Query psy11424
Match_columns 245
No_of_seqs 186 out of 1045
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 18:04:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11424.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11424hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0181 HemC Porphobilinogen d 100.0 1.5E-91 3.2E-96 637.5 23.9 241 1-243 66-306 (307)
2 TIGR00212 hemC porphobilinogen 100.0 5.5E-89 1.2E-93 621.2 25.9 230 1-234 63-292 (292)
3 PLN02691 porphobilinogen deami 100.0 8.4E-88 1.8E-92 624.2 27.2 238 1-241 110-350 (351)
4 cd00494 HMBS Hydroxymethylbila 100.0 8.8E-88 1.9E-92 613.3 25.9 229 1-232 63-292 (292)
5 PRK00072 hemC porphobilinogen 100.0 3.1E-87 6.7E-92 610.4 25.3 228 1-231 67-294 (295)
6 KOG2892|consensus 100.0 1.5E-71 3.3E-76 498.1 8.8 237 1-240 70-313 (320)
7 PF01379 Porphobil_deam: Porph 100.0 3.1E-65 6.7E-70 447.9 14.3 150 1-150 64-215 (215)
8 PRK01066 porphobilinogen deami 100.0 7.2E-64 1.6E-68 441.8 15.0 151 1-156 80-230 (231)
9 PF03900 Porphobil_deamC: Porp 99.8 1.3E-20 2.7E-25 139.9 8.3 72 158-232 1-74 (74)
10 PRK11063 metQ DL-methionine tr 96.3 0.039 8.5E-07 50.3 10.5 148 1-161 74-259 (271)
11 TIGR00363 lipoprotein, YaeC fa 96.2 0.043 9.3E-07 49.8 9.7 153 1-161 61-246 (258)
12 TIGR01096 3A0103s03R lysine-ar 94.0 1.2 2.6E-05 38.1 11.9 141 2-149 78-229 (250)
13 TIGR01729 taurine_ABC_bnd taur 94.0 0.098 2.1E-06 47.0 5.2 107 1-110 42-161 (300)
14 PF00497 SBP_bac_3: Bacterial 93.7 0.082 1.8E-06 43.6 3.8 136 2-149 53-202 (225)
15 PF14503 YhfZ_C: YhfZ C-termin 93.4 0.88 1.9E-05 41.1 10.1 155 1-162 57-220 (232)
16 smart00062 PBPb Bacterial peri 93.3 0.71 1.5E-05 36.7 8.7 103 2-109 54-160 (219)
17 PRK15007 putative ABC transpor 93.3 1.8 3.9E-05 37.1 11.7 140 2-149 75-220 (243)
18 PRK11260 cystine transporter s 93.2 0.72 1.6E-05 40.6 9.3 138 2-149 95-239 (266)
19 PRK09861 cytoplasmic membrane 92.9 1.3 2.7E-05 40.5 10.6 152 1-161 75-260 (272)
20 TIGR03427 ABC_peri_uca ABC tra 92.8 0.7 1.5E-05 43.2 9.0 104 2-110 51-167 (328)
21 COG0834 HisJ ABC-type amino ac 92.5 0.5 1.1E-05 40.8 7.2 143 2-153 92-243 (275)
22 PRK15010 ABC transporter lysin 91.6 4.2 9E-05 35.6 12.1 95 2-103 80-183 (260)
23 cd00134 PBPb Bacterial peripla 91.5 1.4 3.1E-05 35.1 8.3 135 2-145 53-193 (218)
24 PRK11480 tauA taurine transpor 90.2 0.41 9E-06 43.8 4.5 107 1-110 66-183 (320)
25 PF03180 Lipoprotein_9: NLPA l 89.9 2.8 6E-05 37.7 9.5 161 2-178 42-235 (237)
26 PRK09959 hybrid sensory histid 89.3 3.3 7.3E-05 44.2 11.0 137 2-149 357-499 (1197)
27 PF13379 NMT1_2: NMT1-like fam 88.6 0.39 8.4E-06 42.2 3.0 124 1-128 50-202 (252)
28 COG0715 TauA ABC-type nitrate/ 88.1 2.1 4.5E-05 38.8 7.5 122 1-125 76-213 (335)
29 PRK09959 hybrid sensory histid 88.0 2.6 5.7E-05 45.0 9.2 99 2-106 112-215 (1197)
30 PRK10859 membrane-bound lytic 87.9 2.5 5.5E-05 41.2 8.4 102 2-107 96-206 (482)
31 TIGR02995 ectoine_ehuB ectoine 87.2 4.6 9.9E-05 35.8 9.0 140 2-149 87-239 (275)
32 TIGR01098 3A0109s03R phosphate 87.2 4.2 9.1E-05 35.1 8.6 106 2-109 80-207 (254)
33 TIGR01728 SsuA_fam ABC transpo 87.1 4.9 0.00011 34.8 9.0 105 2-110 45-162 (288)
34 PRK11553 alkanesulfonate trans 83.2 6.8 0.00015 35.3 8.3 101 1-104 71-184 (314)
35 cd08429 PBP2_NhaR The C-termin 82.5 3.1 6.8E-05 34.2 5.4 41 63-103 16-56 (204)
36 cd08467 PBP2_SyrM The C-termin 81.8 3.3 7.1E-05 33.4 5.2 49 55-103 1-56 (200)
37 cd08449 PBP2_XapR The C-termin 81.0 4.1 8.9E-05 32.0 5.4 42 63-104 16-57 (197)
38 cd08412 PBP2_PAO1_like The C-t 81.0 4.2 9.2E-05 32.0 5.4 41 63-103 16-56 (198)
39 cd08452 PBP2_AlsR The C-termin 80.5 4.4 9.5E-05 32.4 5.5 41 63-103 16-56 (197)
40 cd08427 PBP2_LTTR_like_2 The C 79.7 4.5 9.8E-05 31.7 5.2 41 64-104 17-57 (195)
41 PRK00489 hisG ATP phosphoribos 79.6 7.9 0.00017 35.2 7.4 97 2-103 59-159 (287)
42 PF09084 NMT1: NMT1/THI5 like; 78.2 1 2.2E-05 38.0 1.1 99 2-104 37-148 (216)
43 cd08458 PBP2_NocR The C-termin 77.9 6.8 0.00015 31.3 5.8 41 63-103 16-56 (196)
44 cd08465 PBP2_ToxR The C-termin 77.5 6.5 0.00014 31.7 5.6 41 64-104 17-57 (200)
45 cd08466 PBP2_LeuO The C-termin 77.2 6.8 0.00015 31.0 5.6 40 64-103 17-56 (200)
46 cd08453 PBP2_IlvR The C-termin 76.9 7.3 0.00016 30.9 5.7 47 57-103 3-56 (200)
47 PRK15437 histidine ABC transpo 76.9 43 0.00094 29.1 11.1 97 2-104 80-184 (259)
48 cd08411 PBP2_OxyR The C-termin 76.0 7.7 0.00017 30.7 5.6 46 57-102 4-56 (200)
49 cd08486 PBP2_CbnR The C-termin 75.7 6.8 0.00015 31.6 5.3 40 64-103 18-57 (198)
50 cd08450 PBP2_HcaR The C-termin 75.7 7.5 0.00016 30.6 5.4 41 63-103 16-56 (196)
51 cd08431 PBP2_HupR The C-termin 74.2 6.1 0.00013 31.2 4.6 40 64-103 17-56 (195)
52 cd08418 PBP2_TdcA The C-termin 74.2 9.6 0.00021 30.0 5.7 41 63-103 16-56 (201)
53 cd08448 PBP2_LTTR_aromatics_li 74.1 9.7 0.00021 29.7 5.7 40 64-103 17-56 (197)
54 cd08442 PBP2_YofA_SoxR_like Th 73.9 8.4 0.00018 30.1 5.3 41 63-103 16-56 (193)
55 cd08456 PBP2_LysR The C-termin 73.5 9 0.00019 30.1 5.4 41 63-103 16-56 (196)
56 cd08439 PBP2_LrhA_like The C-t 73.2 9.9 0.00022 30.0 5.6 39 64-102 17-55 (185)
57 cd05466 PBP2_LTTR_substrate Th 72.9 11 0.00024 28.7 5.6 49 57-105 3-58 (197)
58 cd08415 PBP2_LysR_opines_like 72.8 9.7 0.00021 29.8 5.4 43 63-105 16-58 (196)
59 cd08464 PBP2_DntR_like_2 The C 72.6 7.3 0.00016 30.7 4.7 41 64-104 17-57 (200)
60 cd08423 PBP2_LTTR_like_6 The C 72.6 10 0.00023 29.6 5.6 42 63-104 16-57 (200)
61 cd08447 PBP2_LTTR_aromatics_li 71.9 11 0.00023 29.7 5.5 41 63-103 16-56 (198)
62 cd08413 PBP2_CysB_like The C-t 71.9 11 0.00023 30.3 5.5 41 63-103 16-56 (198)
63 cd08443 PBP2_CysB The C-termin 71.1 11 0.00023 30.3 5.4 41 63-103 16-56 (198)
64 cd08421 PBP2_LTTR_like_1 The C 70.8 10 0.00022 29.8 5.2 41 64-104 17-57 (198)
65 cd08430 PBP2_IlvY The C-termin 69.4 14 0.0003 29.0 5.6 41 63-103 16-56 (199)
66 cd08416 PBP2_MdcR The C-termin 69.3 12 0.00026 29.4 5.3 41 63-103 16-56 (199)
67 PRK11917 bifunctional adhesin/ 68.7 40 0.00087 29.7 9.0 138 2-151 96-241 (259)
68 cd08436 PBP2_LTTR_like_3 The C 68.7 15 0.00033 28.6 5.6 42 63-104 16-57 (194)
69 cd08440 PBP2_LTTR_like_4 TThe 68.6 15 0.00033 28.4 5.7 41 64-104 17-57 (197)
70 cd08441 PBP2_MetR The C-termin 68.5 12 0.00026 29.6 5.1 41 63-103 16-56 (198)
71 cd08446 PBP2_Chlorocatechol Th 67.8 16 0.00034 28.8 5.6 40 64-103 18-57 (198)
72 TIGR03431 PhnD phosphonate ABC 67.7 20 0.00044 31.8 6.9 106 2-109 75-201 (288)
73 cd08438 PBP2_CidR The C-termin 67.6 14 0.00031 28.8 5.3 41 63-103 16-56 (197)
74 cd08445 PBP2_BenM_CatM_CatR Th 67.1 15 0.00032 29.4 5.4 39 64-102 18-56 (203)
75 cd08425 PBP2_CynR The C-termin 66.9 17 0.00036 28.6 5.6 41 63-103 17-57 (197)
76 cd08444 PBP2_Cbl The C-termina 65.6 17 0.00037 29.0 5.5 41 63-103 16-56 (198)
77 cd08457 PBP2_OccR The C-termin 65.5 15 0.00032 29.1 5.1 42 63-104 16-57 (196)
78 PRK09495 glnH glutamine ABC tr 63.9 18 0.00039 31.1 5.7 56 48-106 125-182 (247)
79 PRK10797 glutamate and asparta 63.1 39 0.00085 30.7 7.9 134 2-149 101-249 (302)
80 PRK04056 Maf-like protein; Rev 62.7 7.6 0.00016 33.5 3.0 31 57-89 3-33 (180)
81 cd08437 PBP2_MleR The substrat 62.4 21 0.00047 28.1 5.5 41 63-103 16-56 (198)
82 cd08434 PBP2_GltC_like The sub 62.4 22 0.00047 27.6 5.5 41 64-104 17-57 (195)
83 PRK00078 Maf-like protein; Rev 62.3 7.7 0.00017 33.8 3.0 31 57-89 4-34 (192)
84 PRK04694 Maf-like protein; Rev 62.3 8 0.00017 33.6 3.1 30 57-88 3-32 (190)
85 PF12974 Phosphonate-bd: ABC t 61.8 1.1 2.4E-05 38.9 -2.3 108 2-111 45-172 (243)
86 cd08433 PBP2_Nac The C-teminal 61.8 20 0.00044 28.2 5.2 40 64-103 17-56 (198)
87 cd08462 PBP2_NodD The C-termin 60.9 21 0.00045 28.5 5.2 37 66-103 19-55 (200)
88 PF02621 VitK2_biosynth: Menaq 60.8 21 0.00045 32.0 5.6 95 2-102 39-140 (251)
89 cd08420 PBP2_CysL_like C-termi 60.7 25 0.00054 27.3 5.5 41 63-103 16-56 (201)
90 PRK11716 DNA-binding transcrip 60.3 23 0.00049 30.3 5.6 48 56-103 69-123 (269)
91 TIGR00172 maf MAF protein. Thi 58.4 11 0.00023 32.6 3.3 35 54-90 3-37 (183)
92 PRK00148 Maf-like protein; Rev 57.1 11 0.00024 32.9 3.1 31 56-88 3-33 (194)
93 cd08459 PBP2_DntR_NahR_LinR_li 56.9 21 0.00046 28.2 4.6 41 64-104 17-57 (201)
94 TIGR03870 ABC_MoxJ methanol ox 56.6 58 0.0013 28.3 7.7 19 85-103 152-170 (246)
95 PRK02478 Maf-like protein; Rev 55.8 12 0.00025 32.9 3.0 31 56-88 5-35 (199)
96 PRK14363 Maf-like protein; Pro 55.5 12 0.00025 33.1 3.0 32 56-89 3-34 (204)
97 PRK00234 Maf-like protein; Rev 55.5 12 0.00027 32.5 3.1 32 56-89 4-35 (192)
98 PRK00032 Maf-like protein; Rev 55.2 12 0.00026 32.5 3.0 32 56-89 4-35 (190)
99 cd08451 PBP2_BudR The C-termin 55.0 30 0.00064 27.1 5.1 41 63-103 17-57 (199)
100 cd08426 PBP2_LTTR_like_5 The C 54.7 24 0.00052 27.7 4.5 40 64-103 17-56 (199)
101 cd08414 PBP2_LTTR_aromatics_li 54.4 31 0.00067 26.8 5.1 41 63-103 16-56 (197)
102 cd08435 PBP2_GbpR The C-termin 54.2 29 0.00062 27.1 4.9 41 63-103 16-56 (201)
103 cd08461 PBP2_DntR_like_3 The C 54.2 20 0.00044 28.2 4.0 41 63-103 16-56 (198)
104 PRK12679 cbl transcriptional r 53.1 34 0.00074 30.8 5.8 49 56-104 95-150 (316)
105 PRK14368 Maf-like protein; Pro 53.1 14 0.0003 32.3 3.0 32 56-89 7-38 (193)
106 TIGR03339 phn_lysR aminoethylp 52.7 34 0.00073 29.5 5.5 47 56-102 89-139 (279)
107 PRK01839 Maf-like protein; Rev 52.3 14 0.00031 32.6 3.0 36 55-92 11-46 (209)
108 PRK04425 Maf-like protein; Rev 52.3 15 0.00032 32.2 3.1 31 56-88 7-37 (196)
109 PRK14361 Maf-like protein; Pro 52.2 15 0.00032 32.0 3.0 31 57-89 2-32 (187)
110 PF03466 LysR_substrate: LysR 52.1 26 0.00057 27.8 4.4 43 64-106 23-65 (209)
111 cd00985 Maf_Ham1 Maf_Ham1. Maf 52.1 14 0.00029 29.4 2.7 24 57-80 2-26 (131)
112 PRK03601 transcriptional regul 51.9 31 0.00068 30.3 5.2 48 56-103 91-145 (275)
113 PRK00884 Maf-like protein; Rev 51.9 16 0.00034 32.0 3.2 32 56-89 4-35 (194)
114 cd00555 Maf Nucleotide binding 51.9 14 0.0003 31.8 2.8 33 57-91 2-34 (180)
115 PRK14362 Maf-like protein; Pro 51.6 16 0.00034 32.3 3.2 26 55-80 13-38 (207)
116 PRK14365 Maf-like protein; Pro 51.6 13 0.00029 32.5 2.7 32 56-89 4-36 (197)
117 TIGR02136 ptsS_2 phosphate bin 51.4 18 0.00039 32.6 3.7 47 57-103 39-91 (287)
118 PRK14367 Maf-like protein; Pro 49.6 17 0.00036 32.0 3.0 32 56-89 4-35 (202)
119 cd08417 PBP2_Nitroaromatics_li 48.6 41 0.0009 26.3 5.0 41 64-104 17-57 (200)
120 cd08460 PBP2_DntR_like_1 The C 48.4 38 0.00082 26.9 4.8 39 64-103 17-55 (200)
121 PF02545 Maf: Maf-like protein 48.3 11 0.00023 32.9 1.6 31 57-89 4-34 (195)
122 cd08485 PBP2_ClcR The C-termin 46.4 44 0.00095 26.7 4.9 41 63-103 17-57 (198)
123 PRK14366 Maf-like protein; Pro 45.8 22 0.00048 31.1 3.2 32 56-89 7-39 (195)
124 PRK05593 rplR 50S ribosomal pr 45.5 31 0.00066 27.9 3.7 23 214-236 66-88 (117)
125 PRK02141 Maf-like protein; Rev 45.1 23 0.00049 31.3 3.2 34 54-89 9-42 (207)
126 PRK14364 Maf-like protein; Pro 44.9 17 0.00037 31.3 2.3 32 58-91 1-32 (181)
127 PRK00648 Maf-like protein; Rev 44.9 22 0.00048 30.9 3.0 33 56-89 5-37 (191)
128 COG3265 GntK Gluconate kinase 44.1 29 0.00063 29.8 3.5 40 55-94 69-110 (161)
129 PRK09508 leuO leucine transcri 44.0 49 0.0011 29.7 5.3 48 57-104 115-169 (314)
130 cd08419 PBP2_CbbR_RubisCO_like 43.5 43 0.00093 26.0 4.3 39 65-103 17-55 (197)
131 PRK10341 DNA-binding transcrip 43.1 61 0.0013 29.0 5.8 48 57-104 100-154 (312)
132 TIGR00060 L18_bact ribosomal p 42.7 57 0.0012 26.3 4.9 42 195-236 36-85 (114)
133 PRK12680 transcriptional regul 42.6 63 0.0014 29.5 5.9 49 56-104 95-150 (327)
134 cd08468 PBP2_Pa0477 The C-term 42.2 42 0.00091 26.7 4.2 41 64-104 17-57 (202)
135 PRK12683 transcriptional regul 40.5 66 0.0014 28.9 5.6 47 56-102 95-148 (309)
136 PRK11151 DNA-binding transcrip 40.1 76 0.0016 28.1 5.8 49 56-104 93-148 (305)
137 cd08463 PBP2_DntR_like_4 The C 40.0 65 0.0014 26.0 5.0 38 66-103 19-57 (203)
138 PRK12684 transcriptional regul 39.8 71 0.0015 28.7 5.7 48 56-103 95-149 (313)
139 PRK01526 Maf-like protein; Rev 39.6 31 0.00067 30.4 3.2 32 56-89 10-42 (205)
140 TIGR02122 TRAP_TAXI TRAP trans 39.5 17 0.00038 32.3 1.6 101 1-102 76-196 (320)
141 cd08478 PBP2_CrgA The C-termin 39.1 30 0.00065 27.3 2.8 37 64-103 20-56 (199)
142 PRK10837 putative DNA-binding 39.1 73 0.0016 27.7 5.5 48 56-103 91-145 (290)
143 COG0424 Maf Nucleotide-binding 38.5 32 0.00068 30.3 3.0 100 56-185 5-111 (193)
144 PRK01441 Maf-like protein; Rev 37.3 36 0.00078 30.0 3.2 33 54-88 5-38 (207)
145 cd08479 PBP2_CrgA_like_9 The C 36.7 56 0.0012 25.6 4.0 37 63-102 17-53 (198)
146 TIGR02424 TF_pcaQ pca operon t 36.6 82 0.0018 27.7 5.5 47 56-102 95-148 (300)
147 cd08432 PBP2_GcdR_TrpI_HvrB_Am 36.1 54 0.0012 25.4 3.8 36 65-103 18-53 (194)
148 cd00432 Ribosomal_L18_L5e Ribo 35.8 49 0.0011 25.5 3.4 21 215-235 55-75 (103)
149 PF00861 Ribosomal_L18p: Ribos 35.6 25 0.00054 28.2 1.8 20 216-235 70-89 (119)
150 cd08469 PBP2_PnbR The C-termin 35.6 61 0.0013 26.2 4.2 41 64-104 17-57 (221)
151 COG0256 RplR Ribosomal protein 35.6 39 0.00085 27.8 2.9 23 214-236 74-96 (125)
152 PRK10094 DNA-binding transcrip 34.9 80 0.0017 28.4 5.2 47 56-102 94-148 (308)
153 cd08428 PBP2_IciA_ArgP The C-t 34.5 76 0.0016 24.9 4.5 39 64-103 17-55 (195)
154 PRK09791 putative DNA-binding 34.1 59 0.0013 28.8 4.1 47 57-103 98-151 (302)
155 PRK09906 DNA-binding transcrip 33.7 65 0.0014 28.3 4.3 49 56-104 92-147 (296)
156 PRK15421 DNA-binding transcrip 33.3 71 0.0015 28.9 4.6 41 63-103 105-145 (317)
157 PRK11062 nhaR transcriptional 32.9 97 0.0021 27.5 5.3 47 56-102 95-148 (296)
158 PRK09296 cysteine desufuration 32.4 1.5E+02 0.0032 24.6 6.0 54 143-198 8-72 (138)
159 PRK12682 transcriptional regul 31.9 85 0.0018 28.0 4.8 48 56-103 95-149 (309)
160 PF02657 SufE: Fe-S metabolism 31.2 67 0.0014 26.0 3.6 50 146-198 2-63 (125)
161 PF05494 Tol_Tol_Ttg2: Toluene 30.6 2.9E+02 0.0062 22.8 7.5 55 191-245 115-169 (170)
162 PRK11074 putative DNA-binding 29.1 90 0.002 27.7 4.5 48 56-103 94-148 (300)
163 COG0604 Qor NADPH:quinone redu 29.0 1E+02 0.0023 28.6 5.0 63 57-119 171-240 (326)
164 TIGR03391 FeS_syn_CsdE cystein 28.8 1.6E+02 0.0035 24.3 5.6 54 143-198 13-77 (138)
165 PRK11242 DNA-binding transcrip 28.3 97 0.0021 27.1 4.5 41 63-103 107-147 (296)
166 PF01634 HisG: ATP phosphoribo 26.5 87 0.0019 26.7 3.7 52 47-101 59-111 (163)
167 cd08481 PBP2_GcdR_like The C-t 26.5 91 0.002 24.1 3.6 36 65-103 18-53 (194)
168 PRK15019 CsdA-binding activato 26.4 2.1E+02 0.0046 24.0 5.9 54 143-198 18-82 (147)
169 cd08422 PBP2_CrgA_like The C-t 25.6 1.1E+02 0.0024 23.5 4.0 38 63-103 17-54 (197)
170 cd08474 PBP2_CrgA_like_5 The C 25.4 1.1E+02 0.0023 24.1 3.9 38 63-103 19-56 (202)
171 CHL00180 rbcR LysR transcripti 25.3 1.1E+02 0.0024 27.1 4.4 38 66-103 114-151 (305)
172 PRK11013 DNA-binding transcrip 25.1 1.8E+02 0.0039 25.9 5.7 48 56-103 96-150 (309)
173 PF03466 LysR_substrate: LysR 25.0 3.1E+02 0.0067 21.4 6.6 98 2-105 50-159 (209)
174 cd08437 PBP2_MleR The substrat 24.2 2.8E+02 0.0061 21.5 6.1 97 2-102 44-152 (198)
175 PRK13348 chromosome replicatio 24.0 1.4E+02 0.0031 26.1 4.8 47 56-103 92-145 (294)
176 PRK11233 nitrogen assimilation 23.9 1.4E+02 0.003 26.6 4.7 39 64-102 109-147 (305)
177 cd08488 PBP2_AmpR The C-termin 22.9 1.3E+02 0.0028 23.6 3.9 38 63-103 16-53 (191)
178 smart00187 INB Integrin beta s 22.8 30 0.00065 34.0 0.2 50 94-143 207-258 (423)
179 PF00943 Alpha_E2_glycop: Alph 22.6 61 0.0013 31.6 2.2 33 172-204 12-47 (403)
180 CHL00139 rpl18 ribosomal prote 22.2 86 0.0019 25.0 2.7 22 215-236 59-80 (109)
181 PRK12681 cysB transcriptional 21.6 1.7E+02 0.0037 26.6 4.9 48 56-103 95-149 (324)
182 PRK10216 DNA-binding transcrip 21.4 1.9E+02 0.004 25.9 5.1 50 53-103 94-152 (319)
183 PF07302 AroM: AroM protein; 20.9 48 0.001 29.8 1.0 55 85-141 76-135 (221)
184 cd00755 YgdL_like Family of ac 20.1 1.3E+02 0.0029 26.8 3.7 42 66-107 71-113 (231)
No 1
>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism]
Probab=100.00 E-value=1.5e-91 Score=637.49 Aligned_cols=241 Identities=49% Similarity=0.795 Sum_probs=235.1
Q ss_pred CccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCCCCCCCCCCCCeEeeCcHHHHHHHHHhCCCCeEEe
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKVLIKSFFPSLIIKS 80 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~~~l~~lp~ga~IGTsS~RR~aql~~~~pdl~~~~ 80 (245)
+||++|+||+|||||||||+++|+||.|+||++|+||+|+|||+++.+|.+||+|++|||||+||++||+++|||++|++
T Consensus 66 ~all~g~~DiAVHSlKDvP~~~p~gL~laai~~R~dprDalVs~~~~~l~~LP~Ga~VGTSSlRR~aql~~~rPdl~i~~ 145 (307)
T COG0181 66 QALLEGEIDIAVHSLKDVPTELPEGLVLAAIPEREDPRDALVSRDGYDLEELPEGAVVGTSSLRRQAQLKALRPDLKIEP 145 (307)
T ss_pred HHHHcCCCCEEEeecccCCccCCCCceEEEecCCCChhheEEECCCCchhhCCCCCccccchHHHHHHHHHhCCCCeEEe
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhcCCChhhHHH
Q psy11424 81 LRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQT 160 (245)
Q Consensus 81 iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~l~~~~t~~~ 160 (245)
+||||||||+||++|+|||||||+|||+|||+.++++++|+|+.|+|||||||||||||.+|.++.++|+.|||.+|+.|
T Consensus 146 lRGNVdTRL~KL~~g~yDAIILA~AGL~RLgl~~~~~~~l~p~~~~PA~gQGal~ie~R~~d~~~~~ll~~i~~~~t~~~ 225 (307)
T COG0181 146 LRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLENRITEILDPEEFLPAPGQGALAIECRAGDEKVLELLAELNDEDTRIC 225 (307)
T ss_pred ccCcHHHHHHHhhcCCccHHHHHHHHHHhcCCcccceeecChhhcCCCCCCceEEEEEecCcHHHHHHHHhccCchHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCcceeeEEEEeccCCCeEEEEEEEEcCCCcEEEEEEEecCCCCHHHHHHHHHHHHHHhhHHHHHH
Q psy11424 161 VKAERAVSRNFNGSCKISLAAFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAIEIIK 240 (245)
Q Consensus 161 v~aER~~l~~L~ggC~~Piga~a~~~~~~~~~l~l~~~v~~~dG~~~~~~~~~~~~~~a~~lg~~la~~l~~~ga~~il~ 240 (245)
++|||+||+.|+|||++|||+||+++ .+++|+|+|.|+++||++.++.+..++.++++++|+++|++|+++|+++|+.
