. |++ |++. +++.... +.++.++|.+|++|+|
T Consensus 416 ~~~L~Ig~~~~~~~~~Lp~~----l~~--P~v~----i~v~~~~--------------------s~~vl~~L~~GeiDla 465 (633)
T PRK14498 416 PPTLVIIGSHDPGLDLLLDL----LAR--RGLR----LRSLHVG--------------------SMGGLMALKRGEADIA 465 (633)
T ss_pred ccceEEEccCchHHHHHHHH----hhc--cCCc----eeEEecC--------------------CHHHHHHHHcCCceEE
Confidence 47899999887632222222 222 8652 5444321 3689999999999999
Q ss_pred Eee
Q 020472 145 VHS 147 (326)
Q Consensus 145 VHS 147 (326)
+=.
T Consensus 466 i~~ 468 (633)
T PRK14498 466 GIH 468 (633)
T ss_pred EEc
Confidence 843
No 184
>PRK04056 Maf-like protein; Reviewed
Probab=44.07 E-value=23 Score=32.19 Aligned_cols=23 Identities=13% Similarity=0.101 Sum_probs=19.6
Q ss_pred EEecCChHHHHHHHhhCCCCEEE
Q 020472 190 IVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 190 ~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
++|++|+||+..|..+..+++++
T Consensus 3 ILAS~SprR~elL~~~g~~f~v~ 25 (180)
T PRK04056 3 ILASSSSTRANLLKEAGIEFEQK 25 (180)
T ss_pred EEeCCCHHHHHHHHHCCCCeEEE
Confidence 68999999999999987776655
No 185
>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=43.88 E-value=82 Score=25.71 Aligned_cols=138 Identities=8% Similarity=0.032 Sum_probs=66.2
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+-.+.++.+=.. +...+.+.+ ++ ++++.. ++ ..++.+.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~~~~l~~-~l~~f~~~~-~v----~l~l~~----~~----------------~~~~~~~l~~~~~D~~i~ 54 (195)
T cd08428 1 TLPVAVNADSLATWFLP-ALAPVLKRE-RI----LLDLIV----DD----------------EDRTHDLLRDGEVVGCIS 54 (195)
T ss_pred CEEEEechhHHHHHhHH-HHHHHHhCc-Ce----EEEEEe----CC----------------chhHHHHHHcCcceEEEE
Confidence 47899987666544223 344444443 43 244322 11 136889999999999885
Q ss_pred eCCCCCCCCCCCceeeeecCCCCCcceeecc--------CccCcccCCCCCEEecC--C-hHHHH--HHHhhCCCCEEEe
Q 020472 147 SMKDVPTYLPEKTILPCNLQREDVRDAFISL--------SAASLAELPAGSIVGTA--S-LRRKS--QILHRYPSLKVME 213 (326)
Q Consensus 147 SlKDlPt~lp~gL~iaAv~kReDprD~LV~~--------~~~~l~dLp~ga~IGTS--S-~RR~a--QL~~~~Pdl~v~~ 213 (326)
.. ..+ ++++..-.+. +++--+++.+ +..++++|..-..|..+ + .|+.. +.....++.++.
T Consensus 55 ~~-~~~---~~~~~~~~l~--~~~~~~~~~~~~~~~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~- 127 (195)
T cd08428 55 TQ-AQP---MQGCRSDYLG--SMDYLLVASPDFAARYFPNGLTREALLKAPAVAFNRKDDLHQSFLQQHFGLPPGSYPC- 127 (195)
T ss_pred ec-CCC---CCCceeEEee--eeeEEEEECCcchhhcCCCCCCHHHHhcCcEEEEcCCCchhHHHHHHHhccCCCCceE-
Confidence 42 211 2344322221 1111111111 11245566555566542 2 22211 212223333333
Q ss_pred ccCCCHHHHHhhhccCCccEEeeeh
Q 020472 214 NFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 214 ~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
..-.++++-+.=+.+|.- ..++..
T Consensus 128 ~~~~~~~~~~~~v~~G~G-i~~lp~ 151 (195)
T cd08428 128 HYVPSSEAFVDLAAQGLA-YGMIPE 151 (195)
T ss_pred EEECCHHHHHHHHHhCCe-eEeccH
Confidence 234688888888877743 334444
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=43.77 E-value=60 Score=26.38 Aligned_cols=29 Identities=21% Similarity=0.167 Sum_probs=19.1
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCc
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPEL 96 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l 96 (326)
+|+||+=.|. +..-.-.+...+++.||++
T Consensus 2 ~l~Ig~~~~~-~~~~l~~~l~~f~~~~P~v 30 (197)
T cd08470 2 LLRITCPVAY-GERFIAPLVNDFMQRYPKL 30 (197)
T ss_pred eEEEEcCHHH-HHHHHHHHHHHHHHHCCCe
Confidence 5888885544 3333445567778889975
No 187
>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=43.56 E-value=37 Score=27.81 Aligned_cols=41 Identities=15% Similarity=0.138 Sum_probs=32.6
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+--..++..+|++++. -.-|+-+.-+..|.+|++|..|...
T Consensus 17 ~~l~~~~~~~P~v~v~-i~~~~~~~~~~~l~~g~~D~~i~~~ 57 (201)
T cd08459 17 RLLAALREVAPGVRIE-TVRLPVDELEEALESGEIDLAIGYL 57 (201)
T ss_pred HHHHHHHHHCCCCeEE-EEecCccCHHHHhhCCCceEEEEcC
Confidence 3456778889999997 6677777778889999999988643
No 188
>PRK00078 Maf-like protein; Reviewed
Probab=43.54 E-value=24 Score=32.34 Aligned_cols=24 Identities=25% Similarity=0.357 Sum_probs=20.2
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-++|++|+||+..|+.+..+++++
T Consensus 3 iILAS~SprR~elL~~~g~~f~v~ 26 (192)
T PRK00078 3 IILASASERRQELLKRILEDFQVI 26 (192)
T ss_pred EEEeCCCHHHHHHHHhCCCCeEEe
Confidence 378999999999999987777665
No 189
>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=43.17 E-value=33 Score=27.96 Aligned_cols=41 Identities=12% Similarity=0.039 Sum_probs=33.4
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+.....++..||++++. -..++-++-+..|.+|++|..|..
T Consensus 16 ~~~l~~f~~~~P~v~i~-i~~~~~~~~~~~l~~~~~Di~i~~ 56 (198)
T cd08461 16 PPLLAALRQEAPGVRVA-IRDLESDNLEAQLERGEVDLALTT 56 (198)
T ss_pred HHHHHHHHHHCCCcEEE-EeeCCcccHHHHHhcCCCcEEEec
Confidence 34567788899999997 656777888899999999998864
No 190
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=43.02 E-value=2.8e+02 Score=25.71 Aligned_cols=141 Identities=9% Similarity=-0.007 Sum_probs=70.2
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcE
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDi 143 (326)
..+.|+||+=.+.. ..-.-.+...+...||++ ++..... + +.++.+.|.+|++|+
T Consensus 91 ~~g~l~i~~~~~~~-~~~l~~~l~~f~~~~P~i------~l~~~~~--~----------------~~~~~~~l~~g~~D~ 145 (296)
T PRK11062 91 SNLLFDVGVADALS-KRLVSRVLLTAVPEDESI------HLRCFES--T----------------HEMLLEQLSQHKLDM 145 (296)
T ss_pred CceEEEEEecchhh-HhhHHHHHHHHHhcCCce------EEEEEeC--C----------------HHHHHHHHHcCCCCE
Confidence 34679999955443 333445556666678864 3332211 1 356788999999999
Q ss_pred EEeeCC-CCCCCCCCCceeeeecCCCCCcceeeccCc---cCcccCCCCCEEecC---ChHHH-HH-HHhhCCCCEEEec
Q 020472 144 AVHSMK-DVPTYLPEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTA---SLRRK-SQ-ILHRYPSLKVMEN 214 (326)
Q Consensus 144 AVHSlK-DlPt~lp~gL~iaAv~kReDprD~LV~~~~---~~l~dLp~ga~IGTS---S~RR~-aQ-L~~~~Pdl~v~~~ 214 (326)
++.... +.| .++++. +..-.+++--+++.++. ..+++|-.-..|... +.|+. .+ +.......++. .
T Consensus 146 ~i~~~~~~~~--~~~~l~--~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 220 (296)
T PRK11062 146 ILSDCPVDST--QQEGLF--SKKLGECGVSFFCTNPLPEKPFPACLEERRLLIPGRRTMLGRKLLNWFNSQGLNVEIL-G 220 (296)
T ss_pred EEecCCCccc--cccchh--hhhhhccCcceEecCCCccccChHHHhcCCeeecCCCchHHHHHHHHHHHcCCCceee-e
Confidence 996432 111 123332 12212222222222221 123444443455432 23432 22 22222233333 2
Q ss_pred cCCCHHHHHhhhccCCccEE
Q 020472 215 FRGNVQTRLRKLNERVVQAT 234 (326)
Q Consensus 215 iRGNV~TRL~KL~~ge~DAI 234 (326)
-=.|+.+=++-+.+|..=++
T Consensus 221 ~~~~~~~~~~~v~~g~Gi~~ 240 (296)
T PRK11062 221 EFDDAALMKAFGAYHDAIFV 240 (296)
T ss_pred eeCcHHHHHHHHHcCCceEE
Confidence 33788898888888765333
No 191
>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=42.99 E-value=48 Score=26.94 Aligned_cols=41 Identities=10% Similarity=0.014 Sum_probs=33.9
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++..+.++..+|++++. -..++-.+-.+.|.+|++|..|..
