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Table 3 Transcript-derived fragments (TDFs) from L. rhamnosus PR1019 over-expressed in CB compared to MRS

From: Transcriptomic clues to understand the growth of Lactobacillus rhamnosus in cheese

TDF no Primer combination Length (bp) Biological functiona Organism annotationb Max identity - E-valuec Accession no. