Query 026500
Match_columns 237
No_of_seqs 129 out of 1024
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:49:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026500.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026500hhsearch_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 8.6E-83 1.9E-87 581.9 14.8 211 2-224 27-237 (307)
2 TIGR00212 hemC porphobilinogen 100.0 4.9E-82 1.1E-86 575.8 17.7 211 2-224 24-234 (292)
3 cd00494 HMBS Hydroxymethylbila 100.0 3.1E-81 6.8E-86 570.5 18.3 211 2-224 24-234 (292)
4 PRK00072 hemC porphobilinogen 100.0 4.2E-81 9.2E-86 570.3 17.5 211 2-224 28-238 (295)
5 PLN02691 porphobilinogen deami 100.0 9.3E-80 2E-84 571.4 18.5 214 3-224 68-281 (351)
6 PF01379 Porphobil_deam: Porph 100.0 3.3E-79 7.2E-84 536.9 14.4 189 2-195 25-215 (215)
7 PRK01066 porphobilinogen deami 100.0 1.6E-76 3.4E-81 523.9 17.0 187 2-198 41-227 (231)
8 KOG2892 Porphobilinogen deamin 100.0 1.3E-69 2.8E-74 489.4 8.7 211 2-224 31-245 (320)
9 TIGR00363 lipoprotein, YaeC fa 96.2 0.016 3.4E-07 52.5 7.1 154 42-203 58-243 (258)
10 PRK11063 metQ DL-methionine tr 96.1 0.027 5.8E-07 51.2 8.1 146 41-200 70-253 (271)
11 PRK11260 cystine transporter s 95.7 0.1 2.3E-06 45.5 9.8 145 41-196 90-241 (266)
12 TIGR01096 3A0103s03R lysine-ar 95.6 0.2 4.3E-06 42.5 11.0 148 41-196 73-231 (250)
13 smart00062 PBPb Bacterial peri 95.5 0.19 4.2E-06 39.3 9.8 106 41-152 49-158 (219)
14 PF00497 SBP_bac_3: Bacterial 95.4 0.018 3.9E-07 46.8 3.7 142 41-195 48-203 (225)
15 TIGR01729 taurine_ABC_bnd taur 95.3 0.04 8.7E-07 49.1 6.0 110 41-154 38-160 (300)
16 PRK15007 putative ABC transpor 95.0 0.46 9.9E-06 40.3 11.4 148 41-196 70-222 (243)
17 cd00134 PBPb Bacterial peripla 94.9 0.37 7.9E-06 37.9 9.8 145 40-194 47-197 (218)
18 PRK15010 ABC transporter lysin 94.3 0.96 2.1E-05 39.3 11.9 146 41-196 75-234 (260)
19 TIGR03427 ABC_peri_uca ABC tra 94.0 0.45 9.8E-06 44.4 9.7 102 43-150 48-162 (328)
20 PRK09861 cytoplasmic membrane 93.7 0.18 4E-06 45.9 6.4 145 43-203 73-257 (272)
21 COG0834 HisJ ABC-type amino ac 93.3 0.69 1.5E-05 39.4 9.0 109 41-154 87-202 (275)
22 PRK09959 hybrid sensory histid 93.3 0.68 1.5E-05 48.9 10.7 144 40-195 351-500 (1197)
23 PF14503 YhfZ_C: YhfZ C-termin 93.2 0.64 1.4E-05 42.2 8.9 144 45-197 57-210 (232)
24 PRK09959 hybrid sensory histid 93.1 0.57 1.2E-05 49.5 9.8 141 41-195 107-257 (1197)
25 TIGR01098 3A0109s03R phosphate 92.6 0.75 1.6E-05 39.4 8.3 110 41-153 75-206 (254)
26 PRK11480 tauA taurine transpor 92.1 0.3 6.5E-06 44.4 5.5 107 42-152 63-180 (320)
27 TIGR01728 SsuA_fam ABC transpo 91.7 1.5 3.2E-05 37.7 9.0 108 42-154 41-161 (288)
28 TIGR02995 ectoine_ehuB ectoine 91.3 1.5 3.2E-05 38.6 8.9 145 42-195 83-240 (275)
29 PRK10859 membrane-bound lytic 90.8 0.98 2.1E-05 43.9 7.9 105 41-150 91-204 (482)
30 PF13379 NMT1_2: NMT1-like fam 90.5 0.41 8.8E-06 41.7 4.5 128 41-173 46-202 (252)
31 COG0715 TauA ABC-type nitrate/ 90.4 2 4.3E-05 38.5 8.9 112 42-157 73-200 (335)
32 PF09084 NMT1: NMT1/THI5 like; 89.3 0.5 1.1E-05 39.5 3.9 105 42-151 33-150 (216)
33 PRK00489 hisG ATP phosphoribos 88.7 2.1 4.6E-05 38.8 7.9 101 41-147 54-158 (287)
34 PRK11553 alkanesulfonate trans 88.6 2.1 4.5E-05 38.4 7.7 103 41-149 67-184 (314)
35 PF02621 VitK2_biosynth: Menaq 86.7 2.9 6.3E-05 37.4 7.4 101 40-147 33-140 (251)
36 PRK11917 bifunctional adhesin/ 85.2 14 0.0003 32.5 10.9 142 43-197 93-242 (259)
37 cd08429 PBP2_NhaR The C-termin 81.2 3.7 8.1E-05 33.4 5.3 41 107-148 16-56 (204)
38 cd08449 PBP2_XapR The C-termin 80.7 4 8.7E-05 31.6 5.1 42 107-149 16-57 (197)
39 cd08467 PBP2_SyrM The C-termin 80.6 3.4 7.5E-05 32.8 4.8 49 99-148 1-56 (200)
40 cd08412 PBP2_PAO1_like The C-t 80.2 4.5 9.8E-05 31.3 5.3 42 107-149 16-57 (198)
41 cd08452 PBP2_AlsR The C-termin 79.7 4.3 9.3E-05 32.1 5.1 41 107-148 16-56 (197)
42 PRK09495 glnH glutamine ABC tr 79.1 11 0.00023 32.3 7.7 104 41-150 73-181 (247)
43 TIGR03431 PhnD phosphonate ABC 78.8 5 0.00011 35.4 5.7 108 41-151 70-198 (288)
44 cd08427 PBP2_LTTR_like_2 The C 78.1 4.8 0.0001 31.1 4.8 41 108-149 17-57 (195)
45 cd08453 PBP2_IlvR The C-termin 77.3 6.2 0.00013 30.9 5.3 47 101-148 3-56 (200)
46 cd08465 PBP2_ToxR The C-termin 77.3 6.1 0.00013 31.5 5.3 41 108-149 17-57 (200)
47 PRK10797 glutamate and asparta 77.1 18 0.00038 32.9 8.8 138 42-195 97-250 (302)
48 cd08466 PBP2_LeuO The C-termin 76.7 6.7 0.00015 30.6 5.3 40 108-148 17-56 (200)
49 cd08458 PBP2_NocR The C-termin 76.3 7.6 0.00016 30.6 5.6 41 107-148 16-56 (196)
50 cd08411 PBP2_OxyR The C-termin 76.2 6.8 0.00015 30.6 5.2 47 101-148 4-57 (200)
51 cd08450 PBP2_HcaR The C-termin 75.1 7 0.00015 30.3 5.0 41 107-148 16-56 (196)
52 PRK15437 histidine ABC transpo 74.6 22 0.00048 30.8 8.5 101 42-149 76-184 (259)
53 cd08418 PBP2_TdcA The C-termin 74.1 9 0.00019 29.7 5.4 41 107-148 16-56 (201)
54 cd08431 PBP2_HupR The C-termin 73.7 5.6 0.00012 31.0 4.2 40 108-148 17-56 (195)
55 cd08421 PBP2_LTTR_like_1 The C 73.7 11 0.00024 29.2 5.8 41 108-149 17-57 (198)
56 cd08442 PBP2_YofA_SoxR_like Th 73.1 8.5 0.00018 29.7 5.0 40 108-148 17-56 (193)
57 cd08439 PBP2_LrhA_like The C-t 73.1 9.6 0.00021 29.7 5.4 40 108-148 17-56 (185)
58 cd08448 PBP2_LTTR_aromatics_li 73.1 9.7 0.00021 29.3 5.3 40 108-148 17-56 (197)
59 cd08464 PBP2_DntR_like_2 The C 72.6 6.5 0.00014 30.6 4.3 41 108-149 17-57 (200)
60 cd08415 PBP2_LysR_opines_like 72.6 10 0.00022 29.3 5.3 42 108-150 17-58 (196)
61 cd08486 PBP2_CbnR The C-termin 72.4 8.1 0.00018 30.8 4.9 40 108-148 18-57 (198)
62 PF12974 Phosphonate-bd: ABC t 72.2 0.54 1.2E-05 40.6 -2.2 113 41-156 40-172 (243)
63 cd08456 PBP2_LysR The C-termin 71.9 9.9 0.00021 29.5 5.1 41 107-148 16-56 (196)
64 cd05466 PBP2_LTTR_substrate Th 71.6 11 0.00024 28.3 5.2 49 101-150 3-58 (197)
65 cd08413 PBP2_CysB_like The C-t 71.2 11 0.00023 29.9 5.3 41 107-148 16-56 (198)
66 cd08447 PBP2_LTTR_aromatics_li 71.1 10 0.00022 29.4 5.1 40 108-148 17-56 (198)
67 cd08443 PBP2_CysB The C-termin 71.0 11 0.00023 30.0 5.2 41 107-148 16-56 (198)
68 cd08430 PBP2_IlvY The C-termin 69.9 12 0.00027 28.9 5.3 41 107-148 16-56 (199)
69 cd08423 PBP2_LTTR_like_6 The C 69.8 12 0.00026 28.9 5.2 42 107-149 16-57 (200)
70 cd08440 PBP2_LTTR_like_4 TThe 67.4 16 0.00035 27.9 5.4 41 108-149 17-57 (197)
71 cd08446 PBP2_Chlorocatechol Th 67.3 15 0.00032 28.6 5.3 40 108-148 18-57 (198)
72 cd08416 PBP2_MdcR The C-termin 67.2 13 0.00028 28.9 4.9 42 107-149 16-57 (199)
73 TIGR03870 ABC_MoxJ methanol ox 66.8 25 0.00055 30.4 7.1 19 130-148 152-170 (246)
74 cd08441 PBP2_MetR The C-termin 66.1 12 0.00026 29.2 4.6 40 108-148 17-56 (198)
75 cd08444 PBP2_Cbl The C-termina 65.7 16 0.00036 28.8 5.3 41 107-148 16-56 (198)
76 cd08438 PBP2_CidR The C-termin 65.4 15 0.00033 28.2 5.0 42 107-149 16-57 (197)
77 TIGR00787 dctP tripartite ATP- 65.2 52 0.0011 28.9 8.9 114 40-161 43-194 (257)
78 cd08445 PBP2_BenM_CatM_CatR Th 64.8 15 0.00033 28.9 5.0 39 108-147 18-56 (203)
79 cd08425 PBP2_CynR The C-termin 64.8 18 0.00038 28.2 5.2 42 107-149 17-58 (197)
80 cd08457 PBP2_OccR The C-termin 64.6 14 0.00031 28.9 4.7 42 107-149 16-57 (196)
81 cd08434 PBP2_GltC_like The sub 62.6 20 0.00044 27.4 5.2 41 108-149 17-57 (195)
82 PRK04056 Maf-like protein; Rev 60.8 8.7 0.00019 33.2 3.1 23 101-123 3-25 (180)
83 cd08437 PBP2_MleR The substrat 60.6 22 0.00049 27.7 5.2 42 107-149 16-57 (198)
84 TIGR02122 TRAP_TAXI TRAP trans 60.3 16 0.00035 32.2 4.8 103 41-148 72-197 (320)
85 PRK04694 Maf-like protein; Rev 60.1 9.3 0.0002 33.3 3.1 23 101-123 3-25 (190)
86 cd08433 PBP2_Nac The C-teminal 60.0 22 0.00048 27.6 5.1 40 108-148 17-56 (198)
87 cd08462 PBP2_NodD The C-termin 59.8 20 0.00044 28.2 4.9 37 110-148 19-55 (200)
88 PRK00078 Maf-like protein; Rev 59.7 9.4 0.0002 33.3 3.1 23 101-123 4-26 (192)
89 cd08420 PBP2_CysL_like C-termi 59.6 24 0.00053 27.0 5.1 41 107-148 16-56 (201)
90 PRK11716 DNA-binding transcrip 58.2 23 0.00051 29.9 5.2 39 109-148 85-123 (269)
91 PF03180 Lipoprotein_9: NLPA l 57.0 2.7 5.9E-05 37.9 -0.8 152 42-203 38-222 (237)
92 cd08451 PBP2_BudR The C-termin 55.5 28 0.00061 26.9 4.9 41 107-148 17-57 (199)
93 PRK14363 Maf-like protein; Pro 54.4 13 0.00027 33.0 3.0 23 101-123 4-26 (204)
94 PRK00032 Maf-like protein; Rev 54.3 13 0.00028 32.4 3.1 24 100-123 4-27 (190)
95 PRK00148 Maf-like protein; Rev 54.0 13 0.00029 32.4 3.1 24 100-123 3-26 (194)
96 cd08459 PBP2_DntR_NahR_LinR_li 54.0 21 0.00046 27.9 4.1 41 108-149 17-57 (201)
97 PRK02478 Maf-like protein; Rev 53.9 13 0.00029 32.6 3.1 24 100-123 5-28 (199)
98 TIGR03871 ABC_peri_MoxJ_2 quin 53.2 1.3E+02 0.0029 25.0 10.2 21 129-149 142-162 (232)
99 PRK00234 Maf-like protein; Rev 52.8 15 0.00032 32.1 3.2 24 100-123 4-27 (192)
100 cd08436 PBP2_LTTR_like_3 The C 52.4 34 0.00074 26.2 4.9 41 108-149 17-57 (194)
101 cd08426 PBP2_LTTR_like_5 The C 52.1 26 0.00057 27.1 4.3 40 108-148 17-56 (199)
102 PF03466 LysR_substrate: LysR 51.9 20 0.00044 28.1 3.6 43 108-151 23-65 (209)
103 TIGR00172 maf MAF protein. Thi 51.8 16 0.00036 31.6 3.3 25 99-123 4-28 (183)
104 PRK14368 Maf-like protein; Pro 51.4 15 0.00033 32.1 3.1 24 100-123 7-30 (193)
105 cd08417 PBP2_Nitroaromatics_li 51.3 29 0.00063 26.9 4.4 42 108-150 17-58 (200)
106 cd08414 PBP2_LTTR_aromatics_li 51.3 36 0.00078 26.1 4.9 40 108-148 17-56 (197)
107 cd08435 PBP2_GbpR The C-termin 51.3 32 0.0007 26.5 4.6 41 107-148 16-56 (201)
108 TIGR03339 phn_lysR aminoethylp 51.0 35 0.00076 29.1 5.2 38 109-147 102-139 (279)
109 PRK04425 Maf-like protein; Rev 51.0 16 0.00035 32.1 3.1 24 100-123 7-30 (196)
110 PRK14361 Maf-like protein; Pro 50.9 16 0.00035 31.8 3.1 23 101-123 2-24 (187)
111 PRK14365 Maf-like protein; Pro 50.1 15 0.00032 32.3 2.8 24 100-123 4-28 (197)
112 PRK01839 Maf-like protein; Rev 50.0 17 0.00036 32.2 3.1 25 99-123 11-35 (209)
113 PRK00884 Maf-like protein; Rev 49.7 18 0.0004 31.7 3.3 24 100-123 4-27 (194)
114 PRK14362 Maf-like protein; Pro 49.7 18 0.00039 32.1 3.3 25 99-123 13-37 (207)
115 cd00555 Maf Nucleotide binding 49.5 16 0.00035 31.4 2.9 23 101-123 2-24 (180)
116 cd08461 PBP2_DntR_like_3 The C 49.3 25 0.00053 27.3 3.7 41 107-148 16-56 (198)
117 PRK12679 cbl transcriptional r 49.1 40 0.00087 30.2 5.5 42 107-149 109-150 (316)
118 TIGR02136 ptsS_2 phosphate bin 48.7 21 0.00046 32.1 3.6 47 101-148 39-91 (287)
119 PRK14367 Maf-like protein; Pro 48.5 18 0.00039 31.8 3.1 24 100-123 4-27 (202)
120 cd08460 PBP2_DntR_like_1 The C 48.3 37 0.00079 26.7 4.6 39 108-148 17-55 (200)
121 PF03466 LysR_substrate: LysR 47.9 1.3E+02 0.0029 23.4 8.5 98 41-145 45-154 (209)
122 PRK03601 transcriptional regul 47.6 39 0.00085 29.6 5.1 41 107-148 105-145 (275)
123 PF03480 SBP_bac_7: Bacterial 46.0 87 0.0019 27.8 7.1 119 41-167 44-200 (286)
124 PF02545 Maf: Maf-like protein 45.8 12 0.00027 32.6 1.6 31 101-134 4-34 (195)
125 PRK02141 Maf-like protein; Rev 45.4 22 0.00049 31.5 3.2 25 99-123 10-34 (207)
126 cd08485 PBP2_ClcR The C-termin 45.2 44 0.00094 26.4 4.6 40 108-148 18-57 (198)
127 PRK14364 Maf-like protein; Pro 44.6 18 0.0004 31.3 2.4 22 102-123 1-22 (181)
128 PRK14366 Maf-like protein; Pro 44.1 25 0.00054 30.9 3.3 24 100-123 7-31 (195)
129 PRK00648 Maf-like protein; Rev 44.1 23 0.0005 30.8 3.0 24 100-123 5-28 (191)
130 cd00985 Maf_Ham1 Maf_Ham1. Maf 43.1 25 0.00055 27.7 2.9 23 101-123 2-25 (131)
131 cd08468 PBP2_Pa0477 The C-term 41.2 42 0.00092 26.4 3.9 41 108-149 17-57 (202)
132 KOG0463 GTP-binding protein GP 40.9 15 0.00032 36.6 1.4 57 173-229 304-362 (641)
133 cd08419 PBP2_CbbR_RubisCO_like 40.5 48 0.001 25.4 4.1 38 110-148 18-55 (197)
134 COG3265 GntK Gluconate kinase 40.4 39 0.00084 29.3 3.7 40 99-139 69-110 (161)
135 PRK10341 DNA-binding transcrip 39.8 67 0.0014 28.6 5.4 42 108-150 114-155 (312)
136 PRK12680 transcriptional regul 39.8 68 0.0015 29.2 5.5 42 107-149 109-150 (327)
137 PRK01526 Maf-like protein; Rev 39.5 32 0.00069 30.4 3.2 24 100-123 10-34 (205)
138 PRK09508 leuO leucine transcri 37.9 64 0.0014 28.7 4.9 42 107-149 128-169 (314)
139 cd08463 PBP2_DntR_like_4 The C 37.8 66 0.0014 25.7 4.7 38 110-148 19-57 (203)
140 PRK10837 putative DNA-binding 37.6 73 0.0016 27.5 5.1 40 108-148 106-145 (290)
141 cd08437 PBP2_MleR The substrat 37.5 1.9E+02 0.0041 22.3 8.0 103 40-148 38-152 (198)
142 PRK12684 transcriptional regul 37.3 75 0.0016 28.4 5.3 41 108-149 110-150 (313)
143 PRK11151 DNA-binding transcrip 36.9 83 0.0018 27.7 5.5 40 109-149 109-148 (305)
144 PRK12683 transcriptional regul 36.2 79 0.0017 28.3 5.3 39 108-147 110-148 (309)
145 cd08479 PBP2_CrgA_like_9 The C 35.8 51 0.0011 25.5 3.6 44 101-148 4-54 (198)
146 cd08478 PBP2_CrgA The C-termin 35.3 30 0.00065 27.0 2.2 37 108-148 20-56 (199)
147 COG0424 Maf Nucleotide-binding 35.0 39 0.00085 29.9 3.1 24 100-123 5-28 (193)
148 cd08469 PBP2_PnbR The C-termin 34.5 64 0.0014 25.8 4.0 41 108-149 17-57 (221)
149 TIGR02424 TF_pcaQ pca operon t 34.2 88 0.0019 27.3 5.2 40 107-147 109-148 (300)
150 cd08417 PBP2_Nitroaromatics_li 34.2 54 0.0012 25.3 3.5 20 41-60 39-58 (200)
151 PF04422 FrhB_FdhB_N: Coenzyme 32.6 41 0.00088 25.2 2.4 23 37-59 21-43 (82)
152 cd08436 PBP2_LTTR_like_3 The C 31.7 64 0.0014 24.6 3.5 100 40-146 38-150 (194)
153 PF01634 HisG: ATP phosphoribo 31.5 65 0.0014 27.6 3.8 52 91-146 59-111 (163)
154 cd08452 PBP2_AlsR The C-termin 31.5 62 0.0013 25.3 3.5 20 40-59 38-57 (197)
155 cd08453 PBP2_IlvR The C-termin 31.3 91 0.002 24.2 4.4 98 40-141 38-149 (200)
156 PRK01441 Maf-like protein; Rev 31.3 52 0.0011 29.0 3.2 21 99-119 6-26 (207)
157 cd08466 PBP2_LeuO The C-termin 31.1 59 0.0013 25.2 3.3 19 41-59 39-57 (200)
158 cd08428 PBP2_IciA_ArgP The C-t 31.0 86 0.0019 24.3 4.2 39 108-148 17-55 (195)
159 cd08467 PBP2_SyrM The C-termin 30.9 46 0.001 26.3 2.6 19 41-59 39-57 (200)
160 cd08440 PBP2_LTTR_like_4 TThe 30.5 68 0.0015 24.4 3.4 94 41-141 39-144 (197)
161 PRK15421 DNA-binding transcrip 30.1 81 0.0017 28.4 4.3 41 107-148 105-145 (317)
162 PRK10094 DNA-binding transcrip 29.9 96 0.0021 27.7 4.8 39 108-147 110-148 (308)
163 PRK09791 putative DNA-binding 29.6 82 0.0018 27.7 4.2 40 108-148 112-151 (302)
164 cd08438 PBP2_CidR The C-termin 29.6 68 0.0015 24.5 3.3 19 41-59 39-57 (197)
165 PRK09906 DNA-binding transcrip 29.4 79 0.0017 27.5 4.1 41 108-149 107-147 (296)
166 PRK12682 transcriptional regul 29.2 1E+02 0.0022 27.3 4.8 41 108-149 110-150 (309)
167 PRK11062 nhaR transcriptional 29.1 1.1E+02 0.0024 26.9 5.0 39 108-147 110-148 (296)
168 cd08456 PBP2_LysR The C-termin 28.9 76 0.0017 24.4 3.5 19 41-59 39-57 (196)
169 cd08419 PBP2_CbbR_RubisCO_like 28.7 73 0.0016 24.4 3.4 20 40-59 37-56 (197)
170 PRK11242 DNA-binding transcrip 28.1 94 0.002 26.9 4.3 40 108-148 108-147 (296)
171 COG0604 Qor NADPH:quinone redu 27.9 1.2E+02 0.0025 28.2 5.1 62 101-163 171-239 (326)
172 cd08439 PBP2_LrhA_like The C-t 27.5 60 0.0013 25.2 2.7 20 40-59 38-57 (185)
173 cd08420 PBP2_CysL_like C-termi 27.5 71 0.0015 24.3 3.1 95 41-142 39-148 (201)
174 cd08447 PBP2_LTTR_aromatics_li 26.6 85 0.0018 24.2 3.4 95 40-142 38-147 (198)
175 COG2107 Predicted periplasmic 26.2 4.9E+02 0.011 24.5 8.7 102 40-147 38-142 (272)
176 cd08412 PBP2_PAO1_like The C-t 26.0 95 0.0021 23.8 3.6 96 40-142 38-144 (198)
177 PRK11074 putative DNA-binding 25.8 1.1E+02 0.0024 27.0 4.3 41 107-148 108-148 (300)
178 cd08448 PBP2_LTTR_aromatics_li 25.3 98 0.0021 23.6 3.5 20 40-59 38-57 (197)
179 PRK10343 RNA-binding protein Y 25.1 55 0.0012 26.0 2.0 25 28-52 19-46 (97)
180 cd08422 PBP2_CrgA_like The C-t 24.9 1E+02 0.0022 23.5 3.5 38 107-148 17-54 (197)
181 cd08474 PBP2_CrgA_like_5 The C 23.7 1E+02 0.0022 23.9 3.4 44 101-148 6-56 (202)
182 cd08433 PBP2_Nac The C-teminal 23.5 1E+02 0.0022 23.8 3.3 20 41-60 39-58 (198)
183 COG4623 Predicted soluble lyti 23.0 1.3E+02 0.0027 30.1 4.4 107 41-154 71-189 (473)
184 cd05466 PBP2_LTTR_substrate Th 22.9 3.2E+02 0.0069 20.2 9.4 97 41-145 39-148 (197)
185 cd08481 PBP2_GcdR_like The C-t 22.8 94 0.002 23.7 3.0 36 109-148 18-53 (194)
186 PRK11013 DNA-binding transcrip 22.7 1.9E+02 0.0041 25.6 5.3 40 108-148 111-150 (309)
187 CHL00180 rbcR LysR transcripti 22.7 1.3E+02 0.0028 26.6 4.2 39 109-148 113-151 (305)
188 TIGR00253 RNA_bind_YhbY putati 22.3 68 0.0015 25.2 2.1 35 28-63 17-54 (95)
189 PRK09986 DNA-binding transcrip 21.7 3.7E+02 0.0081 23.1 6.8 103 40-146 135-249 (294)
190 cd08486 PBP2_CbnR The C-termin 21.7 79 0.0017 25.0 2.4 95 40-141 39-147 (198)
191 PRK11013 DNA-binding transcrip 21.3 1.1E+02 0.0024 27.1 3.5 21 41-61 133-153 (309)
192 cd08421 PBP2_LTTR_like_1 The C 21.2 1.2E+02 0.0025 23.4 3.2 94 41-142 39-145 (198)
193 cd08483 PBP2_HvrB The C-termin 20.9 93 0.002 23.8 2.6 37 108-148 17-53 (190)
194 PF00107 ADH_zinc_N: Zinc-bind 20.4 2.5E+02 0.0053 21.2 4.9 48 102-150 19-67 (130)
195 PF06711 DUF1198: Protein of u 20.3 59 0.0013 27.8 1.4 35 98-137 15-49 (148)
196 cd08432 PBP2_GcdR_TrpI_HvrB_Am 20.2 95 0.0021 23.7 2.5 35 110-148 19-53 (194)
197 CHL00180 rbcR LysR transcripti 20.2 2.3E+02 0.0049 25.0 5.2 106 40-150 133-253 (305)
198 cd08469 PBP2_PnbR The C-termin 20.0 1.2E+02 0.0026 24.2 3.2 20 41-60 39-58 (221)
No 1
>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism]
Probab=100.00 E-value=8.6e-83 Score=581.89 Aligned_cols=211 Identities=49% Similarity=0.794 Sum_probs=203.7
Q ss_pred CCCCCCCCCCcEEEEEEeecCcccCCccccccCcccccHHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCC
Q 026500 2 ALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDV 81 (237)
Q Consensus 2 ~~~p~l~~~~~~eiv~i~T~GD~~~~~~L~~iggkGlFtkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dp 81 (237)
+.||++ +|||++|+|+||+++|+||+++||||+||||||+||++|+||+|||||||||+++|+||.++||++|+||
T Consensus 27 ~~~p~~----~~ei~~i~T~GD~i~d~pL~~iGgkGlFtkEle~all~g~~DiAVHSlKDvP~~~p~gL~laai~~R~dp 102 (307)
T COG0181 27 AAYPDL----EVEIVTIKTKGDRILDKPLSKIGGKGLFTKELEQALLEGEIDIAVHSLKDVPTELPEGLVLAAIPEREDP 102 (307)
T ss_pred HhCCCc----eEEEEEEecccchhccchHHHcCCcEEEHHHHHHHHHcCCCCEEEeecccCCccCCCCceEEEecCCCCh
Confidence 467877 7999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEeCCCCCCccCCCCCeeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcc
Q 026500 82 RDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENV 161 (237)
Q Consensus 82 rD~LV~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i 161 (237)
||+||++++.+|.+||+||+|||||+||+|||+++|||++|+ ++||||+|||+||++|+|||||||+|||+|||+++++
T Consensus 103 rDalVs~~~~~l~~LP~Ga~VGTSSlRR~aql~~~rPdl~i~-~lRGNVdTRL~KL~~g~yDAIILA~AGL~RLgl~~~~ 181 (307)
T COG0181 103 RDALVSRDGYDLEELPEGAVVGTSSLRRQAQLKALRPDLKIE-PLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLENRI 181 (307)
T ss_pred hheEEECCCCchhhCCCCCccccchHHHHHHHHHhCCCCeEE-eccCcHHHHHHHhhcCCccHHHHHHHHHHhcCCcccc
Confidence 999999999999999999999999999999999999999998 9999999999999999999999999999999999999
Q ss_pred eeeecCCCCCCCCCCceEEEEEecCchhhhhhhcccccccccccccccchhHHHHHHHHhhhh
Q 026500 162 TNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKLHFGFLNLVE 224 (237)
Q Consensus 162 ~~~l~~~~~lPA~GQGalave~R~~d~~~~~~l~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~ 224 (237)
+++|+|+.|+|||||||||||||.+|+++.++|+.++ +-.+..|+..||.|++-|+
T Consensus 182 ~~~l~p~~~~PA~gQGal~ie~R~~d~~~~~ll~~i~-------~~~t~~~v~aERa~l~~L~ 237 (307)
T COG0181 182 TEILDPEEFLPAPGQGALAIECRAGDEKVLELLAELN-------DEDTRICVTAERAFLRELE 237 (307)
T ss_pred eeecChhhcCCCCCCceEEEEEecCcHHHHHHHHhcc-------CchHHHHHHHHHHHHHhhC
Confidence 9999999999999999999999999999999998887 4447889999999999876
No 2
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=100.00 E-value=4.9e-82 Score=575.77 Aligned_cols=211 Identities=48% Similarity=0.727 Sum_probs=202.4
Q ss_pred CCCCCCCCCCcEEEEEEeecCcccCCccccccCcccccHHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCC
Q 026500 2 ALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDV 81 (237)
Q Consensus 2 ~~~p~l~~~~~~eiv~i~T~GD~~~~~~L~~iggkGlFtkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dp 81 (237)
+.||++ ++|+++|+|+||+++++||+++||||+||||||+||++|+||||||||||||+++|+||+|+||++|+||
T Consensus 24 ~~~p~~----~~ei~~i~T~GD~~~~~~L~~iGgkGlFtkele~aLl~g~iDiAVHSlKDlPt~lp~gl~i~av~~Redp 99 (292)
T TIGR00212 24 AVYPEL----DTEIVIIKTTGDKIQDKPLYDIGGKGLFTKELEQALLDGEIDLAVHSLKDVPTVLPEGLEIAAVLKREDP 99 (292)
T ss_pred HhCCCc----eEEEEEEeeeCcccccCcHHHcCCceeeHHHHHHHHhcCCCCEEEeccccCCCCCCCCcEEEEEecCCCC
Confidence 347877 7999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEeCCCCCCccCCCCCeeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcc
Q 026500 82 RDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENV 161 (237)
Q Consensus 82 rD~LV~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i 161 (237)
||+||++++.++++||+|++|||||+||++||+++|||++|+ ++||||+|||+||++|+|||||||+|||+|||+.+++
T Consensus 100 rD~lv~~~~~~l~~Lp~ga~VGTsS~RR~aql~~~rPdl~i~-~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLgl~~~i 178 (292)
T TIGR00212 100 RDVLVSRKYLSLDSLPQGAKVGTSSLRRKAQLKAIRPDLKIE-PLRGNIDTRLRKLDEGEYDAIILAEAGLKRLGLEDVI 178 (292)
T ss_pred ceEEEECCCCChhHCCCCCEeccCCHHHHHHHHHHCCCCEEE-ECcCCHHHHHHHhcCCCCCEeehHhhHHHhCCCcccc
Confidence 999999998999999999999999999999999999999999 9999999999999999999999999999999999999
Q ss_pred eeeecCCCCCCCCCCceEEEEEecCchhhhhhhcccccccccccccccchhHHHHHHHHhhhh
Q 026500 162 TNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKLHFGFLNLVE 224 (237)
Q Consensus 162 ~~~l~~~~~lPA~GQGalave~R~~d~~~~~~l~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~ 224 (237)
+++|++++|+||||||+||||||++|.++.++++.++ +=.+..|...||.||+.|+
T Consensus 179 ~~~l~~~~~~PA~gQGalaIe~r~~d~~~~~ll~~l~-------d~~t~~~~~aER~~l~~L~ 234 (292)
T TIGR00212 179 TEVLDPEVMLPAPGQGAIAVECRKDDTEIKEILKEIN-------HPPTRVEATAERAFLKELG 234 (292)
T ss_pred ccccChhhcCCccccceEEEEEecCCHHHHHHHHHcC-------CHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999999999999998776 3347889999999999876
No 3
>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=3.1e-81 Score=570.50 Aligned_cols=211 Identities=53% Similarity=0.815 Sum_probs=202.4
Q ss_pred CCCCCCCCCCcEEEEEEeecCcccCCccccccCcccccHHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCC
Q 026500 2 ALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDV 81 (237)
Q Consensus 2 ~~~p~l~~~~~~eiv~i~T~GD~~~~~~L~~iggkGlFtkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dp 81 (237)
+++|++ ++|+++|+|+||+++++||+++||||+||||||+||++|+||||||||||||+++|+||.++||++|+||
T Consensus 24 ~~~p~~----~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVHSlKDlP~~lp~gl~i~av~~Redp 99 (292)
T cd00494 24 ELCPGI----EVEIVIIKTTGDKILDKPLAKIGGKGLFTKELEEALLNGEIDLAVHSLKDVPTELPEGLVLGAIPKREDP 99 (292)
T ss_pred HhCCCC----eEEEEEEEecCcccccccHHHcCCcceeHHHHHHHHHcCCCCEEEeccccCCCCCCCCcEEEEEecCCCC
Confidence 357877 7999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEeCCCCCCccCCCCCeeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcc
Q 026500 82 RDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENV 161 (237)
Q Consensus 82 rD~LV~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i 161 (237)
|||||++++.++++||+|++|||||+||++||+++|||++|+ ++||||+|||+||++|+|||||||+|||+|||+.+++
T Consensus 100 rDvlv~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~rpdl~~~-~iRGNV~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~ 178 (292)
T cd00494 100 RDALVSRNGSSLEDLPAGSVVGTSSLRRQAQLKRKRPDLKFE-PLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRI 178 (292)
T ss_pred ceEEEECCCCChhHCCCCCEEecCCHHHHHHHHHHCCCCEEE-EcCCCHHHHHHHhcCCCCCEeehHhhHHHHcCCcccC
Confidence 999999998899999999999999999999999999999999 9999999999999999999999999999999999999
Q ss_pred eeeecCCCCCCCCCCceEEEEEecCchhhhhhhcccccccccccccccchhHHHHHHHHhhhh
Q 026500 162 TNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKLHFGFLNLVE 224 (237)
Q Consensus 162 ~~~l~~~~~lPA~GQGalave~R~~d~~~~~~l~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~ 224 (237)
+++|++++|+||||||+||||||++|+++.++|+.++ +=.+..|...||.||..|+
T Consensus 179 ~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~i~-------d~~t~~~~~aER~~L~~L~ 234 (292)
T cd00494 179 TQYLSPEVMLPAVGQGALAIECRKGDEELLALLKPLN-------HEETALCVLAERAFLRELE 234 (292)
T ss_pred ccccCccccCCccccceEEEEEecCCHHHHHHHHHCC-------CHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999999999999998877 4447889999999999875
No 4
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=100.00 E-value=4.2e-81 Score=570.32 Aligned_cols=211 Identities=50% Similarity=0.789 Sum_probs=202.3
Q ss_pred CCCCCCCCCCcEEEEEEeecCcccCCccccccCcccccHHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCC
Q 026500 2 ALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDV 81 (237)
Q Consensus 2 ~~~p~l~~~~~~eiv~i~T~GD~~~~~~L~~iggkGlFtkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dp 81 (237)
+.||++ ++|+++|+|+||+++++||+++||||+||||||+||++|+||||||||||||+++|+||.|+||++|+||
T Consensus 28 ~~~p~~----~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVHSlKDlP~~l~~gl~i~avl~R~dp 103 (295)
T PRK00072 28 AAHPGL----EVELVPIKTKGDKILDVPLAKIGGKGLFVKELEEALLEGEIDIAVHSLKDVPTELPEGLVLAAIPEREDP 103 (295)
T ss_pred HHCCCC----eEEEEEeeccCcccccccHHHcCCcceeHHHHHHHHHcCCCCEEEeccCcCCCCCCCCcEEEEEecCCCC
Confidence 346877 7999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEeCCCCCCccCCCCCeeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcc
Q 026500 82 RDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENV 161 (237)
Q Consensus 82 rD~LV~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i 161 (237)
|||||+++++++++||+|++|||||+||++||+++|||++|+ ++||||+|||+||++|+|||||||+|||+|||+++++
T Consensus 104 rDvlv~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~~Pdl~~~-~iRGNV~TRL~KL~~g~~DaivLA~AGL~RLgl~~~~ 182 (295)
T PRK00072 104 RDALVSRDYKSLDDLPEGAVVGTSSLRRQAQLLALRPDLEIK-PLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRI 182 (295)
T ss_pred ceEEEECCCCChhHCCCCCEEecCcHHHHHHHHHHCcCCEEE-ECccCHHHHHHHhhCCCCCEeehHhhHHHHcCCcccc
Confidence 999999988999999999999999999999999999999999 9999999999999999999999999999999999999
Q ss_pred eeeecCCCCCCCCCCceEEEEEecCchhhhhhhcccccccccccccccchhHHHHHHHHhhhh
Q 026500 162 TNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKLHFGFLNLVE 224 (237)
Q Consensus 162 ~~~l~~~~~lPA~GQGalave~R~~d~~~~~~l~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~ 224 (237)
+++|++++|+||||||+||||||++|+++.++|+.++ +=.+..|...||.||+.|+
T Consensus 183 ~~~l~~~~~~PA~gQGaiave~r~~d~~~~~~l~~i~-------d~~t~~~~~aER~~L~~L~ 238 (295)
T PRK00072 183 TEYLDPEEMLPAPGQGALGIECRADDEEILELLAPLN-------HEETRLRVTAERAFLRALE 238 (295)
T ss_pred ceecChhhcCCcccccceeeeeecCCHHHHHHHHHcC-------CHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999999999999998777 4347889999999999875
No 5
>PLN02691 porphobilinogen deaminase
Probab=100.00 E-value=9.3e-80 Score=571.45 Aligned_cols=214 Identities=74% Similarity=1.099 Sum_probs=202.9
Q ss_pred CCCCCCCCCcEEEEEEeecCcccCCccccccCcccccHHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCC
Q 026500 3 LHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVR 82 (237)
Q Consensus 3 ~~p~l~~~~~~eiv~i~T~GD~~~~~~L~~iggkGlFtkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dpr 82 (237)
.+|++....++||++|+|+||+++++||+++||||+||||||+||++|+||||||||||||+++|+||.|+||++|+|||
T Consensus 68 ~~p~~~~~~~~eiv~i~T~GD~~~d~pL~~iGgkGlFtkele~aLl~g~iDiAVHSlKDlP~~l~~gl~i~Avl~Redpr 147 (351)
T PLN02691 68 AHPELAEEGALEIVIIKTTGDKILDQPLADIGGKGLFTKEIDDALLSGRIDIAVHSMKDVPTYLPEGTILPCNLPREDVR 147 (351)
T ss_pred hCCCcCCCCCEEEEEEeecCCccccchHHHcCCceEeHHHHHHHHHcCCCCEEEeccccCCCCCCCCcEEEEEcCCCCCc
Confidence 46766333379999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEeCCCCCCccCCCCCeeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcce
Q 026500 83 DAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVT 162 (237)
Q Consensus 83 D~LV~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i~ 162 (237)
|+||++++++|++||+|++|||||+||++||+++|||++|+ ++||||+|||+||++|+|||||||+|||+|||++++++
T Consensus 148 DvLv~~~~~~L~~Lp~ga~IGTSS~RR~aql~~~rPdl~v~-~iRGNVdTRL~KL~~geyDaiILA~AGL~RLgl~~~i~ 226 (351)
T PLN02691 148 DAFISLKAKSLAELPAGSVVGTASLRRQSQILHKYPHLKVV-NFRGNVQTRLRKLQEGVVDATLLALAGLKRLDMTEHAT 226 (351)
T ss_pred eEEEECCCCChhHCCCCCEeccCcHHHHHHHHHHCCCCEEE-eccCCHHHHHHHhcCCCCCeeehHHHHHHhCCCccccc
Confidence 99999999999999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred eeecCCCCCCCCCCceEEEEEecCchhhhhhhcccccccccccccccchhHHHHHHHHhhhh
Q 026500 163 NILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKLHFGFLNLVE 224 (237)
Q Consensus 163 ~~l~~~~~lPA~GQGalave~R~~d~~~~~~l~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~ 224 (237)
++|++++|+||||||+||||||++|+++.++|+.++ +=.+..|...||.||+.|+
T Consensus 227 ~~l~~~~~~PA~gQGaLaVe~r~~d~~~~~ll~~in-------d~~T~~~~~aER~~L~~L~ 281 (351)
T PLN02691 227 SILSTDEMLPAVAQGAIGIACRTDDDKMLEYLASLN-------HEETRLAVACERAFLAALD 281 (351)
T ss_pred EecchhhcCCccccceEEEEEecCCHHHHHHHHHCC-------CHHHHHHHHHHHHHHHHhC
Confidence 999999999999999999999999999999998877 3346889999999999875
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=3.3e-79 Score=536.93 Aligned_cols=189 Identities=50% Similarity=0.844 Sum_probs=143.7
Q ss_pred CCCCCCCCCCcEEEEEEeecCcccCCccccccCcccccHHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCC
Q 026500 2 ALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDV 81 (237)
Q Consensus 2 ~~~p~l~~~~~~eiv~i~T~GD~~~~~~L~~iggkGlFtkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dp 81 (237)
+++|++ +||+++|+|+||++++.||+++||||+||||||+||++|+||+|||||||||+++|+||.|+||++|+||
T Consensus 25 ~~~P~~----~~ei~~i~T~GD~~~~~~L~~~ggkg~Ftkele~aLl~g~iDiAVHSlKDlP~~l~~gl~iaav~~R~dp 100 (215)
T PF01379_consen 25 KAFPDL----EFEIVTIKTTGDRDLDRPLSKIGGKGLFTKELEEALLDGEIDIAVHSLKDLPTELPEGLVIAAVLKREDP 100 (215)
T ss_dssp HHSTTS----EEEEEEE--CCHH--------TT--HCCCHHHHHHHHTTS-SEEEEEGGGS-SS--TTEEEEEE------
T ss_pred HhCCCc----eEEEEEccCCCCcccccchhhcCCccHHHHHHHHHHHcCCccEEEeccccCCCCCCCCceEeccCCCCCC
Confidence 357888 7999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEe--CCCCCCccCCCCCeeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCC
Q 026500 82 RDAFIS--LSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTE 159 (237)
Q Consensus 82 rD~LV~--~~~~~l~~Lp~ga~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~ 159 (237)
|||||+ +.++++++||+|++|||||+||++||+++|||++|+ ++||||+|||+||++|+|||||||+|||+|||+++
T Consensus 101 rD~Lv~~~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~~pdl~~~-~iRGNv~TRL~KL~~g~~daiiLA~AGL~RLgl~~ 179 (215)
T PF01379_consen 101 RDVLVSRGRDGKSLEDLPKGARIGTSSLRRRAQLKRLRPDLEVV-PIRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLED 179 (215)
T ss_dssp -EEEEE-GCTTSSCCCS-TT-EEE---HHHHHHHHHH-TTSEEE----S-HHHHHHHHHCTS-SEEEEEHHHHHHCT-GG
T ss_pred ccEEEEecCCCCChHHCccccccCCCCHHHHHHHHHhccCCeEE-EecCCHHHHHHHhcccCCCEEEhhhChhhhccccc
Confidence 999999 567899999999999999999999999999999999 99999999999999999999999999999999999
Q ss_pred cceeeecCCCCCCCCCCceEEEEEecCchhhhhhhc
Q 026500 160 NVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTT 195 (237)
Q Consensus 160 ~i~~~l~~~~~lPA~GQGalave~R~~d~~~~~~l~ 195 (237)
+++++|++++|+|||||||||||||++|+++.++|+
T Consensus 180 ~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~llK 215 (215)
T PF01379_consen 180 RISEILDPEEMLPAPGQGALAVECRKDDEEIIELLK 215 (215)
T ss_dssp GESEEE-TTTS-B-TTTT-EEEEEETT-HHHHHHH-
T ss_pred eeeeecCchhcCCCCCCeEEEEEEecCcHHHHHHhC
Confidence 999999999999999999999999999999999885
No 7
>PRK01066 porphobilinogen deaminase; Provisional
Probab=100.00 E-value=1.6e-76 Score=523.88 Aligned_cols=187 Identities=27% Similarity=0.376 Sum_probs=180.7
Q ss_pred CCCCCCCCCCcEEEEEEeecCcccCCccccccCcccccHHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCC
Q 026500 2 ALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDV 81 (237)
Q Consensus 2 ~~~p~l~~~~~~eiv~i~T~GD~~~~~~L~~iggkGlFtkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dp 81 (237)
+.+|++ ++||++|+|+||++++.||+++||||+||||||+||++|+||||||||||||+ |+||.++||++|+||
T Consensus 41 ~~~p~~----~~ei~~i~T~GD~~~~~~L~~iGgkGlFtkele~aLl~g~iDiAVHSlKDlPt--~~gl~l~av~~Redp 114 (231)
T PRK01066 41 SFFPKL----WFQISTTTTQGDLDQKTPLHLVENTGFFTDDVDFLVLSGQCDLAIHSAKDLPE--PPKLTVVAITAGLDP 114 (231)
T ss_pred HhCCCC----cEEEEEEeccCcccccccHHHcCCceeeHHHHHHHHHcCCCCEEEecCCcCCC--CCCCEEEEEcCCCCC
Confidence 347877 79999999999999999999999999999999999999999999999999999 999999999999999
Q ss_pred CeEEEeCCCCCCccCCCCCeeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcc
Q 026500 82 RDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENV 161 (237)
Q Consensus 82 rD~LV~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i 161 (237)
|||||++++.++.+||+|++|||||+||++||+++|||++|+ ++||||+|||+||++|+|||||||+|||+|||+.+++
T Consensus 115 rDvLv~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~rPdl~v~-~iRGNV~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~ 193 (231)
T PRK01066 115 RDLLVYAEKYLSQPLPRRPRIGSSSLRREELLKLLFPSGIIL-DIRGTIEERLKLLEEKKYDAIVVAKAAVLRLGLRLPY 193 (231)
T ss_pred ceEEEECCCCchhhCCCCCEEeCChHHHHHHHHHHCCCCEEE-eCcCCHHHHHHHhcCCCCCchhhHHHHHHhcCCcccc
Confidence 999999998999999999999999999999999999999999 9999999999999999999999999999999999999
Q ss_pred eeeecCCCCCCCCCCceEEEEEecCchhhhhhhcccc
Q 026500 162 TNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQ 198 (237)
Q Consensus 162 ~~~l~~~~~lPA~GQGalave~R~~d~~~~~~l~~~~ 198 (237)
+++|++++ |||||+||||||++|+++.++++.++
T Consensus 194 ~~~l~~~~---A~gQGalaie~R~~d~~~~~ll~~i~ 227 (231)
T PRK01066 194 TKELPPPY---HPLQGRLAITASKHIRSWKGLFLPLG 227 (231)
T ss_pred eeECCCCC---CCCCCeEEEEEecCCHHHHHHHHHhc
Confidence 99999984 99999999999999999999998776
No 8
>KOG2892 consensus Porphobilinogen deaminase [Coenzyme transport and metabolism]
Probab=100.00 E-value=1.3e-69 Score=489.38 Aligned_cols=211 Identities=55% Similarity=0.865 Sum_probs=200.9
Q ss_pred CCCCCCCCCCcEEEEEEeecCcccCCccccccCcccccHHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCC
Q 026500 2 ALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDV 81 (237)
Q Consensus 2 ~~~p~l~~~~~~eiv~i~T~GD~~~~~~L~~iggkGlFtkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dp 81 (237)
++||++ +|+|..++|+||+++++||++||||++||||||++|.+|++||+|||||||||.+|+|+.|+|++||+||
T Consensus 31 k~YP~l----~f~I~t~~T~GDkIl~k~L~~ig~KsLfTkELE~aL~~~~~divVHSLKDlPT~LP~G~~ig~i~kRedp 106 (320)
T KOG2892|consen 31 KKYPEL----AFEIITMSTTGDKILSKPLAKIGGKSLFTKELEDALINGHVDIVVHSLKDLPTYLPEGMIIGCILKREDP 106 (320)
T ss_pred hhCCCc----eeEEEEecccchHHhhchHhhhcccchhHHHHHHHHhcCCccEEEEecccccccCCCCcEeccccCCCCc
Confidence 579999 7999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEeCC---CCCCccCCCCCeeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCC-ccEEeeecccccccCC
Q 026500 82 RDAFISLS---AASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERV-VQATLLALAGLKRLSM 157 (237)
Q Consensus 82 rD~LV~~~---~~~l~~Lp~ga~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge-~DaiILA~AGL~RLgl 157 (237)
+|+||++. |+++++||+|++|||||+||+|||++.||+++|+ ++|||++|||+||+.+. |.|||||.|||.|+||
T Consensus 107 ~DalV~~~~s~~kTladLP~GsVVGTSSlRR~Aql~RkyPHL~f~-~~rgn~~trl~kld~~~~~~~iilA~agl~rmg~ 185 (320)
T KOG2892|consen 107 RDALVFLTYSAYKTLADLPAGSVVGTSSLRRKAQILRKYPHLHVE-SIRGNLQTRLSKLDGGKPFQAIILALAGLKRMGW 185 (320)
T ss_pred cceEEEecccccccHhhCCCCceechHHHhHHHHHHhhCCceEEE-EecChHHHHHHhhcCCCcchhHHHHHHHHHHhhh
Confidence 99999986 7899999999999999999999999999999999 89999999999999987 9999999999999999
Q ss_pred CCcceeeecCCCCCCCCCCceEEEEEecCchhhhhhhcccccccccccccccchhHHHHHHHHhhhh
Q 026500 158 TENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSGKLCYKLHFGFLNLVE 224 (237)
Q Consensus 158 ~~~i~~~l~~~~~lPA~GQGalave~R~~d~~~~~~l~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~ 224 (237)
.+++.+++.|++|+||+||||++||||.+|+++..++..++ ..| +..|.-.||-|++.++
T Consensus 186 ~~ri~qil~p~~~~~avgqgalgie~r~~d~~m~~~l~~l~-----~~~--t~~~~~~eraflrtl~ 245 (320)
T KOG2892|consen 186 TNRIAQILHPDEMLYAVGQGALGIECRADDDKMLTYLASLN-----DLN--TTLRILAERAFLRTLE 245 (320)
T ss_pred HhHHHHhcChHHHHHHhccceeEEEEecChHHHHHHHHHhc-----ChH--HHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999988887665 122 6889999999999886
No 9
>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=96.20 E-value=0.016 Score=52.52 Aligned_cols=154 Identities=16% Similarity=0.100 Sum_probs=85.9
Q ss_pred HHHHHHhcCCccEEEeeCCCCCC--CCCCCceeeeecCCCCCCeEEEeCCCCCCccCCCCCeeecC----ChhHHHHHHH
Q 026500 42 EIDEALINSQIDIAVHSMKDVPT--YLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTA----SLRRKSQILH 115 (237)
Q Consensus 42 eLe~aLl~g~iDiAVHSlKDlP~--~l~~gL~iaav~~R~dprD~LV~~~~~~l~~Lp~ga~IGTS----S~RR~aql~~ 115 (237)
+..+||.+|+||+........-. .-..|..+.++..=.-..=.+.+.+++++++||.|++|+.+ ..=|.-.++.
T Consensus 58 ~~~~Al~~G~ID~~~~q~~~~l~~~~~~~g~~lv~v~~~~~~p~~~ys~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~ 137 (258)
T TIGR00363 58 LPNEAVSKGDLDANAFQHKPYLDQDAKAKGYKLVAVGNTFVYPLAGYSKKIKNVNELQDGAKVAVPNDPTNLGRALLLLQ 137 (258)
T ss_pred HHHHHHHcCCCCeEecCCHHHHHHHHHhCCCcEEEEeeeEEecccccCcCCCCHHHcCCCCEEEEeCCcchHHHHHHHHH
Confidence 67799999999998643222100 01234444444310000001235677899999999999865 2244444444
Q ss_pred h----------------------CCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCc-ceeeecCCCCCC
Q 026500 116 R----------------------YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTEN-VTNILSVDDMLP 172 (237)
Q Consensus 116 ~----------------------~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~-i~~~l~~~~~lP 172 (237)
. ..+++++ ++-- .+=.+.|.+|+.||.++...=....|+... -.-+++...
T Consensus 138 ~aGLi~l~~~~~~~~t~~DI~~n~~~v~~v-el~~--~~~~~al~~g~vDaa~v~~~~~~~agl~~~~~~i~~e~~~--- 211 (258)
T TIGR00363 138 KQGLIKLKDGNGLLPTVLDIVENPKKLNIT-ELET--SQLPRALDDPKVDLAVINTTYAGQVGLNPQDDGVFVEDKD--- 211 (258)
T ss_pred HcCCceecCCCCCcCChhhhhcCCCCCEEE-EcCH--HHHHHHhhcccccEEEEChHHHHHcCCCcCcCceeecCCC---
Confidence 3 4568888 5552 334477889999999984433333333211 112233222
Q ss_pred CCCCceEEEEEecC---chhhhhhhccccccccc
Q 026500 173 AVAQGAIGIACRSN---DEKMVPFTTHSQASILN 203 (237)
Q Consensus 173 A~GQGalave~R~~---d~~~~~~l~~~~~~~~~ 203 (237)
-+|+-.+.+|.+ ++.+.++++.+++....
T Consensus 212 --~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~ 243 (258)
T TIGR00363 212 --SPYVNIIVSREDNKDAENVKDFIQSYQSEEVY 243 (258)
T ss_pred --CCeeEEEEEcCCccCCHHHHHHHHHHcCHHHH
Confidence 146666777764 34677777777754333
No 10
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=96.10 E-value=0.027 Score=51.22 Aligned_cols=146 Identities=20% Similarity=0.215 Sum_probs=85.1
Q ss_pred HHHHHHHhcCCccEEEeeCCCCC--CCCCCCceeeeecCCCCCCeEEEe------CCCCCCccCCCCCeeecCC-h---h
Q 026500 41 KEIDEALINSQIDIAVHSMKDVP--TYLPEKTILPCNLQREDVRDAFIS------LSAASLAELPAGSIVGTAS-L---R 108 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP--~~l~~gL~iaav~~R~dprD~LV~------~~~~~l~~Lp~ga~IGTSS-~---R 108 (237)
.+.-+||.+|++|+......+.= .....|..+..+ ...++. .+.++++|||+|++|++++ + =
T Consensus 70 ~~~~~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~~~------~~~~vvp~~~ys~~i~si~DL~~Gk~IAip~d~~n~~ 143 (271)
T PRK11063 70 VLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLVAV------GNTFVYPIAGYSKKIKSLDELQDGSQVAVPNDPTNLG 143 (271)
T ss_pred HHHHHHHHcCCcceecccCHHHHHHHHHHcCCcEEEE------eEEEEEEeeccccCCCCHHHhcCCCEEEecCCCccHH
Confidence 36779999999999653222110 000122222222 112332 3567899999999999886 2 3
Q ss_pred HHHHHHHh---------------------CC-CCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCC-cceeee
Q 026500 109 RKSQILHR---------------------YP-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTE-NVTNIL 165 (237)
Q Consensus 109 R~aql~~~---------------------~p-dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~-~i~~~l 165 (237)
|.-.+++. +| +++++ ++. -..=-+-|.+|+.||.++..-=....|++. .-.-++
T Consensus 144 r~L~lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v-~~~--~~~~~~al~~g~vDaa~i~~~~a~~a~~~~~~~~l~~ 220 (271)
T PRK11063 144 RSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIV-ELE--APQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFV 220 (271)
T ss_pred HHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEE-ECc--HHHHHHhcccccccEEEEChHHHHHcCCCCCCCeeEE
Confidence 44333332 23 58888 665 344456678999999999665555555543 112234
Q ss_pred cCCCCCCCCCCceEEEEEecC---chhhhhhhcccccc
Q 026500 166 SVDDMLPAVAQGAIGIACRSN---DEKMVPFTTHSQAS 200 (237)
Q Consensus 166 ~~~~~lPA~GQGalave~R~~---d~~~~~~l~~~~~~ 200 (237)
+..+. +++..+.+|++ ++.+..+++.+++.
T Consensus 221 e~~~~-----~~~~~~~v~~~~~~~~~~~~l~~a~~s~ 253 (271)
T PRK11063 221 EDKDS-----PYVNLIVAREDNKDAENVKKFVQAYQSD 253 (271)
T ss_pred CCCCC-----CeEEEEEECCcccCCHHHHHHHHHHcCH
Confidence 43321 46677777764 34667777766654
No 11
>PRK11260 cystine transporter subunit; Provisional
Probab=95.68 E-value=0.1 Score=45.50 Aligned_cols=145 Identities=14% Similarity=0.162 Sum_probs=80.2
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-----CCCccCCCCCeeecC--ChhHHHHH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-----ASLAELPAGSIVGTA--SLRRKSQI 113 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-----~~l~~Lp~ga~IGTS--S~RR~aql 113 (237)
+++.++|.+|++|+++-++-.-|. ..+.+.+....-. ...+++.++. .++++| .|-+||+. +.- ...+
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 578899999999999865422222 2222332221111 1234554432 345666 56677752 222 4556
Q ss_pred HHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcceeeecCCCCCCCCCCceEEEEEecCchhhhhh
Q 026500 114 LHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPF 193 (237)
Q Consensus 114 ~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i~~~l~~~~~lPA~GQGalave~R~~d~~~~~~ 193 (237)
+..+|..++. ....+ .+-++.|.+|++|++|....-...+--.......+....+ .+.+ +++-++++++++.+.
T Consensus 165 ~~~~~~~~i~-~~~~~-~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~--~~~~--~~~~v~~~~~~l~~~ 238 (266)
T PRK11260 165 RQNVQGVDVR-TYDDD-PTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVAGEAF--SRQE--SGVALRKGNPDLLKA 238 (266)
T ss_pred HHhCCCCceE-ecCCH-HHHHHHHHcCCCCEEEechHHHHHHHHhCCCcceecCCcc--ccCc--eEEEEeCCCHHHHHH
Confidence 7788999887 77654 5678999999999999854332222111000001111111 2222 555668888877777
Q ss_pred hcc
Q 026500 194 TTH 196 (237)
Q Consensus 194 l~~ 196 (237)
+.+
T Consensus 239 ln~ 241 (266)
T PRK11260 239 VNQ 241 (266)
T ss_pred HHH
Confidence 653
No 12
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=95.60 E-value=0.2 Score=42.52 Aligned_cols=148 Identities=12% Similarity=0.190 Sum_probs=81.2
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC----CCCccCCCCCeeecCChhH-HHHHHH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA----ASLAELPAGSIVGTASLRR-KSQILH 115 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~----~~l~~Lp~ga~IGTSS~RR-~aql~~ 115 (237)
.+...+|.+|++|+++-++- ...+..+.+.+....- . ..-+++++.. .++++| .|.+||+-+--= ...+..
T Consensus 73 ~~~~~~l~~G~~D~~~~~~~-~~~~r~~~~~~s~p~~-~-~~~~~~~~~~~~~~~~~~dl-~g~~i~~~~g~~~~~~l~~ 148 (250)
T TIGR01096 73 DGLIPSLKAKKVDAIMATMS-ITPKRQKQIDFSDPYY-A-TGQGFVVKKGSDLAKTLEDL-DGKTVGVQSGTTHEQYLKD 148 (250)
T ss_pred HHHHHHHhCCCcCEEEecCc-cCHHHhhccccccchh-c-CCeEEEEECCCCcCCChHHc-CCCEEEEecCchHHHHHHH
Confidence 46678889999999976442 1112222333322111 1 1234444432 245666 477887532111 345666
Q ss_pred hCC-CCeEEeccCCCHHHHHHhhccCCccEEeeecccc----cccCCCCcceeeecCCCCCCCCCCce-EEEEEecCchh
Q 026500 116 RYP-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGL----KRLSMTENVTNILSVDDMLPAVAQGA-IGIACRSNDEK 189 (237)
Q Consensus 116 ~~p-dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL----~RLgl~~~i~~~l~~~~~lPA~GQGa-lave~R~~d~~ 189 (237)
.+| +++++ ... +.+.-+..|.+|++|++|....-+ .+.+....+. +++ ..+.+.+-+|. +++-+++++.+
T Consensus 149 ~~~~~~~~~-~~~-s~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~~~~~~l~-~~~-~~~~~~~~~~~~~~~~~~~~~~~ 224 (250)
T TIGR01096 149 YFKPGVDIV-EYD-SYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFK-FVG-PSVTDEKYFGDGYGIGLRKGDTE 224 (250)
T ss_pred hccCCcEEE-EcC-CHHHHHHHHHcCCCCEEEeCHHHHHHHHHhCCCCCceE-Eec-cccccccccCCceEEEEeCCCHH
Confidence 777 88888 665 567789999999999999855433 3333322221 222 11111111222 67777888776
Q ss_pred hhhhhcc
Q 026500 190 MVPFTTH 196 (237)
Q Consensus 190 ~~~~l~~ 196 (237)
+...+.+
T Consensus 225 l~~~ln~ 231 (250)
T TIGR01096 225 LKAAFNK 231 (250)
T ss_pred HHHHHHH
Confidence 6666643
No 13
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=95.49 E-value=0.19 Score=39.32 Aligned_cols=106 Identities=17% Similarity=0.239 Sum_probs=64.2
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC---CCCccCCCCCeeecCChh-HHHHHHHh
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTASLR-RKSQILHR 116 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~---~~l~~Lp~ga~IGTSS~R-R~aql~~~ 116 (237)
.++.++|.+|++|+++-+.---|.. ...+......- ...-+++++++ .++++| .|-+||+.+-- -...+...
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 5788999999999998764321111 11111111111 11245555443 457777 57778875321 22334445
Q ss_pred CCCCeEEeccCCCHHHHHHhhccCCccEEeeecccc
Q 026500 117 YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGL 152 (237)
Q Consensus 117 ~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL 152 (237)
.++.+++ .. ++...-+..|.+|++||+++...-+
T Consensus 125 ~~~~~~~-~~-~~~~~~~~~l~~g~~d~~~~~~~~~ 158 (219)
T smart00062 125 YPEAKIV-SY-DSQAEALAALKAGRADAAVADAPAL 158 (219)
T ss_pred CCCceEE-Ec-CCHHHHHHHhhcCcccEEEeccHHH
Confidence 6788877 54 4568888999999999999977743
No 14
>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=95.37 E-value=0.018 Score=46.82 Aligned_cols=142 Identities=16% Similarity=0.258 Sum_probs=86.2
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-----C---CCccCCCCCeeecCChhHHH-
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-----A---SLAELPAGSIVGTASLRRKS- 111 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-----~---~l~~Lp~ga~IGTSS~RR~a- 111 (237)
+++-++|.+|++|+++-++-.-|.. .+.+.... +-- ....+++.+++ . ++++| .|.+||+..-....
T Consensus 48 ~~~~~~l~~g~~D~~~~~~~~~~~r-~~~~~~s~-p~~-~~~~~~~~~~~~~~~~~~~~~~~dl-~~~~i~~~~g~~~~~ 123 (225)
T PF00497_consen 48 SRLLEMLENGKADIIIGGLSITPER-AKKFDFSD-PYY-SSPYVLVVRKGDAPPIKTIKSLDDL-KGKRIGVVRGSSYAD 123 (225)
T ss_dssp GGHHHHHHTTSSSEEESSEB-BHHH-HTTEEEES-ESE-EEEEEEEEETTSTCSTSSHSSGGGG-TTSEEEEETTSHHHH
T ss_pred ccccccccccccccccccccccccc-cccccccc-ccc-chhheeeeccccccccccccchhhh-cCcccccccchhHHH
Confidence 3566789999999998544332221 22333322 111 12344555432 1 24477 67788877655544
Q ss_pred HHHHhCC-CCeEEeccCCCHHHHHHhhccCCccEEeeecccc----cccCCCCcceeeecCCCCCCCCCCceEEEEEecC
Q 026500 112 QILHRYP-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGL----KRLSMTENVTNILSVDDMLPAVAQGAIGIACRSN 186 (237)
Q Consensus 112 ql~~~~p-dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL----~RLgl~~~i~~~l~~~~~lPA~GQGalave~R~~ 186 (237)
.+...+| +.+++ .. .|.+.-++.|.+|++|++|....-+ ++.+..... .. .+...+.-+++-++.+
T Consensus 124 ~l~~~~~~~~~~~-~~-~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~--~~-----~~~~~~~~~~~~~~~~ 194 (225)
T PF00497_consen 124 YLKQQYPSNINIV-EV-DSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIV--VI-----PPPISPSPVYFAVRKK 194 (225)
T ss_dssp HHHHHTHHTSEEE-EE-SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEE--EE-----EEEEEEEEEEEEEETT
T ss_pred Hhhhhccchhhhc-cc-ccHHHHHHHHhcCCeeeeeccchhhhhhhhhccccccc--cc-----ccccccceeEEeeccc
Confidence 6677776 89988 54 6899999999999999999876644 343332221 11 3344455566667777
Q ss_pred chhhhhhhc
Q 026500 187 DEKMVPFTT 195 (237)
Q Consensus 187 d~~~~~~l~ 195 (237)
++.+.+.+.
T Consensus 195 ~~~l~~~~n 203 (225)
T PF00497_consen 195 NPELLEIFN 203 (225)
T ss_dssp THHHHHHHH
T ss_pred ccHHHHHHH
Confidence 777666654
No 15
>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=95.32 E-value=0.04 Score=49.08 Aligned_cols=110 Identities=14% Similarity=0.151 Sum_probs=66.6
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCC--ceeeeecCCCCCCeEEEeCCC---CCCccCCCCCeeecC---C-hhHH-
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEK--TILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTA---S-LRRK- 110 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~g--L~iaav~~R~dprD~LV~~~~---~~l~~Lp~ga~IGTS---S-~RR~- 110 (237)
.++-+||.+|++|+++.+.--+-.....| +.+.++.......+.||++++ .+++|| +|.+||+. | -.--
T Consensus 38 ~~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~~~~~lv~~~~s~I~s~~DL-kGK~Igv~~~s~~~~~l~ 116 (300)
T TIGR01729 38 ADISTALASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIGKSEALVAREGSGIEKPEDL-KGKNVAVPFVSTTHYSLL 116 (300)
T ss_pred HHHHHHHHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCCccceEEecCCCCCCChhHc-CCCEEEeCCCCcHHHHHH
Confidence 35779999999999986432110111223 344455555556688888754 456777 68888862 2 2111
Q ss_pred HHHHHhC--C-CCeEEeccCCCHHHHHHhhccCCccEEeeecccccc
Q 026500 111 SQILHRY--P-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKR 154 (237)
Q Consensus 111 aql~~~~--p-dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~R 154 (237)
..|.... | +++++ ..+-...+.-|.+|+.||+++...-..+
T Consensus 117 ~~L~~~Gl~~~dv~~v---~~~~~~~~~al~~G~vDa~~~~~p~~~~ 160 (300)
T TIGR01729 117 AALKHWKTDPREVNIL---NLKPPQIVAAWQRGDIDAAYVWPPALSE 160 (300)
T ss_pred HHHHHcCCChhheEEE---ecCcHHHHHHHHcCCcCEEEEecHHHHH
Confidence 1233222 2 34444 3456778889999999999987654433
No 16
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=95.01 E-value=0.46 Score=40.35 Aligned_cols=148 Identities=14% Similarity=0.192 Sum_probs=79.1
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC--CCCccCCCCCeeecCChh-HHHHHHHhC
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA--ASLAELPAGSIVGTASLR-RKSQILHRY 117 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~--~~l~~Lp~ga~IGTSS~R-R~aql~~~~ 117 (237)
+++.++|.+|++|+++=++-- ..+..+.+..+...- ...-+++.++. .++++| .|-+||+..-- =...+...+
T Consensus 70 ~~~~~~l~~g~~D~~~~~~~~-~~~r~~~~~fs~p~~--~~~~~~v~~~~~~~~~~dL-~g~~Igv~~g~~~~~~l~~~~ 145 (243)
T PRK15007 70 DSLIPSLKFRRVEAVMAGMDI-TPEREKQVLFTTPYY--DNSALFVGQQGKYTSVDQL-KGKKVGVQNGTTHQKFIMDKH 145 (243)
T ss_pred HHHhHHHhCCCcCEEEEcCcc-CHHHhcccceecCcc--ccceEEEEeCCCCCCHHHh-CCCeEEEecCcHHHHHHHHhC
Confidence 357789999999987543211 112223333322111 12234554432 356666 46677652110 123456678
Q ss_pred CCCeEEeccCCCHHHHHHhhccCCccEEeeecccccc-cCCCCcceeeecCCCCC-CCCCCceEEEEEecCchhhhhhhc
Q 026500 118 PSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKR-LSMTENVTNILSVDDML-PAVAQGAIGIACRSNDEKMVPFTT 195 (237)
Q Consensus 118 pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~R-Lgl~~~i~~~l~~~~~l-PA~GQGalave~R~~d~~~~~~l~ 195 (237)
|.++++ .. .+.+..+..|..|++|+++.-..-+.. +...... ..+.. .+. +.....-+++-++.+++++.+.+.
T Consensus 146 ~~~~~~-~~-~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~ln 221 (243)
T PRK15007 146 PEITTV-PY-DSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNPKL-AAVGD-KVTDKDYFGTGLGIAVRQGNTELQQKLN 221 (243)
T ss_pred CCCeEE-Ec-CCHHHHHHHHHcCCCCEEEeCHHHHHHHHhcCCCc-eeecC-cccccccCCcceEEEEeCCCHHHHHHHH
Confidence 999987 55 678899999999999999875432211 1101111 11111 111 112223366777888877776665
Q ss_pred c
Q 026500 196 H 196 (237)
Q Consensus 196 ~ 196 (237)
.
T Consensus 222 ~ 222 (243)
T PRK15007 222 T 222 (243)
T ss_pred H
Confidence 4
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=94.89 E-value=0.37 Score=37.94 Aligned_cols=145 Identities=14% Similarity=0.183 Sum_probs=79.5
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC---CCCccCCCCCeeecCCh-hHHHHHHH
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTASL-RRKSQILH 115 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~---~~l~~Lp~ga~IGTSS~-RR~aql~~ 115 (237)
..++.++|.+|++|+++-+.-..+. ....+.+.. +-..++ -+++.+++ .++++| .|.+||+.+- -=...+..
T Consensus 47 ~~~~~~~l~~g~~D~~~~~~~~~~~-~~~~~~~~~-~~~~~~-~~~~~~~~~~~~~~~dl-~g~~i~~~~~~~~~~~~~~ 122 (218)
T cd00134 47 WDGLITALKSGKVDLIAAGMTITPE-RAKQVDFSD-PYYKSG-QVILVKKGSPIKSVKDL-KGKKVAVQKGSTAEKYLKK 122 (218)
T ss_pred HHHHHHHHhcCCcCEEeecCcCCHH-HHhhccCcc-cceecc-EEEEEECCCCCCChHHh-CCCEEEEEcCchHHHHHHH
Confidence 4688899999999999887622221 111121111 111222 23444333 245666 4667776411 11234555
Q ss_pred hCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCC--CcceeeecCCCCCCCCCCceEEEEEecCchhhhhh
Q 026500 116 RYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMT--ENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPF 193 (237)
Q Consensus 116 ~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~--~~i~~~l~~~~~lPA~GQGalave~R~~d~~~~~~ 193 (237)
..+..+++ ...+ .+.-+..|.+|++|+++........+--. ..+ .++... ...-...+++..+.++.++...
T Consensus 123 ~~~~~~~~-~~~~-~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l-~~~~~~---~~~~~~~~~~~~~~~~~~l~~~ 196 (218)
T cd00134 123 ALPEAKVV-SYDD-NAEALAALENGRADAVIVDEIALAALLKKHPPEL-KIVGPS---IDLEPLGFGVAVGKDNKELLDA 196 (218)
T ss_pred hCCcccEE-EeCC-HHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCc-EEeccc---cCCCccceEEEEcCCCHHHHHH
Confidence 66667776 5554 78899999999999999976654433111 122 222221 1234455667777666544444
Q ss_pred h
Q 026500 194 T 194 (237)
Q Consensus 194 l 194 (237)
+
T Consensus 197 ~ 197 (218)
T cd00134 197 V 197 (218)
T ss_pred H
Confidence 3
No 18
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=94.29 E-value=0.96 Score=39.32 Aligned_cols=146 Identities=14% Similarity=0.194 Sum_probs=73.2
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC----CCCccCCCCCeeec---CChhHHHHH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA----ASLAELPAGSIVGT---ASLRRKSQI 113 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~----~~l~~Lp~ga~IGT---SS~RR~aql 113 (237)
+++-+++..|++|+++=++---|. ..+-+......-. + .-+++.+++ .++++| .|-+||+ |+.- ..+
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 578889999999988754321111 1111111111111 1 123444332 246677 4667776 3221 122
Q ss_pred HHh--CCCCeEEeccCCCHHHHHHhhccCCccEEeeec----ccccccCCCCcceeeecCCC-CCCCCCCceEEEEEecC
Q 026500 114 LHR--YPSLKVMENFRGNVQTRLRKLNERVVQATLLAL----AGLKRLSMTENVTNILSVDD-MLPAVAQGAIGIACRSN 186 (237)
Q Consensus 114 ~~~--~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~----AGL~RLgl~~~i~~~l~~~~-~lPA~GQGalave~R~~ 186 (237)
... .++++++ .. .+.+.-+++|..|++|++|.-. .++..-.....+ .+..+.. -.+..+++ +++-++++
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 222 3456776 54 4678889999999999998732 222222111122 1222211 11222233 55666777
Q ss_pred chhhhhhhcc
Q 026500 187 DEKMVPFTTH 196 (237)
Q Consensus 187 d~~~~~~l~~ 196 (237)
++++.+.+..
T Consensus 225 ~~~L~~~ln~ 234 (260)
T PRK15010 225 DAELTAAFNK 234 (260)
T ss_pred CHHHHHHHHH
Confidence 7777666643
No 19
>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=93.96 E-value=0.45 Score=44.39 Aligned_cols=102 Identities=15% Similarity=0.043 Sum_probs=68.0
Q ss_pred HHHHHhcCCccEEEeeCCCCCCC---CCCC--ceeeeecCCCCCCeEEEeCCCCCCccCCCCCeeec--CChhHHH---H
Q 026500 43 IDEALINSQIDIAVHSMKDVPTY---LPEK--TILPCNLQREDVRDAFISLSAASLAELPAGSIVGT--ASLRRKS---Q 112 (237)
Q Consensus 43 Le~aLl~g~iDiAVHSlKDlP~~---l~~g--L~iaav~~R~dprD~LV~~~~~~l~~Lp~ga~IGT--SS~RR~a---q 112 (237)
.-+||.+|++|++.- =|.|.. ...| +.+.++.......|++|.++.++++|| +|-+||+ +|..--. .
T Consensus 48 ~l~Al~aG~iD~~~~--g~~~~~~~~~a~g~~~~iv~v~~~~~g~~~ivv~~i~svaDL-KGKkIav~~gs~~~~ll~~a 124 (328)
T TIGR03427 48 SINQYTAGKFDGCTM--TNMDALTIPAAGGVDTTALIVGDFSNGNDGIVLKGGKSLADL-KGQKVNLVELSVSHYLLARA 124 (328)
T ss_pred HHHHHHcCCCCEEee--cCHHHHHHHHhCCCCeEEEEEEccCCCceEEEECCCCCHHHc-CCCEEeccCCChHHHHHHHH
Confidence 335899999999854 333321 1234 346666666677899999888889999 7889987 2333211 1
Q ss_pred HHHh---CCCCeEEeccCCCHHHHHHhhccCCccEEeeecc
Q 026500 113 ILHR---YPSLKVMENFRGNVQTRLRKLNERVVQATLLALA 150 (237)
Q Consensus 113 l~~~---~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~A 150 (237)
|... ..|++++ ++. ...-..-|.+|+.||.++..-
T Consensus 125 L~~aGL~~~DV~~v-~~~--~~d~~aAl~~G~VDAa~~~eP 162 (328)
T TIGR03427 125 LESVGLSEKDVKVV-NTS--DADIVAAFITKDVTAVVTWNP 162 (328)
T ss_pred HHHcCCCHHHeEEE-eCC--hHHHHHHHhcCCCcEEEEcCc
Confidence 2221 1478888 774 466788999999999988443
No 20
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=93.68 E-value=0.18 Score=45.92 Aligned_cols=145 Identities=15% Similarity=0.210 Sum_probs=81.0
Q ss_pred HHHHHhcCCccEEEeeCCCCCCC----CCCCceeeeecCCCCCCeEEE------eCCCCCCccCCCCCeeecCC----hh
Q 026500 43 IDEALINSQIDIAVHSMKDVPTY----LPEKTILPCNLQREDVRDAFI------SLSAASLAELPAGSIVGTAS----LR 108 (237)
Q Consensus 43 Le~aLl~g~iDiAVHSlKDlP~~----l~~gL~iaav~~R~dprD~LV------~~~~~~l~~Lp~ga~IGTSS----~R 108 (237)
.-+||.+|+||+.+- -+.|-. -.-|..+.++- ..++ +.+.++++|||+|++|+-+. .=
T Consensus 73 ~n~AL~~G~ID~n~~--qh~~yl~~~~~~~g~~lv~~~------~~~~~P~~~Ys~~iksl~DL~~Ga~IAipnd~~n~~ 144 (272)
T PRK09861 73 PNDATNHGELDANVF--QHRPFLEQDNQAHGYKLVAVG------NTFVFPMAGYSKKIKTVAQIKEGATVAIPNDPTNLG 144 (272)
T ss_pred HHHHHHcCCcceehh--hhHHHHHHHHHhcCCCeEEEe------EEEEEeeeccccCCCCHHHcCCCCEEEEeCCCccHH
Confidence 447999999999863 111100 01223333331 2233 45678999999999999874 22
Q ss_pred HHHHHHHhC----------------------CCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcce-eee
Q 026500 109 RKSQILHRY----------------------PSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVT-NIL 165 (237)
Q Consensus 109 R~aql~~~~----------------------pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i~-~~l 165 (237)
|...|+..- .+++++ ++- -.+=.+-|.+|..|+.++..-=...-|+...-. -++
T Consensus 145 ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~v-e~~--~~q~~~al~dg~vD~a~i~~~~~~~ag~~~~~~~l~~ 221 (272)
T PRK09861 145 RALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIM-ELE--GAQLPRVLDDPKVDVAIISTTYIQQTGLSPVHDSVFI 221 (272)
T ss_pred HHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEE-EcC--HHHhHhhccCcccCEEEEchhHHHHcCCCcccceeEE
Confidence 555544441 357777 554 344566788999999988432222233321111 122
Q ss_pred cCCCCCCCCCCceEEEEEecC---chhhhhhhccccccccc
Q 026500 166 SVDDMLPAVAQGAIGIACRSN---DEKMVPFTTHSQASILN 203 (237)
Q Consensus 166 ~~~~~lPA~GQGalave~R~~---d~~~~~~l~~~~~~~~~ 203 (237)
+.. + .+++..+.+|++ ++.+.++++.+++...+
T Consensus 222 e~~---~--~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~ 257 (272)
T PRK09861 222 EDK---N--SPYVNILVAREDNKNAENVKEFLQSYQSPEVA 257 (272)
T ss_pred cCC---C--CCeEEEEEEcCCccCCHHHHHHHHHHcCHHHH
Confidence 221 1 246666667764 45778888877765433
No 21
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=93.30 E-value=0.69 Score=39.39 Aligned_cols=109 Identities=19% Similarity=0.200 Sum_probs=73.1
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC----CCCccCCC---CCeeecCChhHHHHH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA----ASLAELPA---GSIVGTASLRRKSQI 113 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~----~~l~~Lp~---ga~IGTSS~RR~aql 113 (237)
..+-.+|..|++|+++.++=-.| +..+-+.. ..+--....-+++.... ++++||.. |...||+ .+-....
T Consensus 87 ~~~~~~l~~g~~D~~~~~~~~t~-er~~~~~f-s~py~~~~~~~~~~~~~~~~~~~~~DL~gk~v~v~~gt~-~~~~~~~ 163 (275)
T COG0834 87 DGLIPALKAGKVDIIIAGMTITP-ERKKKVDF-SDPYYYSGQVLLVKKDSDIGIKSLEDLKGKKVGVQLGTT-DEAEEKA 163 (275)
T ss_pred hhhhHHHhcCCcCEEEeccccCH-HHhccccc-cccccccCeEEEEECCCCcCcCCHHHhCCCEEEEEcCcc-hhHHHHH
Confidence 35668999999999999955555 44454544 44444444445553221 24667753 4455666 4556666
Q ss_pred HHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccc
Q 026500 114 LHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKR 154 (237)
Q Consensus 114 ~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~R 154 (237)
....+..+++ ....+ ..-+..|.+|+.||++.-..-+..
T Consensus 164 ~~~~~~~~~~-~~~~~-~~~~~al~~Gr~Da~~~d~~~~~~ 202 (275)
T COG0834 164 KKPGPNAKIV-AYDSN-AEALLALKNGRADAVVSDSAVLAG 202 (275)
T ss_pred hhccCCceEE-eeCCH-HHHHHHHHcCCccEEEcchHhhhh
Confidence 6677888888 66655 778999999999999987665555
No 22
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=93.28 E-value=0.68 Score=48.92 Aligned_cols=144 Identities=15% Similarity=0.169 Sum_probs=80.7
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-CCCccCCCCCeeecCChh-HHHHHHHhC
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-ASLAELPAGSIVGTASLR-RKSQILHRY 117 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-~~l~~Lp~ga~IGTSS~R-R~aql~~~~ 117 (237)
-.+...+|.+|++|++.-.+. -|. ..+.+.+.- |-=..| -++|.++. ....++..|.+||..+-- -...++..+
T Consensus 351 ~~~~~~~l~~g~~D~i~~~~~-t~~-r~~~~~fs~-py~~~~-~~~v~~~~~~~~~~~~~g~~vav~~g~~~~~~~~~~~ 426 (1197)
T PRK09959 351 NIHAGTQLNPGGWDIIPGAIY-SED-RENNVLFAE-AFITTP-YVFVMQKAPDSEQTLKKGMKVAIPYYYELHSQLKEMY 426 (1197)
T ss_pred HHHHHHHHHCCCceEeecccC-Ccc-ccccceecc-ccccCC-EEEEEecCCCCccccccCCEEEEeCCcchHHHHHHHC
Confidence 446777899999998654442 222 112221110 111111 23444432 223444468777753221 135677889
Q ss_pred CCCeEEeccCCCHHHHHHhhccCCccEEeeecccc----cccCCCCcceeeecCCCCCCCCCCceEEEEEecCchhhhhh
Q 026500 118 PSLKVMENFRGNVQTRLRKLNERVVQATLLALAGL----KRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPF 193 (237)
Q Consensus 118 pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL----~RLgl~~~i~~~l~~~~~lPA~GQGalave~R~~d~~~~~~ 193 (237)
|+.+++ .. .|.+.-+..|.+|+.||.|....-. ++.+.. ...... .|+...--+++-++++++.+.++
T Consensus 427 p~~~~~-~~-~~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~-~l~~~~-----~~~~~~~~~~~av~k~~~~L~~~ 498 (1197)
T PRK09959 427 PEVEWI-KV-DNASAAFHKVKEGELDALVATQLNSRYMIDHYYPN-ELYHFL-----IPGVPNASLSFAFPRGEPELKDI 498 (1197)
T ss_pred CCcEEE-Ec-CCHHHHHHHHHcCCCCEEehhhHHHHHHHHhcccc-cceeee-----cCCCCchheEEeeCCCCHHHHHH
Confidence 999998 55 5889999999999999998744322 222211 111111 11111123677789999988888
Q ss_pred hc
Q 026500 194 TT 195 (237)
Q Consensus 194 l~ 195 (237)
+.
T Consensus 499 ln 500 (1197)
T PRK09959 499 IN 500 (1197)
T ss_pred HH
Confidence 75
No 23
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=93.15 E-value=0.64 Score=42.15 Aligned_cols=144 Identities=17% Similarity=0.185 Sum_probs=72.8
Q ss_pred HHHhcCCccEEEee---CCCCCCCCCCCceeeeecCCCC--CCeEEEeCCCCCCccCCCCCeeec--CChhHHHHHHHhC
Q 026500 45 EALINSQIDIAVHS---MKDVPTYLPEKTILPCNLQRED--VRDAFISLSAASLAELPAGSIVGT--ASLRRKSQILHRY 117 (237)
Q Consensus 45 ~aLl~g~iDiAVHS---lKDlP~~l~~gL~iaav~~R~d--prD~LV~~~~~~l~~Lp~ga~IGT--SS~RR~aql~~~~ 117 (237)
++|.+|..|+||-| ++---.+ .+++.++.-+--.. ...+||.+++. -.....|.+||- +|+=.+.--+..+
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 78999999999988 2333333 45666544322211 23677876653 345667999995 4444443334444
Q ss_pred C--CCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcce-eeecCCCCCCCCCCceEEEEEecCchhhhhhh
Q 026500 118 P--SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVT-NILSVDDMLPAVAQGAIGIACRSNDEKMVPFT 194 (237)
Q Consensus 118 p--dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i~-~~l~~~~~lPA~GQGalave~R~~d~~~~~~l 194 (237)
+ ++++| ++++ ..=+..|.+|+.||.|+=...++.-.. .+. ..++...+.-..++. .|.+|++|..+..+|
T Consensus 135 ~gk~Ve~V-ei~Y--~q~~~~l~~g~IDA~IWN~d~i~~~~~--~l~~~~l~~~~~~~~~seA--Vivi~~~~~~i~~ll 207 (232)
T PF14503_consen 135 EGKNVEFV-EIPY--NQLLELLRSGEIDAAIWNYDEIEDKNF--GLKYVPLKDDPMSKDASEA--VIVIRKDNEPIKALL 207 (232)
T ss_dssp TTS--EEE-E--H--HHHHHHHHHTS--EEEEE--HHCCHHC--TEEEEE--SSCHHHHTT-E--EEEEETT-HHHHHHH
T ss_pred CCCceEEE-EecH--HHHHHHHHCCCccEEEECCcccccccC--CeeEEeCCchHHHHhcCee--EEEEeCCCHHHHHHH
Confidence 4 56677 6664 467888899999999997774333321 121 223333333334444 367899999999888
Q ss_pred ccc
Q 026500 195 THS 197 (237)
Q Consensus 195 ~~~ 197 (237)
++.
T Consensus 208 ~~~ 210 (232)
T PF14503_consen 208 RKL 210 (232)
T ss_dssp HHH
T ss_pred HHh
Confidence 743
No 24
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=93.08 E-value=0.57 Score=49.53 Aligned_cols=141 Identities=12% Similarity=0.106 Sum_probs=78.0
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCC---CCCCccCCCCCeeec---CChhHHHHHH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS---AASLAELPAGSIVGT---ASLRRKSQIL 114 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~---~~~l~~Lp~ga~IGT---SS~RR~aql~ 114 (237)
.++-++|.+|+||++..++-.-|. ..+.+.+.. +-=.++- ++|.++ ..++.++ .|.+||. ++. ...++
T Consensus 107 ~~~l~~l~~g~iDl~~~~~~~~~~-r~~~~~fs~-py~~~~~-~~v~~~~~~~~~~~~l-~~~~i~~~~g~~~--~~~~~ 180 (1197)
T PRK09959 107 QKAMDALEEGEVDIVLSHLVASPP-LNDDIAATK-PLIITFP-ALVTTLHDSMRPLTSS-KPVNIARVANYPP--DEVIH 180 (1197)
T ss_pred HHHHHHHHcCCCcEecCccccccc-cccchhcCC-CccCCCc-eEEEeCCCCCCCcccc-cCeEEEEeCCCCC--HHHHH
Confidence 588899999999998765433221 122222111 0001111 122222 1234444 4555553 222 56788
Q ss_pred HhCCCCeEEeccCCCHHHHHHhhccCCccEEeeeccc----ccccCCCCcceeeecCCCCCCCCCCceEEEEEecCchhh
Q 026500 115 HRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAG----LKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKM 190 (237)
Q Consensus 115 ~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AG----L~RLgl~~~i~~~l~~~~~lPA~GQGalave~R~~d~~~ 190 (237)
..+|+.+++ ... |...-+..|.+|+.||+|...+- +++-+... . .+... .+.+-+. .++-++++++.+
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 89999999999999999986543 22221111 1 11111 1112222 345568888878
Q ss_pred hhhhc
Q 026500 191 VPFTT 195 (237)
Q Consensus 191 ~~~l~ 195 (237)
.+++.
T Consensus 253 ~~~ln 257 (1197)
T PRK09959 253 NEVLN 257 (1197)
T ss_pred HHHHH
Confidence 77764
No 25
>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=92.59 E-value=0.75 Score=39.39 Aligned_cols=110 Identities=14% Similarity=0.096 Sum_probs=62.0
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCC-CCCC-ceeee-ecCCCC--CC-eEEEeCCC---CCCccCCCCCeeecCChh---
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTY-LPEK-TILPC-NLQRED--VR-DAFISLSA---ASLAELPAGSIVGTASLR--- 108 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~-l~~g-L~iaa-v~~R~d--pr-D~LV~~~~---~~l~~Lp~ga~IGTSS~R--- 108 (237)
.++.++|.+|++|+++.+.=..+.. ...+ ..+.. +..... .+ -+||.+++ .+++|| .|.+||+.+..
T Consensus 75 ~~~~~~l~~g~~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~~i~~~~dL-~gk~I~~~~~~s~~ 153 (254)
T TIGR01098 75 SAVIEAMRFGRVDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADSPIKSLKDL-KGKTFAFGDPASTS 153 (254)
T ss_pred HHHHHHHHcCCccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCCCCCChHHh-cCCEEEeeCCCCcc
Confidence 3577899999999999765333211 1112 11111 111111 11 25666543 457788 48888864321
Q ss_pred --H--HHHHHHhCC------CCeEEeccCCCHHHHHHhhccCCccEEeeeccccc
Q 026500 109 --R--KSQILHRYP------SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLK 153 (237)
Q Consensus 109 --R--~aql~~~~p------dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~ 153 (237)
- ...++..+. +.+++ . -++.++-+..|.+|+.||.+....-+.
T Consensus 154 ~~~~~~~~l~~~~~~~~~~~~~~i~-~-~~~~~~~~~al~~G~~Da~~~~~~~~~ 206 (254)
T TIGR01098 154 GYLVPRYQLKKEGGLDADGFFSEVV-F-SGSHDASALAVANGKVDAATNNSSAIG 206 (254)
T ss_pred chHhHHHHHHHhcCCChHHhhhhee-e-cCchHHHHHHHHcCCCCeEEecHHHHH
Confidence 1 123343332 24554 3 356678899999999999998765543
No 26
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=92.10 E-value=0.3 Score=44.41 Aligned_cols=107 Identities=8% Similarity=0.076 Sum_probs=64.5
Q ss_pred HHHHHHhcCCccEEEeeCCCCCCC--CCCCceeeeecCCCCCCeEEEeCCC-CCCccCCCCCeeecCC---hhH--HHHH
Q 026500 42 EIDEALINSQIDIAVHSMKDVPTY--LPEKTILPCNLQREDVRDAFISLSA-ASLAELPAGSIVGTAS---LRR--KSQI 113 (237)
Q Consensus 42 eLe~aLl~g~iDiAVHSlKDlP~~--l~~gL~iaav~~R~dprD~LV~~~~-~~l~~Lp~ga~IGTSS---~RR--~aql 113 (237)
++-++|.+|++|+++-+.-.+... ....+.+.++.......+++|.+++ ++++|| +|.+||+.+ ... ...|
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 567999999999996543211111 1122444455555555577887643 678888 599999732 111 1123
Q ss_pred HHh---CCCCeEEeccCCCHHHHHHhhccCCccEEeeecccc
Q 026500 114 LHR---YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGL 152 (237)
Q Consensus 114 ~~~---~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL 152 (237)
+.. ..|++++ ++. -..-..-|.+|+.||+++..--.
T Consensus 142 ~~~Gl~~~dv~~v-~~~--~~~~~~Al~~G~VDAa~~~~p~~ 180 (320)
T PRK11480 142 KHWGIKPGQVEIV-NLQ--PPAIIAAWQRGDIDGAYVWAPAV 180 (320)
T ss_pred HHcCCCHhheEEE-ECC--cHHHHHHHHcCCcCEEEEcchHH
Confidence 332 1356665 543 56677889999999998754433
No 27
>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=91.65 E-value=1.5 Score=37.66 Aligned_cols=108 Identities=11% Similarity=0.007 Sum_probs=59.0
Q ss_pred HHHHHHhcCCccEEEeeCCCCCCCC--CCCceeeeecCCCCCCeEEEeCCC---CCCccCCCCCeeecC---ChhH-HHH
Q 026500 42 EIDEALINSQIDIAVHSMKDVPTYL--PEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTA---SLRR-KSQ 112 (237)
Q Consensus 42 eLe~aLl~g~iDiAVHSlKDlP~~l--~~gL~iaav~~R~dprD~LV~~~~---~~l~~Lp~ga~IGTS---S~RR-~aq 112 (237)
++-++|.+|++|+++-+.=..-... ...+.+.+..... ....+++++. ++++|| .|.+||++ |... -.+
T Consensus 41 ~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~-~~~~~v~~~~~~i~s~~dL-~Gk~i~~~~~~~~~~~~~~ 118 (288)
T TIGR01728 41 PALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSDN-KATAIVVIKGSPIRTVADL-KGKRIAVPKGGSGHDLLLR 118 (288)
T ss_pred HHHHHHhcCCccccccCCcHHHHHHhcCCCEEEEEEecCC-CceEEEECCCCCCCCHHHc-CCCEEEecCCccHHHHHHH
Confidence 4568999999999864321110111 1245555554432 3455555533 456677 57788753 2222 222
Q ss_pred HHHhC---C-CCeEEeccCCCHHHHHHhhccCCccEEeeecccccc
Q 026500 113 ILHRY---P-SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKR 154 (237)
Q Consensus 113 l~~~~---p-dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~R 154 (237)
+.... + +.+++ .. +...-+.-|.+|+.|++++...-...
T Consensus 119 ~l~~~G~~~~~v~~~-~~--~~~~~~~al~~g~vda~~~~~p~~~~ 161 (288)
T TIGR01728 119 ALLKAGLSGDDVTIL-YL--GPSDARAAFAAGQVDAWAIWEPWGSA 161 (288)
T ss_pred HHHHcCCCccceeEE-ec--CcHHHHHHHHCCCCCEEEeccchHhH
Confidence 22221 1 23333 23 35667888999999999986543333
No 28
>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=91.32 E-value=1.5 Score=38.61 Aligned_cols=145 Identities=12% Similarity=0.109 Sum_probs=74.0
Q ss_pred HHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-----CCCccCC--CCCeeecCChhH-HHHH
Q 026500 42 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-----ASLAELP--AGSIVGTASLRR-KSQI 113 (237)
Q Consensus 42 eLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-----~~l~~Lp--~ga~IGTSS~RR-~aql 113 (237)
++-.+|.+|++|++...+-.-|... +.+.+.. +-... ..+++.+++ .++++|. +|.+||+..-== ..++
T Consensus 83 ~~~~~l~~G~~Di~~~~~~~t~eR~-~~~~fs~-py~~~-~~~~~~~~~~~~~i~~~~dl~~~~g~~Igv~~g~~~~~~l 159 (275)
T TIGR02995 83 ALIPGLQAGRFDAIAAGLFIKPERC-KQVAFTQ-PILCD-AEALLVKKGNPKGLKSYKDIAKNPDAKIAAPGGGTEEKLA 159 (275)
T ss_pred HHHHHHHCCCcCEEeecccCCHHHH-hcccccc-ceeec-ceeEEEECCCCCCCCCHHHhccCCCceEEEeCCcHHHHHH
Confidence 5668899999999876443222211 1111111 00111 123333332 2455664 367776533211 2344
Q ss_pred HHh-CCCCeEEeccCCCHHHHHHhhccCCccEEeeeccccc----ccCCCCcceeeecCCCCCCCCCCceEEEEEecCch
Q 026500 114 LHR-YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLK----RLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDE 188 (237)
Q Consensus 114 ~~~-~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~----RLgl~~~i~~~l~~~~~lPA~GQGalave~R~~d~ 188 (237)
... .|..+++ ... +.++-++.|.+|++|++|.-..-+. ..+.. .+. ...+ +.+.+-+.-.++-+++++.
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 4666776 554 6788999999999999998554322 22321 221 1111 1122222223455677777
Q ss_pred hhhhhhc
Q 026500 189 KMVPFTT 195 (237)
Q Consensus 189 ~~~~~l~ 195 (237)
.+.+.+.
T Consensus 234 ~l~~~~n 240 (275)
T TIGR02995 234 ELRDAFN 240 (275)
T ss_pred HHHHHHH
Confidence 7776664
No 29
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=90.85 E-value=0.98 Score=43.90 Aligned_cols=105 Identities=15% Similarity=0.223 Sum_probs=64.1
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC----CCCccCCCCCeee----cCChhHHHH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA----ASLAELPAGSIVG----TASLRRKSQ 112 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~----~~l~~Lp~ga~IG----TSS~RR~aq 112 (237)
.++-.+|.+|++||++-++-.-|. ..+.+.+.... -...-++|.+++ .++++| .|.+|| |+..-.-..
T Consensus 91 ~~ll~aL~~G~iDi~~~~lt~T~e-R~~~~~FS~Py--~~~~~~lv~r~~~~~i~~l~dL-~Gk~I~V~~gS~~~~~L~~ 166 (482)
T PRK10859 91 SQLFDALDKGKADLAAAGLTYTPE-RLKQFRFGPPY--YSVSQQLVYRKGQPRPRSLGDL-KGGTLTVAAGSSHVETLQE 166 (482)
T ss_pred HHHHHHHhCCCCCEEeccCcCChh-hhccCcccCCc--eeeeEEEEEeCCCCCCCCHHHh-CCCeEEEECCCcHHHHHHH
Confidence 577889999999998776633332 12222222111 112344555432 345666 366665 343333344
Q ss_pred HHHhCCCCeEEecc-CCCHHHHHHhhccCCccEEeeecc
Q 026500 113 ILHRYPSLKVMENF-RGNVQTRLRKLNERVVQATLLALA 150 (237)
Q Consensus 113 l~~~~pdl~v~~~i-RGNV~TRL~KL~~ge~DaiILA~A 150 (237)
+...+|+++++ .. -.+.+.-++.|.+|++|++|.-..
T Consensus 167 l~~~~p~i~~~-~~~~~s~~e~l~aL~~G~iDa~v~d~~ 204 (482)
T PRK10859 167 LKKKYPELSWE-ESDDKDSEELLEQVAEGKIDYTIADSV 204 (482)
T ss_pred HHHhCCCceEE-ecCCCCHHHHHHHHHCCCCCEEEECcH
Confidence 55567998876 43 368899999999999999998544
No 30
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=90.54 E-value=0.41 Score=41.74 Aligned_cols=128 Identities=16% Similarity=0.138 Sum_probs=70.1
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCC-------CCCceeeeecCCCCCCeEEEeC------CCCCCccC----C--CCCe
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYL-------PEKTILPCNLQREDVRDAFISL------SAASLAEL----P--AGSI 101 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l-------~~gL~iaav~~R~dprD~LV~~------~~~~l~~L----p--~ga~ 101 (237)
.++-+||++|++|++.= +=.++.-. +..+.+.+-.. .++..++|.+ +.++++|| + .|.+
T Consensus 46 ~~~~~al~~G~iD~a~~-~~~~~~~~~~g~~~~~~~~~~~~~~~-~~g~~lvv~~~~~~~~~~~~~~dl~~~~~~~kGk~ 123 (252)
T PF13379_consen 46 ADILEALAAGEIDIAFV-LAPALIAIAKGAGGPDVDIVVLAGLS-QNGNALVVRNDLKDASDIKSLADLIKKRKAQKGKK 123 (252)
T ss_dssp HHHHHHHHCTSSSEEEE-CTHHHHHHHTTTTT----EEEEEECS-BSSEEEEECGGGTTCSTTCCGHHHHHTCCSCSTEE
T ss_pred HHHHHHHHcCCCCEEEe-chHHHHHHHcCCCCcccceEEeeccC-CCceEEEEcCccccCCCccCHHHHHhhhcccCCcE
Confidence 35679999999999976 32222211 22344444443 3444555542 34566666 1 6889
Q ss_pred eecC---ChhH-----HHHHHHhCC--CCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcceeeecCCCCC
Q 026500 102 VGTA---SLRR-----KSQILHRYP--SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDML 171 (237)
Q Consensus 102 IGTS---S~RR-----~aql~~~~p--dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i~~~l~~~~~l 171 (237)
||++ |.-. ..+-.-+.| |++++ .+.. ...+.-|.+|+.||.++..-=..++--+......++..++.
T Consensus 124 i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~-~~~~--~~~~~al~~g~iDa~~~~eP~~~~~~~~g~g~~v~~~~~~~ 200 (252)
T PF13379_consen 124 IAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLV-NVPP--PEMVAALRAGEIDAAVLWEPFASQAEAKGIGKIVADSGDVW 200 (252)
T ss_dssp EEESSTTSHHHHHHHHHHHHTT--TTTSSEEE-E--G--HHHHHHHHTTS-SEEEEETTHHHHHHHTTS-EEEEEHHHCS
T ss_pred EEEcCCCCHHHHHHHHHHHhCCCCcccceEEE-ecCH--HHHHHHHhCCCcCEEEecCCHHHHHHhccCCeEEEEecccc
Confidence 9985 3222 111112344 78998 7765 88999999999999998655433332111113445555554
Q ss_pred CC
Q 026500 172 PA 173 (237)
Q Consensus 172 PA 173 (237)
|.
T Consensus 201 ~~ 202 (252)
T PF13379_consen 201 GN 202 (252)
T ss_dssp TT
T ss_pred CC
Confidence 43
No 31
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=90.36 E-value=2 Score=38.55 Aligned_cols=112 Identities=19% Similarity=0.125 Sum_probs=76.4
Q ss_pred HHHHHHhcCCccEEEeeCCCCC--CCCCC--CceeeeecCCCCCCeEEEeCCCC---CCccCCCCCeeecCChhH-HHH-
Q 026500 42 EIDEALINSQIDIAVHSMKDVP--TYLPE--KTILPCNLQREDVRDAFISLSAA---SLAELPAGSIVGTASLRR-KSQ- 112 (237)
Q Consensus 42 eLe~aLl~g~iDiAVHSlKDlP--~~l~~--gL~iaav~~R~dprD~LV~~~~~---~l~~Lp~ga~IGTSS~RR-~aq- 112 (237)
..-++|..|.+|+++...-+.| ..... .+.+.+...+....-+++.+++. +++|| +|-+||.+..-- ...
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 3558999999999998888888 33333 48888888888766666665543 46777 788998876654 322
Q ss_pred HHHh-------CCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCC
Q 026500 113 ILHR-------YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSM 157 (237)
Q Consensus 113 l~~~-------~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl 157 (237)
|+.. ..|.+++ .+..+ .-...|.+|+.||.+...--..++-.
T Consensus 152 l~~~L~~~Gl~~~dv~~v-~~~~~--~~~~al~~g~vda~~~~ep~~~~~~~ 200 (335)
T COG0715 152 LRYALAKAGLDPDDVELV-NLPPA--DAVAALAAGQVDAFVVWEPWNAAAEG 200 (335)
T ss_pred HHHHHHHcCCCcccceEE-eeCcH--HHHHHHhcCCcceEEecCCchhhhhc
Confidence 2221 3455555 55544 67778899999997766555555433
No 32
>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=89.27 E-value=0.5 Score=39.47 Aligned_cols=105 Identities=18% Similarity=0.165 Sum_probs=61.2
Q ss_pred HHHHHHhcCCccEEEeeCCCCCCCCCCCc--eeeeecCCCCCCeEEEeCCC---CCCccCCCCCeeecCChhHH-----H
Q 026500 42 EIDEALINSQIDIAVHSMKDVPTYLPEKT--ILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTASLRRK-----S 111 (237)
Q Consensus 42 eLe~aLl~g~iDiAVHSlKDlP~~l~~gL--~iaav~~R~dprD~LV~~~~---~~l~~Lp~ga~IGTSS~RR~-----a 111 (237)
+..++|.+|++|+++=+.=-+......|. .+.+..-...+.. +++++. +++.|| +|-+||.++---. +
T Consensus 33 ~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~-l~~~~~s~i~~~~DL-kGK~i~v~~~s~~~~~~~~ 110 (216)
T PF09084_consen 33 DVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPNA-LVVRKDSGIKSPADL-KGKKIGVSRGSSSEYFLRA 110 (216)
T ss_dssp HHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCEE-EEEETTTS-SSGGGG-TTSEEEESTTSHHHHHHHH
T ss_pred HHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCceE-EEEeccCCCCCHHHh-CCCEEEEecCcchhHHHHH
Confidence 57799999999999876633333333443 3333222233444 444433 567777 6999998883221 2
Q ss_pred HHHHh---CCCCeEEeccCCCHHHHHHhhccCCccEEeeeccc
Q 026500 112 QILHR---YPSLKVMENFRGNVQTRLRKLNERVVQATLLALAG 151 (237)
Q Consensus 112 ql~~~---~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AG 151 (237)
.|+.. ..+++++ .+. -......|.+|+.||+++-...
T Consensus 111 ~l~~~g~~~~~v~~v-~~~--~~~~~~al~~g~vDa~~~~~~~ 150 (216)
T PF09084_consen 111 LLKKNGIDPDDVKIV-NLG--PPELAQALLSGQVDAAILWYPP 150 (216)
T ss_dssp HHHHTTT-GGGSEEE-ES---HHHHHHHHHTTSSSEEEEEEEC
T ss_pred HHHHhccccccceee-eee--hhhhhhhhhcCCCCEEEEccCC
Confidence 22222 2456766 553 3444458999999999944433
No 33
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=88.72 E-value=2.1 Score=38.80 Aligned_cols=101 Identities=13% Similarity=0.119 Sum_probs=60.5
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC---CCCccCCCCCeeecCChhHHHHH-HHh
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTASLRRKSQI-LHR 116 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~---~~l~~Lp~ga~IGTSS~RR~aql-~~~ 116 (237)
.++-.+|.+|++|+++=+. |+..+..........+.-...+=+++.++. .+++|| +|.+|||+...=..+. ...
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 4678999999999998653 221121111222221111223344444433 356777 5889999766543333 333
Q ss_pred CCCCeEEeccCCCHHHHHHhhccCCccEEee
Q 026500 117 YPSLKVMENFRGNVQTRLRKLNERVVQATLL 147 (237)
Q Consensus 117 ~pdl~v~~~iRGNV~TRL~KL~~ge~DaiIL 147 (237)
.-+.+++ ..-|+++. .+..|..||++-
T Consensus 132 gi~~~iv-~~~gs~ea---a~~~G~aDaivd 158 (287)
T PRK00489 132 GIDAEVV-ELSGAVEV---APRLGLADAIVD 158 (287)
T ss_pred CCceEEE-ECCCchhh---hhcCCcccEEEe
Confidence 3457888 88899997 455699999976
No 34
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=88.63 E-value=2.1 Score=38.37 Aligned_cols=103 Identities=14% Similarity=0.077 Sum_probs=59.5
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCC--CCCCceeeee--cCCCCCCeEEEeCCC---CCCccCCCCCeeecCC---hhH-
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTY--LPEKTILPCN--LQREDVRDAFISLSA---ASLAELPAGSIVGTAS---LRR- 109 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~--l~~gL~iaav--~~R~dprD~LV~~~~---~~l~~Lp~ga~IGTSS---~RR- 109 (237)
.++.++|.+|++|+++-+ +.|.. ...|+.+..+ ....+...++|.+++ .+++|| .|.+||+++ .+.
T Consensus 67 ~~~~~aL~~G~iDia~~~--~~~~~~~~~~g~~~~~v~~~~~~~~~~~lvv~~~s~i~s~~dL-~Gk~I~~~~gs~~~~~ 143 (314)
T PRK11553 67 PQMLEALNVGSIDLGSTG--DIPPIFAQAAGADLVYVGVEPPKPKAEVILVAENSPIKTVADL-KGHKVAFQKGSSSHNL 143 (314)
T ss_pred HHHHHHHHcCCCCEEccC--CHHHHHHHhCCCCEEEEEEecCCCcceEEEEeCCCCCCCHHHh-CCCEEeecCCCcHHHH
Confidence 468899999999999854 34332 1344433332 222233356666544 457777 466777643 222
Q ss_pred HHH-HHHhC---CCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 110 KSQ-ILHRY---PSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 110 ~aq-l~~~~---pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
-.+ ++... .+++++ ..+...-..-|.+|++||+++..
T Consensus 144 l~~~l~~~g~~~~dv~~v---~~~~~~~~~al~~G~vDa~~~~e 184 (314)
T PRK11553 144 LLRALRKAGLKFTDIQPT---YLTPADARAAFQQGNVDAWAIWD 184 (314)
T ss_pred HHHHHHHcCCCHHHeEEE---ecChHHHHHHHHcCCCCEEEEcC
Confidence 112 22221 133333 44666778889999999998753
No 35
>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=86.68 E-value=2.9 Score=37.39 Aligned_cols=101 Identities=16% Similarity=0.235 Sum_probs=62.3
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceee--eecCCCCCCeEEEeCCCCCCccCCCCCeeecCChhHHHH--HHH
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILP--CNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQ--ILH 115 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~ia--av~~R~dprD~LV~~~~~~l~~Lp~ga~IGTSS~RR~aq--l~~ 115 (237)
..+|-++|++|++|++.-|+=.-+..-.+-..+. ++..+..+.-+++..+ .+++++. |.+|+.++.-+.+. ++-
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 5789999999999999998866655333222222 4555788888877643 3577774 44777766666433 333
Q ss_pred hCCCC---eEEeccCCCHHHHHHhhccCCccEEee
Q 026500 116 RYPSL---KVMENFRGNVQTRLRKLNERVVQATLL 147 (237)
Q Consensus 116 ~~pdl---~v~~~iRGNV~TRL~KL~~ge~DaiIL 147 (237)
++++. +++ +....+..-+ .+|. ||.++
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 44444 777 7766665533 3666 88877
No 36
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=85.24 E-value=14 Score=32.49 Aligned_cols=142 Identities=17% Similarity=0.215 Sum_probs=70.9
Q ss_pred HHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC---CCCccCCCCCeeecC--ChhH---HHHHH
Q 026500 43 IDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGTA--SLRR---KSQIL 114 (237)
Q Consensus 43 Le~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~---~~l~~Lp~ga~IGTS--S~RR---~aql~ 114 (237)
+..+|.+|++|+++.++..=|.- .+.+.+..-. -.-.-+++.+++ .++++| .|.+||+. |.-- ..+++
T Consensus 93 ~~~~l~~g~~D~~~~~~~~t~eR-~~~~~fs~py--~~~~~~lvv~~~~~~~s~~dL-~g~~V~v~~gs~~~~~l~~~~~ 168 (259)
T PRK11917 93 RGPLLDNGSVDAVIATFTITPER-KRIYNFSEPY--YQDAIGLLVLKEKNYKSLADM-KGANIGVAQAATTKKAIGEAAK 168 (259)
T ss_pred HHHHHHCCCccEEEecccCChhh-hheeeeccCc--eeeceEEEEECCCCCCCHHHh-CCCeEEEecCCcHHHHHHHhhH
Confidence 44788999999999977543321 1111111100 000122333322 356777 47777652 2111 12233
Q ss_pred HhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcceeeecCCCCCCCCCCceEEEEEecCchhhhhhh
Q 026500 115 HRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPFT 194 (237)
Q Consensus 115 ~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i~~~l~~~~~lPA~GQGalave~R~~d~~~~~~l 194 (237)
...+..+++ ..- +...-++.|.+|++||++.-..-+..+ ..+. ...++ +.+.|. -+++-++++|+++.+.+
T Consensus 169 ~~~~~~~~~-~~~-~~~~~~~~l~~GrvDa~~~d~~~~~~~-~~~~-~~~~~-~~~~~~----~~~~a~~k~~~~l~~~l 239 (259)
T PRK11917 169 KIGIDVKFS-EFP-DYPSIKAALDAKRVDAFSVDKSILLGY-VDDK-SEILP-DSFEPQ----SYGIVTKKDDPAFAKYV 239 (259)
T ss_pred hcCCceeEE-ecC-CHHHHHHHHHcCCCcEEEecHHHHHHh-hhcC-CeecC-CcCCCC----ceEEEEeCCCHHHHHHH
Confidence 344555655 443 566678899999999998754322111 1111 11221 122221 13566788888776666
Q ss_pred ccc
Q 026500 195 THS 197 (237)
Q Consensus 195 ~~~ 197 (237)
...
T Consensus 240 n~~ 242 (259)
T PRK11917 240 DDF 242 (259)
T ss_pred HHH
Confidence 543
No 37
>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=81.15 E-value=3.7 Score=33.40 Aligned_cols=41 Identities=12% Similarity=0.158 Sum_probs=36.6
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
++..++++..+|++++. -..|+-.+-++.|.+|++|..|..
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 57778889999999998 889999999999999999998853
No 38
>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=80.70 E-value=4 Score=31.63 Aligned_cols=42 Identities=10% Similarity=0.126 Sum_probs=36.2
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.+.-.+++..+|++++. -..++-++.+..|.+|++|..|...
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 46678889999999998 7788999999999999999988643
No 39
>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=80.56 E-value=3.4 Score=32.82 Aligned_cols=49 Identities=14% Similarity=0.121 Sum_probs=38.9
Q ss_pred CCeeecCC-------hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 99 GSIVGTAS-------LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 99 ga~IGTSS-------~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
|-+||+++ ++-..+++..+|++++. -.-++-.+-+.+|.+|++|..|..
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 45677665 34568888999999998 777777778899999999998853
No 40
>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=80.23 E-value=4.5 Score=31.35 Aligned_cols=42 Identities=17% Similarity=0.130 Sum_probs=35.8
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
...-++++..+|++++. -..++-..-+..|.+|++|..|...
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 35568889999999998 7888888889999999999988743
No 41
>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=79.69 E-value=4.3 Score=32.07 Aligned_cols=41 Identities=15% Similarity=0.139 Sum_probs=35.0
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
...-++++..+|++++. -..|+-..-+..|.+|++|..|..
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 36678888999999997 777888888999999999998863
No 42
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=79.11 E-value=11 Score=32.33 Aligned_cols=104 Identities=14% Similarity=0.104 Sum_probs=58.6
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCC----CCCCccCCCCCeeecCC-hhHHHHHHH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS----AASLAELPAGSIVGTAS-LRRKSQILH 115 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~----~~~l~~Lp~ga~IGTSS-~RR~aql~~ 115 (237)
.++-++|.+|++|+++=.+.--|.. .+-+.... +-..+ .-+++.++ ..++++| .|.+||... .=-...+..
T Consensus 73 ~~~~~~l~~G~vDi~~~~~~~t~~R-~~~~~fs~-p~~~~-~~~~~~~~~~~~~~~~~dL-~g~~I~v~~g~~~~~~l~~ 148 (247)
T PRK09495 73 SGIIPALQTKNVDLALAGITITDER-KKAIDFSD-GYYKS-GLLVMVKANNNDIKSVKDL-DGKVVAVKSGTGSVDYAKA 148 (247)
T ss_pred HHHHHHHhCCCcCEEEecCccCHHH-Hhhccccc-hheec-ceEEEEECCCCCCCChHHh-CCCEEEEecCchHHHHHHh
Confidence 3456889999999986443211111 11111110 11111 12333332 2356666 466665321 112456677
Q ss_pred hCCCCeEEeccCCCHHHHHHhhccCCccEEeeecc
Q 026500 116 RYPSLKVMENFRGNVQTRLRKLNERVVQATLLALA 150 (237)
Q Consensus 116 ~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~A 150 (237)
..|+.+++ ... |.++-+..|.+|++|+++.-..
T Consensus 149 ~~~~~~i~-~~~-~~~~~~~~L~~grvDa~i~~~~ 181 (247)
T PRK09495 149 NIKTKDLR-QFP-NIDNAYLELGTGRADAVLHDTP 181 (247)
T ss_pred cCCCCceE-EcC-CHHHHHHHHHcCceeEEEeChH
Confidence 78888887 554 7888899999999999997543
No 43
>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=78.83 E-value=5 Score=35.45 Aligned_cols=108 Identities=16% Similarity=0.142 Sum_probs=58.7
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCC--CCCCCceeeeecCCCC---CC-eEEEeCCC---CCCccCCCCCeeecC---Ch-
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPT--YLPEKTILPCNLQRED---VR-DAFISLSA---ASLAELPAGSIVGTA---SL- 107 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~--~l~~gL~iaav~~R~d---pr-D~LV~~~~---~~l~~Lp~ga~IGTS---S~- 107 (237)
.++-++|.+|++|+++-+.=.+.. +...+..+ .++.+.+ +. -++|.+++ ++++|| +|.+||+. |.
T Consensus 70 ~~~~~al~~g~~D~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~y~~~lvv~~ds~i~sl~DL-~Gk~v~~~~~~s~~ 147 (288)
T TIGR03431 70 AGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAF-AIEVNADGSTGYYSVLIVKKDSPIKSLEDL-KGKTFGFVDPNSTS 147 (288)
T ss_pred HHHHHHHHcCCccEEEEChHHHHHHHHhcCCeEE-EEeccCCCCCceEEEEEEeCCCCCCcHHHh-CCCEEEeeCCCcch
Confidence 456788999999999865311111 11222112 1111111 11 35565543 467778 58888853 21
Q ss_pred -h--HHHHHHHhC-CC----CeEEeccCCCHHHHHHhhccCCccEEeeeccc
Q 026500 108 -R--RKSQILHRY-PS----LKVMENFRGNVQTRLRKLNERVVQATLLALAG 151 (237)
Q Consensus 108 -R--R~aql~~~~-pd----l~v~~~iRGNV~TRL~KL~~ge~DaiILA~AG 151 (237)
- +...+.... .+ .+.+ ..-|+....+.-|.+|+.||.+....-
T Consensus 148 ~~~~~~~~l~~~~g~~~~~~~~~v-~~~~~~~~~~~al~~G~vDa~~~~~~~ 198 (288)
T TIGR03431 148 GFLVPSYYLFKKNGIKPKEYFKKV-TFSGSHEAAILAVANGTVDAATTNDEN 198 (288)
T ss_pred hhHHHHHHHHHhcCCChHHhHHhh-eecCchHHHHHHHHcCCCCeEeccHHH
Confidence 1 122332221 11 1223 344678889999999999999986543
No 44
>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=78.13 E-value=4.8 Score=31.12 Aligned_cols=41 Identities=20% Similarity=0.286 Sum_probs=34.8
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.--.++++.+|++++. -..|+-++-++.|.+|++|-.|...
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 4457888899999998 7788888889999999999988754
No 45
>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=77.34 E-value=6.2 Score=30.93 Aligned_cols=47 Identities=13% Similarity=0.159 Sum_probs=37.8
Q ss_pred eeecCC-------hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 101 IVGTAS-------LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 101 ~IGTSS-------~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+||+++ ++-.++++..+|++++. -..++-.+-+..|.+|++|..|..
T Consensus 3 ~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08453 3 SLAFVSTADYSVLPELVRRFREAYPDVELQ-LREATSDVQLEALLAGEIDAGIVI 56 (200)
T ss_pred EEEEechHHhHHHHHHHHHHHHhCCCceEE-EEeCCHHHHHHHHHcCCCCEEEEe
Confidence 456654 35678888899999997 777888888999999999987764
No 46
>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=77.33 E-value=6.1 Score=31.49 Aligned_cols=41 Identities=10% Similarity=0.136 Sum_probs=34.5
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.=-+.+++.+|++++. -.-++-++-++.|.+|++|..|...
T Consensus 17 ~~l~~f~~~~P~i~l~-i~~~~~~~~~~~L~~g~~Dl~i~~~ 57 (200)
T cd08465 17 ALMRQLRAEAPGIDLA-VSQASREAMLAQVADGEIDLALGVF 57 (200)
T ss_pred HHHHHHHHHCCCcEEE-EecCChHhHHHHHHCCCccEEEecc
Confidence 4457778889999997 7778889999999999999988643
No 47
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=77.10 E-value=18 Score=32.87 Aligned_cols=138 Identities=17% Similarity=0.173 Sum_probs=71.5
Q ss_pred HHHHHHhcCCccEEEeeCCCCCCCCCCCceeee-ecCCCCCCeEEEeCCC---CCCccCCCCCeee----cCChhHHHHH
Q 026500 42 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPC-NLQREDVRDAFISLSA---ASLAELPAGSIVG----TASLRRKSQI 113 (237)
Q Consensus 42 eLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaa-v~~R~dprD~LV~~~~---~~l~~Lp~ga~IG----TSS~RR~aql 113 (237)
.+..+|.+|++|++.-++---|.- ...+.++. +. ...-.++.+++ .++++| .|-+|| |.+.. ++
T Consensus 97 ~~i~~L~~G~~Di~~~~~~~t~eR-~~~~~fS~Py~---~~~~~lv~r~~~~i~sl~dL-~Gk~V~v~~gs~~~~---~l 168 (302)
T PRK10797 97 NRIPLLQNGTFDFECGSTTNNLER-QKQAAFSDTIF---VVGTRLLTKKGGDIKDFADL-KGKAVVVTSGTTSEV---LL 168 (302)
T ss_pred hHHHHHHCCCccEEecCCccCcch-hhcceecccEe---eccEEEEEECCCCCCChHHc-CCCEEEEeCCCcHHH---HH
Confidence 356899999999988765333321 11111110 10 01122333222 356677 444444 33332 23
Q ss_pred HHh----CCCCeEEeccCCCHHHHHHhhccCCccEEeeec---ccc-cccCCCCcceeeecCCCCCCCCCCceEEEEEec
Q 026500 114 LHR----YPSLKVMENFRGNVQTRLRKLNERVVQATLLAL---AGL-KRLSMTENVTNILSVDDMLPAVAQGAIGIACRS 185 (237)
Q Consensus 114 ~~~----~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~---AGL-~RLgl~~~i~~~l~~~~~lPA~GQGalave~R~ 185 (237)
+.+ .|..+++ . --+.++-++.|.+|++||++.-. ++. ..-.-... ...+. +. ......++-+++
T Consensus 169 ~~~~~~~~~~~~i~-~-~~~~~~~l~~L~~GrvDa~i~d~~~~~~~~~~~~~~~~-l~i~~-~~----~~~~~~~~a~~k 240 (302)
T PRK10797 169 NKLNEEQKMNMRII-S-AKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDN-WEIVG-KP----QSQEAYGCMLRK 240 (302)
T ss_pred HHHhhhcCCceEEE-E-eCCHHHHHHHHHcCCceEEEccHHHHHHHHHcCCCCcc-eEECC-cc----CCcCceeEEEeC
Confidence 332 3456776 3 44688999999999999998643 231 21111111 12222 11 223456777888
Q ss_pred Cchhhhhhhc
Q 026500 186 NDEKMVPFTT 195 (237)
Q Consensus 186 ~d~~~~~~l~ 195 (237)
+++++.+.+.
T Consensus 241 ~~~~L~~~in 250 (302)
T PRK10797 241 DDPQFKKLMD 250 (302)
T ss_pred CCHHHHHHHH
Confidence 8877666664
No 48
>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=76.72 E-value=6.7 Score=30.64 Aligned_cols=40 Identities=10% Similarity=0.101 Sum_probs=33.5
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+--.+++..+|++++. -.-|+-.+-+..|.+|++|..|..
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 4457788889999998 777888888999999999988763
No 49
>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=76.34 E-value=7.6 Score=30.63 Aligned_cols=41 Identities=12% Similarity=-0.026 Sum_probs=35.5
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.+.-+.+++.+|++++. -..+|-.+-.+.|.+|++|..|..
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 46678888999999998 788898889999999999998864
No 50
>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=76.23 E-value=6.8 Score=30.60 Aligned_cols=47 Identities=26% Similarity=0.345 Sum_probs=38.2
Q ss_pred eeecCC-------hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 101 IVGTAS-------LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 101 ~IGTSS-------~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+||+++ ++-.++++..+|++++. -.-++-..-+..|.+|++|-.|..
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 567764 35567888999999998 777888888999999999988753
No 51
>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=75.08 E-value=7 Score=30.31 Aligned_cols=41 Identities=10% Similarity=-0.040 Sum_probs=34.4
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
++-.+.+++.+|++++. -.-++-.+=+..|.+|++|-.|..
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 35568888999999998 777888888899999999998853
No 52
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=74.56 E-value=22 Score=30.78 Aligned_cols=101 Identities=10% Similarity=0.144 Sum_probs=53.0
Q ss_pred HHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC---CCCccCCCCCeeec---CChhHHHHHHH
Q 026500 42 EIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGT---ASLRRKSQILH 115 (237)
Q Consensus 42 eLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~---~~l~~Lp~ga~IGT---SS~RR~aql~~ 115 (237)
.+-+++.+|++|+++-.+-.-|. ....+.... +-=..+.-+++.++. .++++| .|.+||. |+.. ..+..
T Consensus 76 ~~~~~l~~g~~D~~~~~~~~t~e-R~~~~~fs~-p~~~~~~~~~~~~~~~~~~~~~dl-~g~~Igv~~g~~~~--~~~~~ 150 (259)
T PRK15437 76 ALIPSLKAKKIDAIMSSLSITEK-RQQEIAFTD-KLYAADSRLVVAKNSDIQPTVESL-KGKRVGVLQGTTQE--TFGNE 150 (259)
T ss_pred HHHHHHHCCCCCEEEecCCCCHH-Hhhhccccc-hhhcCceEEEEECCCCCCCChHHh-CCCEEEEecCcHHH--HHHHh
Confidence 45577899999999875532221 111121111 111122222222211 246677 5667775 2221 12222
Q ss_pred hC--CCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 116 RY--PSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 116 ~~--pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.. ++++++ ..- +.+.=+++|..|++|+++...
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 456678999999999998754
No 53
>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=74.13 E-value=9 Score=29.74 Aligned_cols=41 Identities=10% Similarity=0.278 Sum_probs=35.0
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
++--++++..+|++++. -.-++-++-+..|.+|++|..|..
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 35578899999999998 777788888999999999999864
No 54
>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=73.74 E-value=5.6 Score=31.03 Aligned_cols=40 Identities=5% Similarity=-0.075 Sum_probs=32.2
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
..-+.++..+|++++. -.-++.+.-++.|.+|++|..|..
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 5567888999999987 555566666888999999998874
No 55
>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=73.67 E-value=11 Score=29.25 Aligned_cols=41 Identities=12% Similarity=0.074 Sum_probs=34.3
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
+.-.+++..+|++++. -.-++-..-+++|.+|++|..|...
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 5668888999999997 6667778888999999999988754
No 56
>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=73.14 E-value=8.5 Score=29.67 Aligned_cols=40 Identities=15% Similarity=0.227 Sum_probs=33.7
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+--++++..+|++++. -.-|+-++-++.|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (193)
T cd08442 17 PLLAAYHARYPKVDLS-LSTGTTGALIQAVLEGRLDGAFVA 56 (193)
T ss_pred HHHHHHHHHCCCceEE-EEeCCcHHHHHHHHCCCccEEEEe
Confidence 5568888999999997 666777888889999999998864
No 57
>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=73.13 E-value=9.6 Score=29.71 Aligned_cols=40 Identities=15% Similarity=0.169 Sum_probs=32.9
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.--+++++.+|++++. -.-++-++-+..|.+|++|..|.-
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 4568888999999997 666677778899999999987763
No 58
>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=73.07 E-value=9.7 Score=29.34 Aligned_cols=40 Identities=13% Similarity=0.171 Sum_probs=34.3
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
..-+++++.+|++++. -.-|+-..-.+.|.+|++|..|..
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 5568888999999997 777888888999999999998863
No 59
>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=72.63 E-value=6.5 Score=30.62 Aligned_cols=41 Identities=5% Similarity=-0.003 Sum_probs=33.6
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
+-...+++.+|++++. -.-++-.+-++.|.+|++|..|...
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 60
>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=72.61 E-value=10 Score=29.32 Aligned_cols=42 Identities=14% Similarity=0.141 Sum_probs=35.4
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecc
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALA 150 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~A 150 (237)
..-..++..+|++++. -.-++-++-...|.+|++|..|....
T Consensus 17 ~~l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (196)
T cd08415 17 RAIARFRARHPDVRIS-LHTLSSSTVVEAVLSGQADLGLASLP 58 (196)
T ss_pred HHHHHHHHHCCCcEEE-EEecchHHHHHHHHcCCccEEEEeCC
Confidence 5667788889999998 77788888889999999999997644
No 61
>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=72.41 E-value=8.1 Score=30.79 Aligned_cols=40 Identities=10% Similarity=0.022 Sum_probs=34.2
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+-.+.++..+|++++. -..++-..=+..|.+|++|..+..
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 4457788889999997 777888889999999999999864
No 62
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=72.23 E-value=0.54 Score=40.55 Aligned_cols=113 Identities=19% Similarity=0.167 Sum_probs=68.5
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCC-CCCCceeeeecCC----CCCCeEEEeCCCC---CCccCCCCCeeecCChh----
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTY-LPEKTILPCNLQR----EDVRDAFISLSAA---SLAELPAGSIVGTASLR---- 108 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~-l~~gL~iaav~~R----~dprD~LV~~~~~---~l~~Lp~ga~IGTSS~R---- 108 (237)
.++.+++.+|++|+++=+.-....- ...|....|...+ ..-+-++|.++.. +++|| +|.+||..+.-
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 5888999999999997643222211 1235665566555 2334556665543 56677 78888876554
Q ss_pred ---HHHHH-HHhCCC----CeEEeccCCCHHHHHHhhccCCccEEeeecccccccC
Q 026500 109 ---RKSQI-LHRYPS----LKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLS 156 (237)
Q Consensus 109 ---R~aql-~~~~pd----l~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLg 156 (237)
-...| ...--+ .+.+ .-||-+.=+.-|.+|++|+.++....++++-
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 121111 3333 4568888899999999999999888777764
No 63
>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=71.88 E-value=9.9 Score=29.46 Aligned_cols=41 Identities=17% Similarity=0.189 Sum_probs=34.7
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.+.-+++++.+|++++. -..++-.+-+..|.+|++|..|..
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 36668889999999998 777887777888999999998864
No 64
>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=71.61 E-value=11 Score=28.28 Aligned_cols=49 Identities=20% Similarity=0.323 Sum_probs=36.3
Q ss_pred eeecCC-------hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecc
Q 026500 101 IVGTAS-------LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALA 150 (237)
Q Consensus 101 ~IGTSS-------~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~A 150 (237)
+||+++ .....++...+|++++. -..++-..-+..|.+|++|..|.-..
T Consensus 3 ~I~~~~~~~~~~l~~~i~~~~~~~p~i~i~-~~~~~~~~~~~~l~~g~~D~~i~~~~ 58 (197)
T cd05466 3 RIGASPSIAAYLLPPLLAAFRQRYPGVELS-LVEGGSSELLEALLEGELDLAIVALP 58 (197)
T ss_pred EEEechhhHHHHhHHHHHHHHHHCCCCEEE-EEECChHHHHHHHHcCCceEEEEcCC
Confidence 456655 24456777889999987 66666666788899999999886543
No 65
>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=71.15 E-value=11 Score=29.90 Aligned_cols=41 Identities=12% Similarity=0.148 Sum_probs=34.7
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.+.-+++...+|++++. -.-++-.+-++.|.+|++|..|..
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 35678899999999998 777887888899999999988864
No 66
>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=71.13 E-value=10 Score=29.42 Aligned_cols=40 Identities=13% Similarity=0.125 Sum_probs=34.5
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+-..+++..+|++++. -..++-.+-+..|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~i~v~-~~~~~~~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08447 17 RLLAAARAALPDVDLV-LREMVTTDQIEALESGRIDLGLLR 56 (198)
T ss_pred HHHHHHHHHCCCeEEE-EEeCCHHHHHHHHHcCCceEEEec
Confidence 5567888999999997 777888899999999999988864
No 67
>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=70.97 E-value=11 Score=30.01 Aligned_cols=41 Identities=12% Similarity=0.233 Sum_probs=35.1
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.+--.++.+.+|++++. -.-++-++-+..|.+|++|-.|..
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 68
>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=69.92 E-value=12 Score=28.92 Aligned_cols=41 Identities=10% Similarity=0.116 Sum_probs=34.0
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.+..+++++.+|++++. -.-++-..=+..|.+|++|..|..
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 46789999999999997 655776667788999999998864
No 69
>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=69.77 E-value=12 Score=28.92 Aligned_cols=42 Identities=14% Similarity=0.078 Sum_probs=35.6
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.+.-.+++..+|++++. -..++-+.-+..|.+|++|..|...
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 36678889999999998 7788888889999999999888654
No 70
>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=67.38 E-value=16 Score=27.89 Aligned_cols=41 Identities=10% Similarity=0.033 Sum_probs=33.0
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
+--..++..+|++++. -..++-..-...|.+|++|..|...
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 4457788899999997 6667777778889999999988753
No 71
>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=67.33 E-value=15 Score=28.60 Aligned_cols=40 Identities=13% Similarity=0.107 Sum_probs=33.7
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+--+++++.+|++++. -.-|+-.+-...|.+|++|-.|..
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 4457788899999997 777888888899999999998864
No 72
>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=67.19 E-value=13 Score=28.91 Aligned_cols=42 Identities=26% Similarity=0.269 Sum_probs=33.6
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.+--++++..+|++++. -..++-.+-+..|.+|++|..|.-.
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 6656666668889999999998743
No 73
>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=66.78 E-value=25 Score=30.44 Aligned_cols=19 Identities=0% Similarity=-0.036 Sum_probs=16.5
Q ss_pred HHHHHHhhccCCccEEeee
Q 026500 130 VQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 130 V~TRL~KL~~ge~DaiILA 148 (237)
..+-++.|.+|..||++.-
T Consensus 152 ~~~~~~aL~~GrvDa~i~~ 170 (246)
T TIGR03870 152 PRKLVSEVATGKADLAVAF 170 (246)
T ss_pred HHHHHHHHHcCCCCEEEee
Confidence 4678999999999999884
No 74
>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=66.05 E-value=12 Score=29.21 Aligned_cols=40 Identities=15% Similarity=0.114 Sum_probs=33.2
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.-.++++..+|++++. -..++-.+-+..|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~i~i~-i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08441 17 PVLDQFRERWPDVELD-LSSGFHFDPLPALLRGELDLVITS 56 (198)
T ss_pred HHHHHHHHhCCCeEEE-EEeCCchhHHHHHHcCCceEEEec
Confidence 5568889999999997 666777777899999999998864
No 75
>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=65.70 E-value=16 Score=28.81 Aligned_cols=41 Identities=7% Similarity=0.136 Sum_probs=33.8
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
++--.++++.+|++++. -.-|+-+.-++.|.+|++|..|..
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 44567888899999998 777887788899999999998863
No 76
>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=65.41 E-value=15 Score=28.23 Aligned_cols=42 Identities=10% Similarity=0.097 Sum_probs=34.8
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.+-.+.+.+.+|++++. -.-+|-++-+..|.+|++|..|...
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 35567888899999998 7778888888999999999988653
No 77
>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=65.18 E-value=52 Score=28.91 Aligned_cols=114 Identities=14% Similarity=0.085 Sum_probs=69.5
Q ss_pred HHHHHHHHhcCCccEEEeeCCC------------CCCCC-----------------------CCCceeeeecCCCCCCeE
Q 026500 40 TKEIDEALINSQIDIAVHSMKD------------VPTYL-----------------------PEKTILPCNLQREDVRDA 84 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKD------------lP~~l-----------------------~~gL~iaav~~R~dprD~ 84 (237)
.+|+=+++..|.+|+++.+.=- ||-.. ..|+.+.++... .-..
T Consensus 43 ~~e~~~~v~~G~~d~~~~~~~~~~~~~p~~~~~~lP~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~~--g~~~ 120 (257)
T TIGR00787 43 DRAMLEALQGGALDMTAPSSSKFGPLVPELAVFDLPFLFRDYNHVHKVLDGEVGKALKKSLEKKGLKGLAYWDN--GFRQ 120 (257)
T ss_pred hHHHHHHHhCCCccEEecccccccccCcchhhccCCeecCCHHHHHHHHcCHHHHHHHHHHHHcCcEEEeecCC--ceeE
Confidence 4688899999999999876432 33111 124443333321 1122
Q ss_pred EEeC--CCCCCccCCCCCeeecCC-hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcc
Q 026500 85 FISL--SAASLAELPAGSIVGTAS-LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENV 161 (237)
Q Consensus 85 LV~~--~~~~l~~Lp~ga~IGTSS-~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i 161 (237)
+.+. .-.+++|| +|.+|++.+ .=-...++.+ ....+ ++ ....=..-|.+|.+||++-....+.-+++.+..
T Consensus 121 ~~~~~~~i~s~~Dl-~G~kir~~~~~~~~~~~~~~--Ga~~v-~~--~~~e~~~aL~~G~vDg~~~~~~~~~~~~~~ev~ 194 (257)
T TIGR00787 121 FTSSKKPITKPEDL-KGLKIRIPNSPMNEAQFKAL--GANPE-PM--AFSEVYTALQTGVVDGQENPLSNVYSSKFYEVQ 194 (257)
T ss_pred eeeCCCccCChHHh-CCCEEecCCCHHHHHHHHHc--CCccc-cc--CHHHHHHHHHcCCcccccCCHHHHhhcchhhhc
Confidence 3322 23467777 699999853 3334444444 34433 33 356667788899999999988888888876444
No 78
>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=64.83 E-value=15 Score=28.95 Aligned_cols=39 Identities=8% Similarity=0.096 Sum_probs=33.2
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 147 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiIL 147 (237)
.--+++.+.+|++++. -..++-+.-+..|.+|++|..|.
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 3457778889999997 77788899999999999999885
No 79
>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=64.76 E-value=18 Score=28.16 Aligned_cols=42 Identities=10% Similarity=0.004 Sum_probs=34.0
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.+.-+.+++.+|++++. -..+.-.+-.+.|.+|++|..|...
T Consensus 17 ~~~l~~~~~~~P~v~i~-i~~~~~~~~~~~l~~g~~Dl~i~~~ 58 (197)
T cd08425 17 GPLIDRFHARYPGIALS-LREMPQERIEAALADDRLDLGIAFA 58 (197)
T ss_pred HHHHHHHHHHCCCcEEE-EEECcHHHHHHHHHcCCccEEEEec
Confidence 35567888899999997 6667777888899999999998653
No 80
>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=64.62 E-value=14 Score=28.86 Aligned_cols=42 Identities=12% Similarity=0.024 Sum_probs=34.7
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.+.-+++.+.+|++++. -.-++.++-+..|.+|++|-.|...
T Consensus 16 ~~~l~~~~~~~P~i~l~-~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08457 16 PRFLAAFLRLRPNLHLS-LMGLSSSQVLEAVASGRADLGIADG 57 (196)
T ss_pred HHHHHHHHHHCCCeEEE-EEecCcHHHHHHHHcCCccEEEecc
Confidence 46778889999999997 6677777778889999999888743
No 81
>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=62.56 E-value=20 Score=27.35 Aligned_cols=41 Identities=15% Similarity=0.213 Sum_probs=33.2
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
+.-++++..+|++++. -.-++-+.-++.|.+|++|..|...
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 4567888899999997 6667777778899999999888654
No 82
>PRK04056 Maf-like protein; Reviewed
Probab=60.81 E-value=8.7 Score=33.25 Aligned_cols=23 Identities=13% Similarity=0.101 Sum_probs=19.5
Q ss_pred eeecCChhHHHHHHHhCCCCeEE
Q 026500 101 IVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 101 ~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
+.|++|+||+..|..+..+.+++
T Consensus 3 ILAS~SprR~elL~~~g~~f~v~ 25 (180)
T PRK04056 3 ILASSSSTRANLLKEAGIEFEQK 25 (180)
T ss_pred EEeCCCHHHHHHHHHCCCCeEEE
Confidence 68999999999999987666655
No 83
>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=60.56 E-value=22 Score=27.67 Aligned_cols=42 Identities=12% Similarity=0.197 Sum_probs=35.0
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
+.--+.+++.+|++++. -..++-++-++.|.+|++|-.|...
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 35567888899999998 7778888888999999999988643
No 84
>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=60.29 E-value=16 Score=32.18 Aligned_cols=103 Identities=16% Similarity=0.121 Sum_probs=54.6
Q ss_pred HHHHHHHhcCCccEEEeeCCCC--------CC---CCCCCceeeeecCCCCCCeEEEeCCC---CCCccCCCCCeeec--
Q 026500 41 KEIDEALINSQIDIAVHSMKDV--------PT---YLPEKTILPCNLQREDVRDAFISLSA---ASLAELPAGSIVGT-- 104 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDl--------P~---~l~~gL~iaav~~R~dprD~LV~~~~---~~l~~Lp~ga~IGT-- 104 (237)
.++-++|.+|++|+++.+.-.. +. .-++.+...+.+-++ + -+++.++. ++++||. |.+|+.
T Consensus 72 ~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~-~-~~lvv~~d~~i~sl~dL~-gk~v~~~~ 148 (320)
T TIGR02122 72 VENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFEGPVEKLRALASLYPE-Y-IQIVVRKDSGIKTVADLK-GKRVAVGA 148 (320)
T ss_pred HHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccCCCCccHHhHHHhccc-c-EEEEEECCCCCCcHHHcC-CCEEecCC
Confidence 4667899999999999763211 00 112334422223222 2 23444432 4567774 444432
Q ss_pred --CChhHH-HHHHHhC---C-CCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 105 --ASLRRK-SQILHRY---P-SLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 105 --SS~RR~-aql~~~~---p-dl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
|+.+.. .++.... | +++.+ ... +....+..|.+|++|+++..
T Consensus 149 ~~s~~~~~~~~~l~~~G~~~~~~~~v-~~~-~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 149 PGSGTELNARAVLKAAGLTYDDVKKV-EYL-GYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred CCcchHHHHHHHHHHcCCCHHHccch-hcC-CHHHHHHHHHCCCccEEEEe
Confidence 334443 2333322 1 12223 333 45677899999999999976
No 85
>PRK04694 Maf-like protein; Reviewed
Probab=60.06 E-value=9.3 Score=33.30 Aligned_cols=23 Identities=13% Similarity=0.216 Sum_probs=19.7
Q ss_pred eeecCChhHHHHHHHhCCCCeEE
Q 026500 101 IVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 101 ~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
+.|++|+||+..|+.+.-+.+++
T Consensus 3 ILAS~SprR~elL~~~g~~f~~~ 25 (190)
T PRK04694 3 YLASRSPRRRELLQRLDVPFQTL 25 (190)
T ss_pred EEcCCCHHHHHHHHHCCCCcEEe
Confidence 67999999999999987777764
No 86
>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=60.04 E-value=22 Score=27.59 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=31.9
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+.-++++..+|++++. -.-++-..=+..|.+|++|..|..
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 554665666778889999998864
No 87
>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=59.80 E-value=20 Score=28.24 Aligned_cols=37 Identities=8% Similarity=0.077 Sum_probs=30.5
Q ss_pred HHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 110 KSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 110 ~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
-++++..+|++++. -..++- ..+..|.+|++|..|..
T Consensus 19 i~~~~~~~P~i~l~-i~~~~~-~~~~~l~~g~~D~~i~~ 55 (200)
T cd08462 19 IERVAREAPGVRFE-LLPPDD-QPHELLERGEVDLLIAP 55 (200)
T ss_pred HHHHHHHCCCCEEE-EecCCh-hHHHHHhcCCeeEEEec
Confidence 46778889999987 665765 88999999999999874
No 88
>PRK00078 Maf-like protein; Reviewed
Probab=59.70 E-value=9.4 Score=33.31 Aligned_cols=23 Identities=26% Similarity=0.398 Sum_probs=19.7
Q ss_pred eeecCChhHHHHHHHhCCCCeEE
Q 026500 101 IVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 101 ~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
+.|++|+||+..|+.+..+.+++
T Consensus 4 ILAS~SprR~elL~~~g~~f~v~ 26 (192)
T PRK00078 4 ILASASERRQELLKRILEDFQVI 26 (192)
T ss_pred EEeCCCHHHHHHHHhCCCCeEEe
Confidence 68999999999999987776665
No 89
>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=59.60 E-value=24 Score=26.97 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=32.1
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.+--.+++..+|++++. -.-++-..-+..|.+|++|..|..
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 34567788899999987 666776666778889999988764
No 90
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=58.22 E-value=23 Score=29.95 Aligned_cols=39 Identities=10% Similarity=0.140 Sum_probs=33.3
Q ss_pred HHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 109 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 109 R~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
--.++...+|++++. -..++.+.-+..|.+|++|..|..
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 777998888999999999988864
No 91
>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=56.96 E-value=2.7 Score=37.86 Aligned_cols=152 Identities=18% Similarity=0.117 Sum_probs=78.3
Q ss_pred HHHHHHhcCCccEEEeeC----CCCCCCCCCCceeeeecCCCCCCeEEEeCCCCCCccCCCCCeeecCC----hhHHHHH
Q 026500 42 EIDEALINSQIDIAVHSM----KDVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTAS----LRRKSQI 113 (237)
Q Consensus 42 eLe~aLl~g~iDiAVHSl----KDlP~~l~~gL~iaav~~R~dprD~LV~~~~~~l~~Lp~ga~IGTSS----~RR~aql 113 (237)
+...||.+|+||+-+.-- +.--.+ .|..+.++-+---..=.|-|.++++++++|+|++|+=+. .=|.-.+
T Consensus 38 ~~N~AL~~G~iDaN~fQh~~yl~~~n~~--~~~~L~~v~~~~~~p~glYS~k~~sl~~lp~Ga~VaIpnD~sN~~RaL~l 115 (237)
T PF03180_consen 38 QPNEALADGEIDANFFQHIPYLEQFNKE--NGYNLVPVGPTYIEPMGLYSKKYKSLDDLPDGATVAIPNDPSNQARALKL 115 (237)
T ss_dssp HHHHHHHTTSSSEEEEEEHHHHHHHHHH--HT--EEEEEEEEE---EEEESSSSSGGGS-TTEEEEEESSHHHHHHHHHH
T ss_pred hcChHHHCCCcceeccCCHHHHHHHHHH--CCCcEEEecceeEEeEEEeecccCchhhcCCCCEEEEeCCccchhHHHHH
Confidence 578999999999987632 111111 233333333221222335578899999999999999654 3455555
Q ss_pred HHhCC----------------------CCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcceeeecCCCCC
Q 026500 114 LHRYP----------------------SLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDML 171 (237)
Q Consensus 114 ~~~~p----------------------dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i~~~l~~~~~l 171 (237)
+...- +++|+ ++-. .+=-+-|. ++|+.|+...=...-|+...-.-++..+.
T Consensus 116 Lq~aGLI~Lk~~~~~~~t~~DI~~Npk~l~~~-evd~--~~l~~~l~--dvD~avi~~~~a~~agl~~~~~~~~~e~~-- 188 (237)
T PF03180_consen 116 LQEAGLITLKDGVGLTATVDDITENPKNLKFK-EVDA--AQLPRALD--DVDAAVINGNYALDAGLDPKKDLLFEEPD-- 188 (237)
T ss_dssp HHHTTSEEE-TT-GCC-SGGGEEEETTSEEEE-EE-G--GGHHHHTT--TSSEEEE-HHHHHHTT--CCCHSSEE-SS--
T ss_pred HHhCCeEEEcCCCCCccChhhhhhcccCceEE-EecH--hhHHhhcc--cCCEEEecHhHHHHcCcCcccceeeeecc--
Confidence 54322 23343 3321 11122233 39999985444455555433211222211
Q ss_pred CCCCCceEEEEEec---Cchhhhhhhccccccccc
Q 026500 172 PAVAQGAIGIACRS---NDEKMVPFTTHSQASILN 203 (237)
Q Consensus 172 PA~GQGalave~R~---~d~~~~~~l~~~~~~~~~ 203 (237)
..-.=+..+.+|+ +++.+..+.+..++....
T Consensus 189 -~~~~y~n~lv~r~~~~d~~~ik~l~ea~~s~~v~ 222 (237)
T PF03180_consen 189 -ADKPYANVLVVREDDKDDPWIKKLVEAYQSPEVK 222 (237)
T ss_dssp -SSCGGEEEEEEEGGGTTCHHHHHHHHHHTSHHHH
T ss_pred -cCcceeEEEEEECCccCCHHHHHHHHHHCCHHHH
Confidence 2455566677776 566777777777654333
No 92
>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=55.49 E-value=28 Score=26.86 Aligned_cols=41 Identities=17% Similarity=0.209 Sum_probs=34.7
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
++--+.++..+|++++. -.-++-+.-+..|.+|++|..|..
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 44578889999999997 777788888899999999998864
No 93
>PRK14363 Maf-like protein; Provisional
Probab=54.40 E-value=13 Score=32.99 Aligned_cols=23 Identities=22% Similarity=0.195 Sum_probs=19.8
Q ss_pred eeecCChhHHHHHHHhCCCCeEE
Q 026500 101 IVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 101 ~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
+.|++|+||+..|..+..+.+++
T Consensus 4 ILAS~SprR~elL~~~G~~f~v~ 26 (204)
T PRK14363 4 ILASSSPRRRQLMELLGIEFEVE 26 (204)
T ss_pred EEeCCCHHHHHHHHhCCCCeEEE
Confidence 78999999999999987776665
No 94
>PRK00032 Maf-like protein; Reviewed
Probab=54.28 E-value=13 Score=32.43 Aligned_cols=24 Identities=17% Similarity=0.232 Sum_probs=19.8
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.|++|+||+..|..+.-+.+++
T Consensus 4 iILAS~SprR~elL~~~g~~f~v~ 27 (190)
T PRK00032 4 LYLASGSPRRRELLTQLGVPFEVL 27 (190)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 378999999999999986666654
No 95
>PRK00148 Maf-like protein; Reviewed
Probab=54.04 E-value=13 Score=32.43 Aligned_cols=24 Identities=17% Similarity=0.004 Sum_probs=20.2
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.|++|+||+..|..+..+.+++
T Consensus 3 iILAS~SprR~elL~~~g~~f~~~ 26 (194)
T PRK00148 3 LVLASASPARLKLLRLAGIPPLVV 26 (194)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 378999999999999987777665
No 96
>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=54.00 E-value=21 Score=27.86 Aligned_cols=41 Identities=15% Similarity=0.138 Sum_probs=32.5
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
+--..+++.+|++++. -.-|+-+.-+..|.+|++|..|...
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 7777767778889999999988643
No 97
>PRK02478 Maf-like protein; Reviewed
Probab=53.89 E-value=13 Score=32.57 Aligned_cols=24 Identities=13% Similarity=0.070 Sum_probs=20.0
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.++||+||+..|..+.-+.+++
T Consensus 5 iILAS~SprR~elL~~~g~~f~v~ 28 (199)
T PRK02478 5 LILASKSPFRRALLENAGLEFSAA 28 (199)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEe
Confidence 478999999999999986666655
No 98
>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.
Probab=53.22 E-value=1.3e+02 Score=25.01 Aligned_cols=21 Identities=5% Similarity=-0.010 Sum_probs=18.5
Q ss_pred CHHHHHHhhccCCccEEeeec
Q 026500 129 NVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 129 NV~TRL~KL~~ge~DaiILA~ 149 (237)
+.++-++.|.+|+.||+|...
T Consensus 142 ~~~~~~~~l~~G~~Da~i~~~ 162 (232)
T TIGR03871 142 PPGRMVEDLAAGEIDVAIVWG 162 (232)
T ss_pred CHHHHHHHHHcCCcCEEEecc
Confidence 578899999999999999853
No 99
>PRK00234 Maf-like protein; Reviewed
Probab=52.84 E-value=15 Score=32.06 Aligned_cols=24 Identities=8% Similarity=0.069 Sum_probs=20.0
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.|++|+||+..|..+.-+.+++
T Consensus 4 iILAS~SprR~elL~~~gi~f~v~ 27 (192)
T PRK00234 4 LLLASSSPYRRELLARLRLPFTWA 27 (192)
T ss_pred EEEecCCHHHHHHHHHCCCCcEEE
Confidence 378999999999999987666655
No 100
>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=52.44 E-value=34 Score=26.17 Aligned_cols=41 Identities=12% Similarity=0.186 Sum_probs=34.0
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
+--+++...+|++++. -.-++-+.-+..|.+|++|-.|...
T Consensus 17 ~~l~~~~~~~P~v~i~-i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (194)
T cd08436 17 ELLARFHRRHPGVDIR-LRQAGSDDLLAAVREGRLDLAFVGL 57 (194)
T ss_pred HHHHHHHHHCCCcEEE-EecCCHHHHHHHHHcCCccEEEEec
Confidence 4458888999999998 6667777788899999999998754
No 101
>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=52.11 E-value=26 Score=27.09 Aligned_cols=40 Identities=13% Similarity=0.059 Sum_probs=33.8
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+--.++++.+|++++. -.-++-..-+..|.+|++|..|..
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 3457888899999998 777888888999999999998864
No 102
>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=51.87 E-value=20 Score=28.12 Aligned_cols=43 Identities=9% Similarity=0.120 Sum_probs=37.1
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeeccc
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAG 151 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AG 151 (237)
.--.+++..+|++++. -.-++-++-++.|.+|++|..|.....
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 4467888899999998 777898999999999999999887665
No 103
>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=51.84 E-value=16 Score=31.59 Aligned_cols=25 Identities=24% Similarity=0.186 Sum_probs=20.3
Q ss_pred CCeeecCChhHHHHHHHhCCCCeEE
Q 026500 99 GSIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 99 ga~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
--+.|++|+||+..|+.+.-+.+++
T Consensus 4 ~lILAS~SprR~elL~~~g~~f~v~ 28 (183)
T TIGR00172 4 ELILASQSPRRKELLEELGISFEQI 28 (183)
T ss_pred CEEEeCCCHHHHHHHHHCCCCeEEE
Confidence 3589999999999999986666654
No 104
>PRK14368 Maf-like protein; Provisional
Probab=51.37 E-value=15 Score=32.10 Aligned_cols=24 Identities=21% Similarity=0.243 Sum_probs=20.0
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.+++|+||+..|+.+.-+.+++
T Consensus 7 lILAS~SprR~eLL~~~g~~f~v~ 30 (193)
T PRK14368 7 IVLASASPRRSELLASAGIEFDVV 30 (193)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 488999999999999986666655
No 105
>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=51.33 E-value=29 Score=26.88 Aligned_cols=42 Identities=5% Similarity=0.036 Sum_probs=34.2
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecc
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALA 150 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~A 150 (237)
+-..+++..+|++++. -.-++-+.-+..|.+|++|..|....
T Consensus 17 ~~i~~~~~~~P~i~l~-~~~~~~~~~~~~l~~g~~D~~i~~~~ 58 (200)
T cd08417 17 PLLARLRQEAPGVRLR-FVPLDRDDLEEALESGEIDLAIGVFP 58 (200)
T ss_pred HHHHHHHhhCCCeEEE-eccCCHHHHHHHHHcCCCCEEEeecc
Confidence 4457888899999997 66677777788999999999987543
No 106
>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=51.33 E-value=36 Score=26.09 Aligned_cols=40 Identities=15% Similarity=0.216 Sum_probs=34.3
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
..-.+++..+|++++. -..++-+.-+..|.+|++|..|..
T Consensus 17 ~~l~~~~~~~p~i~i~-i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08414 17 RLLRRFRARYPDVELE-LREMTTAEQLEALRAGRLDVGFVR 56 (197)
T ss_pred HHHHHHHHHCCCcEEE-EecCChHHHHHHHHcCCccEEEEc
Confidence 5567888899999998 777888888999999999998864
No 107
>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=51.33 E-value=32 Score=26.48 Aligned_cols=41 Identities=20% Similarity=0.213 Sum_probs=34.4
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.+.-++++..+|++++. -.-++-++-...|.+|++|-.|..
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 45668889999999997 667888888889999999988864
No 108
>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=51.04 E-value=35 Score=29.10 Aligned_cols=38 Identities=26% Similarity=0.337 Sum_probs=32.1
Q ss_pred HHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEee
Q 026500 109 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 147 (237)
Q Consensus 109 R~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiIL 147 (237)
--+++...+|++++. -.-++.+.-+..|.+|++|..|.
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 346677889999997 66688888899999999999986
No 109
>PRK04425 Maf-like protein; Reviewed
Probab=51.04 E-value=16 Score=32.07 Aligned_cols=24 Identities=21% Similarity=0.274 Sum_probs=20.0
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.|++|+||+..|+.+.-+.+++
T Consensus 7 iILAS~SprR~elL~~~g~~f~v~ 30 (196)
T PRK04425 7 LVLGTSSVFRREQMERLGIAFQAA 30 (196)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 488999999999999986666655
No 110
>PRK14361 Maf-like protein; Provisional
Probab=50.92 E-value=16 Score=31.79 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=18.8
Q ss_pred eeecCChhHHHHHHHhCCCCeEE
Q 026500 101 IVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 101 ~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
+.|++|+||+..|+.+.-+.+++
T Consensus 2 ILAS~SprR~elL~~~g~~f~v~ 24 (187)
T PRK14361 2 ILASGSPRRRELLENLGVPFQVV 24 (187)
T ss_pred EEccCCHHHHHHHHHCCCCcEEE
Confidence 67999999999999986555554
No 111
>PRK14365 Maf-like protein; Provisional
Probab=50.07 E-value=15 Score=32.28 Aligned_cols=24 Identities=29% Similarity=0.259 Sum_probs=19.5
Q ss_pred CeeecCChhHHHHHHHh-CCCCeEE
Q 026500 100 SIVGTASLRRKSQILHR-YPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~-~pdl~v~ 123 (237)
-+.|+||+||+.-|..+ .-+.+++
T Consensus 4 iILaSsSprR~elL~~~~g~~f~vi 28 (197)
T PRK14365 4 IILASASPRRKELLKQLIGDNFLVY 28 (197)
T ss_pred EEEeCCCHHHHHHHhcCcCcCeEEE
Confidence 47899999999999985 6666665
No 112
>PRK01839 Maf-like protein; Reviewed
Probab=50.05 E-value=17 Score=32.23 Aligned_cols=25 Identities=12% Similarity=0.095 Sum_probs=20.4
Q ss_pred CCeeecCChhHHHHHHHhCCCCeEE
Q 026500 99 GSIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 99 ga~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
--+.|++|+||+..|..+.-+.+++
T Consensus 11 ~lILAS~SprR~elL~~~gi~f~v~ 35 (209)
T PRK01839 11 FLYLASQSPRRQELLQQLGVRFELL 35 (209)
T ss_pred CEEEeCCCHHHHHHHHHCCCCeEEe
Confidence 3689999999999999886556655
No 113
>PRK00884 Maf-like protein; Reviewed
Probab=49.70 E-value=18 Score=31.67 Aligned_cols=24 Identities=13% Similarity=0.121 Sum_probs=20.2
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.+++|+||+..|..+.-+.+++
T Consensus 4 iILAS~SprR~elL~~~g~~f~v~ 27 (194)
T PRK00884 4 LILASTSPYRRALLEKLQLPFECA 27 (194)
T ss_pred EEEeCCCHHHHHHHHHCCCCCEEE
Confidence 478999999999999987666665
No 114
>PRK14362 Maf-like protein; Provisional
Probab=49.67 E-value=18 Score=32.06 Aligned_cols=25 Identities=16% Similarity=0.230 Sum_probs=20.7
Q ss_pred CCeeecCChhHHHHHHHhCCCCeEE
Q 026500 99 GSIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 99 ga~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
.-+.|++|+||+..|+.+.-+.+++
T Consensus 13 ~iILAS~SprR~eLL~~~g~~f~v~ 37 (207)
T PRK14362 13 PVVLASGSPRRREFLEQMGLPFEVI 37 (207)
T ss_pred eEEEeCCCHHHHHHHHHCCCCcEEE
Confidence 3689999999999999986666654
No 115
>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=49.53 E-value=16 Score=31.44 Aligned_cols=23 Identities=26% Similarity=0.317 Sum_probs=20.0
Q ss_pred eeecCChhHHHHHHHhCCCCeEE
Q 026500 101 IVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 101 ~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
+.|++|+||+.-|+.+..+.+++
T Consensus 2 ILaS~SprR~elL~~~g~~f~~~ 24 (180)
T cd00555 2 ILASASPRRRELLEQLGIPFEVV 24 (180)
T ss_pred EECCCCHHHHHHHHhCCCCeEEE
Confidence 67999999999999987777766
No 116
>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=49.33 E-value=25 Score=27.34 Aligned_cols=41 Identities=12% Similarity=0.039 Sum_probs=33.4
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
...-+.++..+|++++. -..++-++-+..|.+|++|..|..
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 34557788899999997 666777788899999999998864
No 117
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=49.09 E-value=40 Score=30.19 Aligned_cols=42 Identities=10% Similarity=0.092 Sum_probs=35.3
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
...-..+...+|++++. -.-|+.+.-+..|.+|++|..|...
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 7788888889999999999988643
No 118
>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=48.72 E-value=21 Score=32.07 Aligned_cols=47 Identities=11% Similarity=0.076 Sum_probs=38.1
Q ss_pred eeecCCh------hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 101 IVGTASL------RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 101 ~IGTSS~------RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+||+|+. .--+..++.+|++++. -.-|+-++-++.|.+|++|..++.
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 6777773 2345667789999998 888899999999999999998764
No 119
>PRK14367 Maf-like protein; Provisional
Probab=48.47 E-value=18 Score=31.84 Aligned_cols=24 Identities=17% Similarity=0.105 Sum_probs=19.8
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.|++|+||+..|+.+.-+.+++
T Consensus 4 iILAS~SprR~eLL~~~Gi~f~v~ 27 (202)
T PRK14367 4 LYLGSNSPRRMEILTQLGYRVVKL 27 (202)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 378999999999999986666655
No 120
>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=48.28 E-value=37 Score=26.67 Aligned_cols=39 Identities=8% Similarity=0.072 Sum_probs=31.5
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+--.++++.+|++++. -.-|+- ..++.|.+|++|..|..
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 4457888899999997 666765 67889999999998863
No 121
>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=47.91 E-value=1.3e+02 Score=23.40 Aligned_cols=98 Identities=15% Similarity=0.031 Sum_probs=57.5
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-------CCCccCCCCCeeecC---ChhHH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA---SLRRK 110 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-------~~l~~Lp~ga~IGTS---S~RR~ 110 (237)
.++.++|.+|++|+++..... .++++....+. .++-=++++++. .++++|..-..|..+ ..+..
T Consensus 45 ~~~~~~l~~g~~Dl~i~~~~~----~~~~~~~~~l~--~~~~~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~ 118 (209)
T PF03466_consen 45 DELIEALRSGELDLAITFGPP----PPPGLESEPLG--EEPLVLVVSPDHPLAQKKPITLEDLADYPLILLSPGSPYRDQ 118 (209)
T ss_dssp HHHHHHHHTTSSSEEEESSSS----SSTTEEEEEEE--EEEEEEEEETTSGGGTTSSSSGGGGTTSEEEEESTTTSHHHH
T ss_pred hhhhHHHhcccccEEEEEeec----ccccccccccc--ceeeeeeeeccccccccccchhhhhhhccccccccccccccc
Confidence 578999999999999998776 45555433332 333333333321 246677655555522 23332
Q ss_pred H--HHHHhCCCCeEEeccCCCHHHHHHhhccCCccEE
Q 026500 111 S--QILHRYPSLKVMENFRGNVQTRLRKLNERVVQAT 145 (237)
Q Consensus 111 a--ql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~Dai 145 (237)
. .+.......+++ -.=.|+++-+.-+.+|..=++
T Consensus 119 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~gi~~ 154 (209)
T PF03466_consen 119 LDRWLREHGFSPNIV-IEVDSFESILSLVASGDGIAI 154 (209)
T ss_dssp HHHHHHHTTEEEEEE-EEESSHHHHHHHHHTTSEBEE
T ss_pred ccccccccccccccc-ccccchhhhccccccccceee
Confidence 1 123334444554 456799999999988864444
No 122
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=47.64 E-value=39 Score=29.56 Aligned_cols=41 Identities=12% Similarity=0.152 Sum_probs=35.0
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
++.-..+...+|++++. -.-|+-..=+..|.+|++|-.|..
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 123
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=45.98 E-value=87 Score=27.83 Aligned_cols=119 Identities=18% Similarity=0.148 Sum_probs=72.7
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCC-----------------------------------CCceeeeecCCCCCCeEE
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLP-----------------------------------EKTILPCNLQREDVRDAF 85 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~-----------------------------------~gL~iaav~~R~dprD~L 85 (237)
.|+-+++.+|.+||++.+.--++...| .|+.+.++.. ..++ .+
T Consensus 44 ~e~~~~v~~G~vdm~~~~~~~~~~~~p~~~~~~lP~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~L~~~~-~g~~-~~ 121 (286)
T PF03480_consen 44 AEVLEAVQDGAVDMAVVSPSYLAGFVPEFGVFDLPFLFRDYEELDRVMDSGYGPELREELEEKGIKLLGWFP-GGPR-QF 121 (286)
T ss_dssp HHHHHHHHTTSSSEEEEEGGGGTTTSGGGGGGGSTTTSSSHHHHHHHHHSHHHHHHHHHHHHTTEEEEEEEE-EEEE-EE
T ss_pred HHHHHHHhCCCccEEeecchhhhhhchhheeeeCCCCCCCHHHHHHHHhCcHHHHHHHHHHhhceEEEEEec-CCce-EE
Confidence 588899999999999987743332222 3444444321 1122 23
Q ss_pred Ee--CCCCCCccCCCCCeeecC-ChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccccCCCCcce
Q 026500 86 IS--LSAASLAELPAGSIVGTA-SLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVT 162 (237)
Q Consensus 86 V~--~~~~~l~~Lp~ga~IGTS-S~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~RLgl~~~i~ 162 (237)
.+ +.-.+++|| +|.+|.|. |.-=...++. =....+ ++..+ .=..-|..|.+||.+-....+..+++.+...
T Consensus 122 ~~~~~pi~s~~Dl-kG~kiR~~~~~~~~~~~~~--lGa~pv-~ip~~--evy~aLq~G~vDg~~~~~~~~~~~~~~ev~~ 195 (286)
T PF03480_consen 122 FSTKKPIRSPEDL-KGLKIRVPGSPVMSDFFEA--LGASPV-PIPWS--EVYQALQQGVVDGAENSASSIYSLGLYEVAK 195 (286)
T ss_dssp EESSS--SSGGGG-TTEEEEETSSHHHHHHHHH--CTSEEE-E-TGG--GHHHHHHTTSSSEEEEEHHHHHHTTGGGTSS
T ss_pred EecccCCccHhhH-hhCeEEecCCHHHHHHHHH--cCCeee-cCcHH--HHHHHHhcCCcCeEecCHHHHHhcChhhhCC
Confidence 33 233567777 79999998 5433333333 244555 55543 3344566999999999999999999876655
Q ss_pred eeecC
Q 026500 163 NILSV 167 (237)
Q Consensus 163 ~~l~~ 167 (237)
++..+
T Consensus 196 y~~~~ 200 (286)
T PF03480_consen 196 YFTDT 200 (286)
T ss_dssp EEEEE
T ss_pred eeEee
Confidence 54443
No 124
>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=45.79 E-value=12 Score=32.58 Aligned_cols=31 Identities=16% Similarity=0.289 Sum_probs=13.5
Q ss_pred eeecCChhHHHHHHHhCCCCeEEeccCCCHHHHH
Q 026500 101 IVGTASLRRKSQILHRYPSLKVMENFRGNVQTRL 134 (237)
Q Consensus 101 ~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL 134 (237)
+.|++|+||+..|+....+.+++ + =+++.+.
T Consensus 4 ILaS~SprR~elL~~~g~~f~v~-~--~~~dE~~ 34 (195)
T PF02545_consen 4 ILASSSPRRRELLKQLGINFEVI-P--SDIDEDA 34 (195)
T ss_dssp EE----HHHHHHHHCTT--EEE------------
T ss_pred EEeCCCHHHHHHHHHCCCCeEEE-c--CCCCCCC
Confidence 68999999999999987666554 3 3355554
No 125
>PRK02141 Maf-like protein; Reviewed
Probab=45.36 E-value=22 Score=31.47 Aligned_cols=25 Identities=16% Similarity=0.165 Sum_probs=20.5
Q ss_pred CCeeecCChhHHHHHHHhCCCCeEE
Q 026500 99 GSIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 99 ga~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
.-+.+++|+||+..|+.+.-+.+++
T Consensus 10 ~iILAS~SprR~elL~~~G~~f~v~ 34 (207)
T PRK02141 10 RLILASSSRYRRELLERLRLPFDVV 34 (207)
T ss_pred CEEEeCCCHHHHHHHHHCCCCeEEE
Confidence 4589999999999999986666655
No 126
>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=45.24 E-value=44 Score=26.44 Aligned_cols=40 Identities=15% Similarity=0.087 Sum_probs=33.4
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+--+.++..+|++++. -..++-++-+..|.+|++|..|..
T Consensus 18 ~~l~~~~~~~P~i~l~-~~~~~~~~~~~~l~~~~~D~~i~~ 57 (198)
T cd08485 18 LLLRQLLSVAPSATVS-LTQMSKNRQIEALDAGTIDIGFGR 57 (198)
T ss_pred HHHHHHHHhCCCcEEE-EEECCHHHHHHHHHcCCccEEEec
Confidence 4457778889999997 777888888889999999998864
No 127
>PRK14364 Maf-like protein; Provisional
Probab=44.57 E-value=18 Score=31.26 Aligned_cols=22 Identities=14% Similarity=0.250 Sum_probs=18.3
Q ss_pred eecCChhHHHHHHHhCCCCeEE
Q 026500 102 VGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 102 IGTSS~RR~aql~~~~pdl~v~ 123 (237)
.|++|+||+..|+.+.-+.+++
T Consensus 1 LAS~SprR~elL~~~g~~f~v~ 22 (181)
T PRK14364 1 LASSSPRRRELLQQLGLNFEIY 22 (181)
T ss_pred CCCCCHHHHHHHHHCCCCeEEE
Confidence 3789999999999987666665
No 128
>PRK14366 Maf-like protein; Provisional
Probab=44.14 E-value=25 Score=30.88 Aligned_cols=24 Identities=13% Similarity=0.077 Sum_probs=18.7
Q ss_pred CeeecCChhHHHHHHHhCC-CCeEE
Q 026500 100 SIVGTASLRRKSQILHRYP-SLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~p-dl~v~ 123 (237)
-+.|++|+||+..|+.+.- ..+++
T Consensus 7 iILAS~SprR~elL~~~G~~~~~v~ 31 (195)
T PRK14366 7 LILASSSKQRLALLEQIGVVPGEIV 31 (195)
T ss_pred EEEeCCCHHHHHHHHhCCCCCCEEe
Confidence 4899999999999998754 44443
No 129
>PRK00648 Maf-like protein; Reviewed
Probab=44.09 E-value=23 Score=30.84 Aligned_cols=24 Identities=25% Similarity=0.245 Sum_probs=19.6
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.|++|+||+..|+.+.-+.+++
T Consensus 5 lILAS~SprR~elL~~~g~~f~v~ 28 (191)
T PRK00648 5 IILASSSPRRKEILEGFRIPFEVV 28 (191)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE
Confidence 478999999999999986665544
No 130
>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=43.05 E-value=25 Score=27.75 Aligned_cols=23 Identities=22% Similarity=0.290 Sum_probs=19.2
Q ss_pred eeecCChhHHHHHHHhC-CCCeEE
Q 026500 101 IVGTASLRRKSQILHRY-PSLKVM 123 (237)
Q Consensus 101 ~IGTSS~RR~aql~~~~-pdl~v~ 123 (237)
+++|+|+||+..+.++. -++.++
T Consensus 2 iLaS~s~~R~~~l~~~~~~~~~~~ 25 (131)
T cd00985 2 ILASGSPRRLEELKQIGGIEFEVL 25 (131)
T ss_pred EEecCChHHHHHHHhcCCCCEEEe
Confidence 68999999999999998 466555
No 131
>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=41.16 E-value=42 Score=26.43 Aligned_cols=41 Identities=15% Similarity=0.079 Sum_probs=33.5
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.--+++++.+|++++. -.-++-++=++.|.+|++|..|...
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 7778878888999999999988643
No 132
>KOG0463 consensus GTP-binding protein GP-1 [General function prediction only]
Probab=40.89 E-value=15 Score=36.62 Aligned_cols=57 Identities=23% Similarity=0.258 Sum_probs=38.8
Q ss_pred CCCCceEEEEEecCchhhhhhhccccccccccccccc--chhHHHHHHHHhhhhhhHHH
Q 026500 173 AVAQGAIGIACRSNDEKMVPFTTHSQASILNTFNCSG--KLCYKLHFGFLNLVELRRII 229 (237)
Q Consensus 173 A~GQGalave~R~~d~~~~~~l~~~~~~~~~~~~~~~--~~c~~~~~~~~~~~~~~~~~ 229 (237)
+||---+-|.+|+-|+-+.........++---|..|+ ..-..+=++|||||+.|+..
T Consensus 304 S~gcrK~PvlVrs~DDVv~~A~NF~Ser~CPIFQvSNVtG~NL~LLkmFLNlls~R~~~ 362 (641)
T KOG0463|consen 304 SPGCRKLPVLVRSMDDVVHAAVNFPSERVCPIFQVSNVTGTNLPLLKMFLNLLSLRRQL 362 (641)
T ss_pred CCCcccCcEEEecccceEEeeccCccccccceEEeccccCCChHHHHHHHhhcCccccc
Confidence 4666678888998887666555555445555554442 34456669999999999753
No 133
>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=40.55 E-value=48 Score=25.39 Aligned_cols=38 Identities=18% Similarity=0.256 Sum_probs=31.4
Q ss_pred HHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 110 KSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 110 ~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
...++..+|++++. -..++-+.-+..|.+|++|..|..
T Consensus 18 l~~~~~~~P~i~l~-i~~~~~~~~~~~l~~g~~Dl~i~~ 55 (197)
T cd08419 18 LGAFCRRHPGVEVS-LRVGNREQVLERLADNEDDLAIMG 55 (197)
T ss_pred HHHHHHHCCCceEE-EEECCHHHHHHHHhcCCccEEEec
Confidence 56778889999987 666777777888999999998864
No 134
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=40.41 E-value=39 Score=29.35 Aligned_cols=40 Identities=15% Similarity=0.409 Sum_probs=34.7
Q ss_pred CCeeecCChhHH--HHHHHhCCCCeEEeccCCCHHHHHHhhcc
Q 026500 99 GSIVGTASLRRK--SQILHRYPSLKVMENFRGNVQTRLRKLNE 139 (237)
Q Consensus 99 ga~IGTSS~RR~--aql~~~~pdl~v~~~iRGNV~TRL~KL~~ 139 (237)
..+|.+|++.|. -+|+.-.|++.|+ -+-|.-++=++++.+
T Consensus 69 ~~vi~CSALKr~YRD~LR~~~~~~~Fv-~L~g~~~~i~~Rm~~ 110 (161)
T COG3265 69 HVVIACSALKRSYRDLLREANPGLRFV-YLDGDFDLILERMKA 110 (161)
T ss_pred ceEEecHHHHHHHHHHHhccCCCeEEE-EecCCHHHHHHHHHh
Confidence 469999999995 6799999999999 999999888887744
No 135
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=39.81 E-value=67 Score=28.58 Aligned_cols=42 Identities=10% Similarity=0.209 Sum_probs=34.7
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeecc
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALA 150 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~A 150 (237)
.--.+++..+|++++. -.-++.+.-+..|.+|++|..|....
T Consensus 114 ~~l~~~~~~~p~v~i~-~~~~~~~~~~~~l~~g~~Dl~i~~~~ 155 (312)
T PRK10341 114 DMINKFKEVFPKAQVS-MYEAQLSSFLPAIRDGRLDFAIGTLS 155 (312)
T ss_pred HHHHHHHHhCCCCEEE-EEeCCHHHHHHHHHcCCCcEEEecCC
Confidence 3357777889999998 77888888999999999999886543
No 136
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=39.77 E-value=68 Score=29.17 Aligned_cols=42 Identities=17% Similarity=0.191 Sum_probs=36.2
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
+..-..+...+|++++. -.-|+-+.=++.|.+|++|..|+..
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 35567788999999998 8888988899999999999999753
No 137
>PRK01526 Maf-like protein; Reviewed
Probab=39.46 E-value=32 Score=30.43 Aligned_cols=24 Identities=13% Similarity=0.090 Sum_probs=18.8
Q ss_pred CeeecCChhHHHHHHHhCC-CCeEE
Q 026500 100 SIVGTASLRRKSQILHRYP-SLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~p-dl~v~ 123 (237)
-+.|++|+||+..|..+.- ..+++
T Consensus 10 lILAS~SprR~elL~~~g~~~~~v~ 34 (205)
T PRK01526 10 IILASSSPARIELLNRIKIIPSQII 34 (205)
T ss_pred EEEeCCCHHHHHHHHhcCCCCceEe
Confidence 5899999999999998854 44443
No 138
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=37.88 E-value=64 Score=28.75 Aligned_cols=42 Identities=12% Similarity=-0.021 Sum_probs=35.4
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.+--+.++..+|++++. -..||-.+=+..|.+|++|..|...
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 34467888899999998 7788888888999999999999754
No 139
>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=37.84 E-value=66 Score=25.72 Aligned_cols=38 Identities=8% Similarity=-0.054 Sum_probs=29.1
Q ss_pred HHHHHHhCCCCeEEeccCC-CHHHHHHhhccCCccEEeee
Q 026500 110 KSQILHRYPSLKVMENFRG-NVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 110 ~aql~~~~pdl~v~~~iRG-NV~TRL~KL~~ge~DaiILA 148 (237)
-.++++.+|++++. -.-+ +-++-+..|.+|++|..|.-
T Consensus 19 l~~~~~~~P~~~v~-~~~~~~~~~l~~~L~~g~lDl~i~~ 57 (203)
T cd08463 19 VARFRREAPGARLE-IHPLGPDFDYERALASGELDLVIGN 57 (203)
T ss_pred HHHHHHHCCCCEEE-EEeCCcchhHHHHHhcCCeeEEEec
Confidence 35667789999997 5444 44677888999999998863
No 140
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=37.55 E-value=73 Score=27.54 Aligned_cols=40 Identities=20% Similarity=0.209 Sum_probs=32.7
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+--++++..+|++++. -.-++-..-+..|.+|++|..|..
T Consensus 106 ~~l~~~~~~~P~i~i~-v~~~~~~~~~~~l~~g~~Di~i~~ 145 (290)
T PRK10837 106 AMIARYRRDYPQLPLE-LSVGNSQDVINAVLDFRVDIGLIE 145 (290)
T ss_pred HHHHHHHHHCCCceEE-EEECCHHHHHHHHHhCCceEEEec
Confidence 5557888899999987 555777778889999999998864
No 141
>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=37.55 E-value=1.9e+02 Score=22.30 Aligned_cols=103 Identities=12% Similarity=0.074 Sum_probs=51.2
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCC-------CCCCccCCCCCeeecCC---hhH
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS-------AASLAELPAGSIVGTAS---LRR 109 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~-------~~~l~~Lp~ga~IGTSS---~RR 109 (237)
+.++.++|.+|++|+++....+. ..++++....+ ..++-=++++++ ..++++|..-..|..++ .|+
T Consensus 38 ~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~l~~~~l--~~~~~~~~~~~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~ 113 (198)
T cd08437 38 SAELLEQLLQGDLDIALLGSLTP--LENSALHSKII--KTQHFMIIVSKDHPLAKAKKVNFADLKKENFILLNEHFVHPK 113 (198)
T ss_pred HHHHHHHHHcCCCCEEEecCCCC--CCcccceEEEe--ecceEEEEecCCCcccccCcccHHHHcCCCeEEecccchHHH
Confidence 35788999999999999643221 11234432211 112222222211 12455555444554432 233
Q ss_pred HH-HHH-HhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 110 KS-QIL-HRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 110 ~a-ql~-~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
.. ++. ......+++ -.-.|+.+-++-+.+|.. ..++.
T Consensus 114 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~g-i~~~p 152 (198)
T cd08437 114 AFDSLCQQANFQPNIV-YRTNDIHILKSMVRENVG-IGFLT 152 (198)
T ss_pred HHHHHHHHcCCCccEE-EEeCcHHHHHHHHHcCCc-EEEEE
Confidence 22 121 222234444 445789999998888854 33444
No 142
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=37.29 E-value=75 Score=28.39 Aligned_cols=41 Identities=10% Similarity=0.176 Sum_probs=34.0
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.-...+...+|++++. -.-++-..-+..|.+|++|..|...
T Consensus 110 ~~l~~~~~~~p~i~l~-~~~~~~~~~~~~L~~g~~D~~i~~~ 150 (313)
T PRK12684 110 AAIKEFKKRYPKVRLS-ILQGSPTQIAEMVLHGQADLAIATE 150 (313)
T ss_pred HHHHHHHHHCCCceEE-EEeCChHHHHHHHHCCCcCEEEeec
Confidence 4556778889999997 7678888888999999999988653
No 143
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=36.89 E-value=83 Score=27.66 Aligned_cols=40 Identities=18% Similarity=0.329 Sum_probs=33.8
Q ss_pred HHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 109 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 109 R~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
--.++...+|++++. -.-++-++-+..|.+|++|-+|...
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 7778889999999999999999753
No 144
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=36.22 E-value=79 Score=28.27 Aligned_cols=39 Identities=13% Similarity=0.120 Sum_probs=33.5
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 147 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiIL 147 (237)
+-...+...+|++++. -.-++.+.-+..|.+|++|..|.
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 77789999999999999998775
No 145
>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=35.80 E-value=51 Score=25.51 Aligned_cols=44 Identities=23% Similarity=0.175 Sum_probs=31.8
Q ss_pred eeecCC-------hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 101 IVGTAS-------LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 101 ~IGTSS-------~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+||+++ ++.-+.+.+.+|++++. -.-++ .+..|.+|++|..|..
T Consensus 4 ~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~-~~~~~---~~~~l~~g~~Dl~i~~ 54 (198)
T cd08479 4 RVNASFGFGRRHIAPALSDFAKRYPELEVQ-LELTD---RPVDLVEEGFDLDIRV 54 (198)
T ss_pred EEeccHHHHHHHHHHHHHHHHHHCCCeEEE-EEecC---ccccccccCccEEEEc
Confidence 566654 36677888899999987 44344 3567889999998763
No 146
>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=35.26 E-value=30 Score=26.97 Aligned_cols=37 Identities=16% Similarity=0.243 Sum_probs=27.6
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+.-.++++.+|++++. -. ....+.++.+|++|..|..
T Consensus 20 ~~l~~f~~~~P~v~i~-~~---~~~~~~~l~~~~~D~~i~~ 56 (199)
T cd08478 20 PLIAKFRERYPDIELE-LV---SNEGIIDLIERKTDVAIRI 56 (199)
T ss_pred HHHHHHHHHCCCeEEE-EE---eccccccchhccccEEEEe
Confidence 5678888899999987 33 2344556778999998864
No 147
>COG0424 Maf Nucleotide-binding protein implicated in inhibition of septum formation [Cell division and chromosome partitioning]
Probab=35.04 E-value=39 Score=29.92 Aligned_cols=24 Identities=21% Similarity=0.270 Sum_probs=18.8
Q ss_pred CeeecCChhHHHHHHHhCCCCeEE
Q 026500 100 SIVGTASLRRKSQILHRYPSLKVM 123 (237)
Q Consensus 100 a~IGTSS~RR~aql~~~~pdl~v~ 123 (237)
-+.|++|+||+..|..+.=+.+++
T Consensus 5 LiLAS~SPrR~elL~~~gi~f~~~ 28 (193)
T COG0424 5 LILASSSPRRRELLEQLGIPFEVI 28 (193)
T ss_pred EEEecCCHHHHHHHHHCCCCeEEe
Confidence 478999999999999985444443
No 148
>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=34.46 E-value=64 Score=25.80 Aligned_cols=41 Identities=5% Similarity=-0.045 Sum_probs=32.2
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
.--..+++.+|++++. -..++-.+-.+.|.+|++|..|...
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 3446788889999997 6666666678888999999988743
No 149
>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=34.24 E-value=88 Score=27.31 Aligned_cols=40 Identities=20% Similarity=0.184 Sum_probs=33.6
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 147 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiIL 147 (237)
+..-.++...+|++++. -.-++-+.=+.-|.+|++|-.|.
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 35678899999999998 77778777788899999999885
No 150
>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=34.20 E-value=54 Score=25.33 Aligned_cols=20 Identities=30% Similarity=0.577 Sum_probs=17.4
Q ss_pred HHHHHHHhcCCccEEEeeCC
Q 026500 41 KEIDEALINSQIDIAVHSMK 60 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlK 60 (237)
.++.+.|.+|++|+|++...
T Consensus 39 ~~~~~~l~~g~~D~~i~~~~ 58 (200)
T cd08417 39 DDLEEALESGEIDLAIGVFP 58 (200)
T ss_pred HHHHHHHHcCCCCEEEeecc
Confidence 47899999999999998654
No 151
>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=32.57 E-value=41 Score=25.22 Aligned_cols=23 Identities=22% Similarity=0.114 Sum_probs=21.5
Q ss_pred cccHHHHHHHHhcCCccEEEeeC
Q 026500 37 GLFTKEIDEALINSQIDIAVHSM 59 (237)
Q Consensus 37 GlFtkeLe~aLl~g~iDiAVHSl 59 (237)
|+||-=+..+|-+|.||-+||--
T Consensus 21 G~vTaLl~~lLe~g~Vd~vv~~~ 43 (82)
T PF04422_consen 21 GVVTALLAYLLESGLVDGVVVVG 43 (82)
T ss_pred HHHHHHHHHHHHcCCceEEEEEe
Confidence 79999999999999999999966
No 152
>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=31.70 E-value=64 Score=24.62 Aligned_cols=100 Identities=15% Similarity=0.110 Sum_probs=49.5
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC--------CCCccCCCCCeeec---CChh
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA--------ASLAELPAGSIVGT---ASLR 108 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~--------~~l~~Lp~ga~IGT---SS~R 108 (237)
+.++.+.|.+|++|+++..... ..++++..-.+ ..++ -+++...+ .++++|..-..|.. ++.|
T Consensus 38 ~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~~~~~l--~~~~-~~~~~~~~~~l~~~~~~~~~~L~~~~~i~~~~~~~~~ 111 (194)
T cd08436 38 SDDLLAAVREGRLDLAFVGLPE---RRPPGLASREL--AREP-LVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGAR 111 (194)
T ss_pred HHHHHHHHHcCCccEEEEecCC---CCCCCcEEEEe--ecce-EEEEecCCCcccCCCccCHHHHhCCCeEEecCcccHH
Confidence 3578899999999999976543 22344433222 1122 22332221 12344433333332 2234
Q ss_pred HH-HHH-HHhCCCCeEEeccCCCHHHHHHhhccCCccEEe
Q 026500 109 RK-SQI-LHRYPSLKVMENFRGNVQTRLRKLNERVVQATL 146 (237)
Q Consensus 109 R~-aql-~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiI 146 (237)
+. .+. .......++. -.=.|..+-++-+.+|..=|++
T Consensus 112 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~gi~~~ 150 (194)
T cd08436 112 RQVDRAFAAAGVRRRVA-FEVSDVDLLLDLVARGLGVALL 150 (194)
T ss_pred HHHHHHHHHcCCCCceE-EEeccHHHHHHHHHcCCceEEe
Confidence 33 222 2222223333 2346888888888888643333
No 153
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=31.55 E-value=65 Score=27.61 Aligned_cols=52 Identities=15% Similarity=0.227 Sum_probs=38.0
Q ss_pred CCCccCCCCCeeecCChhHHHHHH-HhCCCCeEEeccCCCHHHHHHhhccCCccEEe
Q 026500 91 ASLAELPAGSIVGTASLRRKSQIL-HRYPSLKVMENFRGNVQTRLRKLNERVVQATL 146 (237)
Q Consensus 91 ~~l~~Lp~ga~IGTSS~RR~aql~-~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiI 146 (237)
.++.+|+.+.+|.|+-++=..+.. ...-+.+++ .+.|+++-.-. -|-.|+|+
T Consensus 59 ~~~~~l~~~~rIATkyp~l~~~yf~~~g~~~~ii-~l~GsvE~ap~---~glAD~Iv 111 (163)
T PF01634_consen 59 KSVEDLKAGLRIATKYPNLTRRYFAEKGINVEII-KLSGSVELAPP---LGLADAIV 111 (163)
T ss_dssp CCGGGGSSTEEEEES-HHHHHHHHHHCT-EEEEE-E-SS-TTHHHH---TTSSSEEE
T ss_pred CCHHHhccCCEEEECCHHHHHHHHHHcCCcEEEE-EccCCccccCC---CCCCCEEE
Confidence 467888889999999999865554 455689999 99999987644 67789886
No 154
>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=31.52 E-value=62 Score=25.35 Aligned_cols=20 Identities=25% Similarity=0.346 Sum_probs=17.1
Q ss_pred HHHHHHHHhcCCccEEEeeC
Q 026500 40 TKEIDEALINSQIDIAVHSM 59 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSl 59 (237)
+.++.+.|.+|++|+++...
T Consensus 38 ~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08452 38 SPDQVEELLKGRIDIGFLHP 57 (197)
T ss_pred hHHHHHHHHCCCccEEEeeC
Confidence 45789999999999999754
No 155
>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=31.26 E-value=91 Score=24.20 Aligned_cols=98 Identities=13% Similarity=0.028 Sum_probs=48.0
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-------CCCccCCCCCeeec----C-Ch
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGT----A-SL 107 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-------~~l~~Lp~ga~IGT----S-S~ 107 (237)
..++.++|.+|++|+|+... +.+...++++...-+ ..++--+++++.. .++++|-.-..|.- + +.
T Consensus 38 ~~~~~~~l~~g~~D~~i~~~-~~~~~~~~~~~~~~l--~~~~~~~v~~~~hp~~~~~~i~~~~L~~~~~i~~~~~~~~~~ 114 (200)
T cd08453 38 SDVQLEALLAGEIDAGIVIP-PPGASAPPALAYRPL--LSEPLVLAVPAAWAAEGGAPLALAAVAAEPLVIFPRRIAPAF 114 (200)
T ss_pred HHHHHHHHHcCCCCEEEEec-CcccCCCcceeEEEe--eeCceEEEEECCCccccCCCCCHHHhccCCEEeccCCcCCcH
Confidence 35788999999999999753 222223455532221 2233223333221 13344433333321 1 23
Q ss_pred hHH-HHH-HHhCCCCeEEeccCCCHHHHHHhhccCC
Q 026500 108 RRK-SQI-LHRYPSLKVMENFRGNVQTRLRKLNERV 141 (237)
Q Consensus 108 RR~-aql-~~~~pdl~v~~~iRGNV~TRL~KL~~ge 141 (237)
|+. .++ .......++. ---.++.+=++-+.+|.
T Consensus 115 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~ 149 (200)
T cd08453 115 HDAVTGYYRAAGQTPRIA-QEAIQMQTIISLVSAGM 149 (200)
T ss_pred HHHHHHHHHHcCCCCcee-eccccHHHHHHHHHcCC
Confidence 332 122 2222223343 33467888888888874
No 156
>PRK01441 Maf-like protein; Reviewed
Probab=31.25 E-value=52 Score=29.05 Aligned_cols=21 Identities=14% Similarity=0.072 Sum_probs=17.7
Q ss_pred CCeeecCChhHHHHHHHhCCC
Q 026500 99 GSIVGTASLRRKSQILHRYPS 119 (237)
Q Consensus 99 ga~IGTSS~RR~aql~~~~pd 119 (237)
--+.|++|+||+..|+.+.-+
T Consensus 6 ~iILAS~SprR~elL~~~Gi~ 26 (207)
T PRK01441 6 KLVLASGSPRRVELLNQAGIE 26 (207)
T ss_pred cEEEeCCCHHHHHHHHhcCCC
Confidence 358999999999999988554
No 157
>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=31.13 E-value=59 Score=25.20 Aligned_cols=19 Identities=16% Similarity=0.350 Sum_probs=16.3
Q ss_pred HHHHHHHhcCCccEEEeeC
Q 026500 41 KEIDEALINSQIDIAVHSM 59 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSl 59 (237)
.++.+.|.+|++|++++..
T Consensus 39 ~~~~~~l~~g~~Dl~i~~~ 57 (200)
T cd08466 39 EDLFEDLRLQEVDLVIDYV 57 (200)
T ss_pred HhHHHHHHcCCccEEEecc
Confidence 4688999999999999863
No 158
>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=31.00 E-value=86 Score=24.31 Aligned_cols=39 Identities=10% Similarity=0.074 Sum_probs=27.8
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
..-.++++. |++++. -.-++-+.-.+.|.+|++|.+|..
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 345666666 588876 555776666788889999976654
No 159
>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=30.90 E-value=46 Score=26.26 Aligned_cols=19 Identities=26% Similarity=0.356 Sum_probs=16.3
Q ss_pred HHHHHHHhcCCccEEEeeC
Q 026500 41 KEIDEALINSQIDIAVHSM 59 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSl 59 (237)
.++.+.|.+|++|++++..
T Consensus 39 ~~~~~~l~~g~~D~~i~~~ 57 (200)
T cd08467 39 DLAERGLEQGTIDLAVGRF 57 (200)
T ss_pred ccHHHHhhCCCcCEEEecC
Confidence 3688999999999999853
No 160
>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=30.51 E-value=68 Score=24.35 Aligned_cols=94 Identities=14% Similarity=0.117 Sum_probs=47.3
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-------CCCccCCCCCeeec---CChhHH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGT---ASLRRK 110 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-------~~l~~Lp~ga~IGT---SS~RR~ 110 (237)
.++.+.|.+|++|+|+-.... .++++....+. .++.-++++++. .++++|..-..|.. ++.++.
T Consensus 39 ~~~~~~l~~g~~D~~i~~~~~----~~~~~~~~~l~--~~~~~~~~~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~ 112 (197)
T cd08440 39 EQVIEAVRSGEVDFGIGSEPE----ADPDLEFEPLL--RDPFVLVCPKDHPLARRRSVTWAELAGYPLIALGRGSGVRAL 112 (197)
T ss_pred HHHHHHHHcCCccEEEEeCCC----CCCCeeEEEee--cccEEEEecCCCCcccCCccCHHHHccCCEEecCCCccHHHH
Confidence 578899999999999975432 23454433222 233333333221 12344433333332 223332
Q ss_pred -HH-HHHhCCCCeEEeccCCCHHHHHHhhccCC
Q 026500 111 -SQ-ILHRYPSLKVMENFRGNVQTRLRKLNERV 141 (237)
Q Consensus 111 -aq-l~~~~pdl~v~~~iRGNV~TRL~KL~~ge 141 (237)
.+ +.......++. -.-.|+.+-+.-+.+|.
T Consensus 113 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~ 144 (197)
T cd08440 113 IDRALAAAGLTLRPA-YEVSHMSTALGMVAAGL 144 (197)
T ss_pred HHHHHHHcCCCcceE-EEeccHHHHHHHHHcCC
Confidence 12 22222233333 33468888888888874
No 161
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=30.07 E-value=81 Score=28.44 Aligned_cols=41 Identities=7% Similarity=0.071 Sum_probs=34.5
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
...-++++..+|++++. -.-++-.+-+..|.+|++|..|..
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 44678889999999997 667777888999999999999864
No 162
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=29.87 E-value=96 Score=27.71 Aligned_cols=39 Identities=13% Similarity=-0.042 Sum_probs=32.3
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 147 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiIL 147 (237)
.-.++++..+|++++. -..|+-..-...|.+|++|..|.
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 4567888999999997 77777777778999999998774
No 163
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=29.62 E-value=82 Score=27.66 Aligned_cols=40 Identities=18% Similarity=0.255 Sum_probs=33.2
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
..-.++...+|++++. -.-+.....++.|.+|++|..|..
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 667778889999999999998864
No 164
>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=29.62 E-value=68 Score=24.53 Aligned_cols=19 Identities=21% Similarity=0.711 Sum_probs=16.5
Q ss_pred HHHHHHHhcCCccEEEeeC
Q 026500 41 KEIDEALINSQIDIAVHSM 59 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSl 59 (237)
.++.+.|.+|++|+++...
T Consensus 39 ~~~~~~L~~~~~Dl~i~~~ 57 (197)
T cd08438 39 KKVEQAVLNGELDVGITVL 57 (197)
T ss_pred HHHHHHHHcCCCCEEEEec
Confidence 5788999999999999764
No 165
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=29.44 E-value=79 Score=27.53 Aligned_cols=41 Identities=10% Similarity=0.011 Sum_probs=34.5
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
+--.++...+|++++. -.-++-+.-+..|.+|++|..|+..
T Consensus 107 ~~~~~~~~~~p~v~i~-~~~~~~~~~~~~l~~~~~D~~i~~~ 147 (296)
T PRK09906 107 KVLPMFRLRHPDTLIE-LVSLITTQQEEKLRRGELDVGFMRH 147 (296)
T ss_pred HHHHHHHHHCCCeEEE-EEeCCcHHHHHHHHcCCeeEEEecC
Confidence 4557788899999998 7777778889999999999999744
No 166
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=29.20 E-value=1e+02 Score=27.31 Aligned_cols=41 Identities=15% Similarity=0.196 Sum_probs=33.6
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeeec
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLAL 149 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~ 149 (237)
..-..+...+|++++. -.-++.++-++.|.+|++|..|...
T Consensus 110 ~~l~~~~~~~P~i~i~-i~~~~~~~~~~~l~~g~~D~~i~~~ 150 (309)
T PRK12682 110 RVVAAFRKRYPKVNLS-LHQGSPDEIARMVISGEADIGIATE 150 (309)
T ss_pred HHHHHHHHhCCCeEEE-EecCCHHHHHHHHHcCCccEEEecC
Confidence 3356777889999997 6678888899999999999998643
No 167
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=29.09 E-value=1.1e+02 Score=26.89 Aligned_cols=39 Identities=15% Similarity=0.167 Sum_probs=31.6
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLL 147 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiIL 147 (237)
.-.+++...+|++++. -.-++.++-+..|.+|++|-.|.
T Consensus 110 ~~l~~f~~~~P~i~l~-~~~~~~~~~~~~l~~g~~D~~i~ 148 (296)
T PRK11062 110 RVLLTAVPEDESIHLR-CFESTHEMLLEQLSQHKLDMILS 148 (296)
T ss_pred HHHHHHHhcCCceEEE-EEeCCHHHHHHHHHcCCCCEEEe
Confidence 3456667789999987 55578888899999999999875
No 168
>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=28.91 E-value=76 Score=24.39 Aligned_cols=19 Identities=21% Similarity=0.288 Sum_probs=16.2
Q ss_pred HHHHHHHhcCCccEEEeeC
Q 026500 41 KEIDEALINSQIDIAVHSM 59 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSl 59 (237)
.++.++|.+|++|+++...
T Consensus 39 ~~~~~~l~~g~~Dl~i~~~ 57 (196)
T cd08456 39 PTVEQWLSAQQCDLGLVST 57 (196)
T ss_pred HHHHHHHHcCCccEEEEec
Confidence 4688999999999999754
No 169
>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=28.74 E-value=73 Score=24.36 Aligned_cols=20 Identities=20% Similarity=0.325 Sum_probs=16.9
Q ss_pred HHHHHHHHhcCCccEEEeeC
Q 026500 40 TKEIDEALINSQIDIAVHSM 59 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSl 59 (237)
..++.++|.+|++|+|+.+.
T Consensus 37 ~~~~~~~l~~g~~Dl~i~~~ 56 (197)
T cd08419 37 REQVLERLADNEDDLAIMGR 56 (197)
T ss_pred HHHHHHHHhcCCccEEEecC
Confidence 35788999999999999764
No 170
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=28.07 E-value=94 Score=26.92 Aligned_cols=40 Identities=10% Similarity=0.061 Sum_probs=32.3
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+=-..++..+|++++. -.-++-..-+..|.+|++|..|..
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 556788888899999999998864
No 171
>COG0604 Qor NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]
Probab=27.93 E-value=1.2e+02 Score=28.19 Aligned_cols=62 Identities=11% Similarity=0.070 Sum_probs=43.3
Q ss_pred eeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccC-CccEEeeecc------cccccCCCCccee
Q 026500 101 IVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNER-VVQATLLALA------GLKRLSMTENVTN 163 (237)
Q Consensus 101 ~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~g-e~DaiILA~A------GL~RLgl~~~i~~ 163 (237)
++.|||.+....++.+-.|.-+. -.+.++..+++++-.| .+|.++=.-. .+..|....++..
T Consensus 171 v~~~~s~~k~~~~~~lGAd~vi~-y~~~~~~~~v~~~t~g~gvDvv~D~vG~~~~~~~l~~l~~~G~lv~ 239 (326)
T COG0604 171 VAVVSSSEKLELLKELGADHVIN-YREEDFVEQVRELTGGKGVDVVLDTVGGDTFAASLAALAPGGRLVS 239 (326)
T ss_pred EEEecCHHHHHHHHhcCCCEEEc-CCcccHHHHHHHHcCCCCceEEEECCCHHHHHHHHHHhccCCEEEE
Confidence 45566666666788888888876 7888899999999888 5998875332 3555544444433
No 172
>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=27.52 E-value=60 Score=25.17 Aligned_cols=20 Identities=25% Similarity=0.360 Sum_probs=16.9
Q ss_pred HHHHHHHHhcCCccEEEeeC
Q 026500 40 TKEIDEALINSQIDIAVHSM 59 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSl 59 (237)
+.++.++|.+|++|+|+...
T Consensus 38 ~~~~~~~l~~~~~Dl~i~~~ 57 (185)
T cd08439 38 TPRLMEMLERGEVDLALITH 57 (185)
T ss_pred hHHHHHHHHCCCCcEEEEec
Confidence 35788999999999999753
No 173
>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=27.50 E-value=71 Score=24.34 Aligned_cols=95 Identities=16% Similarity=0.113 Sum_probs=47.1
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-------CCCccCCCCCeeecC---ChhH-
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA---SLRR- 109 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-------~~l~~Lp~ga~IGTS---S~RR- 109 (237)
.++.++|.+|++|+|+.+.-.- ++++... +-..++--++++++. .++++|..-..|..+ +.++
T Consensus 39 ~~~~~~l~~g~~D~~i~~~~~~----~~~~~~~--~l~~~~~~~v~~~~~~~~~~~~i~~~~l~~~~~i~~~~~~~~~~~ 112 (201)
T cd08420 39 EEIAERVLDGEIDLGLVEGPVD----HPDLIVE--PFAEDELVLVVPPDHPLAGRKEVTAEELAAEPWILREPGSGTREV 112 (201)
T ss_pred HHHHHHHHCCCccEEEecCCCC----CcceEEE--eecCccEEEEecCCCCccccCccCHHHHhcCCEEEecCCCCHHHH
Confidence 5788999999999999864221 3343322 222233333332221 123444333333321 2232
Q ss_pred HHHHHH---h-CCCCeEEeccCCCHHHHHHhhccCCc
Q 026500 110 KSQILH---R-YPSLKVMENFRGNVQTRLRKLNERVV 142 (237)
Q Consensus 110 ~aql~~---~-~pdl~v~~~iRGNV~TRL~KL~~ge~ 142 (237)
-.+... . .+..++. -.-++..+-++-+.+|..
T Consensus 113 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~g 148 (201)
T cd08420 113 FERALAEAGLDGLDLNIV-MELGSTEAIKEAVEAGLG 148 (201)
T ss_pred HHHHHHHcCcccccCceE-EEECCHHHHHHHHHcCCC
Confidence 222222 1 1223444 445788898888888854
No 174
>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=26.62 E-value=85 Score=24.17 Aligned_cols=95 Identities=12% Similarity=0.041 Sum_probs=48.2
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC--------CCCccCCCCCeeecC--C---
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA--------ASLAELPAGSIVGTA--S--- 106 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~--------~~l~~Lp~ga~IGTS--S--- 106 (237)
..++.+.|.+|++|+++..... .++++..-.+ .+ ++. +++++.+ .++++|.+-..|..+ +
T Consensus 38 ~~~~~~~l~~g~~D~~i~~~~~----~~~~~~~~~l-~~-~~~-~~v~~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~ 110 (198)
T cd08447 38 TTDQIEALESGRIDLGLLRPPF----ARPGLETRPL-VR-EPL-VAAVPAGHPLAGAERLTLEDLDGQPFIMYSPTEARY 110 (198)
T ss_pred HHHHHHHHHcCCceEEEecCCC----CCCCeeEEEe-ec-Cce-EEEecCCCchhhcCcccHHHhCCCeEEEeCCCCCch
Confidence 3578899999999999986332 1344433222 22 222 3333221 234556555555532 1
Q ss_pred hhHH-HH-HHHhCCCCeEEeccCCCHHHHHHhhccCCc
Q 026500 107 LRRK-SQ-ILHRYPSLKVMENFRGNVQTRLRKLNERVV 142 (237)
Q Consensus 107 ~RR~-aq-l~~~~pdl~v~~~iRGNV~TRL~KL~~ge~ 142 (237)
.|+. .+ +.......++. -.-.++.+-+.-+.+|..
T Consensus 111 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~g 147 (198)
T cd08447 111 FHDLVVRLFASAGVQPRYV-QYLSQIHTMLALVRAGLG 147 (198)
T ss_pred HHHHHHHHHHHcCCCCCce-eecCCHHHHHHHHHcCCC
Confidence 1222 12 22222122222 223688888888888864
No 175
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=26.16 E-value=4.9e+02 Score=24.50 Aligned_cols=102 Identities=15% Similarity=0.218 Sum_probs=68.2
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCcee-eeecCCCCCCeEEEeCCCCCCccCCCCCeeecCChhHHHHHHH--h
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTIL-PCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQILH--R 116 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~i-aav~~R~dprD~LV~~~~~~l~~Lp~ga~IGTSS~RR~aql~~--~ 116 (237)
+..|.+..++|+.|+-.-|.--.|.-..+=-.+ ++..--..-.=++|+++.. .+| ++.+|++++..=.|.++. .
T Consensus 38 IetLN~~ale~~~dvtaiSa~~Yp~I~D~Y~ll~~gas~G~gyGPivv~k~~~--~~l-~~~rvavpG~~TTA~lL~rl~ 114 (272)
T COG2107 38 IETLNREALEGRYDVTAISAAAYPYIADDYALLRSGASLGIGYGPIVVAKSEV--KDL-KGKRVAVPGEMTTAALLFRLA 114 (272)
T ss_pred HHHHHHHHHhCCCceEEEchhhhhhhhhhhheeeccccccCCcCCEEEEcccc--ccc-ccceEecCCcccHHHHHHHHh
Confidence 345778889999999999988777542211000 1111112233456666532 223 689999999998776644 6
Q ss_pred CCCCeEEeccCCCHHHHHHhhccCCccEEee
Q 026500 117 YPSLKVMENFRGNVQTRLRKLNERVVQATLL 147 (237)
Q Consensus 117 ~pdl~v~~~iRGNV~TRL~KL~~ge~DaiIL 147 (237)
+|+.+++ .++ .+.=+.-+.+|+.||-++
T Consensus 115 ~p~~~~V-~m~--fdeI~~Avl~G~VDaGvl 142 (272)
T COG2107 115 YPKAEIV-YMP--FDEIIPAVLEGKVDAGVL 142 (272)
T ss_pred CCCceEE-Eee--HHHHHHHHHcCCCccceE
Confidence 8998887 665 888888889999998776
No 176
>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=25.95 E-value=95 Score=23.81 Aligned_cols=96 Identities=15% Similarity=0.149 Sum_probs=47.7
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCC-------CCCCccCCCCCeeecC--ChhHH
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLS-------AASLAELPAGSIVGTA--SLRRK 110 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~-------~~~l~~Lp~ga~IGTS--S~RR~ 110 (237)
..++.+.|.+|++|+++....+. ++++..- +-..++.-+++++. ..++++|..-..|..+ +.++.
T Consensus 38 ~~~~~~~l~~~~~D~~i~~~~~~----~~~~~~~--~l~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~ 111 (198)
T cd08412 38 QEELEEGLRSGELDLALTYDLDL----PEDIAFE--PLARLPPYVWLPADHPLAGKDEVSLADLAAEPLILLDLPHSREY 111 (198)
T ss_pred HHHHHHHHHcCCCcEEEEcCCCC----Cccccee--eeeccceEEEecCCCCCCCCCcCCHHHHcCCcEEecCchhHHHH
Confidence 35788999999999999754432 3444321 11222222222221 1234445444444432 12222
Q ss_pred -HH-HHHhCCCCeEEeccCCCHHHHHHhhccCCc
Q 026500 111 -SQ-ILHRYPSLKVMENFRGNVQTRLRKLNERVV 142 (237)
Q Consensus 111 -aq-l~~~~pdl~v~~~iRGNV~TRL~KL~~ge~ 142 (237)
.+ +....-..++. -.=++..+-++-+.+|..
T Consensus 112 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~g 144 (198)
T cd08412 112 FLSLFAAAGLTPRIA-YRTSSFEAVRSLVANGLG 144 (198)
T ss_pred HHHHHHHcCCCccEE-EEeCcHHHHHHHHHcCCC
Confidence 12 22222233333 334788888888888754
No 177
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=25.80 E-value=1.1e+02 Score=26.98 Aligned_cols=41 Identities=7% Similarity=0.054 Sum_probs=33.8
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
++.-.+++..+|++++. -.-|+-+.-+++|.+|++|-.|..
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 35567888899999997 666777888999999999999863
No 178
>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=25.32 E-value=98 Score=23.63 Aligned_cols=20 Identities=25% Similarity=0.360 Sum_probs=16.8
Q ss_pred HHHHHHHHhcCCccEEEeeC
Q 026500 40 TKEIDEALINSQIDIAVHSM 59 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSl 59 (237)
..++.+.|.+|++|+++...
T Consensus 38 ~~~~~~~l~~~~~Di~i~~~ 57 (197)
T cd08448 38 SAEQIEALLRGELDLGFVHS 57 (197)
T ss_pred HHHHHHHHHcCCcceEEEeC
Confidence 35788999999999999754
No 179
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=25.12 E-value=55 Score=25.95 Aligned_cols=25 Identities=32% Similarity=0.638 Sum_probs=21.6
Q ss_pred ccccccCcccc---cHHHHHHHHhcCCc
Q 026500 28 QPLADIGGKGL---FTKEIDEALINSQI 52 (237)
Q Consensus 28 ~~L~~iggkGl---FtkeLe~aLl~g~i 52 (237)
.|.-.||..|+ |..|+++||...+.
T Consensus 19 ~Pvv~IGk~Glt~~vi~ei~~aL~~hEL 46 (97)
T PRK10343 19 KPVVLLGSNGLTEGVLAEIEQALEHHEL 46 (97)
T ss_pred CCeEEECCCCCCHHHHHHHHHHHHHCCc
Confidence 47788998887 89999999999874
No 180
>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=24.90 E-value=1e+02 Score=23.46 Aligned_cols=38 Identities=21% Similarity=0.290 Sum_probs=27.0
Q ss_pred hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 107 LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 107 ~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
++.-+.++..+|++++. -.-++ .+..+.+|++|..|..
T Consensus 17 ~~~l~~~~~~~P~v~i~-i~~~~---~~~~l~~~~~D~~i~~ 54 (197)
T cd08422 17 APLLAEFLARYPDVRLE-LVLSD---RLVDLVEEGFDLAIRI 54 (197)
T ss_pred HHHHHHHHHhCCceEEE-EecCc---cccchhhcCccEEEEe
Confidence 36678889999999986 33332 3445667889998864
No 181
>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=23.72 E-value=1e+02 Score=23.90 Aligned_cols=44 Identities=14% Similarity=0.202 Sum_probs=31.5
Q ss_pred eeecCC-------hhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 101 IVGTAS-------LRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 101 ~IGTSS-------~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+||++. ++.-+++++.+|++++. -..++ .+..+.+|++|..|..
T Consensus 6 ~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~-~~~~~---~~~~l~~g~~D~~i~~ 56 (202)
T cd08474 6 RINAPRVAARLLLAPLLARFLARYPDIRLE-LVVDD---GLVDIVAEGFDAGIRL 56 (202)
T ss_pred EEeCcHHHHHHHHHHHHHHHHHHCCCeEEE-EEecC---CcccccccCccEEEEc
Confidence 566653 35678888999999987 44344 2556778999998853
No 182
>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=23.55 E-value=1e+02 Score=23.82 Aligned_cols=20 Identities=25% Similarity=0.288 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCccEEEeeCC
Q 026500 41 KEIDEALINSQIDIAVHSMK 60 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlK 60 (237)
.++.+.|.+|++|+++....
T Consensus 39 ~~~~~~l~~~~~D~~i~~~~ 58 (198)
T cd08433 39 GHLLEWLLNGRLDLALLYGP 58 (198)
T ss_pred HHHHHHHhCCCCcEEEEeCC
Confidence 57889999999999998653
No 183
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=22.98 E-value=1.3e+02 Score=30.12 Aligned_cols=107 Identities=17% Similarity=0.174 Sum_probs=67.1
Q ss_pred HHHHHHHhcCCccEEE----eeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC----CCCccCCC-CCeeecCChh--H
Q 026500 41 KEIDEALINSQIDIAV----HSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA----ASLAELPA-GSIVGTASLR--R 109 (237)
Q Consensus 41 keLe~aLl~g~iDiAV----HSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~----~~l~~Lp~-ga~IGTSS~R--R 109 (237)
.+|-.||-+|++|++- .+.+|+-.. +.| |-+-|+.=.||.++| .++.+|.. --.|...|.- -
T Consensus 71 dqLf~aL~ng~~DL~Aagl~~~~~~l~~~-~~g------P~y~svs~qlVyRkG~~Rp~~l~~L~g~~i~v~~gs~~~~~ 143 (473)
T COG4623 71 DQLFDALDNGNADLAAAGLLYNSERLKNF-QPG------PTYYSVSQQLVYRKGQYRPRSLGQLKGRQITVAKGSAHVED 143 (473)
T ss_pred HHHHHHHhCCCcceecccccCChhHhccc-CCC------CceecccHHHHhhcCCCCCCCHHHccCceeeccCCcHHHHH
Confidence 5788999999999983 233333221 111 234455555776655 45666644 2344444442 2
Q ss_pred HHHHHH-hCCCCeEEeccCCCHHHHHHhhccCCccEEeeecccccc
Q 026500 110 KSQILH-RYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKR 154 (237)
Q Consensus 110 ~aql~~-~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA~AGL~R 154 (237)
...+++ .+|++....+-.=-|++=|+++.+|..|-+|.=..-+.+
T Consensus 144 l~~lk~~kyP~l~~k~d~~~~~~dLle~v~~Gkldytiads~~is~ 189 (473)
T COG4623 144 LKLLKETKYPELIWKVDDKLGVEDLLEMVAEGKLDYTIADSVEISL 189 (473)
T ss_pred HHHHHHhhcchhhhhhcccccHHHHHHHHhcCCcceeeeccHHHHH
Confidence 334455 799998875555568899999999999988874444433
No 184
>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=22.92 E-value=3.2e+02 Score=20.18 Aligned_cols=97 Identities=11% Similarity=0.024 Sum_probs=50.4
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCCC--------CCccCCCCCeeecCChh---H
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSAA--------SLAELPAGSIVGTASLR---R 109 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~~--------~l~~Lp~ga~IGTSS~R---R 109 (237)
.++.+.|.+|++|+++..... .++++....+. + ++ -+++.+++. ++++|..-..|..++.- .
T Consensus 39 ~~~~~~l~~g~~D~~i~~~~~----~~~~~~~~~l~-~-~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~ 111 (197)
T cd05466 39 SELLEALLEGELDLAIVALPV----DDPGLESEPLF-E-EP-LVLVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRR 111 (197)
T ss_pred HHHHHHHHcCCceEEEEcCCC----CCCcceEeeee-c-cc-eEEEecCCCCcccCcEecHHHHcCCCEEEecCCchHHH
Confidence 468899999999999986543 23344322221 1 22 223322211 24444333344433221 1
Q ss_pred H--HHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEE
Q 026500 110 K--SQILHRYPSLKVMENFRGNVQTRLRKLNERVVQAT 145 (237)
Q Consensus 110 ~--aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~Dai 145 (237)
. ..+.......+.. -.-.++.+-+.-+.+|..=++
T Consensus 112 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~ 148 (197)
T cd05466 112 LLDRAFAEAGFTPNIA-LEVDSLEAIKALVAAGLGIAL 148 (197)
T ss_pred HHHHHHHHcCCCceEE-EEeccHHHHHHHHHhCCCEEE
Confidence 1 1233444455544 445688888888888874333
No 185
>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=22.81 E-value=94 Score=23.73 Aligned_cols=36 Identities=17% Similarity=0.180 Sum_probs=26.0
Q ss_pred HHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 109 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 109 R~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
--+.+++.+|++++. -..++- ...|.+|++|..|..
T Consensus 18 ~l~~f~~~~P~i~i~-i~~~~~---~~~l~~~~~Dl~l~~ 53 (194)
T cd08481 18 RLPDFLARHPDITVN-LVTRDE---PFDFSQGSFDAAIHF 53 (194)
T ss_pred hhhHHHHHCCCceEE-EEeccc---ccCcccCCCCEEEEc
Confidence 346677789999987 544442 246889999998864
No 186
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=22.70 E-value=1.9e+02 Score=25.61 Aligned_cols=40 Identities=15% Similarity=0.083 Sum_probs=32.5
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
..-.++.+.+|++++. -.-++-..=++.|.+|++|..|..
T Consensus 111 ~~l~~~~~~~P~v~i~-i~~~~~~~~~~~l~~~~~Dl~i~~ 150 (309)
T PRK11013 111 GLCQPFLARYPDVSLN-IVPQESPLLEEWLSAQRHDLGLTE 150 (309)
T ss_pred HHHHHHHHHCCCCeEE-EEeCCHHHHHHHHHcCCCCEEEEc
Confidence 4567788899999998 777777776788999999988864
No 187
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=22.69 E-value=1.3e+02 Score=26.57 Aligned_cols=39 Identities=10% Similarity=0.159 Sum_probs=30.6
Q ss_pred HHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 109 RKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 109 R~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
--+.+...+|++++. -.-++-.+=++.|.+|++|..|..
T Consensus 113 ~l~~~~~~~P~v~i~-~~~~~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 113 LIGLFRQRYPQINVQ-LQVHSTRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred HHHHHHHHCCCceEE-EEeCCHHHHHHHHHcCCccEEEEc
Confidence 346677889999987 555666777789999999998863
No 188
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=22.31 E-value=68 Score=25.21 Aligned_cols=35 Identities=31% Similarity=0.532 Sum_probs=25.6
Q ss_pred ccccccCcccc---cHHHHHHHHhcCCccEEEeeCCCCC
Q 026500 28 QPLADIGGKGL---FTKEIDEALINSQIDIAVHSMKDVP 63 (237)
Q Consensus 28 ~~L~~iggkGl---FtkeLe~aLl~g~iDiAVHSlKDlP 63 (237)
.|.-.||..|+ |..||++||...+. |=|+=++.-+
T Consensus 17 ~p~v~IGK~Glt~~vi~ei~~aL~~hEL-IKVkvl~~~~ 54 (95)
T TIGR00253 17 KPVVLVGKNGLTEGVIKEIEQALEHREL-IKVKVATEDR 54 (95)
T ss_pred CCeEEECCCCCCHHHHHHHHHHHHhCCc-EEEEecCCCh
Confidence 47888998887 69999999999875 3344344443
No 189
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=21.73 E-value=3.7e+02 Score=23.14 Aligned_cols=103 Identities=13% Similarity=0.050 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCCccEEE--ee----CCCCCCCCCCCceeeeecCCCCCCeEEEeCCCCCCccCCCCCeeecCChhHHHH-
Q 026500 40 TKEIDEALINSQIDIAV--HS----MKDVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQ- 112 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAV--HS----lKDlP~~l~~gL~iaav~~R~dprD~LV~~~~~~l~~Lp~ga~IGTSS~RR~aq- 112 (237)
..++.++|.+|++|+++ ++ .+++-...--.-.+.++...+.| +...+..++++|..-..|..++......
T Consensus 135 ~~~~~~~l~~g~~D~~i~~~~~~~~~~~l~~~~l~~~~~~~v~~~~~~---l~~~~~~~~~dL~~~~~i~~~~~~~~~~~ 211 (294)
T PRK09986 135 PSMQMAALERRELDAGIWRMADLEPNPGFTSRRLHESAFAVAVPEEHP---LASRSSVPLKALRNEYFITLPFVHSDWGK 211 (294)
T ss_pred HHHHHHHHHcCCCCEEEecCCccCCCCCeEEEEeecccEEEEEcCCCC---cccCCccCHHHHcCCCEEecCCCchhHHH
Q ss_pred -----HHHhCCCCeEEeccCCCHHHHHHhhccCCccEEe
Q 026500 113 -----ILHRYPSLKVMENFRGNVQTRLRKLNERVVQATL 146 (237)
Q Consensus 113 -----l~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiI 146 (237)
+....-..+++ ---.++.+=+.-+.+|..=+++
T Consensus 212 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~gi~~l 249 (294)
T PRK09986 212 FLQRVCQQAGFSPQII-RQVNEPQTVLAMVSMGIGITLL 249 (294)
T ss_pred HHHHHHHHCCCCCcee-eecCCHHHHHHHHHcCCeEEEc
No 190
>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=21.67 E-value=79 Score=25.01 Aligned_cols=95 Identities=13% Similarity=0.027 Sum_probs=50.3
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-------CCCccCCCCCeeecC-----Ch
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA-----SL 107 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-------~~l~~Lp~ga~IGTS-----S~ 107 (237)
+.++.+.|.+|++|+|+-.- |. .++++....+ ..++-=++++++. -++++|.+-..|+.+ +.
T Consensus 39 ~~~l~~~l~~g~~D~~~~~~---~~-~~~~~~~~~l--~~~~~~lv~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~ 112 (198)
T cd08486 39 KDEQVEGLLAGTIHVGFSRF---FP-RHPGIEIVNI--AQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSF 112 (198)
T ss_pred HHHHHHHHHcCCceEEEecC---CC-CCCceEEEEE--eeccEEEEecCCCccccCCcccHHHHcCCCeEeecCCcCchH
Confidence 46899999999999999532 11 2455543222 2233333333221 235666665566543 23
Q ss_pred hHHHH--HHHhCCCCeEEeccCCCHHHHHHhhccCC
Q 026500 108 RRKSQ--ILHRYPSLKVMENFRGNVQTRLRKLNERV 141 (237)
Q Consensus 108 RR~aq--l~~~~pdl~v~~~iRGNV~TRL~KL~~ge 141 (237)
|+... +.+.....++. -.-.++++=+.-+.+|.
T Consensus 113 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~ 147 (198)
T cd08486 113 ADEVIGLFKHAGIEPRIA-RVVEDATAALALTMAGA 147 (198)
T ss_pred HHHHHHHHHHcCCCcceE-EEeccHHHHHHHHHcCc
Confidence 44322 22222333333 23467888877777763
No 191
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=21.30 E-value=1.1e+02 Score=27.09 Aligned_cols=21 Identities=14% Similarity=0.175 Sum_probs=17.5
Q ss_pred HHHHHHHhcCCccEEEeeCCC
Q 026500 41 KEIDEALINSQIDIAVHSMKD 61 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKD 61 (237)
.++.+.|.+|++|++++...+
T Consensus 133 ~~~~~~l~~~~~Dl~i~~~~~ 153 (309)
T PRK11013 133 PLLEEWLSAQRHDLGLTETLH 153 (309)
T ss_pred HHHHHHHHcCCCCEEEEcCCC
Confidence 468899999999999997543
No 192
>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=21.19 E-value=1.2e+02 Score=23.41 Aligned_cols=94 Identities=11% Similarity=0.018 Sum_probs=47.0
Q ss_pred HHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC--------CCCccCCCCCeeecC---ChhH
Q 026500 41 KEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA--------ASLAELPAGSIVGTA---SLRR 109 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~--------~~l~~Lp~ga~IGTS---S~RR 109 (237)
.++.+.|.+|++|+++-.... .++++..-.+. .++ -++|..++ .++++|-.-..|..+ +.|+
T Consensus 39 ~~~~~~l~~~~~D~~i~~~~~----~~~~~~~~~l~--~~~-~~~v~~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~ 111 (198)
T cd08421 39 ADIVRAVAEGRADLGIVAGNV----DAAGLETRPYR--TDR-LVVVVPRDHPLAGRASVAFADTLDHDFVGLPAGSALHT 111 (198)
T ss_pred HHHHHHHhcCCceEEEEecCC----CCCCcEEEEee--cCc-EEEEeCCCCCccccCCCCHHHhcCCceEeecCCcchHH
Confidence 578899999999999975433 23455433222 222 23333221 134444333344322 2332
Q ss_pred H-HHH-HHhCCCCeEEeccCCCHHHHHHhhccCCc
Q 026500 110 K-SQI-LHRYPSLKVMENFRGNVQTRLRKLNERVV 142 (237)
Q Consensus 110 ~-aql-~~~~pdl~v~~~iRGNV~TRL~KL~~ge~ 142 (237)
. .+. .......++. ..-.++.+=+.-+.+|..
T Consensus 112 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~g 145 (198)
T cd08421 112 FLREAAARLGRRLRLR-VQVSSFDAVCRMVAAGLG 145 (198)
T ss_pred HHHHHHHHcCCCceEE-EEECCHHHHHHHHHcCCC
Confidence 1 111 2222233333 233678888888888754
No 193
>cd08483 PBP2_HvrB The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold. The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transp
Probab=20.94 E-value=93 Score=23.83 Aligned_cols=37 Identities=11% Similarity=0.179 Sum_probs=26.9
Q ss_pred hHHHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 108 RRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 108 RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
+--+.++..+|++++. +. + ...+..|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~i~l~--~~-~-~~~~~~l~~g~~Dl~i~~ 53 (190)
T cd08483 17 PRLGSFWAKHPEIELS--LL-P-SADLVDLRPDGIDVAIRY 53 (190)
T ss_pred hhHHHHHHHCCCceEE--EE-e-cCCcCCCCCCCcCEEEEe
Confidence 4456778889999986 33 1 234678999999998863
No 194
>PF00107 ADH_zinc_N: Zinc-binding dehydrogenase; InterPro: IPR013149 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of alcohols to their corresponding acetaldehyde or ketone with the concomitant reduction of NAD: alcohol + NAD = aldehyde or ketone + NADH Currently three structurally and catalytically different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Zinc-containing ADH's [, ] are dimeric or tetrameric enzymes that bind two atoms of zinc per subunit. One of the zinc atom is essential for catalytic activity while the other is not. Both zinc atoms are coordinated by either cysteine or histidine residues; the catalytic zinc is coordinated by two cysteines and one histidine. Zinc-containing ADH's are found in bacteria, mammals, plants, and in fungi. In many species there is more than one isozyme (for example, humans have at least six isozymes, yeast have three, etc.). A number of other zinc-dependent dehydrogenases are closely related to zinc ADH [] and are included in this family. Sorbitol dehydrogenase (1.1.1.14 from EC) L-threonine 3-dehydrogenase (1.1.1.103 from EC) Glutathione-dependent formaldehyde dehydrogenase (1.1.1.284 from EC) Mannitol dehydrogenase (1.1.1.255 from EC) In addition, this family includes NADP-dependent quinone oxidoreductase (1.6.5.5 from EC), an enzyme found in bacteria (gene qor), in yeast and in mammals where, in some species such as rodents, it has been recruited as an eye lens protein and is known as zeta-crystallin []. The sequence of quinone oxidoreductase is distantly related to that other zinc-containing alcohol dehydrogenases and it lacks the zinc-ligand residues. The torpedo fish and mammalian synaptic vesicle membrane protein vat-1 is related to qor. This entry represents the cofactor-binding domain of these enzymes, which is normally found towards the C terminus. Structural studies indicate that it forms a classical Rossman fold that reversibly binds NAD(H) [, , ].; GO: 0008270 zinc ion binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3PI7_A 3COS_D 1VJ1_A 2ZB3_A 1PIW_B 1Q1N_A 1PS0_A 2EER_B 3KRT_A 1ZSY_A ....
Probab=20.42 E-value=2.5e+02 Score=21.22 Aligned_cols=48 Identities=8% Similarity=-0.012 Sum_probs=36.5
Q ss_pred eecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhhccC-CccEEeeecc
Q 026500 102 VGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNER-VVQATLLALA 150 (237)
Q Consensus 102 IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL~~g-e~DaiILA~A 150 (237)
+-++|..|...++.+.-+.-+- .-..++...++++..| .+|.+|-+..
T Consensus 19 ~~~~~~~k~~~~~~~Ga~~~~~-~~~~~~~~~i~~~~~~~~~d~vid~~g 67 (130)
T PF00107_consen 19 ATDRSEEKLELAKELGADHVID-YSDDDFVEQIRELTGGRGVDVVIDCVG 67 (130)
T ss_dssp EEESSHHHHHHHHHTTESEEEE-TTTSSHHHHHHHHTTTSSEEEEEESSS
T ss_pred EEECCHHHHHHHHhhccccccc-ccccccccccccccccccceEEEEecC
Confidence 4445566777777777676666 7777899999999876 7999988755
No 195
>PF06711 DUF1198: Protein of unknown function (DUF1198); InterPro: IPR009587 This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
Probab=20.32 E-value=59 Score=27.84 Aligned_cols=35 Identities=23% Similarity=0.264 Sum_probs=28.6
Q ss_pred CCCeeecCChhHHHHHHHhCCCCeEEeccCCCHHHHHHhh
Q 026500 98 AGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKL 137 (237)
Q Consensus 98 ~ga~IGTSS~RR~aql~~~~pdl~v~~~iRGNV~TRL~KL 137 (237)
-|.+|+||-.||..|-...+-+++.+ + |++=|.++
T Consensus 15 vGfRvLtSdtR~A~~~Ls~rL~I~Pv-~----iESMl~qM 49 (148)
T PF06711_consen 15 VGFRVLTSDTRRAIRRLSERLNIKPV-Y----IESMLDQM 49 (148)
T ss_pred eeEEecccchHHHHHHHHHHhCCCce-e----HHHHHHHH
Confidence 38899999999999999999888877 4 66666555
No 196
>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=20.17 E-value=95 Score=23.72 Aligned_cols=35 Identities=11% Similarity=0.172 Sum_probs=27.6
Q ss_pred HHHHHHhCCCCeEEeccCCCHHHHHHhhccCCccEEeee
Q 026500 110 KSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLA 148 (237)
Q Consensus 110 ~aql~~~~pdl~v~~~iRGNV~TRL~KL~~ge~DaiILA 148 (237)
-++++..+|++++. -.-++ .+..|.+|++|..|..
T Consensus 19 l~~~~~~~P~v~i~-~~~~~---~~~~l~~g~~D~~i~~ 53 (194)
T cd08432 19 LARFQARHPDIDLR-LSTSD---RLVDFAREGIDLAIRY 53 (194)
T ss_pred hHHHHHHCCCeEEE-EEecC---CccccccccccEEEEe
Confidence 46778889999997 66665 4677899999998863
No 197
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=20.16 E-value=2.3e+02 Score=25.03 Aligned_cols=106 Identities=21% Similarity=0.219 Sum_probs=53.8
Q ss_pred HHHHHHHHhcCCccEEEeeCCCCCCCCCCCceeeeecCCCCCCeEEEeCCC-------CCCccCCCCCeeecC---ChhH
Q 026500 40 TKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSA-------ASLAELPAGSIVGTA---SLRR 109 (237)
Q Consensus 40 tkeLe~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprD~LV~~~~-------~~l~~Lp~ga~IGTS---S~RR 109 (237)
..++.+.|.+|++|+++.+ .+.|...++++..-.+ -.++.-++++++. .++++|..-..|..+ +.|+
T Consensus 133 ~~~~~~~l~~g~~Dl~i~~-~~~~~~~~~~~~~~~l--~~~~~~~v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~ 209 (305)
T CHL00180 133 TRRIAWNVANGQIDIAIVG-GEVPTELKKILEITPY--VEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRK 209 (305)
T ss_pred HHHHHHHHHcCCccEEEEc-CccCcccccceeEEEe--ccCcEEEEECCCCccccCCccCHHHHccCCceEecCCCcHHH
Confidence 4678899999999999975 3444444455543222 2233333333321 123445433344332 2343
Q ss_pred H-HHHHHh---CC-CCeEEeccCCCHHHHHHhhccCCccEEeeecc
Q 026500 110 K-SQILHR---YP-SLKVMENFRGNVQTRLRKLNERVVQATLLALA 150 (237)
Q Consensus 110 ~-aql~~~---~p-dl~v~~~iRGNV~TRL~KL~~ge~DaiILA~A 150 (237)
. .++... .| ++++. -.-+|+++=+.-+.+|.. ..++...
T Consensus 210 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~g-~~~lp~~ 253 (305)
T CHL00180 210 VIDNILIQNGIDSKRFKIE-MELNSIEAIKNAVQSGLG-AAFVSVS 253 (305)
T ss_pred HHHHHHHHcCCCcccceEE-EEeCCHHHHHHHHHcCCc-EEEeEhH
Confidence 2 222222 12 23443 345788888888877743 3344433
No 198
>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=20.01 E-value=1.2e+02 Score=24.19 Aligned_cols=20 Identities=20% Similarity=0.333 Sum_probs=16.6
Q ss_pred HHHHHHHhcCCccEEEeeCC
Q 026500 41 KEIDEALINSQIDIAVHSMK 60 (237)
Q Consensus 41 keLe~aLl~g~iDiAVHSlK 60 (237)
.++.+.|.+|++|+++....
T Consensus 39 ~~~~~~l~~g~~Di~i~~~~ 58 (221)
T cd08469 39 LDLAEQLDLGRIDLVIGIFE 58 (221)
T ss_pred hhHHHHHHCCCccEEEecCC
Confidence 36889999999999997543
Done!