T Consensus 17 ~~~l~~~~~~~P~v~i~-i~~~~~~~~~~~l~~g~~Dl~i~~ 57 (197)
T cd08425 17 GPLIDRFHARYPGIALS-LREMPQERIEAALADDRLDLGIAF 57 (197)
T ss_pred HHHHHHHHHHCCCcEEE-EEECcHHHHHHHHHcCCccEEEEe
Confidence 35667888899999997 666777888889999999998865
No 192
>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=42.60 E-value=47 Score=27.37 Aligned_cols=39 Identities=8% Similarity=0.072 Sum_probs=31.6
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+-..+++..||++++. -.-|+- ..++.|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~v~v~-l~~~~~-~~~~~l~~g~~D~~i~~ 55 (200)
T cd08460 17 ALLAAVAAEAPGVRLR-FVPESD-KDVDALREGRIDLEIGV 55 (200)
T ss_pred HHHHHHHHHCCCCEEE-EecCch-hHHHHHHCCCccEEEec
Confidence 4467888899999997 665765 77889999999998863
No 193
>PRK04694 Maf-like protein; Reviewed
Probab=42.54 E-value=26 Score=32.14 Aligned_cols=23 Identities=13% Similarity=0.216 Sum_probs=19.7
Q ss_pred EEecCChHHHHHHHhhCCCCEEE
Q 020472 190 IVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 190 ~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
+++++|+||+..|+.+.-+++++
T Consensus 3 ILAS~SprR~elL~~~g~~f~~~ 25 (190)
T PRK04694 3 YLASRSPRRRELLQRLDVPFQTL 25 (190)
T ss_pred EEcCCCHHHHHHHHHCCCCcEEe
Confidence 68999999999999987777665
No 194
>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=42.12 E-value=89 Score=25.47 Aligned_cols=54 Identities=13% Similarity=0.281 Sum_probs=34.8
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
+.|+||+=.+.. ...--.+...+++.||++. +++.. ++. + ++|++|++|+++
T Consensus 3 g~l~Ig~~~~~~-~~~l~~~l~~~~~~~P~v~----i~~~~----~~~------------------~-~~l~~g~~D~~i 54 (202)
T cd08474 3 GTLRINAPRVAA-RLLLAPLLARFLARYPDIR----LELVV----DDG------------------L-VDIVAEGFDAGI 54 (202)
T ss_pred cEEEEeCcHHHH-HHHHHHHHHHHHHHCCCeE----EEEEe----cCC------------------c-ccccccCccEEE
Confidence 568999887743 3344556677788899752 55431 111 1 246789999999
Q ss_pred ee
Q 020472 146 HS 147 (326)
Q Consensus 146 HS 147 (326)
-.
T Consensus 55 ~~ 56 (202)
T cd08474 55 RL 56 (202)
T ss_pred Ec
Confidence 54
No 195
>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=41.99 E-value=55 Score=29.33 Aligned_cols=38 Identities=26% Similarity=0.337 Sum_probs=32.1
Q ss_pred HHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEee
Q 020472 198 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 236 (326)
Q Consensus 198 R~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIIL 236 (326)
-.+++...||++++. -.-++.+.-++.|.+|++|..|.
T Consensus 102 ~l~~~~~~~p~v~l~-i~~~~~~~~~~~l~~g~~Dl~i~ 139 (279)
T TIGR03339 102 LVARFRQRYPGIEVS-VRIGNSQEVLQALQSYRVDVAVS 139 (279)
T ss_pred HHHHHHHHCCCcEEE-EEECCHHHHHHHHHcCCCcEEEE
Confidence 345677889999997 66688888899999999999986
No 196
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=40.52 E-value=61 Score=30.50 Aligned_cols=42 Identities=10% Similarity=0.092 Sum_probs=35.3
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+.....+...+|++++. -.-|+.+.-++.|.+|++|..|...
T Consensus 109 ~~~l~~f~~~~P~i~l~-l~~~~~~~~~~~L~~g~~Dl~i~~~ 150 (316)
T PRK12679 109 PEVIKAFRELFPEVRLE-LIQGTPQEIATLLQNGEADIGIASE 150 (316)
T ss_pred HHHHHHHHHHCCCeEEE-EecCCHHHHHHHHHcCCCCEEEecc
Confidence 45667788889999997 7788988889999999999988643
No 197
>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=40.06 E-value=33 Score=32.41 Aligned_cols=47 Identities=11% Similarity=0.076 Sum_probs=38.1
Q ss_pred EEecCCh------HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 190 IVGTASL------RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 190 ~IGTSS~------RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+||+|+. .-...+++.||++++. -.-|+-++-++.|.+|++|..++.
T Consensus 39 rig~s~s~~~~lp~~l~~f~~~~P~i~v~-i~~~~s~~l~~~L~~G~iDlai~~ 91 (287)
T TIGR02136 39 TIDGSTTVAPLAEAAAEEFQKIHPGVSVT-VQGAGSGTGIKALINGTVDIGNSS 91 (287)
T ss_pred EEeccchHHHHHHHHHHHHHhhCCCceEE-EccCCchHHHHHHHcCCCchhhcc
Confidence 6777763 3356667789999997 888899999999999999997764
No 198
>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=39.67 E-value=41 Score=27.80 Aligned_cols=38 Identities=8% Similarity=0.058 Sum_probs=31.0
Q ss_pred HHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 198 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 198 R~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
=.++++..+|++++. -..++- ..++.|.+|++|..|..
T Consensus 18 ~i~~~~~~~P~i~l~-i~~~~~-~~~~~l~~g~~D~~i~~ 55 (200)
T cd08462 18 VIERVAREAPGVRFE-LLPPDD-QPHELLERGEVDLLIAP 55 (200)
T ss_pred HHHHHHHHCCCCEEE-EecCCh-hHHHHHhcCCeeEEEec
Confidence 346778889999987 555775 88999999999999874
No 199
>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=38.69 E-value=59 Score=27.00 Aligned_cols=41 Identities=15% Similarity=0.067 Sum_probs=33.7
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++-.+.++..+|++++. -.-++-++-+..|.+|++|..|..
T Consensus 17 ~~~l~~~~~~~P~i~l~-~~~~~~~~~~~~l~~~~~D~~i~~ 57 (198)
T cd08485 17 PLLLRQLLSVAPSATVS-LTQMSKNRQIEALDAGTIDIGFGR 57 (198)
T ss_pred HHHHHHHHHhCCCcEEE-EEECCHHHHHHHHHcCCccEEEec
Confidence 34457778889999997 667788888889999999998864
No 200
>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=38.62 E-value=59 Score=26.53 Aligned_cols=42 Identities=12% Similarity=0.197 Sum_probs=35.1
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+.-.+.++..+|++++. -..++-++-++.|.+|++|-.|...
T Consensus 16 ~~~l~~~~~~~P~v~i~-~~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (198)
T cd08437 16 PKLAKDLIKTGLMIQID-TYEGGSAELLEQLLQGDLDIALLGS 57 (198)
T ss_pred HHHHHHHHHhCCceEEE-EEEcCHHHHHHHHHcCCCCEEEecC
Confidence 35667888899999997 7778888889999999999988643
No 201
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=38.47 E-value=62 Score=29.76 Aligned_cols=41 Identities=12% Similarity=0.152 Sum_probs=35.1
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++.-..+...||++++. -.-|+-..=+..|.+|++|-.|..
T Consensus 105 ~~~l~~f~~~~P~v~v~-~~~~~~~~~~~~l~~g~~Dl~i~~ 145 (275)
T PRK03601 105 TPWLGRLYQNQEALQFE-ARIAQRQSLVKQLHERQLDLLITT 145 (275)
T ss_pred HHHHHHHHHhCCCcEEE-EEECChHHHHHHHHcCCCCEEEEc
Confidence 45567888899999997 778888888999999999999964
No 202
>PRK00148 Maf-like protein; Reviewed
Probab=37.86 E-value=34 Score=31.48 Aligned_cols=24 Identities=17% Similarity=0.004 Sum_probs=20.4
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-+.|++|+||+..|..+..+++++
T Consensus 3 iILAS~SprR~elL~~~g~~f~~~ 26 (194)
T PRK00148 3 LVLASASPARLKLLRLAGIPPLVV 26 (194)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 478999999999999987777665
No 203
>cd08480 PBP2_CrgA_like_10 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 10. 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=37.85 E-value=86 Score=25.82 Aligned_cols=53 Identities=19% Similarity=0.247 Sum_probs=31.1
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
.|+||+=.+....+= -.+...+.+.||++. +++. .+ + ++.+ +++|++|++++
T Consensus 2 ~l~Ig~~~~~~~~~l-~~~l~~~~~~~P~i~----i~i~--~~--~------------------~~~~-~~~~~~D~~i~ 53 (198)
T cd08480 2 RLRVNASVPFGTHFL-LPLLPAFLARYPEIL----VDLS--LT--D------------------EVVD-LLAERTDVAIR 53 (198)
T ss_pred eEEEEccHHHHhHhh-HHHHHHHHHHCCCeE----EEEE--ec--C------------------Cccc-cccccccEEEE
Confidence 588988554433232 345566677899752 4442 11 1 1222 45899999997
Q ss_pred e
Q 020472 147 S 147 (326)
Q Consensus 147 S 147 (326)
.
T Consensus 54 ~ 54 (198)
T cd08480 54 V 54 (198)
T ss_pred e
Confidence 4
No 204
>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=37.83 E-value=87 Score=25.18 Aligned_cols=53 Identities=17% Similarity=0.227 Sum_probs=33.3
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.+.-..+-...+ ..+.+.||++. +++. + ++.. +.|.+|++|+++.
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l-~~f~~~~P~i~----i~i~---~-~~~~-------------------~~l~~~~~Dl~l~ 52 (194)
T cd08481 1 TLELAVLPTFGTRWLIPRL-PDFLARHPDIT----VNLV---T-RDEP-------------------FDFSQGSFDAAIH 52 (194)
T ss_pred CEEEEecHHHHHHHHHhhh-hHHHHHCCCce----EEEE---e-cccc-------------------cCcccCCCCEEEE
Confidence 4788887776555545555 45667799763 4443 1 2210 1378899999996
Q ss_pred e
Q 020472 147 S 147 (326)
Q Consensus 147 S 147 (326)
.
T Consensus 53 ~ 53 (194)
T cd08481 53 F 53 (194)
T ss_pred c
Confidence 4
No 205
>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=37.46 E-value=1.6e+02 Score=23.72 Aligned_cols=29 Identities=24% Similarity=0.127 Sum_probs=19.7
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCc
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPEL 96 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l 96 (326)
+|+||+=.+. +..-.-.+...+++.+|++
T Consensus 2 ~l~Ig~~~~~-~~~~l~~~l~~~~~~~P~v 30 (199)
T cd08475 2 RLRIDLPVAF-GRLCVAPLLLELARRHPEL 30 (199)
T ss_pred eEEEechHHH-HHhhHHHHHHHHHHHCCCe
Confidence 5888885544 3334555677888889975
No 206
>PRK02478 Maf-like protein; Reviewed
Probab=37.02 E-value=35 Score=31.51 Aligned_cols=24 Identities=13% Similarity=0.070 Sum_probs=20.1
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-+++++|+||+..|..+.-+++++
T Consensus 5 iILAS~SprR~elL~~~g~~f~v~ 28 (199)
T PRK02478 5 LILASKSPFRRALLENAGLEFSAA 28 (199)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEe
Confidence 489999999999999987666655
No 207
>PRK14363 Maf-like protein; Provisional
Probab=36.97 E-value=34 Score=31.82 Aligned_cols=24 Identities=21% Similarity=0.162 Sum_probs=20.3
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-+++++|+||+..|..+..+++++
T Consensus 3 iILAS~SprR~elL~~~G~~f~v~ 26 (204)
T PRK14363 3 IILASSSPRRRQLMELLGIEFEVE 26 (204)
T ss_pred EEEeCCCHHHHHHHHhCCCCeEEE
Confidence 378999999999999987777665
No 208
>TIGR00172 maf MAF protein. This nonessential gene causes inhibition of septation when overexpressed. A member of the family is found in the Archaeon Pyrococcus horikoshii and another in the round worm Caenorhabditis elegans.
Probab=36.96 E-value=38 Score=30.85 Aligned_cols=33 Identities=18% Similarity=0.167 Sum_probs=24.0
Q ss_pred CCCEEecCChHHHHHHHhhCCCCEEEeccCCCHHHH
Q 020472 187 AGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTR 222 (326)
Q Consensus 187 ~ga~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TR 222 (326)
.--++|++|+||+.-|+.+.-+++++ .=||+.+
T Consensus 3 ~~lILAS~SprR~elL~~~g~~f~v~---~~~idE~ 35 (183)
T TIGR00172 3 KELILASQSPRRKELLEELGISFEQI---VSEFDEK 35 (183)
T ss_pred CCEEEeCCCHHHHHHHHHCCCCeEEE---cCCCCCC
Confidence 34689999999999999986666654 3345553
No 209
>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=36.90 E-value=1.4e+02 Score=24.12 Aligned_cols=53 Identities=15% Similarity=0.248 Sum_probs=33.2
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEEe
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVH 146 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAVH 146 (326)
+|+||+=.|.-..+ --.+...+++.||++. +++. + ++ ++.+ +++|++|+++.
T Consensus 2 ~l~Ig~~~~~~~~~-l~~~l~~~~~~~P~v~----i~i~---~-~~------------------~~~~-~~~~~~Dl~i~ 53 (201)
T cd08471 2 LLTVTAPVLFGRLH-VLPIITDFLDAYPEVS----VRLL---L-LD------------------RVVN-LLEEGVDVAVR 53 (201)
T ss_pred eEEEEccHHHHHHH-HHHHHHHHHHHCCCcE----EEEE---E-cC------------------ccch-hhcccccEEEE
Confidence 68999887754433 4445677778899762 5543 1 11 1222 46789999996
Q ss_pred e
Q 020472 147 S 147 (326)
Q Consensus 147 S 147 (326)
.
T Consensus 54 ~ 54 (201)
T cd08471 54 I 54 (201)
T ss_pred e
Confidence 4
No 210
>PRK00032 Maf-like protein; Reviewed
Probab=36.74 E-value=36 Score=31.26 Aligned_cols=24 Identities=17% Similarity=0.232 Sum_probs=20.0
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-++|++|+||+..|..+.-+++++
T Consensus 4 iILAS~SprR~elL~~~g~~f~v~ 27 (190)
T PRK00032 4 LYLASGSPRRRELLTQLGVPFEVL 27 (190)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 488999999999999986666655
No 211
>PRK00234 Maf-like protein; Reviewed
Probab=36.46 E-value=38 Score=31.09 Aligned_cols=24 Identities=8% Similarity=0.069 Sum_probs=20.2
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-++|++|+||+..|+.+.-+++++
T Consensus 4 iILAS~SprR~elL~~~gi~f~v~ 27 (192)
T PRK00234 4 LLLASSSPYRRELLARLRLPFTWA 27 (192)
T ss_pred EEEecCCHHHHHHHHHCCCCcEEE
Confidence 478999999999999987666655
No 212
>PRK07377 hypothetical protein; Provisional
Probab=35.71 E-value=1.3e+02 Score=27.99 Aligned_cols=58 Identities=19% Similarity=0.327 Sum_probs=36.4
Q ss_pred CCceEEEE-----eCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHc
Q 020472 64 KVAIIRIG-----TRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALIN 138 (326)
Q Consensus 64 ~~~~IrIG-----TR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~ 138 (326)
...++|+| ++.+..---=-+.+++.++++| + .+|++.-.+ .+++++||.+
T Consensus 73 ss~~~Rlgv~~~~~~~~~~~~~l~~~l~~~~~~y~--~----rlElv~y~~-------------------~~~l~~aL~~ 127 (184)
T PRK07377 73 SSLVMRLGVLEIETETSSVFDQLIDQLRTILDKYH--L----RLELVVYPD-------------------LQALEQALRD 127 (184)
T ss_pred hccEEEEEEEeccccccccHHHHHHHHHHHHHHhC--c----eeeEEecCC-------------------HHHHHHHHhc
Confidence 45678888 4444432222334566666665 2 366766533 3689999999
Q ss_pred CCCcEEEe
Q 020472 139 SQIDIAVH 146 (326)
Q Consensus 139 g~iDiAVH 146 (326)
|++|++--
T Consensus 128 ~eVh~~c~ 135 (184)
T PRK07377 128 KEVHAICL 135 (184)
T ss_pred CCccEEec
Confidence 99997643
No 213
>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=34.66 E-value=62 Score=26.02 Aligned_cols=39 Identities=18% Similarity=0.231 Sum_probs=31.8
Q ss_pred HHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 198 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 198 R~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
-...++..+|++++. -..++-+.-++.|.+|++|-.|..
T Consensus 17 ~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~g~~Dl~i~~ 55 (197)
T cd08419 17 LLGAFCRRHPGVEVS-LRVGNREQVLERLADNEDDLAIMG 55 (197)
T ss_pred HHHHHHHHCCCceEE-EEECCHHHHHHHHhcCCccEEEec
Confidence 356778889999987 666787777889999999998864
No 214
>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=34.39 E-value=58 Score=26.95 Aligned_cols=41 Identities=15% Similarity=0.079 Sum_probs=33.6
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
.-.+.++..+|++++. -.-++-++=++.|.+|++|..|...
