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Table 1 BCARR-boxes observed in promoter regions of specific genes and repressed gene expression in presence of peptides

From: Genome-wide motif predictions of BCARR-box in the amino-acid repressed genes of Lactobacillus helveticus CM4

No ORF No Repression (%) Strand a Score Location (bp) Gene Function BCARR-box sequence
1 464 97.0 35 −11 dapF Diaminopimelate epimerase AAAATCACTTTTTTA
2 1025 97.0 + 46 254 paaD Predicted metal-sulfur biosynthetic enzyme AAAAATGATATTATC
3 1029 95.0 + 56 7 hisM ABC-type amino acid transportor AATAAGACTATTATT
4 724 93.0 + 60 87 pepO2 Neutral endopeptidase AAAAAATGCTTTTAT
5 726 93.0 + 37 −120 potE Amino acid transporters AAAAAATCATGTTTT
6 1032 93.0 + 37 −229 ddpA ABC-type dipeptide transport system AAAATTCTAAAATAT
7 765 91.0 33 116 himM ABC-type amino acid transporter AAAAGTATTGTCTTT
8 769 91.0 + 45 −116 putative unknown AAAAAATCTATTTTT
9 1099 91.0 37 −19 med Uncharacterized ABC-type transport system GAAAATAATGTTCTT
10 1104 91.0 + 42 150 putative unknown AAAAAAGCCATTCTT
11 513 90.0 + 42 24 nlpA ABC-type metal ion transport AGAAATACAATTATT
12 661 89.0 + 37 −16 pepD Di- and tripeptidases AATAGACTTTTTTAT
13 1113 87.0 + 42 41 purK Phosphoribosylaminoimidazole carboxylase AAAATACCTTGTATT
14 1621 87.0 33 92   Uncharacterized conserved protein AATACAAGATATTGT
15 670 86.0 33 −11 putative unknown AGAAATAGATTTTTT
16 738 85.0 + 35 42 putative unknown AAAGTAAGCGTTTTA
17 1219 85.0 + 46 35 prtH, prtP Protease P&H AAAAAATTAAATGTA
18 123 85.0 38 −15 putative unknown ACAAAAATTATTCTT
19 1102 84.0 + 48 −254 putative unknown TAAAAAAATATTATT
20 737 83.0 36 74 hpt Hypoxanthine-guanine phosphoribosyltransferase TGAAAAAGTATTATT
21 1543 77.0 34 −104 guaA GMP synthase AACAAGAACTTTTTG
22 129 75.0 + 45 −14 putative unknown AAAAATCCGTTTTTT
23 1030 74.0 + 56 −47 putative unknown AATAATAGTCTTATT
24 576 72.0 36 −135 potE Amino acid transporters GAAGAATACTCTTTG
25 1216 72.0 55 −29 putative unknown AATAAAAGGTTTTTA
26 1634 70.0 + 47 −218   ABC-type transportor AAAAAAACTTTCCTA
27 1586 69.0 + 35 −14 guaB IMP dehydrogenase AACAAGTCCTTTTTT
28 1212 69.0 + 51 64 pepN2 Aminopeptidase N2 AGAACAACACTTTTA
29 1541 68.0 + 33 −90 putative unknown AACAAAACGATCATT
30 536 68.0 + 46 −67 pepC2 Aminopeptidase C AAAATGCCAATTATT
31 1585 67.0 + 38 −3 pepE Aminopeptidase C GAACCCGCTTTTATT
32 632 66.0 46 2 putative unknown AAAAAGTCCAATCTT
33 646 65.0 + 40 −89 putative unknown AAACGGACAACCTTT
34 1162 62.0 42 −135 baeS Signal transduction histidine kinase AATTAAAGGTTTTAT
35 950 62.0 + 44 10 ddpA ABC-type dipeptide transportor AAAACATGGTATTAT
36 668 62.0 37 −21 putative unknown AAAAAGCAGCTTAGT
37 691 59.0 + 31 −177 lytT Response regulator AAAATCTCGCTTTTT
38 665 59.0 33 −90 putative unknown AAATATGATATTTTT
39 296 59.0 + 33 −46 uup ATPase components AAAAAGTTTTAATTA
40 1070 59.0 46 60 putative unknown AATAACACTGTTTTT
41 1514 58.0 38 −29   GAF domain-containing protein AATCAAACTTTTTTC
42 701 57.0 37 −30   Uncharacterized conserved protein GAGAAAAGGTTTGTT
43 1529 56.0 40 −89   FOG: CBS domain-containing protein AAGAGATGCTTTTTT
44 1340 56.0 46 39 pepQ Xaa-Pro aminopeptidase AAAAAGAGGCTATTT
45 579 56.0 + 42 125 uvrC Nuclease subunit AAAAACCGGGCTGTT
46 518 55.0 + 46 −29 putative unknown AAAAAAACAATTATA
47 755 53.0 39 99 folB Dihydroneopterin aldolase AATACGAGGAGTTTT
48 1051 52.0 + 40 49 putative unknown AATCAATGTATTATT
49 1406 51.0 49 −51 fatA Acyl-ACP thioesterase AATATAAGTCCTTTT
50 806 50.0 + 57 64 putative unknown AAAAGAAGCTTGTTT
51 807 49.0 + 40 27 putative unknown AACAATAGAATTATA
52 537 48.0 + 38 −1 citT Di- and tricarboxylate transporters AAAAATAACTTTATT
53 1208 47.0 34 64 hflC Membrane protease subunits AACAACAGGACTTTA
54 1151 46.0 + 43 −122 putative unknown AAAAAATTTTTTTGT
55 1254 46.0 + 49 95 putative unknown AAAATAACTATTAAT
56 669 44.0 34 −222 putative unknown ATGAAATCGCTTATT
57 1530 40.0 + 42 149 putative unknown AAAAAAGCTTTGCTT
58 921 38.0 + 44 −12 putative unknown AAAACATCTTTTTTG
59 763 35.0 + 35 55 putative unknown AAAAATGCTTGACTT
60 201 34.0 + 36 109 deoR Transcriptional regulator AAAAATACATTGTTA
61 825 34.0 47 −8   Uncharacterized protein ATTAATAGGTTTTCT
62 954 34.0 + 49 59 dppD ABC-type dipeptide transportor AAAAAAGCTATAAAT
63 1593 32.0 + 46 124 lytR Transcriptional regulator AAAAAACGTCATATT
64 635 32.0 + 51 −19 mdlB. cydC, sunT ATPase and permease components AAAAACACTTTAATT
65 1590 32.0 + 40 −29 putative unknown AAAACAGTTTTCTTA
66 655 31.0 + 41 167 putative unknown AAAAAACGTTTTAGC
67 1535 30.0 36 114 putative unknown AAAAGTAGTTTTCAT
  1. a Waterman-Eggert score by LALIGN analysis