T Consensus 226 v~aERa~l~~L~ggC~~PIg~~a~~~--~~~~l~l~~~v~~~DG~~~~~~~~~g~~~~a~~lG~~~a~~l~~~ga~e~l~ 303 (307)
T COG0181 226 VTAERAFLRELEGGCQVPIGAYAELT--GGGELRLRALVGSPDGSQIIKAEIRGDAEDAEELGKELAEELLEKGAKEILE 303 (307)
T ss_pred HHHHHHHHHhhCCCCCCceEEEEEEc--CCCeEEEEEEEECCCCceeEEEEeecchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999994 3449999999999999999999999999999999999999999999999998
Q ss_pred Hhh
Q psy11424 241 SYE 243 (245)
Q Consensus 241 ~~~ 243 (245)
.++
T Consensus 304 ~~~ 306 (307)
T COG0181 304 GVR 306 (307)
T ss_pred Hhc
Confidence 765
No 2
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=100.00 E-value=5.5e-89 Score=621.17 Aligned_cols=230 Identities=48% Similarity=0.774 Sum_probs=225.4
Q ss_pred CccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCCCCCCCCCCCCeEeeCcHHHHHHHHHhCCCCeEEe
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKVLIKSFFPSLIIKS 80 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~~~l~~lp~ga~IGTsS~RR~aql~~~~pdl~~~~ 80 (245)
+||++|+||||||||||||+++|+||.|+||++|+|||||||++++.+|.+||+|++|||||+||++||+++|||++|++
T Consensus 63 ~aLl~g~iDiAVHSlKDlPt~lp~gl~i~av~~RedprD~lv~~~~~~l~~Lp~ga~VGTsS~RR~aql~~~rPdl~i~~ 142 (292)
T TIGR00212 63 QALLDGEIDLAVHSLKDVPTVLPEGLEIAAVLKREDPRDVLVSRKYLSLDSLPQGAKVGTSSLRRKAQLKAIRPDLKIEP 142 (292)
T ss_pred HHHhcCCCCEEEeccccCCCCCCCCcEEEEEecCCCCceEEEECCCCChhHCCCCCEeccCCHHHHHHHHHHCCCCEEEE
Confidence 48999999999999999999999999999999999999999999989999999999999999999999999999999999
Q ss_pred ccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhcCCChhhHHH
Q psy11424 81 LRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQT 160 (245)
Q Consensus 81 iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~l~~~~t~~~ 160 (245)
|||||+|||+||++|+|||||||+|||+|||+.++++++|++++|+||||||+||||||++|+++.++++.|||++|+.|
T Consensus 143 iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLgl~~~i~~~l~~~~~~PA~gQGalaIe~r~~d~~~~~ll~~l~d~~t~~~ 222 (292)
T TIGR00212 143 LRGNIDTRLRKLDEGEYDAIILAEAGLKRLGLEDVITEVLDPEVMLPAPGQGAIAVECRKDDTEIKEILKEINHPPTRVE 222 (292)
T ss_pred CcCCHHHHHHHhcCCCCCEeehHhhHHHhCCCccccccccChhhcCCccccceEEEEEecCCHHHHHHHHHcCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCcceeeEEEEeccCCCeEEEEEEEEcCCCcEEEEEEEecCCCCHHHHHHHHHHHHHHhh
Q psy11424 161 VKAERAVSRNFNGSCKISLAAFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKG 234 (245)
Q Consensus 161 v~aER~~l~~L~ggC~~Piga~a~~~~~~~~~l~l~~~v~~~dG~~~~~~~~~~~~~~a~~lg~~la~~l~~~g 234 (245)
+.+||+||+.|+|||++|||+||++ ++++++|+|.|+++||++.++.+.+++.+++ ++|.++|++|+++|
T Consensus 223 ~~aER~~l~~L~ggC~~Piga~a~~---~~~~l~l~~~v~~~dG~~~~~~~~~g~~~~a-~lG~~la~~l~~~g 292 (292)
T TIGR00212 223 ATAERAFLKELGGGCQTPIGAYAEY---NGNKLTLIAMVADLDGKEVIREEKEGNIEDA-ELGTEVAEELLKRG 292 (292)
T ss_pred HHHHHHHHHHhCCCCCCceEEEEEE---eCCEEEEEEEEECCCCCEEEEEEEecCHHHH-HHHHHHHHHHHhcC
Confidence 9999999999999999999999999 7889999999999999999999999999999 99999999999876
No 3
>PLN02691 porphobilinogen deaminase
Probab=100.00 E-value=8.4e-88 Score=624.24 Aligned_cols=238 Identities=39% Similarity=0.632 Sum_probs=231.8
Q ss_pred CccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCCCCCCCCCCCCeEeeCcHHHHHHHHHhCCCCeEEe
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKVLIKSFFPSLIIKS 80 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~~~l~~lp~ga~IGTsS~RR~aql~~~~pdl~~~~ 80 (245)
+||++|+||||||||||||+++|+||.|+||++|+|||||||++++.+|++||+|++|||||+||++||+++|||++|++
T Consensus 110 ~aLl~g~iDiAVHSlKDlP~~l~~gl~i~Avl~RedprDvLv~~~~~~L~~Lp~ga~IGTSS~RR~aql~~~rPdl~v~~ 189 (351)
T PLN02691 110 DALLSGRIDIAVHSMKDVPTYLPEGTILPCNLPREDVRDAFISLKAKSLAELPAGSVVGTASLRRQSQILHKYPHLKVVN 189 (351)
T ss_pred HHHHcCCCCEEEeccccCCCCCCCCcEEEEEcCCCCCceEEEECCCCChhHCCCCCEeccCcHHHHHHHHHHCCCCEEEe
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhcCCChhhHHH
Q psy11424 81 LRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQT 160 (245)
Q Consensus 81 iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~l~~~~t~~~ 160 (245)
|||||||||+||++|+|||||||+|||+|||++++++++|++++|+||||||+||||||++|+++.++|+.|||++|+.+
T Consensus 190 iRGNVdTRL~KL~~geyDaiILA~AGL~RLgl~~~i~~~l~~~~~~PA~gQGaLaVe~r~~d~~~~~ll~~ind~~T~~~ 269 (351)
T PLN02691 190 FRGNVQTRLRKLQEGVVDATLLALAGLKRLDMTEHATSILSTDEMLPAVAQGAIGIACRTDDDKMLEYLASLNHEETRLA 269 (351)
T ss_pred ccCCHHHHHHHhcCCCCCeeehHHHHHHhCCCcccccEecchhhcCCccccceEEEEEecCCHHHHHHHHHCCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCcceeeEEEEeccC-CCeEEEEEEEEcCCCcEEEEEEEecC--CCCHHHHHHHHHHHHHHhhHHH
Q psy11424 161 VKAERAVSRNFNGSCKISLAAFAMVNNFN-ESEINLRAIITNPNGLKIITAEVNGP--IDTPETVGLYAAELLKKKGAIE 237 (245)
Q Consensus 161 v~aER~~l~~L~ggC~~Piga~a~~~~~~-~~~l~l~~~v~~~dG~~~~~~~~~~~--~~~a~~lg~~la~~l~~~ga~~ 237 (245)
+.+||+||+.|+|||++|||+||++ + +++|+|+|.|+++||++.++.+..++ .++++++|+++|++|+++|+.+
T Consensus 270 ~~aER~~L~~L~GgC~~Pig~~a~~---~~~~~l~l~~~v~s~dG~~~~~~~~~g~~~~~~a~~lG~~la~~ll~~g~~~ 346 (351)
T PLN02691 270 VACERAFLAALDGSCRTPIAGYARR---DKDGNCDFRGLVASPDGKQVLETSRKGPYVIDDAVAMGKDAGKELKSKAGPG 346 (351)
T ss_pred HHHHHHHHHHhCCCCCCceEEEEEE---cCCCeEEEEEEEECCCCCEEEEEEEecCCCHHHHHHHHHHHHHHHHHhhHHH
Confidence 9999999999999999999999999 6 88999999999999999999988884 6889999999999999999999
Q ss_pred HHHH
Q psy11424 238 IIKS 241 (245)
Q Consensus 238 il~~ 241 (245)
|++.
T Consensus 347 ii~~ 350 (351)
T PLN02691 347 FFDC 350 (351)
T ss_pred HHhc
Confidence 9875
No 4
>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=8.8e-88 Score=613.26 Aligned_cols=229 Identities=49% Similarity=0.781 Sum_probs=223.3
Q ss_pred CccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCCCCCCCCCCCCeEeeCcHHHHHHHHHhCCCCeEEe
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKVLIKSFFPSLIIKS 80 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~~~l~~lp~ga~IGTsS~RR~aql~~~~pdl~~~~ 80 (245)
+||++|+||||||||||||+++|+||.|+||++|+|||||||++++.+|.+||+|++|||||+||++||+++|||++|++
T Consensus 63 ~aLl~g~iDiAVHSlKDlP~~lp~gl~i~av~~RedprDvlv~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~rpdl~~~~ 142 (292)
T cd00494 63 EALLNGEIDLAVHSLKDVPTELPEGLVLGAIPKREDPRDALVSRNGSSLEDLPAGSVVGTSSLRRQAQLKRKRPDLKFEP 142 (292)
T ss_pred HHHHcCCCCEEEeccccCCCCCCCCcEEEEEecCCCCceEEEECCCCChhHCCCCCEEecCCHHHHHHHHHHCCCCEEEE
Confidence 48999999999999999999999999999999999999999999988999999999999999999999999999999999
Q ss_pred ccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhcCCChhhHHH
Q psy11424 81 LRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQT 160 (245)
Q Consensus 81 iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~l~~~~t~~~ 160 (245)
|||||+|||+||++|+|||||||+|||+|||+.++++++|++++|+||||||+||||||++|+++.++|+.|||++|+.+
T Consensus 143 iRGNV~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~i~d~~t~~~ 222 (292)
T cd00494 143 LRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRITQYLSPEVMLPAVGQGALAIECRKGDEELLALLKPLNHEETALC 222 (292)
T ss_pred cCCCHHHHHHHhcCCCCCEeehHhhHHHHcCCcccCccccCccccCCccccceEEEEEecCCHHHHHHHHHCCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCcceeeEEEEeccCCC-eEEEEEEEEcCCCcEEEEEEEecCCCCHHHHHHHHHHHHHH
Q psy11424 161 VKAERAVSRNFNGSCKISLAAFAMVNNFNES-EINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKK 232 (245)
Q Consensus 161 v~aER~~l~~L~ggC~~Piga~a~~~~~~~~-~l~l~~~v~~~dG~~~~~~~~~~~~~~a~~lg~~la~~l~~ 232 (245)
+.+||+||+.|+|||++|||+||++ +++ +++|+|.|+++||++.++.+.+++.++++++|.++|++|++
T Consensus 223 ~~aER~~L~~L~ggC~~Pig~~a~~---~~~~~l~l~~~v~s~dG~~~~~~~~~g~~~~a~~lg~~la~~l~~ 292 (292)
T cd00494 223 VLAERAFLRELEGGCQVPIGVYAEL---DGGEELKLKGLVGSPDGKRLIEGEVRGNIEDAEELGKKLAEELLA 292 (292)
T ss_pred HHHHHHHHHHhCCCCCCceEEEEEE---CCCCEEEEEEEEECCCCCEEEEEEEecCHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999999 777 89999999999999999999999999999999999998863
No 5
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=100.00 E-value=3.1e-87 Score=610.41 Aligned_cols=228 Identities=51% Similarity=0.853 Sum_probs=223.2
Q ss_pred CccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCCCCCCCCCCCCeEeeCcHHHHHHHHHhCCCCeEEe
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKVLIKSFFPSLIIKS 80 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~~~l~~lp~ga~IGTsS~RR~aql~~~~pdl~~~~ 80 (245)
+||++|+||||||||||||+++|+||.|+||++|+|||||||++++.++.+||+|++|||||+||++||+++|||++|++
T Consensus 67 ~aLl~g~iDiAVHSlKDlP~~l~~gl~i~avl~R~dprDvlv~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~~Pdl~~~~ 146 (295)
T PRK00072 67 EALLEGEIDIAVHSLKDVPTELPEGLVLAAIPEREDPRDALVSRDYKSLDDLPEGAVVGTSSLRRQAQLLALRPDLEIKP 146 (295)
T ss_pred HHHHcCCCCEEEeccCcCCCCCCCCcEEEEEecCCCCceEEEECCCCChhHCCCCCEEecCcHHHHHHHHHHCcCCEEEE
Confidence 48999999999999999999999999999999999999999999989999999999999999999999999999999999
Q ss_pred ccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhcCCChhhHHH
Q psy11424 81 LRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQT 160 (245)
Q Consensus 81 iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~l~~~~t~~~ 160 (245)
|||||+|||+||++|+|||||||+|||+|||+.++++++|++++|+||||||+||||||++|+++.++|+.|||++|+.+
T Consensus 147 iRGNV~TRL~KL~~g~~DaivLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGaiave~r~~d~~~~~~l~~i~d~~t~~~ 226 (295)
T PRK00072 147 LRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRITEYLDPEEMLPAPGQGALGIECRADDEEILELLAPLNHEETRLR 226 (295)
T ss_pred CccCHHHHHHHhhCCCCCEeehHhhHHHHcCCccccceecChhhcCCcccccceeeeeecCCHHHHHHHHHcCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCcceeeEEEEeccCCCeEEEEEEEEcCCCcEEEEEEEecCCCCHHHHHHHHHHHHH
Q psy11424 161 VKAERAVSRNFNGSCKISLAAFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLK 231 (245)
Q Consensus 161 v~aER~~l~~L~ggC~~Piga~a~~~~~~~~~l~l~~~v~~~dG~~~~~~~~~~~~~~a~~lg~~la~~l~ 231 (245)
+.+||+||+.|+|||++|||+||++ ++++++|+|.|+++||++.++.+..++.++++++|.++|++|+
T Consensus 227 ~~aER~~L~~L~ggC~~Pig~~a~~---~~~~l~l~~~v~~~dg~~~~~~~~~~~~~~~~~lg~~la~~l~ 294 (295)
T PRK00072 227 VTAERAFLRALEGGCQVPIGAYAEL---EGDELRLRGLVGSPDGSEIIRAEIEGPAADAEELGIELAEELL 294 (295)
T ss_pred HHHHHHHHHHhCCCCCCcceeEEEE---eCCEEEEEEEEECCCCCEEEEEEEecCHHhHHHHHHHHHHHHh
Confidence 9999999999999999999999999 7889999999999999999999988988999999999999886
No 6
>KOG2892|consensus
Probab=100.00 E-value=1.5e-71 Score=498.07 Aligned_cols=237 Identities=41% Similarity=0.659 Sum_probs=219.5
Q ss_pred CccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcC---CCCCCCCCCCCeEeeCcHHHHHHHHHhCCCCe
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISND---YISLSTLPKNAVVGTNSLRRKVLIKSFFPSLI 77 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~---~~~l~~lp~ga~IGTsS~RR~aql~~~~pdl~ 77 (245)
++|.+|++||+|||||||||.+|+|+.|+|++||+||+|+||++. |+++.+||+|++|||||+||+|||++.||+|+
T Consensus 70 ~aL~~~~~divVHSLKDlPT~LP~G~~ig~i~kRedp~DalV~~~~s~~kTladLP~GsVVGTSSlRR~Aql~RkyPHL~ 149 (320)
T KOG2892|consen 70 DALINGHVDIVVHSLKDLPTYLPEGMIIGCILKREDPRDALVFLTYSAYKTLADLPAGSVVGTSSLRRKAQILRKYPHLH 149 (320)
T ss_pred HHHhcCCccEEEEecccccccCCCCcEeccccCCCCccceEEEecccccccHhhCCCCceechHHHhHHHHHHhhCCceE
Confidence 378999999999999999999999999999999999999999987 78999999999999999999999999999999
Q ss_pred EEeccCcHHHHHhhhccCC-ccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhcCCChh
Q psy11424 78 IKSLRGNIDTRLNKLDKGE-YAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYF 156 (245)
Q Consensus 78 ~~~iRGNV~TRL~KL~~g~-~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~l~~~~ 156 (245)
|+++|||++|||+||+.+. |.+||||.|||.|+||.++++++|.|++|+||+|||+++||||.||+.+..++..+||.+
T Consensus 150 f~~~rgn~~trl~kld~~~~~~~iilA~agl~rmg~~~ri~qil~p~~~~~avgqgalgie~r~~d~~m~~~l~~l~~~~ 229 (320)
T KOG2892|consen 150 VESIRGNLQTRLSKLDGGKPFQAIILALAGLKRMGWTNRIAQILHPDEMLYAVGQGALGIECRADDDKMLTYLASLNDLN 229 (320)
T ss_pred EEEecChHHHHHHhhcCCCcchhHHHHHHHHHHhhhHhHHHHhcChHHHHHHhccceeEEEEecChHHHHHHHHHhcChH
Confidence 9999999999999999987 999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHhccCCCcceeeEEEEeccCCCeEEEEEEEEcCCCcEEEEEEEecCCCC--HHHH-HHHHHHHHHHh
Q psy11424 157 SEQTVKAERAVSRNFNGSCKISLAAFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDT--PETV-GLYAAELLKKK 233 (245)
Q Consensus 157 t~~~v~aER~~l~~L~ggC~~Piga~a~~~~~~~~~l~l~~~v~~~dG~~~~~~~~~~~~~~--a~~l-g~~la~~l~~~ 233 (245)
|+.|+.+||+||+.|+|||++||++|+.. +++++.|+|.|+|+||++.++.+..++..+ -... |++.++.|.+.
T Consensus 230 t~~~~~~eraflrtl~Ggcs~piav~s~~---~~g~l~L~g~v~s~dg~~~i~~~~~~~~~~~~~~~~~~~~a~~~L~~~ 306 (320)
T KOG2892|consen 230 TTLRILAERAFLRTLEGGCSVPIAVYSSK---KEGNLILTGLVWSLDGTKVIETSRKGPIVYEKMVKMGGKEAGQQLLSR 306 (320)
T ss_pred HHHHHHHHHHHHHhhCCCccCceeeEeec---cCCcEEEEeeEeccccchHHHHHhhcchhhhhhhhhccccccHHHHhh
Confidence 99999999999999999999999999999 677799999999999999988887776432 1233 46677777777
Q ss_pred hHHHHHH
Q psy11424 234 GAIEIIK 240 (245)
Q Consensus 234 ga~~il~ 240 (245)
++..+..
T Consensus 307 ~~~~~~~ 313 (320)
T KOG2892|consen 307 TAPGIFG 313 (320)
T ss_pred ccCCCCC
Confidence 6665544
No 7
>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=3.1e-65 Score=447.92 Aligned_cols=150 Identities=55% Similarity=0.919 Sum_probs=118.1
Q ss_pred CccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEE--cCCCCCCCCCCCCeEeeCcHHHHHHHHHhCCCCeE
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFIS--NDYISLSTLPKNAVVGTNSLRRKVLIKSFFPSLII 78 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~--~~~~~l~~lp~ga~IGTsS~RR~aql~~~~pdl~~ 78 (245)
+||++|+||||||||||||+++|+||.|+||++|+|||||||+ +++++|++||+|++|||||+||++||+++|||++|
T Consensus 64 ~aLl~g~iDiAVHSlKDlP~~l~~gl~iaav~~R~dprD~Lv~~~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~~pdl~~ 143 (215)
T PF01379_consen 64 EALLDGEIDIAVHSLKDLPTELPEGLVIAAVLKREDPRDVLVSRGRDGKSLEDLPKGARIGTSSLRRRAQLKRLRPDLEV 143 (215)
T ss_dssp HHHHTTS-SEEEEEGGGS-SS--TTEEEEEE-------EEEEE-GCTTSSCCCS-TT-EEE---HHHHHHHHHH-TTSEE
T ss_pred HHHHcCCccEEEeccccCCCCCCCCceEeccCCCCCCccEEEEecCCCCChHHCccccccCCCCHHHHHHHHHhccCCeE
Confidence 4899999999999999999999999999999999999999999 56889999999999999999999999999999999
Q ss_pred EeccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhh
Q psy11424 79 KSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLI 150 (245)
Q Consensus 79 ~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~ 150 (245)
++|||||+|||+||++|+|||||||+|||+|||+.++++++|++++|+|||||||||||||++|+++.++|+
T Consensus 144 ~~iRGNv~TRL~KL~~g~~daiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~llK 215 (215)
T PF01379_consen 144 VPIRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRISEILDPEEMLPAPGQGALAVECRKDDEEIIELLK 215 (215)
T ss_dssp E---S-HHHHHHHHHCTS-SEEEEEHHHHHHCT-GGGESEEE-TTTS-B-TTTT-EEEEEETT-HHHHHHH-
T ss_pred EEecCCHHHHHHHhcccCCCEEEhhhChhhhccccceeeeecCchhcCCCCCCeEEEEEEecCcHHHHHHhC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999985
No 8
>PRK01066 porphobilinogen deaminase; Provisional
Probab=100.00 E-value=7.2e-64 Score=441.83 Aligned_cols=151 Identities=34% Similarity=0.560 Sum_probs=147.1
Q ss_pred CccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCCCCCCCCCCCCeEeeCcHHHHHHHHHhCCCCeEEe
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKVLIKSFFPSLIIKS 80 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~~~l~~lp~ga~IGTsS~RR~aql~~~~pdl~~~~ 80 (245)
+||++|+||||||||||||+ |+||.|+||++|+|||||||++++.++.+||+|++|||||+||++||+++|||++|++
T Consensus 80 ~aLl~g~iDiAVHSlKDlPt--~~gl~l~av~~RedprDvLv~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~rPdl~v~~ 157 (231)
T PRK01066 80 FLVLSGQCDLAIHSAKDLPE--PPKLTVVAITAGLDPRDLLVYAEKYLSQPLPRRPRIGSSSLRREELLKLLFPSGIILD 157 (231)
T ss_pred HHHHcCCCCEEEecCCcCCC--CCCCEEEEEcCCCCCceEEEECCCCchhhCCCCCEEeCChHHHHHHHHHHCCCCEEEe
Confidence 48999999999999999999 9999999999999999999999988999999999999999999999999999999999
Q ss_pred ccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhcCCChh
Q psy11424 81 LRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYF 156 (245)
Q Consensus 81 iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~l~~~~ 156 (245)
|||||+|||+||++|+|||||||+|||+|||+.++++++|+++. |||||+||||||++|+++.++++.|||.+
T Consensus 158 iRGNV~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~~---A~gQGalaie~R~~d~~~~~ll~~i~~~~ 230 (231)
T PRK01066 158 IRGTIEERLKLLEEKKYDAIVVAKAAVLRLGLRLPYTKELPPPY---HPLQGRLAITASKHIRSWKGLFLPLGITE 230 (231)
T ss_pred CcCCHHHHHHHhcCCCCCchhhHHHHHHhcCCcccceeECCCCC---CCCCCeEEEEEecCCHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999999999999984 99999999999999999999999999975
No 9
>PF03900 Porphobil_deamC: Porphobilinogen deaminase, C-terminal domain; InterPro: IPR022418 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the C-terminal domain of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this alpha/beta domain consists of alpha-beta(3)-alpha in two layers []. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 3EQ1_B 3ECR_A 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A.
Probab=99.83 E-value=1.3e-20 Score=139.87 Aligned_cols=72 Identities=36% Similarity=0.651 Sum_probs=64.3
Q ss_pred HHHHHHHHHHHHHhccCCCcceeeEEEEeccCCCe-EEEEEEEEcCCCcE-EEEEEEecCCCCHHHHHHHHHHHHHH
Q psy11424 158 EQTVKAERAVSRNFNGSCKISLAAFAMVNNFNESE-INLRAIITNPNGLK-IITAEVNGPIDTPETVGLYAAELLKK 232 (245)
Q Consensus 158 ~~~v~aER~~l~~L~ggC~~Piga~a~~~~~~~~~-l~l~~~v~~~dG~~-~~~~~~~~~~~~a~~lg~~la~~l~~ 232 (245)
++|+.+||+||+.||||||+|||+||++ +++. ++|+++|+++||++ +++.+.+++.+++.++|+++|++|++
T Consensus 1 ~~~v~aER~fl~~l~ggC~~Piga~a~~---~~~~~l~l~~~v~~~dG~~~~~~~~~~~~~~~a~~lg~~la~~l~~ 74 (74)
T PF03900_consen 1 AIEVEAERAFLKELGGGCHSPIGAYAKI---EGDERLRLRAMVGSPDGSRIIIRVEITGPIEDAEELGKKLAEELLA 74 (74)
T ss_dssp HHHHHHHHHHHHHCT--TTSSEEEEEEE---ETTE-EEEEEEEE-TTSSSEEEEEEEEE-GGGHCCHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHhCCCCCCceeeEEEE---cCCCEEEEEEEEECCCCCEEEEEEEEEcCHHHHHHHHHHHHHHHhC
Confidence 5799999999999999999999999999 6777 99999999999999 89999999999999999999999975
No 10
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=96.33 E-value=0.039 Score=50.25 Aligned_cols=148 Identities=17% Similarity=0.187 Sum_probs=91.4
Q ss_pred CccccCCccEEeecCCCCC--CCCCCCeeEEEecCCCCCCeEEE------EcCCCCCCCCCCCCeEeeCc-H---HHHHH
Q psy11424 1 MAIIKGKADLAVHSLKDIP--MNLPSGFILCAILKREDPRDAFI------SNDYISLSTLPKNAVVGTNS-L---RRKVL 68 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP--~~l~~gL~iaav~~R~dprDvlv------~~~~~~l~~lp~ga~IGTsS-~---RR~aq 68 (245)
+||.+|++|+......+.= .....|..+..+ ...++ +.+.+++++||.|++|++++ . =|...
T Consensus 74 ~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~~~------~~~~vvp~~~ys~~i~si~DL~~Gk~IAip~d~~n~~r~L~ 147 (271)
T PRK11063 74 EALSKGDIDANAFQHKPYLDQQIKDRGYKLVAV------GNTFVYPIAGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLL 147 (271)
T ss_pred HHHHcCCcceecccCHHHHHHHHHHcCCcEEEE------eEEEEEEeeccccCCCCHHHhcCCCEEEecCCCccHHHHHH
Confidence 3789999999553222110 000123232222 11233 23567899999999999886 2 34444
Q ss_pred HHHh---------------------CC-CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCcc-ceeeecCCCCc
Q psy11424 69 IKSF---------------------FP-SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQK-RIRMLFSPNQI 125 (245)
Q Consensus 69 l~~~---------------------~p-dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~-~~~~~l~~~~~ 125 (245)
+++. .| +++|+++.-+ .=-+-|.+|++|+.++..-=..+.|+.. .-.-+++....
T Consensus 148 lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~~~~--~~~~al~~g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~~~ 225 (271)
T PRK11063 148 LLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVELEAP--QLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKDS 225 (271)
T ss_pred HHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEECcHH--HHHHhcccccccEEEEChHHHHHcCCCCCCCeeEECCCCC
Confidence 4443 23 6888888543 3345578999999999887778877754 21223443321
Q ss_pred CCCCCCceEEEEEec---CcHHHHHHhhcCCChhhHHHH
Q psy11424 126 LPAPGQGAIAIEILD---NRKELMEMLIPLNHYFSEQTV 161 (245)
Q Consensus 126 ~PA~gQGalave~r~---~d~~~~~ll~~l~~~~t~~~v 161 (245)
+.+.-+.+|+ +++++..+++.++.++....+
T Consensus 226 -----~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i 259 (271)
T PRK11063 226 -----PYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAA 259 (271)
T ss_pred -----CeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHH
Confidence 4667777775 557889999999988876544
No 11
>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=96.15 E-value=0.043 Score=49.79 Aligned_cols=153 Identities=16% Similarity=0.117 Sum_probs=93.7
Q ss_pred CccccCCccEEeecCCCCCC--CCCCCeeEEEecCCC-CCCeEEEEcCCCCCCCCCCCCeEeeC----cHHHHHHHHHh-
Q psy11424 1 MAIIKGKADLAVHSLKDIPM--NLPSGFILCAILKRE-DPRDAFISNDYISLSTLPKNAVVGTN----SLRRKVLIKSF- 72 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~--~l~~gL~iaav~~R~-dprDvlv~~~~~~l~~lp~ga~IGTs----S~RR~aql~~~- 72 (245)
+||.+|+||+........=. .-..|+.+.++.+=- -|- .+.+++++++++||.|++|+.+ ..=|.-.++..
T Consensus 61 ~Al~~G~ID~~~~q~~~~l~~~~~~~g~~lv~v~~~~~~p~-~~ys~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~~a 139 (258)
T TIGR00363 61 EAVSKGDLDANAFQHKPYLDQDAKAKGYKLVAVGNTFVYPL-AGYSKKIKNVNELQDGAKVAVPNDPTNLGRALLLLQKQ 139 (258)
T ss_pred HHHHcCCCCeEecCCHHHHHHHHHhCCCcEEEEeeeEEecc-cccCcCCCCHHHcCCCCEEEEeCCcchHHHHHHHHHHc
Confidence 37899999998643222100 112345555553100 010 2235678899999999999855 33455455554
Q ss_pred ---------------------CCCCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCccc-eeeecCCCCcCCCCC
Q psy11424 73 ---------------------FPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKR-IRMLFSPNQILPAPG 130 (245)
Q Consensus 73 ---------------------~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~-~~~~l~~~~~~PA~g 130 (245)
.-|++++.+--+- =.+-|.+|+.|+.++..-=+...|+... -.-+++... -
T Consensus 140 GLi~l~~~~~~~~t~~DI~~n~~~v~~vel~~~~--~~~al~~g~vDaa~v~~~~~~~agl~~~~~~i~~e~~~-----~ 212 (258)
T TIGR00363 140 GLIKLKDGNGLLPTVLDIVENPKKLNITELETSQ--LPRALDDPKVDLAVINTTYAGQVGLNPQDDGVFVEDKD-----S 212 (258)
T ss_pred CCceecCCCCCcCChhhhhcCCCCCEEEEcCHHH--HHHHhhcccccEEEEChHHHHHcCCCcCcCceeecCCC-----C
Confidence 4468888876643 3367889999999987666666655421 112333222 2
Q ss_pred CceEEEEEec---CcHHHHHHhhcCCChhhHHHH
Q psy11424 131 QGAIAIEILD---NRKELMEMLIPLNHYFSEQTV 161 (245)
Q Consensus 131 QGalave~r~---~d~~~~~ll~~l~~~~t~~~v 161 (245)
+++--+.+|. +++.+.++++.++.++.....
T Consensus 213 ~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i 246 (258)
T TIGR00363 213 PYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAA 246 (258)
T ss_pred CeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHH
Confidence 4777777775 457899999999988876544
No 12
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=94.02 E-value=1.2 Score=38.11 Aligned_cols=141 Identities=16% Similarity=0.193 Sum_probs=76.4
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCCC----CCCCCCCCCeEeeCcHHH-HHHHHHhCC-C
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYI----SLSTLPKNAVVGTNSLRR-KVLIKSFFP-S 75 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~~----~l~~lp~ga~IGTsS~RR-~aql~~~~p-d 75 (245)
+|.+|++|+++-++- ...+..+.+.+....- . -.-+++++... ++++| .|.+||+-+--= ...+...+| +
T Consensus 78 ~l~~G~~D~~~~~~~-~~~~r~~~~~~s~p~~-~-~~~~~~~~~~~~~~~~~~dl-~g~~i~~~~g~~~~~~l~~~~~~~ 153 (250)
T TIGR01096 78 SLKAKKVDAIMATMS-ITPKRQKQIDFSDPYY-A-TGQGFVVKKGSDLAKTLEDL-DGKTVGVQSGTTHEQYLKDYFKPG 153 (250)
T ss_pred HHhCCCcCEEEecCc-cCHHHhhccccccchh-c-CCeEEEEECCCCcCCChHHc-CCCEEEEecCchHHHHHHHhccCC
Confidence 577899999976542 1112223333322111 1 12344444322 45566 377887522111 245667777 8
Q ss_pred CeEEeccCcHHHHHhhhccCCccEEEehhhhhh----hcCCccceeeecCCCCcCCCCCCce-EEEEEecCcHHHHHHh
Q psy11424 76 LIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLK----RLNLQKRIRMLFSPNQILPAPGQGA-IAIEILDNRKELMEML 149 (245)
Q Consensus 76 l~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~----RLg~~~~~~~~l~~~~~~PA~gQGa-lave~r~~d~~~~~ll 149 (245)
++++.... .+.-+..|.+|++|++|.-..-+. +.+..+.+. +++ ..+.+.+-++. +++.++++++++...+
T Consensus 154 ~~~~~~~s-~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~~~~~~l~-~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~l 229 (250)
T TIGR01096 154 VDIVEYDS-YDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFK-FVG-PSVTDEKYFGDGYGIGLRKGDTELKAAF 229 (250)
T ss_pred cEEEEcCC-HHHHHHHHHcCCCCEEEeCHHHHHHHHHhCCCCCceE-Eec-cccccccccCCceEEEEeCCCHHHHHHH
Confidence 88887754 567899999999999999665543 333322222 222 11111111222 7777788776655544
No 13
>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=93.97 E-value=0.098 Score=47.01 Aligned_cols=107 Identities=17% Similarity=0.185 Sum_probs=65.3
Q ss_pred CccccCCccEEeecCCCCCCCCCCC--eeEEEecCCCCCCeEEEEcCC---CCCCCCCCCCeEeeC---c-HHHH-HHHH
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNLPSG--FILCAILKREDPRDAFISNDY---ISLSTLPKNAVVGTN---S-LRRK-VLIK 70 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l~~g--L~iaav~~R~dprDvlv~~~~---~~l~~lp~ga~IGTs---S-~RR~-aql~ 70 (245)
++|.+|++|+++.+.--+-.....| +.+.++.......+.||.++. .++.+| +|-+||+. | -.-- ..|.
T Consensus 42 ~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~~~~~lv~~~~s~I~s~~DL-kGK~Igv~~~s~~~~~l~~~L~ 120 (300)
T TIGR01729 42 TALASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIGKSEALVAREGSGIEKPEDL-KGKNVAVPFVSTTHYSLLAALK 120 (300)
T ss_pred HHHHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCCccceEEecCCCCCCChhHc-CCCEEEeCCCCcHHHHHHHHHH
Confidence 3789999999986532111111223 445566666566788988764 356777 68888862 2 2111 1233
Q ss_pred HhC--C-CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhc
Q psy11424 71 SFF--P-SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRL 110 (245)
Q Consensus 71 ~~~--p-dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RL 110 (245)
+.- | |++++ ..+-.....-|.+|+.||+++...-..++
T Consensus 121 ~~Gl~~~dv~~v--~~~~~~~~~al~~G~vDa~~~~~p~~~~~ 161 (300)
T TIGR01729 121 HWKTDPREVNIL--NLKPPQIVAAWQRGDIDAAYVWPPALSEL 161 (300)
T ss_pred HcCCChhheEEE--ecCcHHHHHHHHcCCcCEEEEecHHHHHH
Confidence 221 2 34444 44667788899999999999987765554
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=93.67 E-value=0.082 Score=43.61 Aligned_cols=136 Identities=18% Similarity=0.244 Sum_probs=82.9
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC-----C---CCCCCCCCCeEeeCcHHHHH-HHHHh
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY-----I---SLSTLPKNAVVGTNSLRRKV-LIKSF 72 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~-----~---~l~~lp~ga~IGTsS~RR~a-ql~~~ 72 (245)
+|.+|++|+++-++-.-|.. .+.+.... +-- ....+++.+++ . ++.+| .|.+||+..-.... .+...
T Consensus 53 ~l~~g~~D~~~~~~~~~~~r-~~~~~~s~-p~~-~~~~~~~~~~~~~~~~~~~~~~~dl-~~~~i~~~~g~~~~~~l~~~ 128 (225)
T PF00497_consen 53 MLENGKADIIIGGLSITPER-AKKFDFSD-PYY-SSPYVLVVRKGDAPPIKTIKSLDDL-KGKRIGVVRGSSYADYLKQQ 128 (225)
T ss_dssp HHHTTSSSEEESSEB-BHHH-HTTEEEES-ESE-EEEEEEEEETTSTCSTSSHSSGGGG-TTSEEEEETTSHHHHHHHHH
T ss_pred cccccccccccccccccccc-cccccccc-ccc-chhheeeeccccccccccccchhhh-cCcccccccchhHHHHhhhh
Confidence 57789999998554333222 23444432 111 22455555532 1 23477 67788876654444 56777
Q ss_pred CC-CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhh----cCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHH
Q psy11424 73 FP-SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKR----LNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELME 147 (245)
Q Consensus 73 ~p-dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~R----Lg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ 147 (245)
+| +.+++. -.|.+.-++.|.+|++|++|....-+.- .+...... . .+...+.-+++-++.+++.+.+
T Consensus 129 ~~~~~~~~~-~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~--~-----~~~~~~~~~~~~~~~~~~~l~~ 200 (225)
T PF00497_consen 129 YPSNINIVE-VDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVV--I-----PPPISPSPVYFAVRKKNPELLE 200 (225)
T ss_dssp THHTSEEEE-ESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEE--E-----EEEEEEEEEEEEEETTTHHHHH
T ss_pred ccchhhhcc-cccHHHHHHHHhcCCeeeeeccchhhhhhhhhcccccccc--c-----ccccccceeEEeecccccHHHH
Confidence 76 888886 4889999999999999999987776543 33332221 1 2344455566666777776665
Q ss_pred Hh
Q psy11424 148 ML 149 (245)
Q Consensus 148 ll 149 (245)
.+
T Consensus 201 ~~ 202 (225)
T PF00497_consen 201 IF 202 (225)
T ss_dssp HH
T ss_pred HH
Confidence 55
No 15
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=93.39 E-value=0.88 Score=41.07 Aligned_cols=155 Identities=17% Similarity=0.180 Sum_probs=81.1
Q ss_pred CccccCCccEEeec---CCCCCCCCCCCeeEEEec-CCCC-CCeEEEEcCCCCCCCCCCCCeEee--CcHHHHHHHHHhC
Q psy11424 1 MAIIKGKADLAVHS---LKDIPMNLPSGFILCAIL-KRED-PRDAFISNDYISLSTLPKNAVVGT--NSLRRKVLIKSFF 73 (245)
Q Consensus 1 ~aLl~g~iDiAVHS---lKDlP~~l~~gL~iaav~-~R~d-prDvlv~~~~~~l~~lp~ga~IGT--sS~RR~aql~~~~ 73 (245)
++|.+|..|+||-| ++---.+ .+++.++.=+ +..- ...+||++++. -...-.|.+||- +|+=-+.--+..+
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 37899999999988 2333333 5667776433 3222 34788887753 345667999995 4554444444444
Q ss_pred C--CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhc
Q psy11424 74 P--SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIP 151 (245)
Q Consensus 74 p--dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~ 151 (245)
+ ++++++++.| .=+..|.+|+.||.|+=...++.-...-.+ ..|+...+.-..++.+ |.+|++|..+..+|+.
T Consensus 135 ~gk~Ve~Vei~Y~--q~~~~l~~g~IDA~IWN~d~i~~~~~~l~~-~~l~~~~~~~~~seAV--ivi~~~~~~i~~ll~~ 209 (232)
T PF14503_consen 135 EGKNVEFVEIPYN--QLLELLRSGEIDAAIWNYDEIEDKNFGLKY-VPLKDDPMSKDASEAV--IVIRKDNEPIKALLRK 209 (232)
T ss_dssp TTS--EEEE--HH--HHHHHHHHTS--EEEEE--HHCCHHCTEEE-EE--SSCHHHHTT-EE--EEEETT-HHHHHHHHH
T ss_pred CCCceEEEEecHH--HHHHHHHCCCccEEEECCcccccccCCeeE-EeCCchHHHHhcCeeE--EEEeCCCHHHHHHHHH
Confidence 4 5678888765 567888999999999988844433322111 2344433433455544 5678999999999987
Q ss_pred CCChhhHHHHH
Q psy11424 152 LNHYFSEQTVK 162 (245)
Q Consensus 152 l~~~~t~~~v~ 162 (245)
+=|.+.-....
T Consensus 210 ~id~~~vl~iQ 220 (232)
T PF14503_consen 210 LIDVEKVLEIQ 220 (232)
T ss_dssp H--HHHHHHHH
T ss_pred hcCHHHHHHHH
Confidence 77766655443
No 16
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=93.33 E-value=0.71 Score=36.71 Aligned_cols=103 Identities=20% Similarity=0.226 Sum_probs=60.1
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC---CCCCCCCCCCeEeeCcHH-HHHHHHHhCCCCe
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY---ISLSTLPKNAVVGTNSLR-RKVLIKSFFPSLI 77 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~---~~l~~lp~ga~IGTsS~R-R~aql~~~~pdl~ 77 (245)
+|.+|++|+++-++---|.. ...+......- ...-+++.+++ .++++| +|-+||+.+-- -...+....++.+
T Consensus 54 ~l~~g~~D~~~~~~~~~~~~-~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~dL-~g~~i~~~~g~~~~~~~~~~~~~~~ 129 (219)
T smart00062 54 ALKSGKIDVVAAGMTITPER-AKQVDFSDPYY--KSGQVILVRKDSPIKSLEDL-KGKKVAVVAGTTGEELLKKLYPEAK 129 (219)
T ss_pred HHHCCcccEEeccccCCHHH-Hhheeecccee--eceeEEEEecCCCCCChHHh-CCCEEEEecCccHHHHHHHhCCCce
Confidence 57899999999765321111 11111111111 11245555443 356777 56677775321 2233444567787
Q ss_pred EEeccCcHHHHHhhhccCCccEEEehhhhhhh
Q psy11424 78 IKSLRGNIDTRLNKLDKGEYAAIILAAAGLKR 109 (245)
Q Consensus 78 ~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~R 109 (245)
+... ++.+.-+..|..|++|++++...-+..
T Consensus 130 ~~~~-~~~~~~~~~l~~g~~d~~~~~~~~~~~ 160 (219)
T smart00062 130 IVSY-DSQAEALAALKAGRADAAVADAPALAA 160 (219)
T ss_pred EEEc-CCHHHHHHHhhcCcccEEEeccHHHHH
Confidence 7765 456778899999999999998885443
No 17
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=93.27 E-value=1.8 Score=37.07 Aligned_cols=140 Identities=12% Similarity=0.150 Sum_probs=73.2
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC--CCCCCCCCCCeEeeC--cHHHHHHHHHhCCCCe
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY--ISLSTLPKNAVVGTN--SLRRKVLIKSFFPSLI 77 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~--~~l~~lp~ga~IGTs--S~RR~aql~~~~pdl~ 77 (245)
+|.+|++|+++=++--- .+..+.+...... -...-+++.++. .++.+| .|-+||+. +.= ...+...+|.++
T Consensus 75 ~l~~g~~D~~~~~~~~~-~~r~~~~~fs~p~--~~~~~~~v~~~~~~~~~~dL-~g~~Igv~~g~~~-~~~l~~~~~~~~ 149 (243)
T PRK15007 75 SLKFRRVEAVMAGMDIT-PEREKQVLFTTPY--YDNSALFVGQQGKYTSVDQL-KGKKVGVQNGTTH-QKFIMDKHPEIT 149 (243)
T ss_pred HHhCCCcCEEEEcCccC-HHHhcccceecCc--cccceEEEEeCCCCCCHHHh-CCCeEEEecCcHH-HHHHHHhCCCCe
Confidence 57789999875433111 1122333332211 112245555432 345666 46667652 111 134566789998
Q ss_pred EEeccCcHHHHHhhhccCCccEEEehhhhhhhc-CCccceeeecCCCCcCC-CCCCceEEEEEecCcHHHHHHh
Q psy11424 78 IKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRL-NLQKRIRMLFSPNQILP-APGQGAIAIEILDNRKELMEML 149 (245)
Q Consensus 78 ~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RL-g~~~~~~~~l~~~~~~P-A~gQGalave~r~~d~~~~~ll 149 (245)
++.. .|.+..+..|..|++|+++.-..-+... ....... .+.. .+.+ .....-+++-++.+++++.+.+
T Consensus 150 ~~~~-~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~l 220 (243)
T PRK15007 150 TVPY-DSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNPKLA-AVGD-KVTDKDYFGTGLGIAVRQGNTELQQKL 220 (243)
T ss_pred EEEc-CCHHHHHHHHHcCCCCEEEeCHHHHHHHHhcCCCce-eecC-cccccccCCcceEEEEeCCCHHHHHHH
Confidence 8765 7788999999999999999765433221 1111111 1111 1111 1112336777788776665554
No 18
>PRK11260 cystine transporter subunit; Provisional
Probab=93.22 E-value=0.72 Score=40.58 Aligned_cols=138 Identities=9% Similarity=0.120 Sum_probs=73.4
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC-----CCCCCCCCCCeEee--CcHHHHHHHHHhCC
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY-----ISLSTLPKNAVVGT--NSLRRKVLIKSFFP 74 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~-----~~l~~lp~ga~IGT--sS~RR~aql~~~~p 74 (245)
+|.+|++|+++-++-.-|. ..+.+.+....-+ ...+++.++. .++++| .|-+||+ ++.- ...++..+|
T Consensus 95 ~l~~G~~D~~~~~~~~~~~-r~~~~~fs~p~~~--~~~~~~~~~~~~~~~~~~~dL-~g~~Igv~~G~~~-~~~l~~~~~ 169 (266)
T PRK11260 95 SLDSKRIDVVINQVTISDE-RKKKYDFSTPYTV--SGIQALVKKGNEGTIKTAADL-KGKKVGVGLGTNY-EQWLRQNVQ 169 (266)
T ss_pred HHhcCCCCEEEeccccCHH-HHhccccCCceee--cceEEEEEcCCcCCCCCHHHc-CCCEEEEecCCcH-HHHHHHhCC
Confidence 5778999999865421122 1222222211111 1234554432 345566 4667775 2222 445677889
Q ss_pred CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHh
Q psy11424 75 SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEML 149 (245)
Q Consensus 75 dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll 149 (245)
+.++.....+ ++-++.|..|++|++|....-...+--...-...+....+ ... -+++.++++++++.+.+
T Consensus 170 ~~~i~~~~~~-~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~--~~~--~~~~~v~~~~~~l~~~l 239 (266)
T PRK11260 170 GVDVRTYDDD-PTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVAGEAF--SRQ--ESGVALRKGNPDLLKAV 239 (266)
T ss_pred CCceEecCCH-HHHHHHHHcCCCCEEEechHHHHHHHHhCCCcceecCCcc--ccC--ceEEEEeCCCHHHHHHH
Confidence 9998887776 4568999999999999755433332111000001111111 222 35566688887666655
No 19
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=92.87 E-value=1.3 Score=40.55 Aligned_cols=152 Identities=18% Similarity=0.151 Sum_probs=86.8
Q ss_pred CccccCCccEEeecCCCCCC----CCCCCeeEEEecCCCCCCeEEEEcCCCCCCCCCCCCeEeeCc----HHHHHHHHHh
Q psy11424 1 MAIIKGKADLAVHSLKDIPM----NLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNS----LRRKVLIKSF 72 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~----~l~~gL~iaav~~R~dprDvlv~~~~~~l~~lp~ga~IGTsS----~RR~aql~~~ 72 (245)
+||.+|+||+.+- -+.|. .---|..+.++-.=--....+-+.+.++++|||.|++|.-+. .=|...|+..
T Consensus 75 ~AL~~G~ID~n~~--qh~~yl~~~~~~~g~~lv~~~~~~~~P~~~Ys~~iksl~DL~~Ga~IAipnd~~n~~ral~lL~~ 152 (272)
T PRK09861 75 DATNHGELDANVF--QHRPFLEQDNQAHGYKLVAVGNTFVFPMAGYSKKIKTVAQIKEGATVAIPNDPTNLGRALLLLQK 152 (272)
T ss_pred HHHHcCCcceehh--hhHHHHHHHHHhcCCCeEEEeEEEEEeeeccccCCCCHHHcCCCCEEEEeCCCccHHHHHHHHHH
Confidence 3788999999763 22221 001233334432100000112245678999999999999874 3355555554
Q ss_pred C----------------------CCCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCcccee-eecCCCCcCCCC
Q psy11424 73 F----------------------PSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIR-MLFSPNQILPAP 129 (245)
Q Consensus 73 ~----------------------pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~-~~l~~~~~~PA~ 129 (245)
- .+++|+.+--. .=.+-|.+|..|+.++..-=...-|+...-. -+++. ..
T Consensus 153 agli~l~~~~g~~~t~~di~~np~~l~~ve~~~~--q~~~al~dg~vD~a~i~~~~~~~ag~~~~~~~l~~e~-----~~ 225 (272)
T PRK09861 153 EKLITLKEGKGLLPTALDITDNPRHLQIMELEGA--QLPRVLDDPKVDVAIISTTYIQQTGLSPVHDSVFIED-----KN 225 (272)
T ss_pred CCCEEEcCCCCCCCCHhHHhcCCCCCEEEEcCHH--HhHhhccCcccCEEEEchhHHHHcCCCcccceeEEcC-----CC
Confidence 2 25777766543 2345678899999988654444444432111 12221 11
Q ss_pred CCceEEEEEec---CcHHHHHHhhcCCChhhHHHH
Q psy11424 130 GQGAIAIEILD---NRKELMEMLIPLNHYFSEQTV 161 (245)
Q Consensus 130 gQGalave~r~---~d~~~~~ll~~l~~~~t~~~v 161 (245)
.+++.-+.+|+ +++.+.++++.++.++...-+
T Consensus 226 ~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i 260 (272)
T PRK09861 226 SPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAA 260 (272)
T ss_pred CCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHH
Confidence 24666677775 467899999999988875544
No 20
>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=92.80 E-value=0.7 Score=43.24 Aligned_cols=104 Identities=13% Similarity=0.088 Sum_probs=69.1
Q ss_pred ccccCCccEEeecCCCCCCC---CCCC--eeEEEecCCCCCCeEEEEcCCCCCCCCCCCCeEee--CcHHHHH--H-HHH
Q psy11424 2 AIIKGKADLAVHSLKDIPMN---LPSG--FILCAILKREDPRDAFISNDYISLSTLPKNAVVGT--NSLRRKV--L-IKS 71 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~---l~~g--L~iaav~~R~dprDvlv~~~~~~l~~lp~ga~IGT--sS~RR~a--q-l~~ 71 (245)
||..|++|++.- =|.|.. ...| +.+.++....+..|++|.++.+++.|| +|-+||+ +|..--. + |..
T Consensus 51 Al~aG~iD~~~~--g~~~~~~~~~a~g~~~~iv~v~~~~~g~~~ivv~~i~svaDL-KGKkIav~~gs~~~~ll~~aL~~ 127 (328)
T TIGR03427 51 QYTAGKFDGCTM--TNMDALTIPAAGGVDTTALIVGDFSNGNDGIVLKGGKSLADL-KGQKVNLVELSVSHYLLARALES 127 (328)
T ss_pred HHHcCCCCEEee--cCHHHHHHHHhCCCCeEEEEEEccCCCceEEEECCCCCHHHc-CCCEEeccCCChHHHHHHHHHHH
Confidence 678999999753 444321 1234 457777777778899999888889999 6778876 3333211 1 111
Q ss_pred h--C-CCCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhc
Q psy11424 72 F--F-PSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRL 110 (245)
Q Consensus 72 ~--~-pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RL 110 (245)
. - .|++++++. ...-..-|.+|+.||.++-.--+.++
T Consensus 128 aGL~~~DV~~v~~~--~~d~~aAl~~G~VDAa~~~eP~~s~~ 167 (328)
T TIGR03427 128 VGLSEKDVKVVNTS--DADIVAAFITKDVTAVVTWNPQLSEI 167 (328)
T ss_pred cCCCHHHeEEEeCC--hHHHHHHHhcCCCcEEEEcCchHHHH
Confidence 1 1 368888874 35667889999999998855444433
No 21
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=92.55 E-value=0.5 Score=40.77 Aligned_cols=143 Identities=19% Similarity=0.140 Sum_probs=87.5
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC----CCCCCCCC---CCeEeeCcHHHHHHHHHhCC
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY----ISLSTLPK---NAVVGTNSLRRKVLIKSFFP 74 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~----~~l~~lp~---ga~IGTsS~RR~aql~~~~p 74 (245)
+|..|++|+.+.++=-.| +..+-+.. ..+--..+.-+++.++. .++.+|.. |...||+ .+-........+
T Consensus 92 ~l~~g~~D~~~~~~~~t~-er~~~~~f-s~py~~~~~~~~~~~~~~~~~~~~~DL~gk~v~v~~gt~-~~~~~~~~~~~~ 168 (275)
T COG0834 92 ALKAGKVDIIIAGMTITP-ERKKKVDF-SDPYYYSGQVLLVKKDSDIGIKSLEDLKGKKVGVQLGTT-DEAEEKAKKPGP 168 (275)
T ss_pred HHhcCCcCEEEeccccCH-HHhccccc-cccccccCeEEEEECCCCcCcCCHHHhCCCEEEEEcCcc-hhHHHHHhhccC
Confidence 578999999999965555 54455555 45555555555553322 24566653 3445666 555666666778
Q ss_pred CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhc--CCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhcC
Q psy11424 75 SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRL--NLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPL 152 (245)
Q Consensus 75 dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RL--g~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~l 152 (245)
..+++....+ ..-+..|.+|..|+++.-..-+..+ ..............+.+ ...+++..++++ . .++.+.+
T Consensus 169 ~~~~~~~~~~-~~~~~al~~Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~-~-~~l~~~i 242 (275)
T COG0834 169 NAKIVAYDSN-AEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLS---VEYLGIALRKGD-D-PELLEAV 242 (275)
T ss_pred CceEEeeCCH-HHHHHHHHcCCccEEEcchHhhhhhhhhhcCCCCceeeeccCCC---cceeEEEeccCC-c-HHHHHHH
Confidence 8899988877 7789999999999999887776664 21111000111111111 357888888873 2 3444444
Q ss_pred C
Q psy11424 153 N 153 (245)
Q Consensus 153 ~ 153 (245)
|
T Consensus 243 n 243 (275)
T COG0834 243 N 243 (275)
T ss_pred H
Confidence 4
No 22
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=91.64 E-value=4.2 Score=35.60 Aligned_cols=95 Identities=16% Similarity=0.139 Sum_probs=50.0
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC----CCCCCCCCCCeEee---CcHHHHHHHHHh--
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY----ISLSTLPKNAVVGT---NSLRRKVLIKSF-- 72 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~----~~l~~lp~ga~IGT---sS~RR~aql~~~-- 72 (245)
++..|++|+++=++---|. .-+-+......-. + .-+++.+++ .++.+|+ |-+||+ |+.-. .+...
T Consensus 80 ~l~~g~~Di~~~~~~~t~e-R~~~~~fs~p~~~-~-~~~~~~~~~~~~~~~~~dl~-g~~Igv~~gs~~~~--~~~~~~~ 153 (260)
T PRK15010 80 SLKAKKIDAIISSLSITDK-RQQEIAFSDKLYA-A-DSRLIAAKGSPIQPTLDSLK-GKHVGVLQGSTQEA--YANETWR 153 (260)
T ss_pred HHHCCCCCEEEecCcCCHH-HHhhcccccceEe-c-cEEEEEECCCCCCCChhHcC-CCEEEEecCchHHH--HHHHhcc
Confidence 5778999988754321111 1111111111101 1 123444332 1456674 666766 33211 22222
Q ss_pred CCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 73 FPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 73 ~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.++++++.. .+.+.-+++|..|++|++|.-
T Consensus 154 ~~~~~~~~~-~~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 154 SKGVDVVAY-ANQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred cCCceEEec-CCHHHHHHHHHcCCccEEEeC
Confidence 345666655 577888999999999999963
No 23
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=91.48 E-value=1.4 Score=35.13 Aligned_cols=135 Identities=18% Similarity=0.218 Sum_probs=72.8
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCCC---CCCCCCCCCeEeeCc-HHHHHHHHHhCCCCe
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYI---SLSTLPKNAVVGTNS-LRRKVLIKSFFPSLI 77 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~~---~l~~lp~ga~IGTsS-~RR~aql~~~~pdl~ 77 (245)
+|.+|++|+++-+.-..+. ....+.+.. +-..++ -+++.+++. ++.+| .|.+||+.+ .-=...+....+..+
T Consensus 53 ~l~~g~~D~~~~~~~~~~~-~~~~~~~~~-~~~~~~-~~~~~~~~~~~~~~~dl-~g~~i~~~~~~~~~~~~~~~~~~~~ 128 (218)
T cd00134 53 ALKSGKVDLIAAGMTITPE-RAKQVDFSD-PYYKSG-QVILVKKGSPIKSVKDL-KGKKVAVQKGSTAEKYLKKALPEAK 128 (218)
T ss_pred HHhcCCcCEEeecCcCCHH-HHhhccCcc-cceecc-EEEEEECCCCCCChHHh-CCCEEEEEcCchHHHHHHHhCCccc
Confidence 5789999999877622221 111111111 111122 233433322 45666 466776641 111234555566677
Q ss_pred EEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCc--cceeeecCCCCcCCCCCCceEEEEEecCcHHH
Q psy11424 78 IKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQ--KRIRMLFSPNQILPAPGQGAIAIEILDNRKEL 145 (245)
Q Consensus 78 ~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~--~~~~~~l~~~~~~PA~gQGalave~r~~d~~~ 145 (245)
+....+ .+.-+..|.+|.+|+++........+--. ..+. ++... ...-...+++..+.+++++
T Consensus 129 ~~~~~~-~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l~-~~~~~---~~~~~~~~~~~~~~~~~~l 193 (218)
T cd00134 129 VVSYDD-NAEALAALENGRADAVIVDEIALAALLKKHPPELK-IVGPS---IDLEPLGFGVAVGKDNKEL 193 (218)
T ss_pred EEEeCC-HHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCcE-Eeccc---cCCCccceEEEEcCCCHHH
Confidence 776655 78899999999999999987766554221 2221 22221 1234556777777666433
No 24
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=90.20 E-value=0.41 Score=43.80 Aligned_cols=107 Identities=9% Similarity=0.127 Sum_probs=64.2
Q ss_pred CccccCCccEEeecCCCCCCC--CCCCeeEEEecCCCCCCeEEEEcC-CCCCCCCCCCCeEeeC---cHHHH--HHHHHh
Q psy11424 1 MAIIKGKADLAVHSLKDIPMN--LPSGFILCAILKREDPRDAFISND-YISLSTLPKNAVVGTN---SLRRK--VLIKSF 72 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~--l~~gL~iaav~~R~dprDvlv~~~-~~~l~~lp~ga~IGTs---S~RR~--aql~~~ 72 (245)
++|.+|++|+++.+.--+... ....+.+.++.......+.+|.++ -+++.+| +|-+||+. |.... ..|+..
T Consensus 66 ~al~~G~~D~a~~~~~~~~~a~~~g~~~~~v~~~~~~~~~~~lv~~~~I~s~~DL-kGK~Iav~~~s~~~~~l~~~L~~~ 144 (320)
T PRK11480 66 RALASGDVQIGNLGSSPLAVAASQQVPIEVFLLASKLGNSEALVVKKTISKPEDL-IGKRIAVPFISTTHYSLLAALKHW 144 (320)
T ss_pred HHHHCCCCCEECcCchHHHHHHHCCCCeEEEEeeccCCcceEEEecCCCCChHHc-CCCEEecCCCCchHHHHHHHHHHc
Confidence 378899999996543211111 112355556656655667888764 3577888 58899963 22211 123322
Q ss_pred --C-CCCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhc
Q psy11424 73 --F-PSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRL 110 (245)
Q Consensus 73 --~-pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RL 110 (245)
- .|++++++. -..-..-|.+|+.||+++..--..++
T Consensus 145 Gl~~~dv~~v~~~--~~~~~~Al~~G~VDAa~~~~p~~~~~ 183 (320)
T PRK11480 145 GIKPGQVEIVNLQ--PPAIIAAWQRGDIDGAYVWAPAVNAL 183 (320)
T ss_pred CCCHhheEEEECC--cHHHHHHHHcCCcCEEEEcchHHHHH
Confidence 2 255665553 46677888999999998776554444
No 25
>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=89.94 E-value=2.8 Score=37.75 Aligned_cols=161 Identities=15% Similarity=0.133 Sum_probs=88.9
Q ss_pred ccccCCccEEeecC----CCCCCCCCCCeeEEEecCCCCCCeEEEEcCCCCCCCCCCCCeEeeCc----HHHHHHHHHhC
Q psy11424 2 AIIKGKADLAVHSL----KDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNS----LRRKVLIKSFF 73 (245)
Q Consensus 2 aLl~g~iDiAVHSl----KDlP~~l~~gL~iaav~~R~dprDvlv~~~~~~l~~lp~ga~IGTsS----~RR~aql~~~~ 73 (245)
||.+|+||+-+.-- +.--.+ .|..|.++-+=--..=.|-|+++++++++|.|++|+=+. .=|.-.|+...
T Consensus 42 AL~~G~iDaN~fQh~~yl~~~n~~--~~~~L~~v~~~~~~p~glYS~k~~sl~~lp~Ga~VaIpnD~sN~~RaL~lLq~a 119 (237)
T PF03180_consen 42 ALADGEIDANFFQHIPYLEQFNKE--NGYNLVPVGPTYIEPMGLYSKKYKSLDDLPDGATVAIPNDPSNQARALKLLQEA 119 (237)
T ss_dssp HHHTTSSSEEEEEEHHHHHHHHHH--HT--EEEEEEEEE---EEEESSSSSGGGS-TTEEEEEESSHHHHHHHHHHHHHT
T ss_pred HHHCCCcceeccCCHHHHHHHHHH--CCCcEEEecceeEEeEEEeecccCchhhcCCCCEEEEeCCccchhHHHHHHHhC
Confidence 67778888775421 111111 244444443322223345578899999999999999543 44565665532
Q ss_pred ------C----------------CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCC
Q psy11424 74 ------P----------------SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQ 131 (245)
Q Consensus 74 ------p----------------dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQ 131 (245)
| +++|+++-..-- -+-| .++|+.|+.-.=...-|+...-.-++..+ +..-+
T Consensus 120 GLI~Lk~~~~~~~t~~DI~~Npk~l~~~evd~~~l--~~~l--~dvD~avi~~~~a~~agl~~~~~~~~~e~---~~~~~ 192 (237)
T PF03180_consen 120 GLITLKDGVGLTATVDDITENPKNLKFKEVDAAQL--PRAL--DDVDAAVINGNYALDAGLDPKKDLLFEEP---DADKP 192 (237)
T ss_dssp TSEEE-TT-GCC-SGGGEEEETTSEEEEEE-GGGH--HHHT--TTSSEEEE-HHHHHHTT--CCCHSSEE-S---SSSCG
T ss_pred CeEEEcCCCCCccChhhhhhcccCceEEEecHhhH--Hhhc--ccCCEEEecHhHHHHcCcCcccceeeeec---ccCcc
Confidence 2 344444433211 1222 35999999665556666654321122221 12456
Q ss_pred ceEEEEEec---CcHHHHHHhhcCCChhhHHHHHHHHHHHHHhccCCCcc
Q psy11424 132 GAIAIEILD---NRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKIS 178 (245)
Q Consensus 132 Galave~r~---~d~~~~~ll~~l~~~~t~~~v~aER~~l~~L~ggC~~P 178 (245)
=+..+.+|+ ||+++..+.+.+++++++ .|+..--+|.-.|
T Consensus 193 y~n~lv~r~~~~d~~~ik~l~ea~~s~~v~-------~~i~~~~~g~~iP 235 (237)
T PF03180_consen 193 YANVLVVREDDKDDPWIKKLVEAYQSPEVK-------KFIEETYKGSVIP 235 (237)
T ss_dssp GEEEEEEEGGGTTCHHHHHHHHHHTSHHHH-------HHHHHHCTTSSEE
T ss_pred eeEEEEEECCccCCHHHHHHHHHHCCHHHH-------HHHHHHcCCceEe
Confidence 677888886 789999999999998874 4444445666655
No 26
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=89.25 E-value=3.3 Score=44.24 Aligned_cols=137 Identities=14% Similarity=0.197 Sum_probs=73.5
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC-CCCCCCCCCCeEeeCcHH-HHHHHHHhCCCCeEE
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY-ISLSTLPKNAVVGTNSLR-RKVLIKSFFPSLIIK 79 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~-~~l~~lp~ga~IGTsS~R-R~aql~~~~pdl~~~ 79 (245)
+|.+|++|+..-.+. -|. ..+.+.+.- |-=..| -++|.++. ....++..|.+||..+-- =...++..+|+.+++
T Consensus 357 ~l~~g~~D~i~~~~~-t~~-r~~~~~fs~-py~~~~-~~~v~~~~~~~~~~~~~g~~vav~~g~~~~~~~~~~~p~~~~~ 432 (1197)
T PRK09959 357 QLNPGGWDIIPGAIY-SED-RENNVLFAE-AFITTP-YVFVMQKAPDSEQTLKKGMKVAIPYYYELHSQLKEMYPEVEWI 432 (1197)
T ss_pred HHHCCCceEeecccC-Ccc-ccccceecc-ccccCC-EEEEEecCCCCccccccCCEEEEeCCcchHHHHHHHCCCcEEE
Confidence 477899998654442 222 111111110 111112 23444332 223444467777653211 134677889999987
Q ss_pred eccCcHHHHHhhhccCCccEEEehhhhhhh----cCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHh
Q psy11424 80 SLRGNIDTRLNKLDKGEYAAIILAAAGLKR----LNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEML 149 (245)
Q Consensus 80 ~iRGNV~TRL~KL~~g~~DaiiLA~AGL~R----Lg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll 149 (245)
.. .|.+.=|..|.+|+.||.|....-... .+....+ ... .|....--+++-+|++|+.+.+++
T Consensus 433 ~~-~~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~~l~-~~~-----~~~~~~~~~~~av~k~~~~L~~~l 499 (1197)
T PRK09959 433 KV-DNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNELY-HFL-----IPGVPNASLSFAFPRGEPELKDII 499 (1197)
T ss_pred Ec-CCHHHHHHHHHcCCCCEEehhhHHHHHHHHhcccccce-eee-----cCCCCchheEEeeCCCCHHHHHHH
Confidence 66 688999999999999999975433322 2211111 111 111112236777899887665554
No 27
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=88.62 E-value=0.39 Score=42.17 Aligned_cols=124 Identities=16% Similarity=0.182 Sum_probs=69.1
Q ss_pred CccccCCccEEeecCCCCCCCC-------CCCeeEEEecCCCCCCeEEEEc------CCCCCCCC----C--CCCeEeeC
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNL-------PSGFILCAILKREDPRDAFISN------DYISLSTL----P--KNAVVGTN 61 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l-------~~gL~iaav~~R~dprDvlv~~------~~~~l~~l----p--~ga~IGTs 61 (245)
+||++|++|++.= .=.++.-. +..+.+.+-... ++..+++.+ +.+++.+| + +|.+||++
T Consensus 50 ~al~~G~iD~a~~-~~~~~~~~~~g~~~~~~~~~~~~~~~~-~g~~lvv~~~~~~~~~~~~~~dl~~~~~~~kGk~i~~~ 127 (252)
T PF13379_consen 50 EALAAGEIDIAFV-LAPALIAIAKGAGGPDVDIVVLAGLSQ-NGNALVVRNDLKDASDIKSLADLIKKRKAQKGKKIAVP 127 (252)
T ss_dssp HHHHCTSSSEEEE-CTHHHHHHHTTTTT----EEEEEECSB-SSEEEEECGGGTTCSTTCCGHHHHHTCCSCSTEEEEES
T ss_pred HHHHcCCCCEEEe-chHHHHHHHcCCCCcccceEEeeccCC-CceEEEEcCccccCCCccCHHHHHhhhcccCCcEEEEc
Confidence 3789999999876 32222211 224555554443 455556653 24566666 1 78899984
Q ss_pred ---cHHH-----HHHHHHhCC--CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCC
Q psy11424 62 ---SLRR-----KVLIKSFFP--SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPA 128 (245)
Q Consensus 62 ---S~RR-----~aql~~~~p--dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA 128 (245)
|.-. ..+-.-+.| |++++.+.. ...+.-|.+|+.||.++..-=..++--...-...++..++.|.
T Consensus 128 ~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~--~~~~~al~~g~iDa~~~~eP~~~~~~~~g~g~~v~~~~~~~~~ 202 (252)
T PF13379_consen 128 FPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP--PEMVAALRAGEIDAAVLWEPFASQAEAKGIGKIVADSGDVWGN 202 (252)
T ss_dssp STTSHHHHHHHHHHHHTT--TTTSSEEEE--G--HHHHHHHHTTS-SEEEEETTHHHHHHHTTS-EEEEEHHHCSTT
T ss_pred CCCCHHHHHHHHHHHhCCCCcccceEEEecCH--HHHHHHHhCCCcCEEEecCCHHHHHHhccCCeEEEEeccccCC
Confidence 3332 222222345 789998877 8899999999999999976665555222111234455555443
No 28
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=88.12 E-value=2.1 Score=38.76 Aligned_cols=122 Identities=17% Similarity=0.127 Sum_probs=82.0
Q ss_pred CccccCCccEEeecCCCCC--CCCCC--CeeEEEecCCCCCCeEEEEcCCC---CCCCCCCCCeEeeCcHHH-HHHHHHh
Q psy11424 1 MAIIKGKADLAVHSLKDIP--MNLPS--GFILCAILKREDPRDAFISNDYI---SLSTLPKNAVVGTNSLRR-KVLIKSF 72 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP--~~l~~--gL~iaav~~R~dprDvlv~~~~~---~l~~lp~ga~IGTsS~RR-~aql~~~ 72 (245)
++|..|.+|+++..+-+.| ..... .+.+.+...+....-.++.++.. ++.+| +|-+||.+-.-- ...+.++
T Consensus 76 ~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~~va~~~~~~~~~~i~~~~~~~i~~~adl-kGk~vg~~~~~~~~~~~l~~ 154 (335)
T COG0715 76 EALAAGALDFAVYYTGDTPLIAAGAAGAPVKVVAALVQNGNGIALLVLKDSGIKSVADL-KGKKVGVPFGGSTSDFLLRY 154 (335)
T ss_pred HHHhcCCcCccccccCchHHHHhhccCCCeEEeeecccCCceeEEEeccCCCcccccCC-CCceEEEeCCCchHHHHHHH
Confidence 4688999999999888888 44444 48889999998766666665543 45777 888998876654 3333222
Q ss_pred --------CCCCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCc
Q psy11424 73 --------FPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQI 125 (245)
Q Consensus 73 --------~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~ 125 (245)
..|.+++.+-.+ .-...|..|..||.+...--..++.........++....
T Consensus 155 ~L~~~Gl~~~dv~~v~~~~~--~~~~al~~g~vda~~~~ep~~~~~~~~~~~~~~~~~~~~ 213 (335)
T COG0715 155 ALAKAGLDPDDVELVNLPPA--DAVAALAAGQVDAFVVWEPWNAAAEGEGGGRVLLDGADL 213 (335)
T ss_pred HHHHcCCCcccceEEeeCcH--HHHHHHhcCCcceEEecCCchhhhhccCCeEEEEcchhh
Confidence 235665666555 667788899999987777666666554433333443333
No 29
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=87.97 E-value=2.6 Score=45.01 Aligned_cols=99 Identities=16% Similarity=0.127 Sum_probs=57.1
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcC--CCCCCCCCCCCeEee---CcHHHHHHHHHhCCCC
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISND--YISLSTLPKNAVVGT---NSLRRKVLIKSFFPSL 76 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~--~~~l~~lp~ga~IGT---sS~RR~aql~~~~pdl 76 (245)
+|.+|+||++..++-.-|.. .+.+.+.. +-=.++--+++.++ ..++.++ .|.+||. ++. ...++..+|+.
T Consensus 112 ~l~~g~iDl~~~~~~~~~~r-~~~~~fs~-py~~~~~~~v~~~~~~~~~~~~l-~~~~i~~~~g~~~--~~~~~~~~p~~ 186 (1197)
T PRK09959 112 ALEEGEVDIVLSHLVASPPL-NDDIAATK-PLIITFPALVTTLHDSMRPLTSS-KPVNIARVANYPP--DEVIHQSFPKA 186 (1197)
T ss_pred HHHcCCCcEecCcccccccc-ccchhcCC-CccCCCceEEEeCCCCCCCcccc-cCeEEEEeCCCCC--HHHHHHhCCCC
Confidence 68899999987655332211 11221111 00111111222211 1233443 4455543 222 46788899999
Q ss_pred eEEeccCcHHHHHhhhccCCccEEEehhhh
Q psy11424 77 IIKSLRGNIDTRLNKLDKGEYAAIILAAAG 106 (245)
Q Consensus 77 ~~~~iRGNV~TRL~KL~~g~~DaiiLA~AG 106 (245)
+++... |.+.-|..|.+|+.||+|-..+-
T Consensus 187 ~i~~~~-s~~~al~av~~G~~Da~i~~~~~ 215 (1197)
T PRK09959 187 TIISFT-NLYQALASVSAGQNDYFIGSNII 215 (1197)
T ss_pred EEEeCC-CHHHHHHHHHcCCCCEEEccHHH
Confidence 998665 78888999999999999987643
No 30
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=87.87 E-value=2.5 Score=41.24 Aligned_cols=102 Identities=21% Similarity=0.237 Sum_probs=60.7
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC----CCCCCCCCCCeEe----eCcHHHHHHHHHhC
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY----ISLSTLPKNAVVG----TNSLRRKVLIKSFF 73 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~----~~l~~lp~ga~IG----TsS~RR~aql~~~~ 73 (245)
+|.+|++||++-++-.-|. ..+.+.+.. +=-...-+||.+++ .++++| .|.+|| |+..-.-..+...+
T Consensus 96 aL~~G~iDi~~~~lt~T~e-R~~~~~FS~--Py~~~~~~lv~r~~~~~i~~l~dL-~Gk~I~V~~gS~~~~~L~~l~~~~ 171 (482)
T PRK10859 96 ALDKGKADLAAAGLTYTPE-RLKQFRFGP--PYYSVSQQLVYRKGQPRPRSLGDL-KGGTLTVAAGSSHVETLQELKKKY 171 (482)
T ss_pred HHhCCCCCEEeccCcCChh-hhccCcccC--CceeeeEEEEEeCCCCCCCCHHHh-CCCeEEEECCCcHHHHHHHHHHhC
Confidence 6789999998876643332 112222211 00112344555432 245555 355554 44444444555668
Q ss_pred CCCeEEecc-CcHHHHHhhhccCCccEEEehhhhh
Q psy11424 74 PSLIIKSLR-GNIDTRLNKLDKGEYAAIILAAAGL 107 (245)
Q Consensus 74 pdl~~~~iR-GNV~TRL~KL~~g~~DaiiLA~AGL 107 (245)
|++.++... .+.+.-|+.|.+|++|++|.-..-+
T Consensus 172 p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d~~~~ 206 (482)
T PRK10859 172 PELSWEESDDKDSEELLEQVAEGKIDYTIADSVEI 206 (482)
T ss_pred CCceEEecCCCCHHHHHHHHHCCCCCEEEECcHHH
Confidence 998877543 6899999999999999999865443
No 31
>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=87.22 E-value=4.6 Score=35.79 Aligned_cols=140 Identities=15% Similarity=0.128 Sum_probs=69.2
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC-----CCCCCCC--CCCeEeeCcHHH-HHHHHHh-
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY-----ISLSTLP--KNAVVGTNSLRR-KVLIKSF- 72 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~-----~~l~~lp--~ga~IGTsS~RR-~aql~~~- 72 (245)
+|.+|++|+....+-.-|... +.+.+.- +-... ..+++.+++ .++++|. +|.+||+..-== ..++...
T Consensus 87 ~l~~G~~Di~~~~~~~t~eR~-~~~~fs~-py~~~-~~~~~~~~~~~~~i~~~~dl~~~~g~~Igv~~g~~~~~~l~~~~ 163 (275)
T TIGR02995 87 GLQAGRFDAIAAGLFIKPERC-KQVAFTQ-PILCD-AEALLVKKGNPKGLKSYKDIAKNPDAKIAAPGGGTEEKLAREAG 163 (275)
T ss_pred HHHCCCcCEEeecccCCHHHH-hcccccc-ceeec-ceeEEEECCCCCCCCCHHHhccCCCceEEEeCCcHHHHHHHHcC
Confidence 467899999876543222111 1111111 11111 123333332 1345553 366776432111 2344443
Q ss_pred CCCCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhc----CCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHH
Q psy11424 73 FPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRL----NLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEM 148 (245)
Q Consensus 73 ~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RL----g~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~l 148 (245)
.|..+++... |.++-++.|..|++|++|.-..-+..+ +.. .+. .+.+ +.+.+-+...++-.+.+++++.+.
T Consensus 164 ~~~~~i~~~~-~~~~~i~~L~~grvDa~i~d~~~~~~~~~~~~~~-~~~-~~~~--~~~~~~~~~~~~~~~~~~~~l~~~ 238 (275)
T TIGR02995 164 VKREQIIVVP-DGQSGLKMVQDGRADAYSLTVLTINDLASKAGDP-NVE-VLAP--FKDAPVRYYGGAAFRPEDKELRDA 238 (275)
T ss_pred CChhhEEEeC-CHHHHHHHHHcCCCCEEecChHHHHHHHHhCCCC-Cce-eecC--ccCCccccceeEEECCCCHHHHHH
Confidence 4666676554 678899999999999999866543322 321 221 1111 112232233355567777766665
Q ss_pred h
Q psy11424 149 L 149 (245)
Q Consensus 149 l 149 (245)
+
T Consensus 239 ~ 239 (275)
T TIGR02995 239 F 239 (275)
T ss_pred H
Confidence 5
No 32
>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=87.18 E-value=4.2 Score=35.07 Aligned_cols=106 Identities=14% Similarity=0.101 Sum_probs=58.3
Q ss_pred ccccCCccEEeecCCCCCCC-CCCC-eeEEE-ecCCCC--CC-eEEEEcCC---CCCCCCCCCCeEeeCcHH-----H--
Q psy11424 2 AIIKGKADLAVHSLKDIPMN-LPSG-FILCA-ILKRED--PR-DAFISNDY---ISLSTLPKNAVVGTNSLR-----R-- 65 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~-l~~g-L~iaa-v~~R~d--pr-Dvlv~~~~---~~l~~lp~ga~IGTsS~R-----R-- 65 (245)
+|.+|++|+++.+.=..+.. ...+ ..+.. +..... .. -+||.+++ .++.+| .|-+||+.... -
T Consensus 80 ~l~~g~~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~~i~~~~dL-~gk~I~~~~~~s~~~~~~~ 158 (254)
T TIGR01098 80 AMRFGRVDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADSPIKSLKDL-KGKTFAFGDPASTSGYLVP 158 (254)
T ss_pred HHHcCCccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCCCCCChHHh-cCCEEEeeCCCCccchHhH
Confidence 57899999999765333311 1111 11111 111110 11 25665543 356778 47888864211 1
Q ss_pred HHHHHHhCC------CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhh
Q psy11424 66 KVLIKSFFP------SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKR 109 (245)
Q Consensus 66 ~aql~~~~p------dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~R 109 (245)
...|+..+. +.++.. -++.++-+..|.+|+.|+.+....-+..
T Consensus 159 ~~~l~~~~~~~~~~~~~~i~~-~~~~~~~~~al~~G~~Da~~~~~~~~~~ 207 (254)
T TIGR01098 159 RYQLKKEGGLDADGFFSEVVF-SGSHDASALAVANGKVDAATNNSSAIGR 207 (254)
T ss_pred HHHHHHhcCCChHHhhhheee-cCchHHHHHHHHcCCCCeEEecHHHHHH
Confidence 122343332 134443 3566788999999999999988776654
No 33
>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=87.14 E-value=4.9 Score=34.76 Aligned_cols=105 Identities=10% Similarity=-0.022 Sum_probs=57.6
Q ss_pred ccccCCccEEeecCCCCCCC--CCCCeeEEEecCCCCCCeEEEEcCC---CCCCCCCCCCeEeeC---cHHH-HHHHHHh
Q psy11424 2 AIIKGKADLAVHSLKDIPMN--LPSGFILCAILKREDPRDAFISNDY---ISLSTLPKNAVVGTN---SLRR-KVLIKSF 72 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~--l~~gL~iaav~~R~dprDvlv~~~~---~~l~~lp~ga~IGTs---S~RR-~aql~~~ 72 (245)
+|.+|++|+++-+.=..... -...+.+.+..... ...+++.++. .++++| +|.+||++ |... ..++...
T Consensus 45 ~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~-~~~~~v~~~~~~i~s~~dL-~Gk~i~~~~~~~~~~~~~~~l~~ 122 (288)
T TIGR01728 45 ALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSDN-KATAIVVIKGSPIRTVADL-KGKRIAVPKGGSGHDLLLRALLK 122 (288)
T ss_pred HHhcCCccccccCCcHHHHHHhcCCCEEEEEEecCC-CceEEEECCCCCCCCHHHc-CCCEEEecCCccHHHHHHHHHHH
Confidence 68899999986432111111 11346666655543 3455555543 356677 46678752 2222 2222222
Q ss_pred C---C-CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhc
Q psy11424 73 F---P-SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRL 110 (245)
Q Consensus 73 ~---p-dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RL 110 (245)
. + +.+++. .+...-+.-|.+|+.|++++..--..++
T Consensus 123 ~G~~~~~v~~~~--~~~~~~~~al~~g~vda~~~~~p~~~~~ 162 (288)
T TIGR01728 123 AGLSGDDVTILY--LGPSDARAAFAAGQVDAWAIWEPWGSAL 162 (288)
T ss_pred cCCCccceeEEe--cCcHHHHHHHHCCCCCEEEeccchHhHH
Confidence 1 1 233333 3456678889999999999976444443
No 34
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=83.24 E-value=6.8 Score=35.30 Aligned_cols=101 Identities=14% Similarity=0.087 Sum_probs=55.9
Q ss_pred CccccCCccEEeecCCCCCCC--CCCCeeEEEe--cCCCCCCeEEEEcCC---CCCCCCCCCCeEeeCc---HHH-HHH-
Q psy11424 1 MAIIKGKADLAVHSLKDIPMN--LPSGFILCAI--LKREDPRDAFISNDY---ISLSTLPKNAVVGTNS---LRR-KVL- 68 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~--l~~gL~iaav--~~R~dprDvlv~~~~---~~l~~lp~ga~IGTsS---~RR-~aq- 68 (245)
++|.+|++|+++-+ +.|.. ...|+.+..+ .+..+...++|.+++ .++++|. |.+||++. .+. -.+
T Consensus 71 ~aL~~G~iDia~~~--~~~~~~~~~~g~~~~~v~~~~~~~~~~~lvv~~~s~i~s~~dL~-Gk~I~~~~gs~~~~~l~~~ 147 (314)
T PRK11553 71 EALNVGSIDLGSTG--DIPPIFAQAAGADLVYVGVEPPKPKAEVILVAENSPIKTVADLK-GHKVAFQKGSSSHNLLLRA 147 (314)
T ss_pred HHHHcCCCCEEccC--CHHHHHHHhCCCCEEEEEEecCCCcceEEEEeCCCCCCCHHHhC-CCEEeecCCCcHHHHHHHH
Confidence 36889999999854 44332 1344444333 233333456776543 3567774 66677532 222 122
Q ss_pred HHHhCCC-CeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 69 IKSFFPS-LIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 69 l~~~~pd-l~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
++..--+ -.+..+..+...-..-|.+|++||+++..
T Consensus 148 l~~~g~~~~dv~~v~~~~~~~~~al~~G~vDa~~~~e 184 (314)
T PRK11553 148 LRKAGLKFTDIQPTYLTPADARAAFQQGNVDAWAIWD 184 (314)
T ss_pred HHHcCCCHHHeEEEecChHHHHHHHHcCCCCEEEEcC
Confidence 2222111 12223444666677889999999998754
No 35
>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=82.54 E-value=3.1 Score=34.21 Aligned_cols=41 Identities=10% Similarity=0.124 Sum_probs=37.3
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++...++...||++++.-..||-.+-++.|.+|++|..|..
T Consensus 16 ~~~l~~f~~~~P~v~l~i~~~~~~~~~~~L~~~~~D~~i~~ 56 (204)
T cd08429 16 YRLLEPAMDLHEPIRLVCREGKLEQLLADLALHRLDMVLAD 56 (204)
T ss_pred HHHHHHHHHhCCCcEEEEEeCCHHHHHHHHHcCCccEEEec
Confidence 57788889999999999999999999999999999998753
No 36
>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=81.79 E-value=3.3 Score=33.36 Aligned_cols=49 Identities=12% Similarity=0.041 Sum_probs=40.4
Q ss_pred CCeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 55 NAVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 55 ga~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
|-+||+++ ++-..++++.+|++++...-++-++-+.+|.+|++|..|..
T Consensus 1 ~~~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08467 1 GFTLAMPDYAEVALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGR 56 (200)
T ss_pred CeEEEechhhHHHHHHHHHHHHHhhCCCCEEEEecCCcccHHHHhhCCCcCEEEec
Confidence 45677655 35568888999999999999998888999999999998853
No 37
>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=81.02 E-value=4.1 Score=32.03 Aligned_cols=42 Identities=7% Similarity=-0.045 Sum_probs=37.1
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
.+.-.+++..+|++++.-..+|-++.+..|.+|++|..|...
T Consensus 16 ~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08449 16 GPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRF 57 (197)
T ss_pred HHHHHHHHHHCCCeEEEEEECCHHHHHHHHhCCCccEEEecc
Confidence 466788899999999999999999999999999999988643
No 38
>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=80.95 E-value=4.2 Score=31.97 Aligned_cols=41 Identities=15% Similarity=0.212 Sum_probs=36.6
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
...-.++++.+|++++.-..+|-+.-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~ 56 (198)
T cd08412 16 PGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTY 56 (198)
T ss_pred HHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEc
Confidence 36678889999999999999999999999999999998874
No 39
>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=80.53 E-value=4.4 Score=32.42 Aligned_cols=41 Identities=17% Similarity=0.092 Sum_probs=36.2
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
...-.+++..+|++++.-..|+-+.-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08452 16 PPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLH 56 (197)
T ss_pred HHHHHHHHHHCCCcEEEEEecChHHHHHHHHCCCccEEEee
Confidence 46678888999999999999999999999999999998863
No 40
>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=79.75 E-value=4.5 Score=31.73 Aligned_cols=41 Identities=24% Similarity=0.353 Sum_probs=35.9
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
+--.++.+.+|++++.-..|+-++-++.|.+|++|-.|...
T Consensus 17 ~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (195)
T cd08427 17 RALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVE 57 (195)
T ss_pred HHHHHHHHHCCCceEEEEeCCcHHHHHHHHCCCCCEEEEcC
Confidence 44578888999999999999999999999999999988754
No 41
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=79.57 E-value=7.9 Score=35.22 Aligned_cols=97 Identities=13% Similarity=0.010 Sum_probs=56.5
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC---CCCCCCCCCCeEeeCcHHHHHHHH-HhCCCCe
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY---ISLSTLPKNAVVGTNSLRRKVLIK-SFFPSLI 77 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~---~~l~~lp~ga~IGTsS~RR~aql~-~~~pdl~ 77 (245)
+|.+|++|+++=++ |+..+............-...+=+++.++. .++++| +|-+|||+...=..+.. ...-+.+
T Consensus 59 ~L~sG~vDlgi~g~-~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~~i~sl~DL-~Gk~ia~~~~~~~~~~l~~~gi~~~ 136 (287)
T PRK00489 59 YVADGVVDLGITGE-DLLEESGADVEELLDLGFGKCRLVLAVPEDSDWQGVEDL-AGKRIATSYPNLTRRYLAEKGIDAE 136 (287)
T ss_pred HHHcCCCCEEEcch-HHHHHCCCCceEeeeccCCceEEEEEEECCCCCCChHHh-CCCEEEEcCcHHHHHHHHHcCCceE
Confidence 57889999998664 221121111222222112223444444432 356777 57899997665433332 2223578
Q ss_pred EEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 78 IKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 78 ~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++..-|+++. -+..|..|||+--
T Consensus 137 iv~~~gs~ea---a~~~G~aDaivd~ 159 (287)
T PRK00489 137 VVELSGAVEV---APRLGLADAIVDV 159 (287)
T ss_pred EEECCCchhh---hhcCCcccEEEee
Confidence 8889999997 4556999999873
No 42
>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=78.21 E-value=1 Score=37.96 Aligned_cols=99 Identities=24% Similarity=0.228 Sum_probs=55.8
Q ss_pred ccccCCccEEeecCCCCCCCCCCCe--eEEEecCCCCCCeEEEEcCC---CCCCCCCCCCeEeeCcHHHH-----HHHHH
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGF--ILCAILKREDPRDAFISNDY---ISLSTLPKNAVVGTNSLRRK-----VLIKS 71 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL--~iaav~~R~dprDvlv~~~~---~~l~~lp~ga~IGTsS~RR~-----aql~~ 71 (245)
+|.+|++|+++=+.=-+......|. .+.+..-..++. .+|+++. +++.+| +|-+||.++---. ..|+.
T Consensus 37 ~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~-~l~~~~~s~i~~~~DL-kGK~i~v~~~s~~~~~~~~~l~~ 114 (216)
T PF09084_consen 37 ALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPN-ALVVRKDSGIKSPADL-KGKKIGVSRGSSSEYFLRALLKK 114 (216)
T ss_dssp HHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCE-EEEEETTTS-SSGGGG-TTSEEEESTTSHHHHHHHHHHHH
T ss_pred HHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCce-EEEEeccCCCCCHHHh-CCCEEEEecCcchhHHHHHHHHH
Confidence 6889999999876533332333343 333323323344 4444433 456677 6889998872111 12222
Q ss_pred h---CCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 72 F---FPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 72 ~---~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
. ..+++++.+. -.....-|.+|+.||+++-.
T Consensus 115 ~g~~~~~v~~v~~~--~~~~~~al~~g~vDa~~~~~ 148 (216)
T PF09084_consen 115 NGIDPDDVKIVNLG--PPELAQALLSGQVDAAILWY 148 (216)
T ss_dssp TTT-GGGSEEEES---HHHHHHHHHTTSSSEEEEEE
T ss_pred hccccccceeeeee--hhhhhhhhhcCCCCEEEEcc
Confidence 2 1356666553 34444589999999999333
No 43
>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=77.93 E-value=6.8 Score=31.26 Aligned_cols=41 Identities=12% Similarity=-0.113 Sum_probs=36.5
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+.-..+++.+|++++.-..+|-++-.+.|.+|++|-.|..
T Consensus 16 ~~~l~~f~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08458 16 SGVIQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGISI 56 (196)
T ss_pred HHHHHHHHHHCCCcEEEEeccChHHHHHHHHcCCCCEEEEe
Confidence 46678888999999999999999999999999999998864
No 44
>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=77.48 E-value=6.5 Score=31.68 Aligned_cols=41 Identities=10% Similarity=0.097 Sum_probs=35.5
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
.=-+.+++.+|++++...-++-++-++.|.+|++|-.|...
T Consensus 17 ~~l~~f~~~~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~ 57 (200)
T cd08465 17 ALMRQLRAEAPGIDLAVSQASREAMLAQVADGEIDLALGVF 57 (200)
T ss_pred HHHHHHHHHCCCcEEEEecCChHhHHHHHHCCCccEEEecc
Confidence 44577788899999999999999999999999999988643
No 45
>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=77.20 E-value=6.8 Score=31.01 Aligned_cols=40 Identities=15% Similarity=0.180 Sum_probs=34.6
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+--.++++.+|++++.-.-|+-++-+..|.+|++|..|..
T Consensus 17 ~~l~~f~~~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (200)
T cd08466 17 RLLARLKQLAPNISLRESPSSEEDLFEDLRLQEVDLVIDY 56 (200)
T ss_pred HHHHHHHHHCCCCEEEEecCchHhHHHHHHcCCccEEEec
Confidence 4457788889999999999999999999999999987753
No 46
>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=76.94 E-value=7.3 Score=30.94 Aligned_cols=47 Identities=19% Similarity=0.179 Sum_probs=38.8
Q ss_pred eEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 57 VVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 57 ~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+||+++ ++-..++...+|++++.-.-++-.+-+..|.+|++|..|..
T Consensus 3 ~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~ 56 (200)
T cd08453 3 SLAFVSTADYSVLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVI 56 (200)
T ss_pred EEEEechHHhHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHcCCCCEEEEe
Confidence 466654 35678888899999999999998888999999999987754
No 47
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=76.87 E-value=43 Score=29.10 Aligned_cols=97 Identities=14% Similarity=0.144 Sum_probs=48.9
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC---CCCCCCCCCCeEee---CcHHHHHHHHHhC--
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY---ISLSTLPKNAVVGT---NSLRRKVLIKSFF-- 73 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~---~~l~~lp~ga~IGT---sS~RR~aql~~~~-- 73 (245)
++.+|++|+++..+-.-|. ...-+.... +-=.++.-+++.++. .++.+| +|.+||. |+-. ..+....
T Consensus 80 ~l~~g~~D~~~~~~~~t~e-R~~~~~fs~-p~~~~~~~~~~~~~~~~~~~~~dl-~g~~Igv~~g~~~~--~~~~~~~~~ 154 (259)
T PRK15437 80 SLKAKKIDAIMSSLSITEK-RQQEIAFTD-KLYAADSRLVVAKNSDIQPTVESL-KGKRVGVLQGTTQE--TFGNEHWAP 154 (259)
T ss_pred HHHCCCCCEEEecCCCCHH-Hhhhccccc-hhhcCceEEEEECCCCCCCChHHh-CCCEEEEecCcHHH--HHHHhhccc
Confidence 5779999999875532221 111111111 111222222222211 245666 5666765 3221 1222222
Q ss_pred CCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 74 PSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 74 pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
++++++..- +.+.=+++|..|++|++|.-.
T Consensus 155 ~~~~~~~~~-~~~~~i~~L~~grvD~~v~~~ 184 (259)
T PRK15437 155 KGIEIVSYQ-GQDNIYSDLTAGRIDAAFQDE 184 (259)
T ss_pred cCceEEecC-CHHHHHHHHHcCCccEEEech
Confidence 346666433 445668899999999998755
No 48
>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=75.98 E-value=7.7 Score=30.70 Aligned_cols=46 Identities=24% Similarity=0.323 Sum_probs=39.0
Q ss_pred eEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 57 VVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 57 ~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
+||+++ ++-..+++..+|++++.-.-+|-+.-+..|.+|++|-.|.
T Consensus 4 ~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~ 56 (200)
T cd08411 4 RLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALL 56 (200)
T ss_pred EEEecHHHHhhhhHHHHHHHHHHCCCcEEEEEeCcHHHHHHHHHcCCccEEEE
Confidence 577764 3557788889999999999899999999999999998875
No 49
>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=75.75 E-value=6.8 Score=31.58 Aligned_cols=40 Identities=10% Similarity=-0.043 Sum_probs=35.2
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+-.+.++..+|++++.-..++-..=+..|.+|++|..+..
T Consensus 18 ~~l~~f~~~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~ 57 (198)
T cd08486 18 LLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSR 57 (198)
T ss_pred HHHHHHHHhCCCeEEEEEECCHHHHHHHHHcCCceEEEec
Confidence 4457778889999999888999999999999999999864
No 50
>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=75.72 E-value=7.5 Score=30.57 Aligned_cols=41 Identities=10% Similarity=0.049 Sum_probs=35.7
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++-...+++.+|++++.-.-++-.+=+..|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (196)
T cd08450 16 PEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMR 56 (196)
T ss_pred HHHHHHHHhhCCCcEEEEEecChHHHHHHHhcCCccEEEEe
Confidence 45668888999999999988998888999999999998853
No 51
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=74.23 E-value=6.1 Score=31.24 Aligned_cols=40 Identities=13% Similarity=0.017 Sum_probs=34.5
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+.-..++..+|++++.-.-++.+.-++.|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~g~~D~~i~~ 56 (195)
T cd08431 17 PLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGA 56 (195)
T ss_pred HHHHHHHHHCCCCceEEEEeccchHHHHHhCCCCCEEEEe
Confidence 5567888999999999888888888899999999998864
No 52
>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=74.21 E-value=9.6 Score=29.97 Aligned_cols=41 Identities=22% Similarity=0.248 Sum_probs=36.3
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+--.++++.+|++++.-.-++-++-+..|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (201)
T cd08418 16 PAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGT 56 (201)
T ss_pred HHHHHHHHHHCCCceEEEEeCcHHHHHHHHHcCCCcEEEEe
Confidence 35578899999999999998999999999999999999864
No 53
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=74.07 E-value=9.7 Score=29.75 Aligned_cols=40 Identities=13% Similarity=0.161 Sum_probs=35.4
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
..-.++.+.+|++++.-.-||-..-.+.|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~ 56 (197)
T cd08448 17 RILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVH 56 (197)
T ss_pred HHHHHHHHHCCCCeEEEEeCCHHHHHHHHHcCCcceEEEe
Confidence 5568888899999999999999999999999999998853
No 54
>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=73.89 E-value=8.4 Score=30.09 Aligned_cols=41 Identities=10% Similarity=0.142 Sum_probs=35.7
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+--.++...+|++++.-.-|+-+.-++.|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (193)
T cd08442 16 PPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVA 56 (193)
T ss_pred HHHHHHHHHHCCCceEEEEeCCcHHHHHHHHCCCccEEEEe
Confidence 35568888899999999988999999999999999998864
No 55
>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=73.47 E-value=9 Score=30.10 Aligned_cols=41 Identities=12% Similarity=0.000 Sum_probs=36.0
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+.-.++++.+|++++.-..++-.+-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08456 16 PRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVS 56 (196)
T ss_pred HHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEe
Confidence 36678889999999999999998888889999999998864
No 56
>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=73.20 E-value=9.9 Score=29.98 Aligned_cols=39 Identities=18% Similarity=0.259 Sum_probs=34.3
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
.-.+++++.+|++++.-.-++-++-+..|.+|++|..|.
T Consensus 17 ~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~~~~Dl~i~ 55 (185)
T cd08439 17 FLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALI 55 (185)
T ss_pred HHHHHHHHHCCCeEEEEEECChHHHHHHHHCCCCcEEEE
Confidence 556888899999999988888888899999999998775
No 57
>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=72.93 E-value=11 Score=28.75 Aligned_cols=49 Identities=18% Similarity=0.282 Sum_probs=38.1
Q ss_pred eEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehhh
Q psy11424 57 VVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAA 105 (245)
Q Consensus 57 ~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~A 105 (245)
+||+++ .....++...+|++++.-..++-+.-+..|.+|++|..|.-..
T Consensus 3 ~I~~~~~~~~~~l~~~i~~~~~~~p~i~i~~~~~~~~~~~~~l~~g~~D~~i~~~~ 58 (197)
T cd05466 3 RIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALP 58 (197)
T ss_pred EEEechhhHHHHhHHHHHHHHHHCCCCEEEEEECChHHHHHHHHcCCceEEEEcCC
Confidence 456655 3445677788999999988888777788999999999986544
No 58
>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=72.84 E-value=9.7 Score=29.81 Aligned_cols=43 Identities=12% Similarity=0.036 Sum_probs=37.0
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehhh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAA 105 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~A 105 (245)
...-..++..+|++++.-.-++-+.-...|.+|++|-.|....
T Consensus 16 ~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (196)
T cd08415 16 PRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLP 58 (196)
T ss_pred HHHHHHHHHHCCCcEEEEEecchHHHHHHHHcCCccEEEEeCC
Confidence 3566778888999999999999999999999999999997543
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=72.64 E-value=7.3 Score=30.75 Aligned_cols=41 Identities=15% Similarity=0.017 Sum_probs=35.2
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
+-..++++.+|++++.-.-++-++-+..|.+|++|..|...
T Consensus 17 ~~l~~~~~~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~ 57 (200)
T cd08464 17 PLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVF 57 (200)
T ss_pred HHHHHHHHHCCCcEEEEecCCcccHHHHHhcCcccEEEecC
Confidence 44578888999999999888888889999999999998643
No 60
>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=72.60 E-value=10 Score=29.63 Aligned_cols=42 Identities=14% Similarity=0.197 Sum_probs=36.6
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
.+...+++..+|++++.-.-++-+.-+..|.+|++|-.|...
T Consensus 16 ~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (200)
T cd08423 16 PPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFD 57 (200)
T ss_pred hHHHHHHHHhCCCCeEEEEeCCHHHHHHHHhcCCccEEEEec
Confidence 466788899999999999999999999999999999877643
No 61
>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=71.94 E-value=11 Score=29.70 Aligned_cols=41 Identities=12% Similarity=0.122 Sum_probs=36.1
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++-..+++..+|++++.-..++-+.-+..|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08447 16 PRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLR 56 (198)
T ss_pred HHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHcCCceEEEec
Confidence 35567888899999999989999999999999999988864
No 62
>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=71.90 E-value=11 Score=30.25 Aligned_cols=41 Identities=15% Similarity=0.136 Sum_probs=35.9
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+.-.++...+|++++...-++-++-++.|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08413 16 PPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIAT 56 (198)
T ss_pred cHHHHHHHHhCCceEEEEEeCCHHHHHHHHHcCCCCEEEEc
Confidence 36678889999999999999998888899999999987764
No 63
>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=71.12 E-value=11 Score=30.34 Aligned_cols=41 Identities=12% Similarity=0.055 Sum_probs=36.2
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+--.++.+.+|++++.-.-++-++-+..|.+|++|-.|..
T Consensus 16 ~~~l~~f~~~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08443 16 PPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIAT 56 (198)
T ss_pred cHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHCCCccEEEEe
Confidence 45567888899999999999999999999999999998864
No 64
>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=70.78 E-value=10 Score=29.80 Aligned_cols=41 Identities=12% Similarity=0.039 Sum_probs=35.7
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
+.-.++.+.+|++++.-.-++-+.-+++|.+|++|..|...
T Consensus 17 ~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~ 57 (198)
T cd08421 17 EDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAG 57 (198)
T ss_pred HHHHHHHHHCCCceEEEEecCcHHHHHHHhcCCceEEEEec
Confidence 56788888999999998888888889999999999988643
No 65
>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=69.38 E-value=14 Score=29.03 Aligned_cols=41 Identities=22% Similarity=0.194 Sum_probs=35.8
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+...++.+.+|++++.-.-++-+.=+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (199)
T cd08430 16 PPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAA 56 (199)
T ss_pred cHHHHHHHHHCCCceEEEEeCCHHHHHHHHHCCCCCEEEEe
Confidence 57789999999999999888888777889999999998864
No 66
>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=69.25 E-value=12 Score=29.43 Aligned_cols=41 Identities=34% Similarity=0.323 Sum_probs=35.1
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+--+++++.+|++++.-.-++-.+-+..|.+|++|..|.-
T Consensus 16 ~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (199)
T cd08416 16 PRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVA 56 (199)
T ss_pred HHHHHHHHHhCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEe
Confidence 36678899999999999888877777889999999999874
No 67
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=68.72 E-value=40 Score=29.73 Aligned_cols=138 Identities=12% Similarity=0.144 Sum_probs=67.2
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcC---CCCCCCCCCCCeEee----CcHHH-HHHHHHhC
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISND---YISLSTLPKNAVVGT----NSLRR-KVLIKSFF 73 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~---~~~l~~lp~ga~IGT----sS~RR-~aql~~~~ 73 (245)
+|.+|++|+++.++..=|.. .+.+....- -=.+ .-+|+.++ ..++++| +|.+||+ ++... ..+++...
T Consensus 96 ~l~~g~~D~~~~~~~~t~eR-~~~~~fs~p-y~~~-~~~lvv~~~~~~~s~~dL-~g~~V~v~~gs~~~~~l~~~~~~~~ 171 (259)
T PRK11917 96 LLDNGSVDAVIATFTITPER-KRIYNFSEP-YYQD-AIGLLVLKEKNYKSLADM-KGANIGVAQAATTKKAIGEAAKKIG 171 (259)
T ss_pred HHHCCCccEEEecccCChhh-hheeeeccC-ceee-ceEEEEECCCCCCCHHHh-CCCeEEEecCCcHHHHHHHhhHhcC
Confidence 46789999999987643321 111111100 0001 12233222 2356667 4666654 22211 12223334
Q ss_pred CCCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHHHHhhc
Q psy11424 74 PSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIP 151 (245)
Q Consensus 74 pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~ 151 (245)
++.+++..- +...-++.|..|++||++.-..=+..+ ..+.. ..++ +.+.|. -+++-++++|+++.+.+..
T Consensus 172 ~~~~~~~~~-~~~~~~~~l~~GrvDa~~~d~~~~~~~-~~~~~-~~~~-~~~~~~----~~~~a~~k~~~~l~~~ln~ 241 (259)
T PRK11917 172 IDVKFSEFP-DYPSIKAALDAKRVDAFSVDKSILLGY-VDDKS-EILP-DSFEPQ----SYGIVTKKDDPAFAKYVDD 241 (259)
T ss_pred CceeEEecC-CHHHHHHHHHcCCCcEEEecHHHHHHh-hhcCC-eecC-CcCCCC----ceEEEEeCCCHHHHHHHHH
Confidence 555554443 456667889999999998765322211 11111 1221 222221 2466678888777666643
No 68
>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=68.68 E-value=15 Score=28.56 Aligned_cols=42 Identities=12% Similarity=0.114 Sum_probs=36.0
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
.+--.++.+.+|++++.-.-++-+.-+..|.+|++|-.|...
T Consensus 16 ~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (194)
T cd08436 16 PELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGL 57 (194)
T ss_pred HHHHHHHHHHCCCcEEEEecCCHHHHHHHHHcCCccEEEEec
Confidence 345688889999999999889888888999999999998753
No 69
>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=68.62 E-value=15 Score=28.39 Aligned_cols=41 Identities=10% Similarity=0.074 Sum_probs=34.7
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
+-...+.+.+|++++.-..++-+.-...|.+|++|..|...
T Consensus 17 ~~l~~~~~~~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~ 57 (197)
T cd08440 17 PVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSE 57 (197)
T ss_pred HHHHHHHHhCCCcEEEEEeCChHHHHHHHHcCCccEEEEeC
Confidence 45577888899999998888888888999999999988643
No 70
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=68.48 E-value=12 Score=29.60 Aligned_cols=41 Identities=17% Similarity=0.169 Sum_probs=35.4
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
..-..++++.+|++++.-..++-.+-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08441 16 MPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITS 56 (198)
T ss_pred HHHHHHHHHhCCCeEEEEEeCCchhHHHHHHcCCceEEEec
Confidence 35568888999999999888888888899999999998864
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=67.77 E-value=16 Score=28.85 Aligned_cols=40 Identities=13% Similarity=0.042 Sum_probs=34.8
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+--+++++.+|++++.-.-|+-++-...|.+|++|-.|..
T Consensus 18 ~~i~~~~~~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~ 57 (198)
T cd08446 18 RLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGR 57 (198)
T ss_pred HHHHHHHHHCCCeEEEEeeCCHHHHHHHHHCCCccEEEEe
Confidence 4467788899999999888998888999999999998864
No 72
>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=67.73 E-value=20 Score=31.79 Aligned_cols=106 Identities=18% Similarity=0.118 Sum_probs=56.4
Q ss_pred ccccCCccEEeecCCCCCC--CCCCCeeEEEecCCCC---CC-eEEEEcCC---CCCCCCCCCCeEeeC---cH--H--H
Q psy11424 2 AIIKGKADLAVHSLKDIPM--NLPSGFILCAILKRED---PR-DAFISNDY---ISLSTLPKNAVVGTN---SL--R--R 65 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~--~l~~gL~iaav~~R~d---pr-Dvlv~~~~---~~l~~lp~ga~IGTs---S~--R--R 65 (245)
+|.+|++|+++-++=.+.. +......+ ..+.+.+ +. -+||.+++ .++.+| +|.+||+. |. - +
T Consensus 75 al~~g~~D~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~y~~~lvv~~ds~i~sl~DL-~Gk~v~~~~~~s~~~~~~~ 152 (288)
T TIGR03431 75 GMRFGKVDIAWYGPSSYAEAYQKANAEAF-AIEVNADGSTGYYSVLIVKKDSPIKSLEDL-KGKTFGFVDPNSTSGFLVP 152 (288)
T ss_pred HHHcCCccEEEEChHHHHHHHHhcCCeEE-EEeccCCCCCceEEEEEEeCCCCCCcHHHh-CCCEEEeeCCCcchhhHHH
Confidence 5788999999865321111 22222222 1111111 11 35565543 356777 58888853 21 1 1
Q ss_pred HHHHHHhC-CC----CeEEeccCcHHHHHhhhccCCccEEEehhhhhhh
Q psy11424 66 KVLIKSFF-PS----LIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKR 109 (245)
Q Consensus 66 ~aql~~~~-pd----l~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~R 109 (245)
...+.+.. .+ +..+..-|+....+.-|.+|+.|+.+....-+..
T Consensus 153 ~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~G~vDa~~~~~~~~~~ 201 (288)
T TIGR03431 153 SYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVANGTVDAATTNDENLDR 201 (288)
T ss_pred HHHHHHhcCCChHHhHHhheecCchHHHHHHHHcCCCCeEeccHHHHHH
Confidence 22332221 11 1223344688889999999999999987654433
No 73
>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=67.63 E-value=14 Score=28.75 Aligned_cols=41 Identities=10% Similarity=0.050 Sum_probs=35.8
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+-...+.+.+|++++.-.-+|-++-+..|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~ 56 (197)
T cd08438 16 APLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITV 56 (197)
T ss_pred HHHHHHHHHHCcCeEEEEEEcCcHHHHHHHHcCCCCEEEEe
Confidence 35567888899999999998999988999999999998864
No 74
>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=67.07 E-value=15 Score=29.41 Aligned_cols=39 Identities=10% Similarity=0.061 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
.-..++.+.+|++++...-++-+.-+..|.+|++|-.|.
T Consensus 18 ~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~ 56 (203)
T cd08445 18 ELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFG 56 (203)
T ss_pred HHHHHHHHHCCCeEEEEEeCChHHHHHHHHcCCCcEEEe
Confidence 445777888999999999999999999999999999885
No 75
>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=66.93 E-value=17 Score=28.65 Aligned_cols=41 Identities=7% Similarity=-0.092 Sum_probs=35.5
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+.-+.+.+.+|++++.-.-++-.+-.+.|.+|++|..|..
T Consensus 17 ~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~ 57 (197)
T cd08425 17 GPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAF 57 (197)
T ss_pred HHHHHHHHHHCCCcEEEEEECcHHHHHHHHHcCCccEEEEe
Confidence 35667888899999999888888888899999999998864
No 76
>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=65.57 E-value=17 Score=29.03 Aligned_cols=41 Identities=17% Similarity=0.140 Sum_probs=35.2
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+--.++++.+|++++.-.-|+-++-++.|.+|++|-.|.-
T Consensus 16 ~~~l~~~~~~~P~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08444 16 PWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIAT 56 (198)
T ss_pred hHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHCCCccEEEec
Confidence 45567788889999999999998888899999999998753
No 77
>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=65.52 E-value=15 Score=29.10 Aligned_cols=42 Identities=14% Similarity=0.062 Sum_probs=36.4
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
.+.-+++.+.+|++++.-.-+|-++-+..|.+|++|-.|...
T Consensus 16 ~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08457 16 PRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADG 57 (196)
T ss_pred HHHHHHHHHHCCCeEEEEEecCcHHHHHHHHcCCccEEEecc
Confidence 467788899999999999889888888899999999888653
No 78
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=63.89 E-value=18 Score=31.12 Aligned_cols=56 Identities=20% Similarity=0.233 Sum_probs=38.6
Q ss_pred CCCCCCCCCeEeeC--cHHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehhhh
Q psy11424 48 SLSTLPKNAVVGTN--SLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAG 106 (245)
Q Consensus 48 ~l~~lp~ga~IGTs--S~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AG 106 (245)
++++| .|.+||.. |. -...+....|+.+++... |.++=+..|.+|++|++|.-..-
T Consensus 125 ~~~dL-~g~~I~v~~g~~-~~~~l~~~~~~~~i~~~~-~~~~~~~~L~~grvDa~i~~~~~ 182 (247)
T PRK09495 125 SVKDL-DGKVVAVKSGTG-SVDYAKANIKTKDLRQFP-NIDNAYLELGTGRADAVLHDTPN 182 (247)
T ss_pred ChHHh-CCCEEEEecCch-HHHHHHhcCCCCceEEcC-CHHHHHHHHHcCceeEEEeChHH
Confidence 45566 45566422 11 235666778888887654 78888999999999999975543
No 79
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=63.07 E-value=39 Score=30.73 Aligned_cols=134 Identities=13% Similarity=0.145 Sum_probs=66.7
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC---CCCCCCCCCCeE----eeCcHHHHHHHHHhC-
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY---ISLSTLPKNAVV----GTNSLRRKVLIKSFF- 73 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~---~~l~~lp~ga~I----GTsS~RR~aql~~~~- 73 (245)
+|.+|++|++..++---|.. -+.+.+.. |- -...-.|+.+++ .++.+|+ |-+| ||.+.. +++.+.
T Consensus 101 ~L~~G~~Di~~~~~~~t~eR-~~~~~fS~-Py-~~~~~~lv~r~~~~i~sl~dL~-Gk~V~v~~gs~~~~---~l~~~~~ 173 (302)
T PRK10797 101 LLQNGTFDFECGSTTNNLER-QKQAAFSD-TI-FVVGTRLLTKKGGDIKDFADLK-GKAVVVTSGTTSEV---LLNKLNE 173 (302)
T ss_pred HHHCCCccEEecCCccCcch-hhcceecc-cE-eeccEEEEEECCCCCCChHHcC-CCEEEEeCCCcHHH---HHHHHhh
Confidence 57889999988766333321 11111110 00 011122232222 3456663 4344 344333 233332
Q ss_pred ---CCCeEEeccCcHHHHHhhhccCCccEEEehh---hhh-hhcCCccceeeecCCCCcCCCCCCceEEEEEecCcHHHH
Q psy11424 74 ---PSLIIKSLRGNIDTRLNKLDKGEYAAIILAA---AGL-KRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELM 146 (245)
Q Consensus 74 ---pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~---AGL-~RLg~~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~ 146 (245)
|+.+++. --+.++-++.|.+|++|++|.-. ++. ..-.....+ ..+. +.+ .....++-.|++++++.
T Consensus 174 ~~~~~~~i~~-~~~~~~~l~~L~~GrvDa~i~d~~~~~~~~~~~~~~~~l-~i~~-~~~----~~~~~~~a~~k~~~~L~ 246 (302)
T PRK10797 174 EQKMNMRIIS-AKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNW-EIVG-KPQ----SQEAYGCMLRKDDPQFK 246 (302)
T ss_pred hcCCceEEEE-eCCHHHHHHHHHcCCceEEEccHHHHHHHHHcCCCCcce-EECC-ccC----CcCceeEEEeCCCHHHH
Confidence 4455554 45678899999999999998643 232 211111122 2222 212 33457778888887655
Q ss_pred HHh
Q psy11424 147 EML 149 (245)
Q Consensus 147 ~ll 149 (245)
+.+
T Consensus 247 ~~i 249 (302)
T PRK10797 247 KLM 249 (302)
T ss_pred HHH
Confidence 554
No 80
>PRK04056 Maf-like protein; Reviewed
Probab=62.73 E-value=7.6 Score=33.52 Aligned_cols=31 Identities=16% Similarity=0.141 Sum_probs=23.4
Q ss_pred eEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 57 VVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 57 ~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
+.|++|+||+..|..+..++ ..+.=++|.+.
T Consensus 3 ILAS~SprR~elL~~~g~~f--~v~~~~idE~~ 33 (180)
T PRK04056 3 ILASSSSTRANLLKEAGIEF--EQKSLDFDEES 33 (180)
T ss_pred EEeCCCHHHHHHHHHCCCCe--EEEcCCCCCCC
Confidence 68999999999999986554 44455677653
No 81
>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=62.44 E-value=21 Score=28.11 Aligned_cols=41 Identities=15% Similarity=0.118 Sum_probs=36.0
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++--..+++.+|++++.-..++-++-++.|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08437 16 PKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLG 56 (198)
T ss_pred HHHHHHHHHhCCceEEEEEEcCHHHHHHHHHcCCCCEEEec
Confidence 35667888899999999999999999999999999998864
No 82
>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=62.42 E-value=22 Score=27.55 Aligned_cols=41 Identities=17% Similarity=0.314 Sum_probs=35.1
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
+.-.++...+|++++.-.-++-+.-++.|.+|++|-.|...
T Consensus 17 ~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (195)
T cd08434 17 DLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSP 57 (195)
T ss_pred HHHHHHHHhCCCeEEEEecCcHHHHHHHHHcCCccEEEEcc
Confidence 55678888899999999889888888999999999888653
No 83
>PRK00078 Maf-like protein; Reviewed
Probab=62.32 E-value=7.7 Score=33.77 Aligned_cols=31 Identities=19% Similarity=0.407 Sum_probs=23.3
Q ss_pred eEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 57 VVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 57 ~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
+.|++|+||+..|+.+..++++ +.=++|...
T Consensus 4 ILAS~SprR~elL~~~g~~f~v--~~~~idE~~ 34 (192)
T PRK00078 4 ILASASERRQELLKRILEDFQV--IVSDFDESS 34 (192)
T ss_pred EEeCCCHHHHHHHHhCCCCeEE--eCCCCCCCC
Confidence 6899999999999998655544 455677653
No 84
>PRK04694 Maf-like protein; Reviewed
Probab=62.25 E-value=8 Score=33.65 Aligned_cols=30 Identities=17% Similarity=0.228 Sum_probs=22.9
Q ss_pred eEeeCcHHHHHHHHHhCCCCeEEeccCcHHHH
Q psy11424 57 VVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTR 88 (245)
Q Consensus 57 ~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TR 88 (245)
+.+++|+||+..|+.+.-++++ +-=|||..
T Consensus 3 ILAS~SprR~elL~~~g~~f~~--~~~~idE~ 32 (190)
T PRK04694 3 YLASRSPRRRELLQRLDVPFQT--LQLDVPEV 32 (190)
T ss_pred EEcCCCHHHHHHHHHCCCCcEE--ecCCCCCC
Confidence 6799999999999998665554 45566664
No 85
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=61.79 E-value=1.1 Score=38.88 Aligned_cols=108 Identities=20% Similarity=0.175 Sum_probs=66.7
Q ss_pred ccccCCccEEeecCCCCCCCC-CCCeeEEEecCC----CCCCeEEEEcCCC---CCCCCCCCCeEeeCcHH-------HH
Q psy11424 2 AIIKGKADLAVHSLKDIPMNL-PSGFILCAILKR----EDPRDAFISNDYI---SLSTLPKNAVVGTNSLR-------RK 66 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l-~~gL~iaav~~R----~dprDvlv~~~~~---~l~~lp~ga~IGTsS~R-------R~ 66 (245)
++.+|++|+++=+.-....-. ..|....|...+ ..-+-++|.+... ++++| +|.+||..+.- -.
T Consensus 45 ~l~~g~~D~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds~i~~l~dL-~Gk~v~~~~~~s~sg~l~~~ 123 (243)
T PF12974_consen 45 ALRSGEIDLAFMGPLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADSPITSLADL-KGKRVAFPDPSSTSGYLIPR 123 (243)
T ss_dssp HHHTTS-SEEE--HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTSS--SHHHH-GGSEEEEE-TT-TTTTHHHH
T ss_pred HHHcCCccEEEECcHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCCCCCChhhc-CCCEEEEecCCccHHHHHHH
Confidence 577899999975432222111 236666666665 3334556666554 45666 78888876554 23
Q ss_pred HHH-HHhC--C--CCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcC
Q psy11424 67 VLI-KSFF--P--SLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLN 111 (245)
Q Consensus 67 aql-~~~~--p--dl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg 111 (245)
..| ...- | ++..+ .-||-+.=+.-|.+|++|+.++....++++.
T Consensus 124 ~~L~~~~Gl~~~~~~~~~-~~~~~~~~~~~l~~G~~Da~~~~~~~~~~~~ 172 (243)
T PF12974_consen 124 YELLREAGLDPGDDFKQV-FVGSHDAVLEALLNGKADAAAIPSDAFERLE 172 (243)
T ss_dssp HHTCCCCT--HHHHSSEE-EEE-HHHHHHHHHTTSSSEEEEEHHHHHHHH
T ss_pred HHHHHHcCCChhHceeEE-EeCCHHHHHHHHHcCCccEEEEechhHHHHH
Confidence 333 1211 2 24566 7789999999999999999999988888774
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=61.75 E-value=20 Score=28.18 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=33.8
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+..++++..+|++++.-.-++-..=++.|.+|++|-.|..
T Consensus 17 ~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~ 56 (198)
T cd08433 17 PLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLY 56 (198)
T ss_pred HHHHHHHHHCCCcEEEEEecCcHHHHHHHhCCCCcEEEEe
Confidence 5678889999999999877777777788999999998864
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=60.90 E-value=21 Score=28.50 Aligned_cols=37 Identities=16% Similarity=0.150 Sum_probs=31.7
Q ss_pred HHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 66 KVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 66 ~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-++++..+|++++.-.-++- ..++.|.+|++|..|..
T Consensus 19 i~~~~~~~P~i~l~i~~~~~-~~~~~l~~g~~D~~i~~ 55 (200)
T cd08462 19 IERVAREAPGVRFELLPPDD-QPHELLERGEVDLLIAP 55 (200)
T ss_pred HHHHHHHCCCCEEEEecCCh-hHHHHHhcCCeeEEEec
Confidence 46678889999999887876 88999999999999864
No 88
>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=60.77 E-value=21 Score=31.96 Aligned_cols=95 Identities=14% Similarity=0.214 Sum_probs=57.5
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEE--EecCCCCCCeEEEEcCCCCCCCCCCCCeEeeCcHHHHHH--HHHhCCCC-
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILC--AILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKVL--IKSFFPSL- 76 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~ia--av~~R~dprDvlv~~~~~~l~~lp~ga~IGTsS~RR~aq--l~~~~pdl- 76 (245)
+|++|++|++.=|+=.-+....+-..+- ++..+....-|++..+ .+++++. |.+|..++.-+.+. ++-++++.
T Consensus 39 ~l~~g~~Dv~~iSs~~y~~~~~~y~ilp~~~i~s~g~v~Sv~l~s~-~p~~~l~-~~~ial~~~S~TS~~Llrill~~~~ 116 (251)
T PF02621_consen 39 MLLEGELDVALISSIEYARNADDYLILPDLSISSDGPVYSVLLFSK-VPIEELD-GKKIALTGESTTSVALLRILLEEFY 116 (251)
T ss_dssp HHHTTS-SEEEEEHHHHCTCTTTEEEESCECEEECCSSSSEEEEES-S-CCC-T-TSEEEESTTTSHHHHHHHHHHCCTT
T ss_pred HHHcCCCCEEEcCHHHHHHhhhhheecCCcEEEEcCCccceEEEEC-CChHHcC-CCeEEcCCCCHHHHHHHHHHHHhcc
Confidence 5889999999999866665333322222 4555777788877653 3567774 34777776666433 33344555
Q ss_pred --eEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 77 --IIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 77 --~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
++++....+..-+ .+|. ||.+|
T Consensus 117 ~p~~~~~~~~~~~~~---~~~~-da~Ll 140 (251)
T PF02621_consen 117 KPEYVPMPDDIPPAM---LAGA-DAALL 140 (251)
T ss_dssp --EEEEE-CGHHHHH---HTTS-SEEEE
T ss_pred ccceeecCchhhHHh---hcCC-CEEEE
Confidence 8888887666533 3566 87776
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=60.69 E-value=25 Score=27.31 Aligned_cols=41 Identities=15% Similarity=0.206 Sum_probs=33.9
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+--.++...+|++++.-.-++-..-+..|.+|++|..|..
T Consensus 16 ~~~l~~~~~~~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~ 56 (201)
T cd08420 16 PRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVE 56 (201)
T ss_pred HHHHHHHHHHCCCceEEEEeCCcHHHHHHHHCCCccEEEec
Confidence 35567788889999999888887777888999999987764
No 90
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=60.35 E-value=23 Score=30.34 Aligned_cols=48 Identities=19% Similarity=0.125 Sum_probs=39.8
Q ss_pred CeEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 56 AVVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 56 a~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-+||+++. .--.++...+|++++....++.+.-+..|.+|++|..|.-
T Consensus 69 l~I~~~~~~~~~~~~~~l~~~~~~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~ 123 (269)
T PRK11716 69 LSLFCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAA 123 (269)
T ss_pred EEEEecchHHHHHHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHHCCCccEEEEe
Confidence 46888764 3357777889999999999999999999999999988764
No 91
>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=58.44 E-value=11 Score=32.62 Aligned_cols=35 Identities=20% Similarity=0.333 Sum_probs=26.2
Q ss_pred CCCeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHHh
Q psy11424 54 KNAVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRLN 90 (245)
Q Consensus 54 ~ga~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL~ 90 (245)
..-+.|++|+||+.-|+.+. +.|..+-=|||.+..
T Consensus 3 ~~lILAS~SprR~elL~~~g--~~f~v~~~~idE~~~ 37 (183)
T TIGR00172 3 KELILASQSPRRKELLEELG--ISFEQIVSEFDEKSL 37 (183)
T ss_pred CCEEEeCCCHHHHHHHHHCC--CCeEEEcCCCCCCCC
Confidence 34689999999999999875 445555667887543
No 92
>PRK00148 Maf-like protein; Reviewed
Probab=57.10 E-value=11 Score=32.90 Aligned_cols=31 Identities=16% Similarity=0.136 Sum_probs=23.4
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTR 88 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TR 88 (245)
-+.|++|+||+..|..+.-+++++ -=+||..
T Consensus 3 iILAS~SprR~elL~~~g~~f~~~--~~~idE~ 33 (194)
T PRK00148 3 LVLASASPARLKLLRLAGIPPLVV--VSHVDED 33 (194)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE--CCCCCCC
Confidence 478999999999999987665544 4456664
No 93
>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=56.89 E-value=21 Score=28.21 Aligned_cols=41 Identities=22% Similarity=0.258 Sum_probs=34.3
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
+--..+++.+|++++.-.-|+-+.-+..|.+|++|..|...
T Consensus 17 ~~l~~~~~~~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~ 57 (201)
T cd08459 17 RLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYL 57 (201)
T ss_pred HHHHHHHHHCCCCeEEEEecCccCHHHHhhCCCceEEEEcC
Confidence 34567788899999999989888888999999999988643
No 94
>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=56.60 E-value=58 Score=28.27 Aligned_cols=19 Identities=5% Similarity=0.062 Sum_probs=16.4
Q ss_pred HHHHHhhhccCCccEEEeh
Q psy11424 85 IDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 85 V~TRL~KL~~g~~DaiiLA 103 (245)
..+-++.|.+|..||+|.-
T Consensus 152 ~~~~~~aL~~GrvDa~i~~ 170 (246)
T TIGR03870 152 PRKLVSEVATGKADLAVAF 170 (246)
T ss_pred HHHHHHHHHcCCCCEEEee
Confidence 4678999999999999873
No 95
>PRK02478 Maf-like protein; Reviewed
Probab=55.84 E-value=12 Score=32.87 Aligned_cols=31 Identities=19% Similarity=0.285 Sum_probs=23.5
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTR 88 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TR 88 (245)
-+.+++|+||+..|..+.-+ |..+.=|||.+
T Consensus 5 iILAS~SprR~elL~~~g~~--f~v~~~~idE~ 35 (199)
T PRK02478 5 LILASKSPFRRALLENAGLE--FSAAAADIDER 35 (199)
T ss_pred EEEeCCCHHHHHHHHHCCCC--eEEecCCCCCC
Confidence 47899999999999998544 44455566665
No 96
>PRK14363 Maf-like protein; Provisional
Probab=55.49 E-value=12 Score=33.10 Aligned_cols=32 Identities=13% Similarity=0.256 Sum_probs=24.1
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
-+.+++|+||+..|..+..+++ .+.=++|.+.
T Consensus 3 iILAS~SprR~elL~~~G~~f~--v~~~~iDE~~ 34 (204)
T PRK14363 3 IILASSSPRRRQLMELLGIEFE--VEKPDVEEEF 34 (204)
T ss_pred EEEeCCCHHHHHHHHhCCCCeE--EEcCCCCCCC
Confidence 3789999999999999865544 4456677764
No 97
>PRK00234 Maf-like protein; Reviewed
Probab=55.48 E-value=12 Score=32.47 Aligned_cols=32 Identities=16% Similarity=0.182 Sum_probs=24.1
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
-+.|++|+||+..|..+.-++++ +-=|+|.+.
T Consensus 4 iILAS~SprR~elL~~~gi~f~v--~~~~iDE~~ 35 (192)
T PRK00234 4 LLLASSSPYRRELLARLRLPFTW--ASPDIDESH 35 (192)
T ss_pred EEEecCCHHHHHHHHHCCCCcEE--ECCCCCCCC
Confidence 47899999999999998655544 455677753
No 98
>PRK00032 Maf-like protein; Reviewed
Probab=55.16 E-value=12 Score=32.53 Aligned_cols=32 Identities=19% Similarity=0.245 Sum_probs=24.2
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
-+.|++|+||+..|..+.-++ ..+-=|||.+.
T Consensus 4 iILAS~SprR~elL~~~g~~f--~v~~~~idE~~ 35 (190)
T PRK00032 4 LYLASGSPRRRELLTQLGVPF--EVLVPGIEEQR 35 (190)
T ss_pred EEEeCCCHHHHHHHHHCCCCe--EEEcCCCCCCC
Confidence 478999999999999885544 44456777754
No 99
>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=54.96 E-value=30 Score=27.06 Aligned_cols=41 Identities=15% Similarity=0.177 Sum_probs=36.1
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++--..+++.+|++++...-++-+.-+..|.+|++|-.|.-
T Consensus 17 ~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~ 57 (199)
T cd08451 17 PGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVR 57 (199)
T ss_pred HHHHHHHHHHCCCcEEEEecCChHHHHHHHHCCCccEEEEe
Confidence 45578889999999999999999999999999999998863
No 100
>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=54.67 E-value=24 Score=27.67 Aligned_cols=40 Identities=10% Similarity=0.058 Sum_probs=35.2
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+--.++++.+|++++.-.-+|-+.-+..|.+|++|..|..
T Consensus 17 ~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~ 56 (199)
T cd08426 17 SLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAF 56 (199)
T ss_pred HHHHHHHHhCCCeEEEEEeCCcHHHHHHHHCCCccEEEec
Confidence 4457888899999999999999999999999999998864
No 101
>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=54.40 E-value=31 Score=26.82 Aligned_cols=41 Identities=12% Similarity=0.146 Sum_probs=35.9
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
...-.++++.+|++++.-..++-+.-+..|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08414 16 PRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVR 56 (197)
T ss_pred HHHHHHHHHHCCCcEEEEecCChHHHHHHHHcCCccEEEEc
Confidence 35567888899999999999999999999999999998864
No 102
>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=54.21 E-value=29 Score=27.12 Aligned_cols=41 Identities=22% Similarity=0.246 Sum_probs=35.8
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+..++++..+|++++.-.-+|-++-...|.+|++|-.|..
T Consensus 16 ~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (201)
T cd08435 16 PPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGR 56 (201)
T ss_pred HHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHcCCccEEEEe
Confidence 46678889999999999888999988999999999988864
No 103
>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=54.19 E-value=20 Score=28.17 Aligned_cols=41 Identities=12% Similarity=0.092 Sum_probs=35.2
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
...-.++++.+|++++.-..++-++-+..|.+|++|-.|..
T Consensus 16 ~~~l~~f~~~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~ 56 (198)
T cd08461 16 PPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTT 56 (198)
T ss_pred HHHHHHHHHHCCCcEEEEeeCCcccHHHHHhcCCCcEEEec
Confidence 34567788899999999888988889999999999998864
No 104
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=53.13 E-value=34 Score=30.85 Aligned_cols=49 Identities=16% Similarity=0.238 Sum_probs=41.1
Q ss_pred CeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 56 AVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 56 a~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
-+||++. ...-..+...+|++++.-.-||.+.-+..|.+|++|..|...
T Consensus 95 lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~ 150 (316)
T PRK12679 95 LTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASE 150 (316)
T ss_pred EEEEechHhhhcchHHHHHHHHHHCCCeEEEEecCCHHHHHHHHHcCCCCEEEecc
Confidence 4577764 566778888899999999999999999999999999988643
No 105
>PRK14368 Maf-like protein; Provisional
Probab=53.12 E-value=14 Score=32.34 Aligned_cols=32 Identities=22% Similarity=0.197 Sum_probs=23.5
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
-+.+++|+||+..|+.+.-++ ..+-=|+|.+.
T Consensus 7 lILAS~SprR~eLL~~~g~~f--~v~~~~iDE~~ 38 (193)
T PRK14368 7 IVLASASPRRSELLASAGIEF--DVVPADIPEEP 38 (193)
T ss_pred EEEeCCCHHHHHHHHHCCCCe--EEEcCCCCCCC
Confidence 579999999999999875544 44455566643
No 106
>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=52.74 E-value=34 Score=29.47 Aligned_cols=47 Identities=11% Similarity=0.126 Sum_probs=38.2
Q ss_pred CeEeeCcH----HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 56 AVVGTNSL----RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 56 a~IGTsS~----RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
-+||+++. .--+++...+|++++.-.-++.+.-+..|.+|++|..|.
T Consensus 89 l~ig~~~~~~~~~~l~~~~~~~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~ 139 (279)
T TIGR03339 89 LRIAATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVS 139 (279)
T ss_pred EEEeCchHHHHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEE
Confidence 36787754 234566778999999988899999999999999999986
No 107
>PRK01839 Maf-like protein; Reviewed
Probab=52.34 E-value=14 Score=32.59 Aligned_cols=36 Identities=19% Similarity=0.158 Sum_probs=27.1
Q ss_pred CCeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHHhhh
Q psy11424 55 NAVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKL 92 (245)
Q Consensus 55 ga~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL~KL 92 (245)
.-+.|++|+||+..|.++.-+ |..+-=|+|....++
T Consensus 11 ~lILAS~SprR~elL~~~gi~--f~v~~~~idE~~~~~ 46 (209)
T PRK01839 11 FLYLASQSPRRQELLQQLGVR--FELLLPRPDEDAEAL 46 (209)
T ss_pred CEEEeCCCHHHHHHHHHCCCC--eEEeCCCCCcCcccc
Confidence 368999999999999987544 455556788876554
No 108
>PRK04425 Maf-like protein; Reviewed
Probab=52.27 E-value=15 Score=32.23 Aligned_cols=31 Identities=19% Similarity=0.240 Sum_probs=23.2
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTR 88 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TR 88 (245)
-+.|++|+||+..|.++.-+++++ .=|+|.+
T Consensus 7 iILAS~SprR~elL~~~g~~f~v~--~~~iDE~ 37 (196)
T PRK04425 7 LVLGTSSVFRREQMERLGIAFQAA--SPDFDET 37 (196)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEE--CCCCCCC
Confidence 589999999999999886555544 4456664
No 109
>PRK14361 Maf-like protein; Provisional
Probab=52.18 E-value=15 Score=31.96 Aligned_cols=31 Identities=13% Similarity=0.209 Sum_probs=23.3
Q ss_pred eEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 57 VVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 57 ~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
+.|++|+||+..|..+.-++ ..+-=++|.+.
T Consensus 2 ILAS~SprR~elL~~~g~~f--~v~~~~~dE~~ 32 (187)
T PRK14361 2 ILASGSPRRRELLENLGVPF--QVVVSGEAEDS 32 (187)
T ss_pred EEccCCHHHHHHHHHCCCCc--EEECCCCCCCC
Confidence 67999999999999985444 44455677764
No 110
>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=52.12 E-value=26 Score=27.80 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=38.2
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehhhh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAG 106 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AG 106 (245)
.--.++++.+|++++...-++-++-++.|.+|++|..|.....
T Consensus 23 ~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~ 65 (209)
T PF03466_consen 23 PLLAEFRERHPNIRIEIREGDSDELIEALRSGELDLAITFGPP 65 (209)
T ss_dssp HHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSS
T ss_pred HHHHHHHHHCCCcEEEEEeccchhhhHHHhcccccEEEEEeec
Confidence 4567888899999999999999999999999999999887665
No 111
>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=52.09 E-value=14 Score=29.36 Aligned_cols=24 Identities=17% Similarity=0.156 Sum_probs=19.1
Q ss_pred eEeeCcHHHHHHHHHhCC-CCeEEe
Q psy11424 57 VVGTNSLRRKVLIKSFFP-SLIIKS 80 (245)
Q Consensus 57 ~IGTsS~RR~aql~~~~p-dl~~~~ 80 (245)
+++|+|+||+..|.++.+ ++.+.+
T Consensus 2 iLaS~s~~R~~~l~~~~~~~~~~~~ 26 (131)
T cd00985 2 ILASGSPRRLEELKQIGGIEFEVLP 26 (131)
T ss_pred EEecCChHHHHHHHhcCCCCEEEeC
Confidence 689999999999999984 444443
No 112
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=51.90 E-value=31 Score=30.35 Aligned_cols=48 Identities=8% Similarity=0.067 Sum_probs=41.4
Q ss_pred CeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 56 AVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 56 a~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-+||+++ ++.-..+.+.+|++++...-|+-..=+..|.+|++|-.|..
T Consensus 91 l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~ 145 (275)
T PRK03601 91 LSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLITT 145 (275)
T ss_pred EEEeccHHHHHHHHHHHHHHHHHhCCCcEEEEEECChHHHHHHHHcCCCCEEEEc
Confidence 4788877 45567888899999999999999998999999999999964
No 113
>PRK00884 Maf-like protein; Reviewed
Probab=51.88 E-value=16 Score=31.97 Aligned_cols=32 Identities=13% Similarity=0.201 Sum_probs=25.0
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
-+.+++|+||+..|..+.-+++++ .=|||...
T Consensus 4 iILAS~SprR~elL~~~g~~f~v~--~~~idE~~ 35 (194)
T PRK00884 4 LILASTSPYRRALLEKLQLPFECA--APEVDETP 35 (194)
T ss_pred EEEeCCCHHHHHHHHHCCCCCEEE--CCCCCCCC
Confidence 478999999999999987666655 44787754
No 114
>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=51.88 E-value=14 Score=31.76 Aligned_cols=33 Identities=21% Similarity=0.324 Sum_probs=24.9
Q ss_pred eEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHHhh
Q psy11424 57 VVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRLNK 91 (245)
Q Consensus 57 ~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL~K 91 (245)
+.|++|+||+.-|+.+..++++ +.=|+|.+.-+
T Consensus 2 ILaS~SprR~elL~~~g~~f~~--~~~~iDE~~~~ 34 (180)
T cd00555 2 ILASASPRRRELLEQLGIPFEV--VPSDIDETPIK 34 (180)
T ss_pred EECCCCHHHHHHHHhCCCCeEE--EcCCCCCCCCC
Confidence 6799999999999998665554 45578877543
No 115
>PRK14362 Maf-like protein; Provisional
Probab=51.59 E-value=16 Score=32.31 Aligned_cols=26 Identities=15% Similarity=0.204 Sum_probs=20.9
Q ss_pred CCeEeeCcHHHHHHHHHhCCCCeEEe
Q psy11424 55 NAVVGTNSLRRKVLIKSFFPSLIIKS 80 (245)
Q Consensus 55 ga~IGTsS~RR~aql~~~~pdl~~~~ 80 (245)
.-+.|++|+||+..|+.+.-++++.+
T Consensus 13 ~iILAS~SprR~eLL~~~g~~f~v~~ 38 (207)
T PRK14362 13 PVVLASGSPRRREFLEQMGLPFEVIL 38 (207)
T ss_pred eEEEeCCCHHHHHHHHHCCCCcEEEC
Confidence 36899999999999999866665543
No 116
>PRK14365 Maf-like protein; Provisional
Probab=51.58 E-value=13 Score=32.50 Aligned_cols=32 Identities=19% Similarity=0.320 Sum_probs=23.2
Q ss_pred CeEeeCcHHHHHHHHHh-CCCCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSF-FPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~-~pdl~~~~iRGNV~TRL 89 (245)
-+.|+||+||+.-|..+ .-++++ +-=++|.+.
T Consensus 4 iILaSsSprR~elL~~~~g~~f~v--i~~~idE~~ 36 (197)
T PRK14365 4 IILASASPRRKELLKQLIGDNFLV--YPSSYEEPP 36 (197)
T ss_pred EEEeCCCHHHHHHHhcCcCcCeEE--ECCCCCCCC
Confidence 47999999999999885 544444 444577654
No 117
>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=51.42 E-value=18 Score=32.61 Aligned_cols=47 Identities=9% Similarity=0.065 Sum_probs=39.1
Q ss_pred eEeeCcH------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 57 VVGTNSL------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 57 ~IGTsS~------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+||+|+. .--...++.+|++++.-.-|+-++-++.|.+|++|..++.
T Consensus 39 rig~s~s~~~~lp~~l~~f~~~~P~i~v~i~~~~s~~l~~~L~~G~iDlai~~ 91 (287)
T TIGR02136 39 TIDGSTTVAPLAEAAAEEFQKIHPGVSVTVQGAGSGTGIKALINGTVDIGNSS 91 (287)
T ss_pred EEeccchHHHHHHHHHHHHHhhCCCceEEEccCCchHHHHHHHcCCCchhhcc
Confidence 6787773 3345667789999999999999999999999999997764
No 118
>PRK14367 Maf-like protein; Provisional
Probab=49.64 E-value=17 Score=32.00 Aligned_cols=32 Identities=25% Similarity=0.376 Sum_probs=23.6
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
-+.|++|+||+..|..+.-+++ .+.=|||...
T Consensus 4 iILAS~SprR~eLL~~~Gi~f~--v~~~~iDE~~ 35 (202)
T PRK14367 4 LYLGSNSPRRMEILTQLGYRVV--KLPAGIDETV 35 (202)
T ss_pred EEEeCCCHHHHHHHHHCCCCeE--EECCCCCCCC
Confidence 4789999999999998865444 4455666653
No 119
>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=48.56 E-value=41 Score=26.32 Aligned_cols=41 Identities=15% Similarity=0.085 Sum_probs=35.4
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
+-..+++..+|++++.-.-++-+.-+..|.+|++|..|...
T Consensus 17 ~~i~~~~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~ 57 (200)
T cd08417 17 PLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVF 57 (200)
T ss_pred HHHHHHHhhCCCeEEEeccCCHHHHHHHHHcCCCCEEEeec
Confidence 44578888999999999889888889999999999998754
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=48.36 E-value=38 Score=26.89 Aligned_cols=39 Identities=10% Similarity=0.079 Sum_probs=32.8
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+--.++++.+|++++.-.-|+- ..++.|.+|++|..|.-
T Consensus 17 ~~l~~~~~~~P~v~v~l~~~~~-~~~~~l~~g~~D~~i~~ 55 (200)
T cd08460 17 ALLAAVAAEAPGVRLRFVPESD-KDVDALREGRIDLEIGV 55 (200)
T ss_pred HHHHHHHHHCCCCEEEEecCch-hHHHHHHCCCccEEEec
Confidence 4467888899999999887876 77899999999998863
No 121
>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=48.30 E-value=11 Score=32.93 Aligned_cols=31 Identities=23% Similarity=0.406 Sum_probs=13.4
Q ss_pred eEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 57 VVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 57 ~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
+.|++|+||+..|+.+. ++|..+.=++|.+.
T Consensus 4 ILaS~SprR~elL~~~g--~~f~v~~~~~dE~~ 34 (195)
T PF02545_consen 4 ILASSSPRRRELLKQLG--INFEVIPSDIDEDA 34 (195)
T ss_dssp EE----HHHHHHHHCTT----EEE---------
T ss_pred EEeCCCHHHHHHHHHCC--CCeEEEcCCCCCCC
Confidence 68999999999998887 55666677799887
No 122
>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=46.45 E-value=44 Score=26.69 Aligned_cols=41 Identities=15% Similarity=0.037 Sum_probs=35.0
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++-.+.++..+|++++...-++-++-+..|.+|++|..|..
T Consensus 17 ~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~ 57 (198)
T cd08485 17 PLLLRQLLSVAPSATVSLTQMSKNRQIEALDAGTIDIGFGR 57 (198)
T ss_pred HHHHHHHHHhCCCcEEEEEECCHHHHHHHHHcCCccEEEec
Confidence 34457778889999999988999998999999999998764
No 123
>PRK14366 Maf-like protein; Provisional
Probab=45.76 E-value=22 Score=31.07 Aligned_cols=32 Identities=19% Similarity=0.160 Sum_probs=22.9
Q ss_pred CeEeeCcHHHHHHHHHhCC-CCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFP-SLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~p-dl~~~~iRGNV~TRL 89 (245)
-+.|++|+||+..|+.+.- ..++. -=+||...
T Consensus 7 iILAS~SprR~elL~~~G~~~~~v~--~~~iDE~~ 39 (195)
T PRK14366 7 LILASSSKQRLALLEQIGVVPGEIV--SPDIDESP 39 (195)
T ss_pred EEEeCCCHHHHHHHHhCCCCCCEEe--CCCCCCCC
Confidence 5799999999999998754 33443 44566643
No 124
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=45.48 E-value=31 Score=27.90 Aligned_cols=23 Identities=35% Similarity=0.406 Sum_probs=18.5
Q ss_pred cCCCCHHHHHHHHHHHHHHhhHH
Q psy11424 214 GPIDTPETVGLYAAELLKKKGAI 236 (245)
Q Consensus 214 ~~~~~a~~lg~~la~~l~~~ga~ 236 (245)
++.+.|..+|..+|+..+++|..
T Consensus 66 ~n~~aa~~vG~~la~ra~~~gi~ 88 (117)
T PRK05593 66 GNKEAAKKVGKLIAERAKAKGIK 88 (117)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCC
Confidence 45556899999999999998743
No 125
>PRK02141 Maf-like protein; Reviewed
Probab=45.14 E-value=23 Score=31.30 Aligned_cols=34 Identities=15% Similarity=0.240 Sum_probs=25.0
Q ss_pred CCCeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 54 KNAVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 54 ~ga~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
+.-+.+++|+||+..|..+.-++++ +-=|||...
T Consensus 9 ~~iILAS~SprR~elL~~~G~~f~v--~~~~iDE~~ 42 (207)
T PRK02141 9 PRLILASSSRYRRELLERLRLPFDV--VSPDIDETP 42 (207)
T ss_pred CCEEEeCCCHHHHHHHHHCCCCeEE--EcCCCCCCC
Confidence 3468999999999999988555444 455677654
No 126
>PRK14364 Maf-like protein; Provisional
Probab=44.90 E-value=17 Score=31.34 Aligned_cols=32 Identities=19% Similarity=0.306 Sum_probs=23.3
Q ss_pred EeeCcHHHHHHHHHhCCCCeEEeccCcHHHHHhh
Q psy11424 58 VGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRLNK 91 (245)
Q Consensus 58 IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL~K 91 (245)
.|++|+||+..|+.+.-+++ .+.=++|.+.-+
T Consensus 1 LAS~SprR~elL~~~g~~f~--v~~~~~dE~~~~ 32 (181)
T PRK14364 1 LASSSPRRRELLQQLGLNFE--IYSPDIDESVHE 32 (181)
T ss_pred CCCCCHHHHHHHHHCCCCeE--EECCCCCCCCCC
Confidence 37899999999999865544 445678876543
No 127
>PRK00648 Maf-like protein; Reviewed
Probab=44.86 E-value=22 Score=30.89 Aligned_cols=33 Identities=15% Similarity=0.285 Sum_probs=23.7
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL 89 (245)
-+.+++|+||+.-|+.+.-++++++ --++|...
T Consensus 5 lILAS~SprR~elL~~~g~~f~v~~-~~~~dE~~ 37 (191)
T PRK00648 5 IILASSSPRRKEILEGFRIPFEVVP-SPFVEESY 37 (191)
T ss_pred EEEeCCCHHHHHHHHHCCCCeEEEe-CCCCCCCC
Confidence 5789999999999999865544432 55666543
No 128
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=44.05 E-value=29 Score=29.76 Aligned_cols=40 Identities=25% Similarity=0.457 Sum_probs=35.1
Q ss_pred CCeEeeCcHHHH--HHHHHhCCCCeEEeccCcHHHHHhhhcc
Q psy11424 55 NAVVGTNSLRRK--VLIKSFFPSLIIKSLRGNIDTRLNKLDK 94 (245)
Q Consensus 55 ga~IGTsS~RR~--aql~~~~pdl~~~~iRGNV~TRL~KL~~ 94 (245)
..+|.+|++.|. -+|+.-.|++.|+-+-|+-++=++++..
T Consensus 69 ~~vi~CSALKr~YRD~LR~~~~~~~Fv~L~g~~~~i~~Rm~~ 110 (161)
T COG3265 69 HVVIACSALKRSYRDLLREANPGLRFVYLDGDFDLILERMKA 110 (161)
T ss_pred ceEEecHHHHHHHHHHHhccCCCeEEEEecCCHHHHHHHHHh
Confidence 369999999995 5789999999999999999998888753
No 129
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=44.00 E-value=49 Score=29.67 Aligned_cols=48 Identities=13% Similarity=-0.042 Sum_probs=40.0
Q ss_pred eEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 57 VVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 57 ~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
+||+++. +--+.++..+|++++.-..||-.+=+..|.+|++|..|...
T Consensus 115 ~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 169 (314)
T PRK09508 115 NLCICSPLDIRLTSQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISYE 169 (314)
T ss_pred EEEechhHHHHHHHHHHHHHHHhCCCcEEEEEeCcchhHHHHHhcCCccEEEecC
Confidence 5776643 44677888999999999999998889999999999999754
No 130
>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=43.45 E-value=43 Score=26.00 Aligned_cols=39 Identities=18% Similarity=0.144 Sum_probs=33.2
Q ss_pred HHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 65 RKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 65 R~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-...+++.+|++++.-..++-+.-+..|.+|++|-.|..
T Consensus 17 ~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~ 55 (197)
T cd08419 17 LLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMG 55 (197)
T ss_pred HHHHHHHHCCCceEEEEECCHHHHHHHHhcCCccEEEec
Confidence 356677889999999888988888889999999999864
No 131
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=43.14 E-value=61 Score=29.00 Aligned_cols=48 Identities=19% Similarity=0.209 Sum_probs=40.0
Q ss_pred eEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 57 VVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 57 ~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
+||+++. .--.+++..+|++++.-.-+|.+.-+..|.+|++|..|...
T Consensus 100 ~ig~~~~~~~~~l~~~l~~~~~~~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~ 154 (312)
T PRK10341 100 SFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTL 154 (312)
T ss_pred EEEechHHhHhhHHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHcCCCcEEEecC
Confidence 6888754 33467777899999999999999999999999999998654
No 132
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=42.67 E-value=57 Score=26.32 Aligned_cols=42 Identities=26% Similarity=0.391 Sum_probs=27.9
Q ss_pred EEEEEEcCCCcEEEEEEE--------ecCCCCHHHHHHHHHHHHHHhhHH
Q psy11424 195 LRAIITNPNGLKIITAEV--------NGPIDTPETVGLYAAELLKKKGAI 236 (245)
Q Consensus 195 l~~~v~~~dG~~~~~~~~--------~~~~~~a~~lg~~la~~l~~~ga~ 236 (245)
+.+.+.+..+...+-... .++.+.|..+|..+|+.++++|..
T Consensus 36 iyaQiIdd~~~~tlasaST~ek~~~~~~n~~aA~~vG~~la~ra~~~gi~ 85 (114)
T TIGR00060 36 IYAQVIDDSKSEVLASASTLEKKLKYTGNKDAAKKVGKLVAERLKEKGIK 85 (114)
T ss_pred EEEEEEECCCCEEEEEEecchhhhcCCCCHHHHHHHHHHHHHHHHHCCCC
Confidence 445555555555443322 345567899999999999998843
No 133
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=42.59 E-value=63 Score=29.50 Aligned_cols=49 Identities=16% Similarity=0.241 Sum_probs=41.3
Q ss_pred CeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 56 AVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 56 a~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
-+||+++ +..-..+...+|++++.-.-|+-+.=++.|.+|++|..|+..
T Consensus 95 lrIg~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~ 150 (327)
T PRK12680 95 LTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVST 150 (327)
T ss_pred EEEEecchhHHHhhHHHHHHHHHHCCCcEEEEEeCChHHHHHHHHCCCCcEEEEec
Confidence 4677755 356677888999999999999999999999999999998753
No 134
>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=42.24 E-value=42 Score=26.73 Aligned_cols=41 Identities=17% Similarity=0.186 Sum_probs=35.0
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
.--+++++.+|++++.-.-++-++=++.|.+|++|..|...
T Consensus 17 ~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (202)
T cd08468 17 RLMARLEELAPSVRLNLVHAEQKLPLDALLAGEIDFALGYS 57 (202)
T ss_pred HHHHHHHhhCCCCEEEEEECChHhHHHHHHCCCccEEEecc
Confidence 34577788899999999999988899999999999988643
No 135
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=40.45 E-value=66 Score=28.91 Aligned_cols=47 Identities=21% Similarity=0.184 Sum_probs=39.0
Q ss_pred CeEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 56 AVVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 56 a~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
-+||++.. +-...+.+.+|++++.-.-++.+.-+..|.+|++|-.|.
T Consensus 95 l~Ig~~~~~~~~~l~~~i~~f~~~~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~ 148 (309)
T PRK12683 95 LTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIA 148 (309)
T ss_pred EEEEeccchHHHHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEe
Confidence 35777543 556677888999999999999999999999999998775
No 136
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=40.09 E-value=76 Score=28.12 Aligned_cols=49 Identities=22% Similarity=0.287 Sum_probs=39.5
Q ss_pred CeEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 56 AVVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 56 a~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
.+||+++. +--.++...+|++++...-++-++-+..|.+|++|-+|...
T Consensus 93 l~i~~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~ 148 (305)
T PRK11151 93 LHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILAL 148 (305)
T ss_pred EEEEecchhHHHHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEec
Confidence 46777442 33456777899999999999999999999999999999753
No 137
>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=40.02 E-value=65 Score=25.98 Aligned_cols=38 Identities=13% Similarity=-0.051 Sum_probs=30.4
Q ss_pred HHHHHHhCCCCeEEeccC-cHHHHHhhhccCCccEEEeh
Q psy11424 66 KVLIKSFFPSLIIKSLRG-NIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 66 ~aql~~~~pdl~~~~iRG-NV~TRL~KL~~g~~DaiiLA 103 (245)
-.++++.+|++++.-.-+ |-++-++.|.+|++|..|.-
T Consensus 19 l~~~~~~~P~~~v~~~~~~~~~~l~~~L~~g~lDl~i~~ 57 (203)
T cd08463 19 VARFRREAPGARLEIHPLGPDFDYERALASGELDLVIGN 57 (203)
T ss_pred HHHHHHHCCCCEEEEEeCCcchhHHHHHhcCCeeEEEec
Confidence 356677899999998764 55677889999999998863
No 138
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=39.79 E-value=71 Score=28.70 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=39.8
Q ss_pred CeEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 56 AVVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 56 a~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-+||+++. .-..++...+|++++...-++-+.-+..|.+|++|..|..
T Consensus 95 l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 95 LTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred EEEEechHHHHHHhHHHHHHHHHHCCCceEEEEeCChHHHHHHHHCCCcCEEEee
Confidence 36887654 4556778889999999988999999999999999998864
No 139
>PRK01526 Maf-like protein; Reviewed
Probab=39.64 E-value=31 Score=30.41 Aligned_cols=32 Identities=19% Similarity=0.165 Sum_probs=22.6
Q ss_pred CeEeeCcHHHHHHHHHhCC-CCeEEeccCcHHHHH
Q psy11424 56 AVVGTNSLRRKVLIKSFFP-SLIIKSLRGNIDTRL 89 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~p-dl~~~~iRGNV~TRL 89 (245)
-+.|++|+||+..|..+.- ..+++ -=+||.+.
T Consensus 10 lILAS~SprR~elL~~~g~~~~~v~--~~~iDE~~ 42 (205)
T PRK01526 10 IILASSSPARIELLNRIKIIPSQII--PADIDETP 42 (205)
T ss_pred EEEeCCCHHHHHHHHhcCCCCceEe--cCCCCCCC
Confidence 5899999999999998853 44343 34566543
No 140
>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=39.49 E-value=17 Score=32.28 Aligned_cols=101 Identities=15% Similarity=0.078 Sum_probs=0.0
Q ss_pred CccccCCccEEeecCCCCCCCC-----------CCCeeEEEecCCCCCCeEEEEcC--CCCCCCCCCCCeE---eeCcHH
Q psy11424 1 MAIIKGKADLAVHSLKDIPMNL-----------PSGFILCAILKREDPRDAFISND--YISLSTLPKNAVV---GTNSLR 64 (245)
Q Consensus 1 ~aLl~g~iDiAVHSlKDlP~~l-----------~~gL~iaav~~R~dprDvlv~~~--~~~l~~lp~ga~I---GTsS~R 64 (245)
++|.+|++|+++.+.-...... ++.+...+.+-++... +++.++ ..++++|....++ ++|+.+
T Consensus 76 ~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~-lvv~~d~~i~sl~dL~gk~v~~~~~~s~~~ 154 (320)
T TIGR02122 76 NLLEAGEADLAIVQSDVAYYAYEGDGEFEFEGPVEKLRALASLYPEYIQ-IVVRKDSGIKTVADLKGKRVAVGAPGSGTE 154 (320)
T ss_pred HHHhCCCCcEEEEcchhHHHHhcCcCccccCCCCccHHhHHHhccccEE-EEEECCCCCCcHHHcCCCEEecCCCCcchH
Q ss_pred HHHHHHHhCCCCeEEecc----CcHHHHHhhhccCCccEEEe
Q psy11424 65 RKVLIKSFFPSLIIKSLR----GNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 65 R~aql~~~~pdl~~~~iR----GNV~TRL~KL~~g~~DaiiL 102 (245)
+..+.....-+++...+. .+....+..|.+|++|+++.
T Consensus 155 ~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~ 196 (320)
T TIGR02122 155 LNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFY 196 (320)
T ss_pred HHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEE
No 141
>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=39.13 E-value=30 Score=27.30 Aligned_cols=37 Identities=8% Similarity=0.117 Sum_probs=28.1
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+.-.++.+.+|++++.-. + ...+.++.+|++|..|..
T Consensus 20 ~~l~~f~~~~P~v~i~~~--~-~~~~~~l~~~~~D~~i~~ 56 (199)
T cd08478 20 PLIAKFRERYPDIELELV--S-NEGIIDLIERKTDVAIRI 56 (199)
T ss_pred HHHHHHHHHCCCeEEEEE--e-ccccccchhccccEEEEe
Confidence 667888889999998865 2 344555778999998853
No 142
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=39.06 E-value=73 Score=27.75 Aligned_cols=48 Identities=13% Similarity=0.053 Sum_probs=38.9
Q ss_pred CeEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 56 AVVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 56 a~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+||+++. +--.+++..+|++++...-++-+.-+..|.+|++|-.|..
T Consensus 91 l~i~~~~~~~~~~~~~~l~~~~~~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~ 145 (290)
T PRK10837 91 LRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIE 145 (290)
T ss_pred EEEEecchhHhhhhHHHHHHHHHHCCCceEEEEECCHHHHHHHHHhCCceEEEec
Confidence 35777663 5557888889999999877888888899999999998864
No 143
>COG0424 Maf Nucleotide-binding protein implicated in inhibition of septum formation [Cell division and chromosome partitioning]
Probab=38.48 E-value=32 Score=30.31 Aligned_cols=100 Identities=20% Similarity=0.297 Sum_probs=56.8
Q ss_pred CeEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehhhhhhhcCCccc--eeeecCCCCcCCCCCCce
Q psy11424 56 AVVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKR--IRMLFSPNQILPAPGQGA 133 (245)
Q Consensus 56 a~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~--~~~~l~~~~~~PA~gQGa 133 (245)
-+.+++|+||+..|..+.= .|..+-=+||+.+.+-.. +..=..||-...- +...++ +++
T Consensus 5 LiLAS~SPrR~elL~~~gi--~f~~~~~~iDE~~~~~~~--------P~~~v~~LA~~KA~~va~~~~---------~~~ 65 (193)
T COG0424 5 LILASSSPRRRELLEQLGI--PFEVIPSDIDEPLLKAEE--------PREYVLRLAEEKARAVAARLP---------PDA 65 (193)
T ss_pred EEEecCCHHHHHHHHHCCC--CeEEecCCCCCCcccCCC--------HHHHHHHHHHHHHHHHHHhCC---------CCC
Confidence 4789999999999999873 555556677755543332 2233334433221 111222 222
Q ss_pred EEEE-----EecCcHHHHHHhhcCCChhhHHHHHHHHHHHHHhccCCCcceeeEEEE
Q psy11424 134 IAIE-----ILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLAAFAMV 185 (245)
Q Consensus 134 lave-----~r~~d~~~~~ll~~l~~~~t~~~v~aER~~l~~L~ggC~~Piga~a~~ 185 (245)
+-|- +- |+ + -+.-|.+...+ +++|+.|.|-.|.=+-++|-+
T Consensus 66 ~VigaDtvv~l-dg-r------ilgKP~~~~eA---~~~L~~lSG~~h~v~T~v~li 111 (193)
T COG0424 66 LVIGADTVVVL-DG-R------ILGKPKDEEEA---REMLRKLSGRTHQVYTGVALI 111 (193)
T ss_pred EEEecCeEEEE-CC-E------EecCCCCHHHH---HHHHHHhcCCeEEEEEEEEEE
Confidence 2222 11 11 1 12233333333 789999999999988888888
No 144
>PRK01441 Maf-like protein; Reviewed
Probab=37.28 E-value=36 Score=29.98 Aligned_cols=33 Identities=21% Similarity=0.161 Sum_probs=22.7
Q ss_pred CCCeEeeCcHHHHHHHHHhCCCCe-EEeccCcHHHH
Q psy11424 54 KNAVVGTNSLRRKVLIKSFFPSLI-IKSLRGNIDTR 88 (245)
Q Consensus 54 ~ga~IGTsS~RR~aql~~~~pdl~-~~~iRGNV~TR 88 (245)
.--+.|++|+||+..|..+.-+.. +. -=|||.+
T Consensus 5 ~~iILAS~SprR~elL~~~Gi~f~~v~--~~~iDE~ 38 (207)
T PRK01441 5 PKLVLASGSPRRVELLNQAGIEPDRLM--PADIDET 38 (207)
T ss_pred CcEEEeCCCHHHHHHHHhcCCCCeEEe--CCCCCCC
Confidence 336899999999999998855432 32 3355554
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=36.72 E-value=56 Score=25.58 Aligned_cols=37 Identities=11% Similarity=-0.030 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
++.-..+.+.+|++++.-.-++. +..|.+|++|..|.
T Consensus 17 ~~~l~~f~~~~P~i~i~~~~~~~---~~~l~~g~~Dl~i~ 53 (198)
T cd08479 17 APALSDFAKRYPELEVQLELTDR---PVDLVEEGFDLDIR 53 (198)
T ss_pred HHHHHHHHHHCCCeEEEEEecCc---cccccccCccEEEE
Confidence 36677888899999988765553 46788999999775
No 146
>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=36.60 E-value=82 Score=27.69 Aligned_cols=47 Identities=15% Similarity=0.154 Sum_probs=40.4
Q ss_pred CeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 56 AVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 56 a~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
-+||++. +..-.++...+|++++...-++-+.=++-|.+|++|-.|.
T Consensus 95 l~I~~~~~~~~~~~~~~l~~~~~~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~ 148 (300)
T TIGR02424 95 VRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVG 148 (300)
T ss_pred EEEecccHHHHhhhHHHHHHHHHhCCCcEEEEEeCchHHHHHHHHCCCCCEEEE
Confidence 4688875 4667889999999999999999888888999999999885
No 147
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=36.12 E-value=54 Score=25.41 Aligned_cols=36 Identities=14% Similarity=0.169 Sum_probs=28.9
Q ss_pred HHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 65 RKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 65 R~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
--.++.+.+|++++.-.-++ .+..|.+|++|-.|.-
T Consensus 18 ~l~~~~~~~P~v~i~~~~~~---~~~~l~~g~~D~~i~~ 53 (194)
T cd08432 18 RLARFQARHPDIDLRLSTSD---RLVDFAREGIDLAIRY 53 (194)
T ss_pred HhHHHHHHCCCeEEEEEecC---CccccccccccEEEEe
Confidence 35677888999999988777 4677899999998753
No 148
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=35.79 E-value=49 Score=25.54 Aligned_cols=21 Identities=24% Similarity=0.267 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHHHHHHHHhhH
Q psy11424 215 PIDTPETVGLYAAELLKKKGA 235 (245)
Q Consensus 215 ~~~~a~~lg~~la~~l~~~ga 235 (245)
+.+.|..+|+.+|+.++++|.
T Consensus 55 n~~aA~~vG~~la~r~~~~gi 75 (103)
T cd00432 55 NVEAAYLVGRLLAKRALEKGI 75 (103)
T ss_pred cHHHHHHHHHHHHHHHHHCCC
Confidence 445689999999999998864
No 149
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=35.63 E-value=25 Score=28.20 Aligned_cols=20 Identities=25% Similarity=0.285 Sum_probs=16.6
Q ss_pred CCCHHHHHHHHHHHHHHhhH
Q psy11424 216 IDTPETVGLYAAELLKKKGA 235 (245)
Q Consensus 216 ~~~a~~lg~~la~~l~~~ga 235 (245)
.+.|..+|..+|+.++++|.
T Consensus 70 ~~aa~~vG~lla~ra~~~gi 89 (119)
T PF00861_consen 70 VEAAYLVGELLAKRALEKGI 89 (119)
T ss_dssp HHHHHHHHHHHHHHHHHTTS
T ss_pred EehHHHHHHHHHHHHHHcCC
Confidence 45578999999999999874
No 150
>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=35.62 E-value=61 Score=26.21 Aligned_cols=41 Identities=12% Similarity=-0.006 Sum_probs=34.0
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
.--..+++.+|++++.-..++-.+-.+.|.+|++|-.|...
T Consensus 17 ~~l~~f~~~~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 17 ALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred HHHHHHHHHCCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 34567888899999998888877788899999999988743
No 151
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=35.61 E-value=39 Score=27.80 Aligned_cols=23 Identities=30% Similarity=0.265 Sum_probs=19.6
Q ss_pred cCCCCHHHHHHHHHHHHHHhhHH
Q psy11424 214 GPIDTPETVGLYAAELLKKKGAI 236 (245)
Q Consensus 214 ~~~~~a~~lg~~la~~l~~~ga~ 236 (245)
++.+.|..+|..+|+..+++|..
T Consensus 74 ~N~~aA~~vG~lia~ra~~kgi~ 96 (125)
T COG0256 74 GNTEAAYLVGKLIAERALAKGIE 96 (125)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCc
Confidence 46778999999999999999854
No 152
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=34.92 E-value=80 Score=28.36 Aligned_cols=47 Identities=11% Similarity=-0.012 Sum_probs=38.2
Q ss_pred CeEeeCc--------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 56 AVVGTNS--------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 56 a~IGTsS--------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
-+||+++ +.-..+++..+|++++.-..||-..-.+.|.+|++|..|.
T Consensus 94 l~Ig~~~~~~~~~~l~~~l~~~~~~~P~i~l~l~~~~~~~~~~~l~~g~~D~~i~ 148 (308)
T PRK10094 94 VNIVINNLLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIG 148 (308)
T ss_pred EEEEecccccCHHHHHHHHHHHHHhCCCcEEEEEeehhhhHHHHHhCCCccEEEe
Confidence 4677653 2455788889999999999998888889999999998774
No 153
>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=34.48 E-value=76 Score=24.90 Aligned_cols=39 Identities=13% Similarity=0.142 Sum_probs=30.0
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
..-.++.+. |++++.-.-+|-+.-.+.|.+|++|.+|..
T Consensus 17 ~~l~~f~~~-~~v~l~l~~~~~~~~~~~l~~~~~D~~i~~ 55 (195)
T cd08428 17 PALAPVLKR-ERILLDLIVDDEDRTHDLLRDGEVVGCIST 55 (195)
T ss_pred HHHHHHHhC-cCeEEEEEeCCchhHHHHHHcCcceEEEEe
Confidence 346666666 588888877887777788999999976654
No 154
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=34.08 E-value=59 Score=28.77 Aligned_cols=47 Identities=17% Similarity=0.291 Sum_probs=38.6
Q ss_pred eEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 57 VVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 57 ~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
+||++.. ..-.++.+.+|++++...-++....++.|.+|++|..|..
T Consensus 98 ~I~~~~~~~~~~l~~~l~~~~~~~p~i~~~~~~~~~~~~~~~l~~g~~Di~i~~ 151 (302)
T PRK09791 98 NIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINT 151 (302)
T ss_pred EEEechHHHHhhhHHHHHHHHHHCCCeEEEEEeCChHHHHHHHHCCCccEEEEe
Confidence 5666553 3456778889999999988999999999999999998864
No 155
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=33.71 E-value=65 Score=28.28 Aligned_cols=49 Identities=14% Similarity=0.163 Sum_probs=40.2
Q ss_pred CeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEehh
Q psy11424 56 AVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAA 104 (245)
Q Consensus 56 a~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~ 104 (245)
-+||++. .+--.++...+|++++.-.-++-++-+..|.+|++|..|+..
T Consensus 92 l~Ig~~~~~~~~~l~~~~~~~~~~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~ 147 (296)
T PRK09906 92 LTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRH 147 (296)
T ss_pred EEEEEecchhhhHHHHHHHHHHHHCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecC
Confidence 5666532 255677888999999999999989999999999999999744
No 156
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=33.30 E-value=71 Score=28.92 Aligned_cols=41 Identities=12% Similarity=0.109 Sum_probs=35.5
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
...-.+++..+|++++...-++-++-+..|.+|++|..|..
T Consensus 105 ~~~l~~~~~~~P~i~l~~~~~~~~~~~~~L~~g~~Dl~i~~ 145 (317)
T PRK15421 105 TPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTS 145 (317)
T ss_pred HHHHHHHHHHCCCceEEEEeCccHHHHHHHHCCCcCEEEec
Confidence 34568888899999999888888888999999999999864
No 157
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=32.88 E-value=97 Score=27.47 Aligned_cols=47 Identities=15% Similarity=0.138 Sum_probs=37.5
Q ss_pred CeEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 56 AVVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 56 a~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
-+||++.. .-.+++...+|++++...-++.++-+..|.+|++|-.|.
T Consensus 95 l~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~ 148 (296)
T PRK11062 95 FDVGVADALSKRLVSRVLLTAVPEDESIHLRCFESTHEMLLEQLSQHKLDMILS 148 (296)
T ss_pred EEEEecchhhHhhHHHHHHHHHhcCCceEEEEEeCCHHHHHHHHHcCCCCEEEe
Confidence 36777642 445666777999999987789999999999999999885
No 158
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=32.45 E-value=1.5e+02 Score=24.56 Aligned_cols=54 Identities=11% Similarity=0.089 Sum_probs=38.9
Q ss_pred HHHHHHhhcCCChhhHHHHHHHHHH-HHHhc----------cCCCcceeeEEEEeccCCCeEEEEEE
Q psy11424 143 KELMEMLIPLNHYFSEQTVKAERAV-SRNFN----------GSCKISLAAFAMVNNFNESEINLRAI 198 (245)
Q Consensus 143 ~~~~~ll~~l~~~~t~~~v~aER~~-l~~L~----------ggC~~Piga~a~~~~~~~~~l~l~~~ 198 (245)
.++.+-++.+.|++.+.....|.+= |-.|. .||++++=..++.. +++++++.|.
T Consensus 8 ~~i~~~f~~~~dwe~Ry~~LI~lgk~Lp~lpe~~r~~~~~V~GCqS~VWl~~~~~--~~g~~~f~~d 72 (138)
T PRK09296 8 EKLLRNFSRCANWEEKYLYIIELGQRLPPLTDEDRSPQNLIQGCQSQVWIVMRQN--AQGIIELQGD 72 (138)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhhCCCCCHHHcCccccCCCcccceeeeEeec--CCCEEEEEEe
Confidence 4677888899999998887776542 22222 69999999988772 3368888764
No 159
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=31.86 E-value=85 Score=27.97 Aligned_cols=48 Identities=17% Similarity=0.178 Sum_probs=38.9
Q ss_pred CeEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 56 AVVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 56 a~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-+||+++. .....+...+|++++.-.-++.++-++.|.+|++|..|..
T Consensus 95 l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~ 149 (309)
T PRK12682 95 LTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAT 149 (309)
T ss_pred EEEeeCchHHHHHHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHcCCccEEEec
Confidence 46777642 3345667789999999999999999999999999999864
No 160
>PF02657 SufE: Fe-S metabolism associated domain; InterPro: IPR003808 This entry represents the core domain of SufE and related proteins. This domain of SufE shows strong structural similarity to IscU, and the sulfur-acceptor site in SufE coincides with the location of the cysteine residues mediating Fe-S cluster assembly in IscU. Thus, a conserved core structure is implicated in mediating the interactions of both SufE and IscU with the mutually homologous cysteine desulfurase enzymes present in their respective operons [].; PDB: 1MZG_B 1WLO_A 3G0M_A 1NI7_A.
Probab=31.21 E-value=67 Score=25.99 Aligned_cols=50 Identities=10% Similarity=0.121 Sum_probs=29.1
Q ss_pred HHHhhcCCChhhHHHHHHHHHH-HHH----------hccCCCcceee-EEEEeccCCCeEEEEEE
Q psy11424 146 MEMLIPLNHYFSEQTVKAERAV-SRN----------FNGSCKISLAA-FAMVNNFNESEINLRAI 198 (245)
Q Consensus 146 ~~ll~~l~~~~t~~~v~aER~~-l~~----------L~ggC~~Piga-~a~~~~~~~~~l~l~~~ 198 (245)
.+.|+.+.|++.+.....|-+= |.. +=.||++++-. +... +++++++.|.
T Consensus 2 ~~~f~~~~~~~~ry~~Li~lgk~lp~l~~~~~~~~~~V~GC~S~vWl~~~~~---~~g~~~f~ad 63 (125)
T PF02657_consen 2 IEDFSSLDDWEERYRYLIDLGKKLPPLPEELRTDENLVHGCQSQVWLHVEED---EDGKVHFRAD 63 (125)
T ss_dssp HHHHHCSSSHHHHHHHHHHHHHTS----CCCCSCCEEETSSSS-EEEEEEEE---TTSEEEEEEE
T ss_pred HhHHhcCCCHHHHHHHHHHHHhcCCCCCHHHhcccccCCCCccceeEeeeec---cCCEEEEEec
Confidence 3445666666666655444221 000 11799999999 4455 7788888774
No 161
>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []. Many proteins are involved in these processes. This family is a transporter which shows similarity to ABC transporters [].; PDB: 2QGU_A.
Probab=30.56 E-value=2.9e+02 Score=22.84 Aligned_cols=55 Identities=18% Similarity=0.163 Sum_probs=36.2
Q ss_pred CeEEEEEEEEcCCCcEEEEEEEecCCCCHHHHHHHHHHHHHHhhHHHHHHHhhcC
Q psy11424 191 SEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAIEIIKSYEKK 245 (245)
Q Consensus 191 ~~l~l~~~v~~~dG~~~~~~~~~~~~~~a~~lg~~la~~l~~~ga~~il~~~~~~ 245 (245)
..+.+.=.+...+|.+.+..-..-..+-...--......|.+.|...+++.+++|
T Consensus 115 ~~i~v~y~l~~~~g~Wki~Dv~ieGvSl~~~~R~qF~~~l~~~Gid~li~~l~~k 169 (170)
T PF05494_consen 115 QPIPVDYRLRKKDGKWKIYDVIIEGVSLVATYRSQFQSILRKNGIDGLIEKLKKK 169 (170)
T ss_dssp EEEEEEEEEEEETTEEEEEEEEETTEEHHHHHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred CcEEEEEEEEEcCCCeEEEEEEEcceeHHHHHHHHHHHHHHhCCHHHHHHHHHhc
Confidence 3444444444456655554333223566677778889999999999999998764
No 162
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=29.09 E-value=90 Score=27.67 Aligned_cols=48 Identities=13% Similarity=0.072 Sum_probs=39.1
Q ss_pred CeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 56 AVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 56 a~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-+||++. ++.-.+++..+|++++...-|+-+.-+++|.+|++|-.|..
T Consensus 94 l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~ 148 (300)
T PRK11074 94 LSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGA 148 (300)
T ss_pred EEEEEcCccchhHHHHHHHHHHHhCCCceEEEEehhhhHHHHHHHCCCCCEEEec
Confidence 4677642 34567788889999999888998889999999999999963
No 163
>COG0604 Qor NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]
Probab=29.04 E-value=1e+02 Score=28.56 Aligned_cols=63 Identities=16% Similarity=0.186 Sum_probs=46.1
Q ss_pred eEeeCcHHHHHHHHHhCCCCeEEeccCcHHHHHhhhccC-CccEEEehhh------hhhhcCCccceeee
Q psy11424 57 VVGTNSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKG-EYAAIILAAA------GLKRLNLQKRIRML 119 (245)
Q Consensus 57 ~IGTsS~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g-~~DaiiLA~A------GL~RLg~~~~~~~~ 119 (245)
++.|||.+....++.+-.|..+.-.+.|+..+++++..| .||.++=..- .+.-|...-++..+
T Consensus 171 v~~~~s~~k~~~~~~lGAd~vi~y~~~~~~~~v~~~t~g~gvDvv~D~vG~~~~~~~l~~l~~~G~lv~i 240 (326)
T COG0604 171 VAVVSSSEKLELLKELGADHVINYREEDFVEQVRELTGGKGVDVVLDTVGGDTFAASLAALAPGGRLVSI 240 (326)
T ss_pred EEEecCHHHHHHHHhcCCCEEEcCCcccHHHHHHHHcCCCCceEEEECCCHHHHHHHHHHhccCCEEEEE
Confidence 466666766678888888888888899999999999988 5999874433 45556555555443
No 164
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=28.82 E-value=1.6e+02 Score=24.34 Aligned_cols=54 Identities=7% Similarity=0.005 Sum_probs=38.5
Q ss_pred HHHHHHhhcCCChhhHHHHHHHHHH-HHHhc----------cCCCcceeeEEEEeccCCCeEEEEEE
Q psy11424 143 KELMEMLIPLNHYFSEQTVKAERAV-SRNFN----------GSCKISLAAFAMVNNFNESEINLRAI 198 (245)
Q Consensus 143 ~~~~~ll~~l~~~~t~~~v~aER~~-l~~L~----------ggC~~Piga~a~~~~~~~~~l~l~~~ 198 (245)
.++.+-|+.+.|++.+.....|.+= |-.|. .||++++=.++... +++++++.|.
T Consensus 13 ~~i~~~f~~~~dwe~ry~~lI~lgk~Lp~lpe~~r~~~~~V~GCqS~VWl~~~~~--~dg~~~f~~d 77 (138)
T TIGR03391 13 ADLIATFAACRQWEDRYRQLILLAKQLPALPEALKTQATELTGCENRVWLGHQVL--PDGTLHFYGD 77 (138)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHhhCCCCChHHcChhhccCCcccceeeeeeec--CCCEEEEEec
Confidence 4678888999999988887776542 21222 69999998888631 5668887653
No 165
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=28.31 E-value=97 Score=27.05 Aligned_cols=41 Identities=10% Similarity=-0.042 Sum_probs=34.8
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
.+=-..+...+|++++...-++-..-++.|.+|++|-.|..
T Consensus 107 ~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 147 (296)
T PRK11242 107 GPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAF 147 (296)
T ss_pred HHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHCCCCcEEEEe
Confidence 44556777789999999888999999999999999998864
No 166
>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=26.50 E-value=87 Score=26.68 Aligned_cols=52 Identities=17% Similarity=0.049 Sum_probs=38.5
Q ss_pred CCCCCCCCCCeEeeCcHHHHHHHHHh-CCCCeEEeccCcHHHHHhhhccCCccEEE
Q psy11424 47 ISLSTLPKNAVVGTNSLRRKVLIKSF-FPSLIIKSLRGNIDTRLNKLDKGEYAAII 101 (245)
Q Consensus 47 ~~l~~lp~ga~IGTsS~RR~aql~~~-~pdl~~~~iRGNV~TRL~KL~~g~~Daii 101 (245)
.++.+|+.+.+|.|+-++=..+.... .-+.+++.+-|+++--- ..|-.|+||
T Consensus 59 ~~~~~l~~~~rIATkyp~l~~~yf~~~g~~~~ii~l~GsvE~ap---~~glAD~Iv 111 (163)
T PF01634_consen 59 KSVEDLKAGLRIATKYPNLTRRYFAEKGINVEIIKLSGSVELAP---PLGLADAIV 111 (163)
T ss_dssp CCGGGGSSTEEEEES-HHHHHHHHHHCT-EEEEEE-SS-TTHHH---HTTSSSEEE
T ss_pred CCHHHhccCCEEEECCHHHHHHHHHHcCCcEEEEEccCCccccC---CCCCCCEEE
Confidence 45778888999999999986665554 55899999999998763 378889997
No 167
>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=26.48 E-value=91 Score=24.08 Aligned_cols=36 Identities=14% Similarity=0.182 Sum_probs=27.2
Q ss_pred HHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 65 RKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 65 R~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
--..+.+.+|++++.-..++-. ..|.+|++|-.|..
T Consensus 18 ~l~~f~~~~P~i~i~i~~~~~~---~~l~~~~~Dl~l~~ 53 (194)
T cd08481 18 RLPDFLARHPDITVNLVTRDEP---FDFSQGSFDAAIHF 53 (194)
T ss_pred hhhHHHHHCCCceEEEEecccc---cCcccCCCCEEEEc
Confidence 3466677899999987766532 46889999998864
No 168
>PRK15019 CsdA-binding activator; Provisional
Probab=26.40 E-value=2.1e+02 Score=23.97 Aligned_cols=54 Identities=9% Similarity=0.073 Sum_probs=39.3
Q ss_pred HHHHHHhhcCCChhhHHHHHHHHHH-HHHhc----------cCCCcceeeEEEEeccCCCeEEEEEE
Q psy11424 143 KELMEMLIPLNHYFSEQTVKAERAV-SRNFN----------GSCKISLAAFAMVNNFNESEINLRAI 198 (245)
Q Consensus 143 ~~~~~ll~~l~~~~t~~~v~aER~~-l~~L~----------ggC~~Piga~a~~~~~~~~~l~l~~~ 198 (245)
.++.+-++.+.|++.+.....|.+= |-.|. .||++++=..+... +++++++.|.
T Consensus 18 ~~i~~~f~~~~dweeRy~~LI~lgk~Lp~lpe~~r~~~~~V~GCqS~VWL~~~~~--~dg~~~f~~d 82 (147)
T PRK15019 18 ETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVA--ENGKMHFFGD 82 (147)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhhCCCCChHHcCccCcCCCcccceeeeeeec--CCCEEEEEee
Confidence 4688889999999999988776542 22221 69999998877762 4568888764
No 169
>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=25.58 E-value=1.1e+02 Score=23.50 Aligned_cols=38 Identities=13% Similarity=0.141 Sum_probs=27.9
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++.-..++..+|++++.-.-++ .+..+.+|++|..|..
T Consensus 17 ~~~l~~~~~~~P~v~i~i~~~~---~~~~l~~~~~D~~i~~ 54 (197)
T cd08422 17 APLLAEFLARYPDVRLELVLSD---RLVDLVEEGFDLAIRI 54 (197)
T ss_pred HHHHHHHHHhCCceEEEEecCc---cccchhhcCccEEEEe
Confidence 4667888899999988765443 3445667889998863
No 170
>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=25.41 E-value=1.1e+02 Score=24.06 Aligned_cols=38 Identities=11% Similarity=0.045 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++.-.++++.+|++++....++. +..+.+|++|..|..
T Consensus 19 ~~~l~~~~~~~P~v~i~~~~~~~---~~~l~~g~~D~~i~~ 56 (202)
T cd08474 19 APLLARFLARYPDIRLELVVDDG---LVDIVAEGFDAGIRL 56 (202)
T ss_pred HHHHHHHHHHCCCeEEEEEecCC---cccccccCccEEEEc
Confidence 36678888999999998766653 556778999998753
No 171
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=25.32 E-value=1.1e+02 Score=27.12 Aligned_cols=38 Identities=11% Similarity=0.155 Sum_probs=32.1
Q ss_pred HHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 66 KVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 66 ~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
..++...+|++++.-.-++-++=++.|.+|++|..|.-
T Consensus 114 l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 114 IGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred HHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEEc
Confidence 45667789999999888888888889999999998863
No 172
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=25.14 E-value=1.8e+02 Score=25.90 Aligned_cols=48 Identities=4% Similarity=-0.107 Sum_probs=38.9
Q ss_pred CeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 56 AVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 56 a~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-+||.++ ...-.++.+.+|++++.-.-++-..=++.|.+|++|..|..
T Consensus 96 l~I~~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~ 150 (309)
T PRK11013 96 LSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTE 150 (309)
T ss_pred EEEEEcHHHHHhhHHHHHHHHHHHCCCCeEEEEeCCHHHHHHHHHcCCCCEEEEc
Confidence 4677665 34456788899999999999998887889999999988864
No 173
>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=24.96 E-value=3.1e+02 Score=21.43 Aligned_cols=98 Identities=21% Similarity=0.209 Sum_probs=57.4
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcCC-------CCCCCCCCCCeEeeC---cHHHHHH--H
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDY-------ISLSTLPKNAVVGTN---SLRRKVL--I 69 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~~-------~~l~~lp~ga~IGTs---S~RR~aq--l 69 (245)
+|.+|++|+++..... .++++...-+. .++.=++++++. .++++|..-..|..+ ..+.... +
T Consensus 50 ~l~~g~~Dl~i~~~~~----~~~~~~~~~l~--~~~~~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~ 123 (209)
T PF03466_consen 50 ALRSGELDLAITFGPP----PPPGLESEPLG--EEPLVLVVSPDHPLAQKKPITLEDLADYPLILLSPGSPYRDQLDRWL 123 (209)
T ss_dssp HHHTTSSSEEEESSSS----SSTTEEEEEEE--EEEEEEEEETTSGGGTTSSSSGGGGTTSEEEEESTTTSHHHHHHHHH
T ss_pred HHhcccccEEEEEeec----ccccccccccc--ceeeeeeeeccccccccccchhhhhhhcccccccccccccccccccc
Confidence 5789999999998877 45566544443 333333333332 245666554455422 2333211 2
Q ss_pred HHhCCCCeEEeccCcHHHHHhhhccCCccEEEehhh
Q psy11424 70 KSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAA 105 (245)
Q Consensus 70 ~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA~A 105 (245)
.......+....=.|+++-+.-+.+|..=+++-...
T Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~ 159 (209)
T PF03466_consen 124 REHGFSPNIVIEVDSFESILSLVASGDGIAILPDSL 159 (209)
T ss_dssp HHTTEEEEEEEEESSHHHHHHHHHTTSEBEEEEHHH
T ss_pred ccccccccccccccchhhhccccccccceeecCccc
Confidence 333334455556799999999999997666655444
No 174
>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=24.18 E-value=2.8e+02 Score=21.54 Aligned_cols=97 Identities=12% Similarity=0.027 Sum_probs=46.7
Q ss_pred ccccCCccEEeecCCCCCCCCCCCeeEEEecCCCCCCeEEEEcC-------CCCCCCCCCCCeEeeCc---HHHHHH-HH
Q psy11424 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISND-------YISLSTLPKNAVVGTNS---LRRKVL-IK 70 (245)
Q Consensus 2 aLl~g~iDiAVHSlKDlP~~l~~gL~iaav~~R~dprDvlv~~~-------~~~l~~lp~ga~IGTsS---~RR~aq-l~ 70 (245)
.|.+|++|+++....+. ..++++...-+. +++-=++++++ ..++++|..-..|..++ .|+... +.
T Consensus 44 ~l~~g~~Dl~i~~~~~~--~~~~~l~~~~l~--~~~~~~~~~~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~ 119 (198)
T cd08437 44 QLLQGDLDIALLGSLTP--LENSALHSKIIK--TQHFMIIVSKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLC 119 (198)
T ss_pred HHHcCCCCEEEecCCCC--CCcccceEEEee--cceEEEEecCCCcccccCcccHHHHcCCCeEEecccchHHHHHHHHH
Confidence 57889999999653221 112344322211 11211122221 12344444334454432 233221 22
Q ss_pred -HhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 71 -SFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 71 -~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
......++.-.-.|+.+-++-+.+|..=+++-
T Consensus 120 ~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p 152 (198)
T cd08437 120 QQANFQPNIVYRTNDIHILKSMVRENVGIGFLT 152 (198)
T ss_pred HHcCCCccEEEEeCcHHHHHHHHHcCCcEEEEE
Confidence 22223455555689999999999887544443
No 175
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=24.01 E-value=1.4e+02 Score=26.08 Aligned_cols=47 Identities=13% Similarity=0.250 Sum_probs=35.0
Q ss_pred CeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 56 AVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 56 a~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-+||+++ +..-.++... |++++.-.-+|-+.-++.|.+|++|.+|..
T Consensus 92 l~I~~~~~~~~~~~~~~l~~~~~~-~~i~i~~~~~~~~~~~~~L~~~~~d~~i~~ 145 (294)
T PRK13348 92 LAIAVNADSLATWFLPALAAVLAG-ERILLELIVDDQDHTFALLERGEVVGCVST 145 (294)
T ss_pred EEEEecchhHHHHHHHHHHHHHhC-CCeEEEEEEcchHHHHHHHhcCCeEEEEec
Confidence 4678753 2344555444 898888888999888999999999988753
No 176
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=23.95 E-value=1.4e+02 Score=26.62 Aligned_cols=39 Identities=15% Similarity=0.217 Sum_probs=32.9
Q ss_pred HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEe
Q psy11424 64 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIIL 102 (245)
Q Consensus 64 RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiL 102 (245)
.....+.+.+|++++.-..++-.+-...|.+|++|..|.
T Consensus 109 ~~l~~~~~~~p~i~l~~~~~~~~~~~~~l~~g~~Di~i~ 147 (305)
T PRK11233 109 PLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVI 147 (305)
T ss_pred HHHHHHHHHCCCcEEEEEECCcHHHHHHHHCCCCCEEEE
Confidence 345677778999999888888888889999999999885
No 177
>cd08488 PBP2_AmpR The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold. AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsibl
Probab=22.90 E-value=1.3e+02 Score=23.57 Aligned_cols=38 Identities=13% Similarity=0.047 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 63 LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 63 ~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
++--.++++.+|++++.-.-+|-.. .+.+|++|..|..
T Consensus 16 ~~~l~~f~~~~P~v~i~~~~~~~~~---~l~~~~~D~~i~~ 53 (191)
T cd08488 16 LPRLADFQNRHPFIDLRLSTNNNRV---DIAAEGLDYAIRF 53 (191)
T ss_pred HhHHHHHHHHCCCcEEEEEecCCcc---ccCCCCccEEEEe
Confidence 3567888999999999876555332 4667899987753
No 178
>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).
Probab=22.82 E-value=30 Score=33.98 Aligned_cols=50 Identities=24% Similarity=0.384 Sum_probs=39.2
Q ss_pred cCCccEEEehhhhhhhcCCcccee--eecCCCCcCCCCCCceEEEEEecCcH
Q psy11424 94 KGEYAAIILAAAGLKRLNLQKRIR--MLFSPNQILPAPGQGAIAIEILDNRK 143 (245)
Q Consensus 94 ~g~~DaiiLA~AGL~RLg~~~~~~--~~l~~~~~~PA~gQGalave~r~~d~ 143 (245)
||.||||.-|+.=-+.+||....+ -+|..|....-+|.|-||=.+.-+|.
T Consensus 207 EgG~DAimQaaVC~~~IGWR~~a~rllv~~TDa~fH~AGDGkLaGIv~PNDg 258 (423)
T smart00187 207 EGGFDAIMQAAVCTEQIGWREDARRLLVFSTDAGFHFAGDGKLAGIVQPNDG 258 (423)
T ss_pred cccHHHHHHHHhhccccccCCCceEEEEEEcCCCccccCCcceeeEecCCCC
Confidence 688999999888888999975433 36778887788999999877765553
No 179
>PF00943 Alpha_E2_glycop: Alphavirus E2 glycoprotein; InterPro: IPR000936 Alphaviruses are enveloped RNA viruses that use arthropods such as mosquitoes for transmission to their vertebrate hosts, and include Semliki Forest and Sindbis viruses []. Alphaviruses consist of three structural proteins: the core nucleocapsid protein C, and the envelope proteins P62 and E1 (IPR002548 from INTERPRO) that associate as a heterodimer. The viral membrane-anchored surface glycoproteins are responsible for receptor recognition and entry into target cells through membrane fusion. The proteolytic maturation of P62 into E2 and E3 (IPR002533 from INTERPRO) causes a change in the viral surface. Together the E1, E2, and sometimes E3 glycoprotein "spikes" form an E1/E2 dimer or an E1/E2/E3 trimer, where E2 extends from the centre to the vertices, E1 fills the space between the vertices, and E3, if present, is at the distal end of the spike [, ]. Upon exposure of the virus to the acidity of the endosome, E1 dissociates from E2 to form an E1 homotrimer, which is necessary for the fusion step to drive the cellular and viral membranes together []. This entry represents the alphaviral E2 glycoprotein. The E2 glycoprotein functions to interact with the nucleocapsid through its cytoplasmic domain, while its ectodomain is responsible for binding a cellular receptor.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2XFC_B 3N42_B 3N41_B 2XFB_E 3N40_P 3N43_B 3N44_B 3MUU_B 1Z8Y_P 3J0C_H ....
Probab=22.61 E-value=61 Score=31.64 Aligned_cols=33 Identities=18% Similarity=0.377 Sum_probs=19.6
Q ss_pred ccCCCcceeeEEEEeccCCCeEEEE--EEEE-cCCC
Q psy11424 172 NGSCKISLAAFAMVNNFNESEINLR--AIIT-NPNG 204 (245)
Q Consensus 172 ~ggC~~Piga~a~~~~~~~~~l~l~--~~v~-~~dG 204 (245)
+..|++||++-..+.++.|+.|.+. +.+. +.+|
T Consensus 12 g~~C~SPiaIE~V~~ea~DG~lrIQ~SaQ~Gl~ksg 47 (403)
T PF00943_consen 12 GESCHSPIAIEEVRSEADDGTLRIQVSAQIGLDKSG 47 (403)
T ss_dssp SS-EEETT-EEEEEE--TTSEEEEEEEEEEEECTTS
T ss_pred CCccCChHhhhhhhccCCCceEEEEEeeeeccccCC
Confidence 4489999999998876677766554 4443 2444
No 180
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=22.21 E-value=86 Score=25.00 Aligned_cols=22 Identities=32% Similarity=0.283 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHHHHHHHHhhHH
Q psy11424 215 PIDTPETVGLYAAELLKKKGAI 236 (245)
Q Consensus 215 ~~~~a~~lg~~la~~l~~~ga~ 236 (245)
+.+.|..+|..+|+.++++|..
T Consensus 59 n~~aA~~vG~lla~ra~~~gi~ 80 (109)
T CHL00139 59 TCDASKLVGQKLAKKSLKKGIT 80 (109)
T ss_pred CHHHHHHHHHHHHHHHHHCCCC
Confidence 4556889999999999998843
No 181
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=21.59 E-value=1.7e+02 Score=26.56 Aligned_cols=48 Identities=13% Similarity=0.068 Sum_probs=39.5
Q ss_pred CeEeeCc-------HHHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 56 AVVGTNS-------LRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 56 a~IGTsS-------~RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
-+||++. +.--.++...+|++++.-.-|+-+.-++.|.+|++|..|..
T Consensus 95 l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~~~~L~~g~iDl~i~~ 149 (324)
T PRK12681 95 LYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIAT 149 (324)
T ss_pred EEEEechhHHHHhhHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCCCEEEec
Confidence 4677765 33457788889999999999999999999999999998863
No 182
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=21.36 E-value=1.9e+02 Score=25.94 Aligned_cols=50 Identities=20% Similarity=0.227 Sum_probs=37.7
Q ss_pred CCC--CeEeeCcH-------HHHHHHHHhCCCCeEEeccCcHHHHHhhhccCCccEEEeh
Q psy11424 53 PKN--AVVGTNSL-------RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILA 103 (245)
Q Consensus 53 p~g--a~IGTsS~-------RR~aql~~~~pdl~~~~iRGNV~TRL~KL~~g~~DaiiLA 103 (245)
|.| -+||+++. .=.+.++..+|++++.-.-++-+ .+..|.+|++|..|+.
T Consensus 94 ~~~~~l~I~~~~~~~~~~~~~~l~~f~~~~P~v~v~i~~~~~~-~~~~l~~g~~D~~i~~ 152 (319)
T PRK10216 94 PRGLKFELAAESPLMMIMLNALSKRIYQRYPQATIKLRNWDYD-SLDAITRGEVDIGFTG 152 (319)
T ss_pred ccCCEEEEEecchhHHHHHHHHHHHHHHHCCCCEEEEEeCCcc-hHHHHhcCCccEEEec
Confidence 455 47887763 34566778899998887767654 5899999999998874
No 183
>PF07302 AroM: AroM protein; InterPro: IPR010843 This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL []. The function of this family is unknown.
Probab=20.88 E-value=48 Score=29.79 Aligned_cols=55 Identities=24% Similarity=0.419 Sum_probs=42.5
Q ss_pred HHHHHhhhccCCccEEEehhhhhhhcCCccceeeecCCCCcCCC-----CCCceEEEEEecC
Q psy11424 85 IDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILPA-----PGQGAIAIEILDN 141 (245)
Q Consensus 85 V~TRL~KL~~g~~DaiiLA~AGL~RLg~~~~~~~~l~~~~~~PA-----~gQGalave~r~~ 141 (245)
++..+++|++..||.|+|...|--. ++..+.. .+.|+.++|. ++.+-+||.+-..
T Consensus 76 lq~~i~~le~~G~d~illlCTG~F~-~l~~~~~-lleP~ril~~lV~al~~~~~vGVivP~~ 135 (221)
T PF07302_consen 76 LQACIAQLEAQGYDVILLLCTGEFP-GLTARNP-LLEPDRILPPLVAALVGGHQVGVIVPLP 135 (221)
T ss_pred HHHHHHHHHHCCCCEEEEeccCCCC-CCCCCcc-eeehHHhHHHHHHHhcCCCeEEEEecCH
Confidence 5567788999999999999999777 7776665 7778877663 3346899998754
No 184
>cd00755 YgdL_like Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of the substrate. The exact function of this family is unknown.
Probab=20.12 E-value=1.3e+02 Score=26.76 Aligned_cols=42 Identities=12% Similarity=0.151 Sum_probs=31.8
Q ss_pred HHHHHHhCCCCeEEeccCcHH-HHHhhhccCCccEEEehhhhh
Q psy11424 66 KVLIKSFFPSLIIKSLRGNID-TRLNKLDKGEYAAIILAAAGL 107 (245)
Q Consensus 66 ~aql~~~~pdl~~~~iRGNV~-TRL~KL~~g~~DaiiLA~AGL 107 (245)
+.+|+.++|++++..+...+. +-+..+...+||-||-|-.-+
T Consensus 71 ~~~l~~inP~~~V~~~~~~i~~~~~~~l~~~~~D~VvdaiD~~ 113 (231)
T cd00755 71 AERIRDINPECEVDAVEEFLTPDNSEDLLGGDPDFVVDAIDSI 113 (231)
T ss_pred HHHHHHHCCCcEEEEeeeecCHhHHHHHhcCCCCEEEEcCCCH
Confidence 345778899999999988776 355566667799999985543
Done!