T Consensus 17 ~~l~~~~~~~P~v~i~-~~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (202)
T cd08468 17 RLMARLEELAPSVRLN-LVHAEQKLPLDALLAGEIDFALGYS 57 (202)
T ss_pred HHHHHHHhhCCCCEEE-EEECChHhHHHHHHCCCccEEEecc
Confidence 3457778889999997 7778888889999999999988643
No 215
>PRK14361 Maf-like protein; Provisional
Probab=33.89 E-value=42 Score=30.71 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=19.0
Q ss_pred EEecCChHHHHHHHhhCCCCEEE
Q 020472 190 IVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 190 ~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
++|++|+||+..|+.+.-+++++
T Consensus 2 ILAS~SprR~elL~~~g~~f~v~ 24 (187)
T PRK14361 2 ILASGSPRRRELLENLGVPFQVV 24 (187)
T ss_pred EEccCCHHHHHHHHHCCCCcEEE
Confidence 68999999999999986556554
No 216
>PRK04425 Maf-like protein; Reviewed
Probab=33.85 E-value=43 Score=30.94 Aligned_cols=24 Identities=21% Similarity=0.274 Sum_probs=20.1
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-++|++|+||+..|+.+.-+++++
T Consensus 7 iILAS~SprR~elL~~~g~~f~v~ 30 (196)
T PRK04425 7 LVLGTSSVFRREQMERLGIAFQAA 30 (196)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 589999999999999986666655
No 217
>PRK01839 Maf-like protein; Reviewed
Probab=33.67 E-value=43 Score=31.21 Aligned_cols=35 Identities=9% Similarity=0.012 Sum_probs=25.3
Q ss_pred CCEEecCChHHHHHHHhhCCCCEEEeccCCCHHHHHhh
Q 020472 188 GSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRK 225 (326)
Q Consensus 188 ga~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~K 225 (326)
.-++|++|+||+..|+.+.-+++++ -=|++....+
T Consensus 11 ~lILAS~SprR~elL~~~gi~f~v~---~~~idE~~~~ 45 (209)
T PRK01839 11 FLYLASQSPRRQELLQQLGVRFELL---LPRPDEDAEA 45 (209)
T ss_pred CEEEeCCCHHHHHHHHHCCCCeEEe---CCCCCcCccc
Confidence 3699999999999999886566655 3346665433
No 218
>PRK14368 Maf-like protein; Provisional
Probab=33.61 E-value=43 Score=30.87 Aligned_cols=24 Identities=21% Similarity=0.243 Sum_probs=20.2
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-+++++|+||+..|+.+.-+++++
T Consensus 7 lILAS~SprR~eLL~~~g~~f~v~ 30 (193)
T PRK14368 7 IVLASASPRRSELLASAGIEFDVV 30 (193)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 589999999999999986666655
No 219
>PRK00884 Maf-like protein; Reviewed
Probab=33.42 E-value=46 Score=30.69 Aligned_cols=24 Identities=13% Similarity=0.121 Sum_probs=20.5
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-+++++|+||+..|..+.-+++++
T Consensus 4 iILAS~SprR~elL~~~g~~f~v~ 27 (194)
T PRK00884 4 LILASTSPYRRALLEKLQLPFECA 27 (194)
T ss_pred EEEeCCCHHHHHHHHHCCCCCEEE
Confidence 488999999999999987667665
No 220
>PRK14365 Maf-like protein; Provisional
Probab=33.31 E-value=40 Score=31.14 Aligned_cols=24 Identities=29% Similarity=0.259 Sum_probs=19.7
Q ss_pred CEEecCChHHHHHHHhh-CCCCEEE
Q 020472 189 SIVGTASLRRKSQILHR-YPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~-~Pdl~v~ 212 (326)
-++|++|+||+.-|..+ .-+++++
T Consensus 4 iILaSsSprR~elL~~~~g~~f~vi 28 (197)
T PRK14365 4 IILASASPRRKELLKQLIGDNFLVY 28 (197)
T ss_pred EEEeCCCHHHHHHHhcCcCcCeEEE
Confidence 48999999999999985 6666665
No 221
>cd00555 Maf Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or nucleic acid-binding protein with structural similarity to the hypoxanthine/xanthine NTP pyrophosphatase Ham1 from Methanococcus jannaschii, RNase H from Escherichia coli, and some other nucleotide or RNA-binding proteins.
Probab=32.68 E-value=43 Score=30.34 Aligned_cols=31 Identities=19% Similarity=0.235 Sum_probs=24.0
Q ss_pred EEecCChHHHHHHHhhCCCCEEEeccCCCHHHHH
Q 020472 190 IVGTASLRRKSQILHRYPSLKVMENFRGNVQTRL 223 (326)
Q Consensus 190 ~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TRL 223 (326)
++|++|+||+.-|+.+..+++++ +- |+|.+.
T Consensus 2 ILaS~SprR~elL~~~g~~f~~~-~~--~iDE~~ 32 (180)
T cd00555 2 ILASASPRRRELLEQLGIPFEVV-PS--DIDETP 32 (180)
T ss_pred EECCCCHHHHHHHHhCCCCeEEE-cC--CCCCCC
Confidence 68999999999999987777766 43 465554
No 222
>PRK14362 Maf-like protein; Provisional
Probab=32.62 E-value=48 Score=30.94 Aligned_cols=25 Identities=16% Similarity=0.230 Sum_probs=20.8
Q ss_pred CCEEecCChHHHHHHHhhCCCCEEE
Q 020472 188 GSIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 188 ga~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
.-++|++|+||+..|+.+.-+++++
T Consensus 13 ~iILAS~SprR~eLL~~~g~~f~v~ 37 (207)
T PRK14362 13 PVVLASGSPRRREFLEQMGLPFEVI 37 (207)
T ss_pred eEEEeCCCHHHHHHHHHCCCCcEEE
Confidence 3689999999999999987666654
No 223
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=31.49 E-value=2.6e+02 Score=25.79 Aligned_cols=57 Identities=18% Similarity=0.181 Sum_probs=35.4
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.++|+||+-.+.+..+-...+ ..+.+. |++ ++++.. |+ ..++.+.|.+|++|++
T Consensus 89 ~g~l~I~~~~~~~~~~l~~~l-~~f~~~-~~i----~i~l~~----~~----------------~~~~~~~l~~~~~d~~ 142 (294)
T PRK03635 89 PLTLSIAVNADSLATWFLPAL-APVLAR-SGV----LLDLVV----ED----------------QDHTAELLRRGEVVGA 142 (294)
T ss_pred ceEEEEeecchhHHHHHHHHH-HHHHhC-CCc----EEEEEe----cC----------------cHHHHHHHhCCCceEE
Confidence 578999997655544445544 444444 443 233322 11 2467889999999999
Q ss_pred Eee
Q 020472 145 VHS 147 (326)
Q Consensus 145 VHS 147 (326)
+-+
T Consensus 143 i~~ 145 (294)
T PRK03635 143 VTT 145 (294)
T ss_pred Eec
Confidence 865
No 224
>PF02545 Maf: Maf-like protein; InterPro: IPR003697 Maf is a putative inhibitor of septum formation in eukaryotes, bacteria, and archaea. The Maf protein shares substantial amino acid sequence identity with the Escherichia coli OrfE protein [].; GO: 0005737 cytoplasm; PDB: 2P5X_A 1EXC_B 1EX2_A.
Probab=31.29 E-value=32 Score=31.55 Aligned_cols=31 Identities=16% Similarity=0.289 Sum_probs=13.8
Q ss_pred EEecCChHHHHHHHhhCCCCEEEeccCCCHHHHH
Q 020472 190 IVGTASLRRKSQILHRYPSLKVMENFRGNVQTRL 223 (326)
Q Consensus 190 ~IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TRL 223 (326)
++|++|+||+..|+.+..+++++ .=+++.+.
T Consensus 4 ILaS~SprR~elL~~~g~~f~v~---~~~~dE~~ 34 (195)
T PF02545_consen 4 ILASSSPRRRELLKQLGINFEVI---PSDIDEDA 34 (195)
T ss_dssp EE----HHHHHHHHCTT--EEE------------
T ss_pred EEeCCCHHHHHHHHHCCCCeEEE---cCCCCCCC
Confidence 78999999999999988666655 34577766
No 225
>PRK14367 Maf-like protein; Provisional
Probab=31.15 E-value=50 Score=30.62 Aligned_cols=24 Identities=17% Similarity=0.105 Sum_probs=19.9
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-++|++|+||+..|+.+.-+++++
T Consensus 4 iILAS~SprR~eLL~~~Gi~f~v~ 27 (202)
T PRK14367 4 LYLGSNSPRRMEILTQLGYRVVKL 27 (202)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 478999999999999986666655
No 226
>cd08476 PBP2_CrgA_like_7 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 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=31.03 E-value=1.4e+02 Score=23.93 Aligned_cols=27 Identities=19% Similarity=0.177 Sum_probs=17.4
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCc
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPEL 96 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l 96 (326)
+|+||+= .+....-.+...+++.||++
T Consensus 2 ~l~ig~~---~~~~~l~~~l~~~~~~~P~v 28 (197)
T cd08476 2 RLRVSLP---LVGGLLLPVLAAFMQRYPEI 28 (197)
T ss_pred eEEEEec---chHHHHHHHHHHHHHHCCCe
Confidence 5899974 33222234677788889975
No 227
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=31.02 E-value=1.6e+02 Score=23.94 Aligned_cols=29 Identities=21% Similarity=0.246 Sum_probs=20.1
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCc
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPEL 96 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l 96 (326)
+++||+=.+. +..---.+...+.+.||++
T Consensus 2 ~l~Ig~~~~~-~~~~l~~~l~~~~~~~P~i 30 (202)
T cd08472 2 RLRVDVPGSL-ARLLLIPALPDFLARYPDI 30 (202)
T ss_pred eEEEeccHHH-HHHHHHHHHHHHHHHCCCc
Confidence 5889887764 4344455667788889976
No 228
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=30.95 E-value=90 Score=29.21 Aligned_cols=42 Identities=12% Similarity=-0.021 Sum_probs=35.6
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
++--+.++..+|++++. -..||-.+=+..|.+|++|..|...
T Consensus 128 ~~~l~~f~~~~P~i~l~-i~~~~~~~~~~~l~~g~~Di~i~~~ 169 (314)
T PRK09508 128 SQIYNRIEQIAPNIHVV-FKSSLNQNIEHQLRYQETEFVISYE 169 (314)
T ss_pred HHHHHHHHHhCCCcEEE-EEeCcchhHHHHHhcCCccEEEecC
Confidence 45567888899999997 7788888889999999999999754
No 229
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=30.94 E-value=1.1e+02 Score=28.73 Aligned_cols=41 Identities=10% Similarity=0.205 Sum_probs=34.5
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
.-..+++..+|++++. -.-++.+.-+..|.+|++|..|...
T Consensus 114 ~~l~~~~~~~p~v~i~-~~~~~~~~~~~~l~~g~~Dl~i~~~ 154 (312)
T PRK10341 114 DMINKFKEVFPKAQVS-MYEAQLSSFLPAIRDGRLDFAIGTL 154 (312)
T ss_pred HHHHHHHHhCCCCEEE-EEeCCHHHHHHHHHcCCCcEEEecC
Confidence 4457777889999997 7778889999999999999988654
No 230
>cd08477 PBP2_CrgA_like_8 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 8. 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=30.43 E-value=1.5e+02 Score=23.91 Aligned_cols=29 Identities=14% Similarity=0.106 Sum_probs=18.5
Q ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhCCCc
Q 020472 67 IIRIGTRGSPLALAQAHETRNKLMALHPEL 96 (326)
Q Consensus 67 ~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l 96 (326)
.|+||+=.+.-..+ .-.+...+++.||++
T Consensus 2 ~l~Ig~~~~~~~~~-l~~~l~~~~~~~P~i 30 (197)
T cd08477 2 KLRISAPVTFGSHV-LTPALAEYLARYPDV 30 (197)
T ss_pred eEEEeCCHHHHHHH-HHHHHHHHHHHCCCc
Confidence 58888876643222 334566777889986
No 231
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=29.82 E-value=1.6e+02 Score=29.14 Aligned_cols=56 Identities=9% Similarity=-0.025 Sum_probs=41.3
Q ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccE-EEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCc
Q 020472 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAI-QIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQID 142 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~-eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iD 142 (326)
+.++|+||.=+..=..+.++.+...|++.+ +++ +++...+ .-+-++|.+|++|
T Consensus 27 ~~~~V~~~~~~W~~~~~~t~v~~~iLe~~G------Y~V~e~~~~~~--------------------~~~~~ala~GdiD 80 (331)
T PRK11119 27 KGITVQPAQSTIAEETFQTLLVSRALEKLG------YDVNKPKEVDY--------------------NVFYTSIANGDAT 80 (331)
T ss_pred CCeEEEEeecCccHHHHHHHHHHHHHHHcC------CceeeecccCc--------------------HHHHHHHHcCCCe
Confidence 457899999999999999999999998653 246 5544422 1356778888888
Q ss_pred EEE
Q 020472 143 IAV 145 (326)
Q Consensus 143 iAV 145 (326)
+.+
T Consensus 81 v~~ 83 (331)
T PRK11119 81 FTA 83 (331)
T ss_pred Eeh
Confidence 754
No 232
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=29.27 E-value=1.1e+02 Score=27.74 Aligned_cols=41 Identities=20% Similarity=0.186 Sum_probs=33.3
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++-.++++..||++++. -.-++-+.-+..|.+|++|..|..
T Consensus 105 ~~~l~~~~~~~P~i~i~-v~~~~~~~~~~~l~~g~~Di~i~~ 145 (290)
T PRK10837 105 PAMIARYRRDYPQLPLE-LSVGNSQDVINAVLDFRVDIGLIE 145 (290)
T ss_pred HHHHHHHHHHCCCceEE-EEECCHHHHHHHHHhCCceEEEec
Confidence 35567888899999987 555787888899999999998864
No 233
>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=29.14 E-value=44 Score=27.35 Aligned_cols=37 Identities=16% Similarity=0.260 Sum_probs=27.8
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+.-.++...||++++. -. + ...+.++.+|++|..|..
T Consensus 20 ~~l~~f~~~~P~v~i~-~~--~-~~~~~~l~~~~~D~~i~~ 56 (199)
T cd08478 20 PLIAKFRERYPDIELE-LV--S-NEGIIDLIERKTDVAIRI 56 (199)
T ss_pred HHHHHHHHHCCCeEEE-EE--e-ccccccchhccccEEEEe
Confidence 6678888899999997 33 2 344556788999998864
No 234
>PRK00648 Maf-like protein; Reviewed
Probab=28.84 E-value=57 Score=29.90 Aligned_cols=24 Identities=25% Similarity=0.245 Sum_probs=20.0
Q ss_pred CEEecCChHHHHHHHhhCCCCEEE
Q 020472 189 SIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
-++|++|+||+.-|+.+.-+++++
T Consensus 5 lILAS~SprR~elL~~~g~~f~v~ 28 (191)
T PRK00648 5 IILASSSPRRKEILEGFRIPFEVV 28 (191)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 589999999999999986666654
No 235
>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=28.83 E-value=4.6e+02 Score=24.10 Aligned_cols=65 Identities=14% Similarity=0.061 Sum_probs=45.1
Q ss_pred cCcccCCCCCEEecC-ChHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhcccCCCccc
Q 020472 180 ASLAELPAGSIVGTA-SLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENV 250 (326)
Q Consensus 180 ~~l~dLp~ga~IGTS-S~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RLgl~~~i 250 (326)
++++|| +|.+|++. +.--...++.+ ....+ ++ ....=..-|..|.+||.+-....+.-+++.+-.
T Consensus 129 ~s~~Dl-~G~kir~~~~~~~~~~~~~~--Ga~~v-~~--~~~e~~~aL~~G~vDg~~~~~~~~~~~~~~ev~ 194 (257)
T TIGR00787 129 TKPEDL-KGLKIRIPNSPMNEAQFKAL--GANPE-PM--AFSEVYTALQTGVVDGQENPLSNVYSSKFYEVQ 194 (257)
T ss_pred CChHHh-CCCEEecCCCHHHHHHHHHc--CCccc-cc--CHHHHHHHHHcCCcccccCCHHHHhhcchhhhc
Confidence 467777 69999985 33334445554 34433 33 466777788999999999998888888886554
No 236
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=28.56 E-value=1.2e+02 Score=28.59 Aligned_cols=39 Identities=13% Similarity=0.120 Sum_probs=33.5
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 236 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIIL 236 (326)
+-...+...+|++++. -.-++-+.-+..|.+|++|..|.
T Consensus 110 ~~i~~f~~~~P~i~l~-~~~~~~~~~~~~L~~~~~D~~i~ 148 (309)
T PRK12683 110 KVVRQFKEVFPKVHLA-LRQGSPQEIAEMLLNGEADIGIA 148 (309)
T ss_pred HHHHHHHHHCCCceEE-EEeCCHHHHHHHHHcCCccEEEe
Confidence 4557788889999997 77799999999999999998775
No 237
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=28.43 E-value=1.2e+02 Score=28.50 Aligned_cols=40 Identities=10% Similarity=0.204 Sum_probs=33.7
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.-...+...+|++++. -.-++-+.-+..|.+|++|..|..
T Consensus 110 ~~l~~~~~~~p~i~l~-~~~~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 110 AAIKEFKKRYPKVRLS-ILQGSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred HHHHHHHHHCCCceEE-EEeCChHHHHHHHHCCCcCEEEee
Confidence 4566788889999997 667888888999999999998865
No 238
>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=28.22 E-value=86 Score=26.32 Aligned_cols=41 Identities=5% Similarity=-0.045 Sum_probs=32.3
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
.-...++..+|++++. -..++-.+-.+.|.+|++|..|...
T Consensus 17 ~~l~~f~~~~P~v~l~-i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 17 ALVRRLETEAPGIDLR-IRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred HHHHHHHHHCCCcEEE-EeeCChhhHHHHHHCCCccEEEecC
Confidence 3456788889999997 6667766778888999999988743
No 239
>PRK02141 Maf-like protein; Reviewed
Probab=27.98 E-value=62 Score=30.18 Aligned_cols=25 Identities=16% Similarity=0.165 Sum_probs=20.6
Q ss_pred CCEEecCChHHHHHHHhhCCCCEEE
Q 020472 188 GSIVGTASLRRKSQILHRYPSLKVM 212 (326)
Q Consensus 188 ga~IGTSS~RR~aQL~~~~Pdl~v~ 212 (326)
.-+++++|+||+..|+.+.-+++++
T Consensus 10 ~iILAS~SprR~elL~~~G~~f~v~ 34 (207)
T PRK02141 10 RLILASSSRYRRELLERLRLPFDVV 34 (207)
T ss_pred CEEEeCCCHHHHHHHHHCCCCeEEE
Confidence 3699999999999999986666655
No 240
>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=27.34 E-value=3.2e+02 Score=24.99 Aligned_cols=143 Identities=9% Similarity=-0.002 Sum_probs=71.4
Q ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEE
Q 020472 65 VAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIA 144 (326)
Q Consensus 65 ~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiA 144 (326)
.+.|+||+-......+=...+.+..++ + ++ ++++. .|+ ..++.+.|.+|++|++
T Consensus 89 ~g~l~i~~~~~~~~~~l~~~l~~~~~~-~-~i----~i~l~----~~~----------------~~~~~~~l~~g~~d~~ 142 (292)
T TIGR03298 89 PVTLSIAVNADSLATWFLPALAPVLAQ-E-GV----LLDLV----VED----------------QDHTAELLRSGEVLGA 142 (292)
T ss_pred CceEEEecccchhhhhhHHHHHHHHhC-C-Cc----eEEEE----eCc----------------chhHHHHHhCCCceEE
Confidence 468999986444444444444444433 3 32 23332 132 2467899999999999
Q ss_pred EeeCCCCCCCCCCCceeeeecCCCCCcceeec-cC--------ccCcccCCCCCEEecCCh---HHHH--HHHhhCCCCE
Q 020472 145 VHSMKDVPTYLPEKTILPCNLQREDVRDAFIS-LS--------AASLAELPAGSIVGTASL---RRKS--QILHRYPSLK 210 (326)
Q Consensus 145 VHSlKDlPt~lp~gL~iaAv~kReDprD~LV~-~~--------~~~l~dLp~ga~IGTSS~---RR~a--QL~~~~Pdl~ 210 (326)
|-+... | .+++....+. .++ -++|+ ++ ..+++||..-..|..+.. ++.. ++........
T Consensus 143 i~~~~~-~---~~~l~~~~l~-~~~--~~~v~~~~~~~~~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 215 (292)
T TIGR03298 143 VTTQAK-P---VQGCRVVPLG-AMR--YLAVASPAFAARYFPDGVTAEALARAPVIVFNRKDDLQDRFLRRLFGLPVSPP 215 (292)
T ss_pred EecCCC-C---CCCceEEecC-Cce--EEEEECchhhhhccCCCCCHHHhcCCCEEEeCCCCccHHHHHHHHhcCCCCCC
Confidence 965332 1 3455433221 111 12222 21 124566666666665432 2321 1111110111
Q ss_pred EEeccCCCHHHHHhhhccCCccEEeeehhhhcc
Q 020472 211 VMENFRGNVQTRLRKLNERVVQATLLALAGLKR 243 (326)
Q Consensus 211 v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~R 243 (326)
+. .+ .|+++-+.=+..| ....+++..-+.+
T Consensus 216 ~~-~~-~~~~~~~~~v~~g-~Gi~~~p~~~~~~ 245 (292)
T TIGR03298 216 RH-YV-PSSEGFVEAARAG-LGWGMVPELQAEP 245 (292)
T ss_pred eE-ec-CCHHHHHHHHHhC-CCeEeCcHHHHHH
Confidence 22 23 4888877777777 3456666665554
No 241
>PRK14364 Maf-like protein; Provisional
Probab=27.09 E-value=50 Score=30.07 Aligned_cols=30 Identities=10% Similarity=0.237 Sum_probs=21.8
Q ss_pred EecCChHHHHHHHhhCCCCEEEeccCCCHHHHH
Q 020472 191 VGTASLRRKSQILHRYPSLKVMENFRGNVQTRL 223 (326)
Q Consensus 191 IGTSS~RR~aQL~~~~Pdl~v~~~iRGNV~TRL 223 (326)
.|++|+||+..|+.+.-+++++ +- +++.+.
T Consensus 1 LAS~SprR~elL~~~g~~f~v~-~~--~~dE~~ 30 (181)
T PRK14364 1 LASSSPRRRELLQQLGLNFEIY-SP--DIDESV 30 (181)
T ss_pred CCCCCHHHHHHHHHCCCCeEEE-CC--CCCCCC
Confidence 3789999999999987667665 33 455543
No 242
>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=27.00 E-value=90 Score=25.37 Aligned_cols=37 Identities=24% Similarity=0.204 Sum_probs=28.1
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 236 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIIL 236 (326)
++.-+.+...||++++. -.-++ .+..|.+|++|..|.
T Consensus 17 ~~~l~~f~~~~P~i~i~-~~~~~---~~~~l~~g~~Dl~i~ 53 (198)
T cd08479 17 APALSDFAKRYPELEVQ-LELTD---RPVDLVEEGFDLDIR 53 (198)
T ss_pred HHHHHHHHHHCCCeEEE-EEecC---ccccccccCccEEEE
Confidence 46677888899999987 44344 356788999999876
No 243
>PRK14366 Maf-like protein; Provisional
Probab=26.96 E-value=69 Score=29.61 Aligned_cols=24 Identities=13% Similarity=0.077 Sum_probs=18.8
Q ss_pred CEEecCChHHHHHHHhhCC-CCEEE
Q 020472 189 SIVGTASLRRKSQILHRYP-SLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~P-dl~v~ 212 (326)
-++|++|+||+..|+.+-- ..+++
T Consensus 7 iILAS~SprR~elL~~~G~~~~~v~ 31 (195)
T PRK14366 7 LILASSSKQRLALLEQIGVVPGEIV 31 (195)
T ss_pred EEEeCCCHHHHHHHHhCCCCCCEEe
Confidence 5899999999999998754 44444
No 244
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=26.83 E-value=97 Score=29.36 Aligned_cols=41 Identities=7% Similarity=0.071 Sum_probs=34.5
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+..-.+++..||++++. -.-++-++-+..|.+|++|..|..
T Consensus 105 ~~~l~~~~~~~P~i~l~-~~~~~~~~~~~~L~~g~~Dl~i~~ 145 (317)
T PRK15421 105 TPALENFHKNWPQVEMD-FKSGVTFDPQPALQQGELDLVMTS 145 (317)
T ss_pred HHHHHHHHHHCCCceEE-EEeCccHHHHHHHHCCCcCEEEec
Confidence 44678888999999997 666777888999999999999864
No 245
>cd00985 Maf_Ham1 Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard nucleotides, such as hypoxanthine/xanthine NTP, but not standard nucleotides.
Probab=26.17 E-value=70 Score=26.52 Aligned_cols=23 Identities=22% Similarity=0.290 Sum_probs=19.2
Q ss_pred EEecCChHHHHHHHhhC-CCCEEE
Q 020472 190 IVGTASLRRKSQILHRY-PSLKVM 212 (326)
Q Consensus 190 ~IGTSS~RR~aQL~~~~-Pdl~v~ 212 (326)
+++|+|+||..-+..+. -++.++
T Consensus 2 iLaS~s~~R~~~l~~~~~~~~~~~ 25 (131)
T cd00985 2 ILASGSPRRLEELKQIGGIEFEVL 25 (131)
T ss_pred EEecCChHHHHHHHhcCCCCEEEe
Confidence 68999999999999998 466555
No 246
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=25.97 E-value=1.2e+02 Score=28.30 Aligned_cols=40 Identities=15% Similarity=0.224 Sum_probs=33.5
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
.....+...+|++++. -.-++.++-++.|.+|++|..|..
T Consensus 110 ~~l~~~~~~~P~i~i~-i~~~~~~~~~~~l~~g~~D~~i~~ 149 (309)
T PRK12682 110 RVVAAFRKRYPKVNLS-LHQGSPDEIARMVISGEADIGIAT 149 (309)
T ss_pred HHHHHHHHhCCCeEEE-EecCCHHHHHHHHHcCCccEEEec
Confidence 3456778889999997 667888899999999999999864
No 247
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=25.92 E-value=95 Score=28.43 Aligned_cols=41 Identities=10% Similarity=0.011 Sum_probs=34.5
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+-..++...+|++++. -.-++-+.-+..|.+|++|..|+..
T Consensus 107 ~~~~~~~~~~p~v~i~-~~~~~~~~~~~~l~~~~~D~~i~~~ 147 (296)
T PRK09906 107 KVLPMFRLRHPDTLIE-LVSLITTQQEEKLRRGELDVGFMRH 147 (296)
T ss_pred HHHHHHHHHCCCeEEE-EEeCCcHHHHHHHHcCCeeEEEecC
Confidence 4567788899999997 7777888889999999999999744
No 248
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=25.74 E-value=95 Score=28.67 Aligned_cols=40 Identities=18% Similarity=0.255 Sum_probs=33.4
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
..-.++...+|++++. -.-++....++.|.+|++|..|..
T Consensus 112 ~~l~~~~~~~p~i~~~-~~~~~~~~~~~~l~~g~~Di~i~~ 151 (302)
T PRK09791 112 AVISRFHQQHPQVKVR-IMEGQLVSMINELRQGELDFTINT 151 (302)
T ss_pred HHHHHHHHHCCCeEEE-EEeCChHHHHHHHHCCCccEEEEe
Confidence 3456788889999997 667788899999999999998864
No 249
>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=25.73 E-value=1.4e+02 Score=27.37 Aligned_cols=40 Identities=20% Similarity=0.184 Sum_probs=33.5
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 236 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIIL 236 (326)
+..-.++...+|++++. -.-++-+.=++-|.+|++|-.|.
T Consensus 109 ~~~l~~~~~~~P~~~i~-~~~~~~~~~~~~l~~g~~D~~i~ 148 (300)
T TIGR02424 109 PEVVKRFLARAPRLRVR-IMTGPNAYLLDQLRVGALDLVVG 148 (300)
T ss_pred HHHHHHHHHhCCCcEEE-EEeCchHHHHHHHHCCCCCEEEE
Confidence 35678889999999998 66678777788899999999885
No 250
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=24.81 E-value=1e+02 Score=32.25 Aligned_cols=150 Identities=19% Similarity=0.244 Sum_probs=90.0
Q ss_pred CCceEEEEeCCCHHHHHHHH--------HHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHH
Q 020472 64 KVAIIRIGTRGSPLALAQAH--------ETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEA 135 (326)
Q Consensus 64 ~~~~IrIGTR~S~LAlaQa~--------~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~A 135 (326)
..+.+||+|+.|++.-.+-+ +...+..++ | .++++.+.- |. ..+|..+
T Consensus 21 ~rGvLrV~tinsp~sy~~~~~~p~G~eYelak~Fa~y---L----gV~Lki~~~--~n---------------~dqLf~a 76 (473)
T COG4623 21 ARGVLRVSTINSPLSYFEDKGGPTGLEYELAKAFADY---L----GVKLKIIPA--DN---------------IDQLFDA 76 (473)
T ss_pred hcCeEEEEeecCccceeccCCCccchhHHHHHHHHHH---h----CCeEEEEec--CC---------------HHHHHHH
Confidence 34779999999998765532 122223222 1 144433321 11 2468899
Q ss_pred HHcCCCcEEE----eeCCCCCCCCCCCceeeeecCCCCCcceeeccCc----cCcccCCC-CCEEecCChHH--HHHHHh
Q 020472 136 LINSQIDIAV----HSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA----ASLAELPA-GSIVGTASLRR--KSQILH 204 (326)
Q Consensus 136 Ll~g~iDiAV----HSlKDlPt~lp~gL~iaAv~kReDprD~LV~~~~----~~l~dLp~-ga~IGTSS~RR--~aQL~~ 204 (326)
|-+|++|++- ...+|+-.. +.| +-+-|+.=.||.++| +++.+|.. --.|-..|.-= ...++.
T Consensus 77 L~ng~~DL~Aagl~~~~~~l~~~-~~g------P~y~svs~qlVyRkG~~Rp~~l~~L~g~~i~v~~gs~~~~~l~~lk~ 149 (473)
T COG4623 77 LDNGNADLAAAGLLYNSERLKNF-QPG------PTYYSVSQQLVYRKGQYRPRSLGQLKGRQITVAKGSAHVEDLKLLKE 149 (473)
T ss_pred HhCCCcceecccccCChhHhccc-CCC------CceecccHHHHhhcCCCCCCCHHHccCceeeccCCcHHHHHHHHHHH
Confidence 9999999983 222332211 111 234555556777655 45777654 23454555432 233444
Q ss_pred -hCCCCEEEeccCCCHHHHHhhhccCCccEEeeehhhhccc
Q 020472 205 -RYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRL 244 (326)
Q Consensus 205 -~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~AGL~RL 244 (326)
.||++....+--=.+++=|+++.+|.+|-+|.=..-+.+.
T Consensus 150 ~kyP~l~~k~d~~~~~~dLle~v~~Gkldytiads~~is~~ 190 (473)
T COG4623 150 TKYPELIWKVDDKLGVEDLLEMVAEGKLDYTIADSVEISLF 190 (473)
T ss_pred hhcchhhhhhcccccHHHHHHHHhcCCcceeeeccHHHHHH
Confidence 7999998755666689999999999999998855554444
No 251
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=24.39 E-value=1e+02 Score=28.16 Aligned_cols=43 Identities=14% Similarity=0.367 Sum_probs=35.7
Q ss_pred CCEEecCChHHH--HHHHhhCCCCEEEeccCCCHHHHHhhhc--cCCc
Q 020472 188 GSIVGTASLRRK--SQILHRYPSLKVMENFRGNVQTRLRKLN--ERVV 231 (326)
Q Consensus 188 ga~IGTSS~RR~--aQL~~~~Pdl~v~~~iRGNV~TRL~KL~--~ge~ 231 (326)
..+|.+|++.|. -+|+.-.|++.|+ -+-|+-++=++++. .|.|
T Consensus 69 ~~vi~CSALKr~YRD~LR~~~~~~~Fv-~L~g~~~~i~~Rm~~R~gHF 115 (161)
T COG3265 69 HVVIACSALKRSYRDLLREANPGLRFV-YLDGDFDLILERMKARKGHF 115 (161)
T ss_pred ceEEecHHHHHHHHHHHhccCCCeEEE-EecCCHHHHHHHHHhcccCC
Confidence 479999999995 5799999999999 99999888777773 4444
No 252
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=24.33 E-value=1.3e+02 Score=28.24 Aligned_cols=39 Identities=13% Similarity=-0.042 Sum_probs=32.5
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 236 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIIL 236 (326)
.-..+++..||++++. -..|+-..-.+.|.+|++|..|.
T Consensus 110 ~~l~~~~~~~P~i~l~-l~~~~~~~~~~~l~~g~~D~~i~ 148 (308)
T PRK10094 110 QLLAWLNERYPFTQFH-ISRQIYMGVWDSLLYEGFSLAIG 148 (308)
T ss_pred HHHHHHHHhCCCcEEE-EEeehhhhHHHHHhCCCccEEEe
Confidence 4567889999999997 77777777788999999998774
No 253
>PF04422 FrhB_FdhB_N: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term; InterPro: IPR007516 Coenzyme F420 hydrogenase (1.12.99.1 from EC) reduces the low-potential two-electron acceptor coenzyme F420. This entry contains the N termini of F420 hydrogenase and dehydrogenase beta subunits [, ]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (1.2.1.2 from EC, P06130 from SWISSPROT) is also represented in this entry []. This region is often found in association with the 4Fe-4S binding domain, fer4 (IPR001450 from INTERPRO), and the C terminus IPR007525 from INTERPRO.
Probab=23.61 E-value=67 Score=25.34 Aligned_cols=24 Identities=21% Similarity=0.094 Sum_probs=21.8
Q ss_pred ccccHHHHHHHHHcCCCcEEEeeC
Q 020472 125 KGLFTKEIDEALINSQIDIAVHSM 148 (326)
Q Consensus 125 kGlFtkELe~ALl~g~iDiAVHSl 148 (326)
-|+||.=+..+|-+|.||-+||--
T Consensus 20 GG~vTaLl~~lLe~g~Vd~vv~~~ 43 (82)
T PF04422_consen 20 GGVVTALLAYLLESGLVDGVVVVG 43 (82)
T ss_pred HHHHHHHHHHHHHcCCceEEEEEe
Confidence 379999999999999999999976
No 254
>PRK01526 Maf-like protein; Reviewed
Probab=23.33 E-value=86 Score=29.18 Aligned_cols=24 Identities=13% Similarity=0.090 Sum_probs=18.8
Q ss_pred CEEecCChHHHHHHHhhCC-CCEEE
Q 020472 189 SIVGTASLRRKSQILHRYP-SLKVM 212 (326)
Q Consensus 189 a~IGTSS~RR~aQL~~~~P-dl~v~ 212 (326)
-++|++|+||+..|..+.- ..+++
T Consensus 10 lILAS~SprR~elL~~~g~~~~~v~ 34 (205)
T PRK01526 10 IILASSSPARIELLNRIKIIPSQII 34 (205)
T ss_pred EEEeCCCHHHHHHHHhcCCCCceEe
Confidence 5899999999999998853 44443
No 255
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=23.13 E-value=1.2e+02 Score=28.04 Aligned_cols=41 Identities=7% Similarity=0.054 Sum_probs=34.1
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
++.-.+++..||++++. -.-|+-+.-+++|.+|++|-.|..
T Consensus 108 ~~~l~~~~~~~p~i~i~-i~~~~~~~~~~~l~~g~~Dl~i~~ 148 (300)
T PRK11074 108 RQLIVDFYRHFDDVELI-IRQEVFNGVWDALADGRVDIAIGA 148 (300)
T ss_pred HHHHHHHHHhCCCceEE-EEehhhhHHHHHHHCCCCCEEEec
Confidence 35677888999999997 666777888999999999999863
No 256
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=22.67 E-value=1.3e+02 Score=27.50 Aligned_cols=40 Identities=10% Similarity=0.061 Sum_probs=32.2
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
+=...++..+|++++. -.-++-..-++.|.+|++|..|..
T Consensus 108 ~~l~~~~~~~p~~~i~-~~~~~~~~~~~~l~~g~~Dl~i~~ 147 (296)
T PRK11242 108 PLIDAFHARYPGITLT-IREMSQERIEALLADDELDVGIAF 147 (296)
T ss_pred HHHHHHHHHCCCCEEE-EEeCCHHHHHHHHHCCCCcEEEEe
Confidence 3356677789999997 556788888899999999988864
No 257
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=22.55 E-value=5.5e+02 Score=22.77 Aligned_cols=58 Identities=16% Similarity=0.289 Sum_probs=37.6
Q ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCcEEE
Q 020472 66 AIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAV 145 (326)
Q Consensus 66 ~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iDiAV 145 (326)
+.++||+-.+.- ....-.+...+.+.||++ ++.... ..++.+.|.+|++|+++
T Consensus 92 ~~~~i~~~~~~~-~~~l~~~l~~~~~~~P~~------~~~~~~--------------------~~~~~~~l~~~~~D~~i 144 (297)
T COG0583 92 GLLRIAAPSTAA-SSLLPPLLARFRARYPEI------ELELGT--------------------SDRLLEDLVEGELDLAI 144 (297)
T ss_pred ceEEEEecchhh-hhhhHHHHHHHHHhCCCe------EEEeCc--------------------hHHHHHHHHcCCCCEEE
Confidence 478888877665 323444556666777743 232221 12367888899999999
Q ss_pred eeCCC
Q 020472 146 HSMKD 150 (326)
Q Consensus 146 HSlKD 150 (326)
.....
T Consensus 145 ~~~~~ 149 (297)
T COG0583 145 RAGPP 149 (297)
T ss_pred ecCCC
Confidence 98876
No 258
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=22.48 E-value=1.5e+02 Score=27.35 Aligned_cols=40 Identities=18% Similarity=0.329 Sum_probs=33.7
Q ss_pred HHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 198 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 198 R~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
-..++...+|++++. -.-++-++-+..|.+|++|-+|...
T Consensus 109 ~l~~~~~~~P~v~i~-~~~~~~~~~~~~l~~g~~Dl~i~~~ 148 (305)
T PRK11151 109 IIPMLHQTFPKLEMY-LHEAQTHQLLAQLDSGKLDCAILAL 148 (305)
T ss_pred HHHHHHHHCCCcEEE-EEeCCHHHHHHHHHcCCccEEEEec
Confidence 345677889999998 7777889999999999999999753
No 259
>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=22.15 E-value=1.5e+02 Score=24.10 Aligned_cols=39 Identities=10% Similarity=0.074 Sum_probs=28.0
Q ss_pred HHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeee
Q 020472 197 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 237 (326)
Q Consensus 197 RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA 237 (326)
....+++.. |++++. -.-+|-+.-.+.|.+|++|.+|..
T Consensus 17 ~~l~~f~~~-~~v~l~-l~~~~~~~~~~~l~~~~~D~~i~~ 55 (195)
T cd08428 17 PALAPVLKR-ERILLD-LIVDDEDRTHDLLRDGEVVGCIST 55 (195)
T ss_pred HHHHHHHhC-cCeEEE-EEeCCchhHHHHHHcCcceEEEEe
Confidence 346677776 588876 555776667788899999976654
No 260
>COG1732 OpuBC Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]
Probab=21.06 E-value=2.5e+02 Score=28.08 Aligned_cols=192 Identities=15% Similarity=0.124 Sum_probs=104.2
Q ss_pred cCCceEEEEeCCCHHHHHHHHHHHHHHHhhCCCcccCccEEEEEeeccCccccCccccccCCccccHHHHHHHHHcCCCc
Q 020472 63 TKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQID 142 (326)
Q Consensus 63 ~~~~~IrIGTR~S~LAlaQa~~V~~~L~~~~p~l~~~~~~eiv~i~T~GD~~~~~pL~~iGgkGlFtkELe~ALl~g~iD 142 (326)
....+|+||+..-.=..+=+++..+.|++. ++. ++. .. .+|+. -=+.+||.+|+||
T Consensus 30 ~~~~~I~VgsK~~tE~~IL~~m~~~lle~~--~~k----v~~--~~------------~lG~t----~v~~~Al~~G~ID 85 (300)
T COG1732 30 SAAKTIVVGSKIFTEQYILGNILKQLLEKN--GIK----VED--KT------------GLGGT----AVVRNALKSGDID 85 (300)
T ss_pred ccCCCEEEecCCCcHHHHHHHHHHHHHHhc--CCc----eee--cc------------CCCch----HHHHHHHHcCCCC
Confidence 356789999999888888888999988875 221 211 11 23332 2257899999999
Q ss_pred EEEee--------CCCCC-CCCCC-------------CceeeeecCCCCCcc--eeeccC-------ccCcccCC---CC
Q 020472 143 IAVHS--------MKDVP-TYLPE-------------KTILPCNLQREDVRD--AFISLS-------AASLAELP---AG 188 (326)
Q Consensus 143 iAVHS--------lKDlP-t~lp~-------------gL~iaAv~kReDprD--~LV~~~-------~~~l~dLp---~g 188 (326)
|-+-= +|.=| ....+ ...+ -.+++-..+| +|..++ -.+++||- ++
T Consensus 86 iYpEYTGt~~~~~lk~~~~~~~dp~~~y~~vK~~~~k~~~l-~wl~p~~~nNTyA~av~~~~A~~~~i~TiSDLak~~~~ 164 (300)
T COG1732 86 IYPEYTGTALFSFLKKDPPASKDPKKVYETVKKLDAKQFKL-VWLKPAGFNNTYALAVRKDVAEKYNLETISDLAKHSNQ 164 (300)
T ss_pred eEeeecchhhhhhcccCccccCCHHHHHHHHHHHHHhcCCE-EEecccCCCcceEEEecHHHHHHhCCccHHHHHHhhhh
Confidence 98531 23211 11111 1111 1233333333 343321 13455653 34
Q ss_pred CEEecCChH--H----HHHHHhhCCCCE--EEeccCCCHHHHHhhhccCCccEEee--ehhhhcccCCCccceeeecCCC
Q 020472 189 SIVGTASLR--R----KSQILHRYPSLK--VMENFRGNVQTRLRKLNERVVQATLL--ALAGLKRLSMTENVTNILSVDD 258 (326)
Q Consensus 189 a~IGTSS~R--R----~aQL~~~~Pdl~--v~~~iRGNV~TRL~KL~~ge~DAIIL--A~AGL~RLgl~~~i~~~L~~~~ 258 (326)
-+.|.++-= | .+.-+.+--++. +. .+-+. =+.+-+.+|+.|++.. --+.|.+.|+. +|.-+.
T Consensus 165 l~~g~~~eF~~R~DG~~~l~k~Yg~~~~~~~~-~m~~g--l~y~Al~~g~~d~~~~YsTDg~I~~~~L~-----VLkDDK 236 (300)
T COG1732 165 LKLGADSEFAERADGLPALQKAYGFDFKPDLR-TMDGG--LTYQALKNGTVDAADAYSTDGRIAAYGLK-----VLKDDK 236 (300)
T ss_pred ceecCChhhhccccccHHHHHHhCCccCCCce-ecCch--HHHHHHHcCCCCeEeeccccccccccCcE-----EEecCC
Confidence 577777632 2 123333322222 44 55544 6788899999998765 22357777763 222222
Q ss_pred CCCCcccceeee--EeecCchhHHhhhhccc
Q 020472 259 MLPAVAQGAIGI--ACRSNDEKMVPFTTHSQ 287 (326)
Q Consensus 259 ~lPA~GQGaLAV--e~R~dD~~~~~lL~~~~ 287 (326)
=.=+|-|++.-| ++-++.+++.++|+.+.
T Consensus 237 ~~fP~Y~~apvvre~vlk~~Pel~~~l~~l~ 267 (300)
T COG1732 237 GFFPPYQAAPVVREEVLKKHPELKTILNKLS 267 (300)
T ss_pred cCCCCCcccceecHHHHhHCHHHHHHHHHHh
Confidence 122345555444 45567788888887664
No 261
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=20.79 E-value=1.7e+02 Score=28.06 Aligned_cols=42 Identities=17% Similarity=0.191 Sum_probs=36.2
Q ss_pred hHHHHHHHhhCCCCEEEeccCCCHHHHHhhhccCCccEEeeeh
Q 020472 196 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 238 (326)
Q Consensus 196 ~RR~aQL~~~~Pdl~v~~~iRGNV~TRL~KL~~ge~DAIILA~ 238 (326)
+.....+...||++++. -.-|+-+.=++.|.+|++|..|+..
T Consensus 109 ~~~l~~f~~~~P~v~i~-l~~~~~~~~~~~l~~g~~Dl~i~~~ 150 (327)
T PRK12680 109 PPAVAQIKQAYPQVSVH-LQQAAESAALDLLGQGDADIAIVST 150 (327)
T ss_pred HHHHHHHHHHCCCcEEE-EEeCChHHHHHHHHCCCCcEEEEec
Confidence 45677788999999998 8889999999999999999998753
Done!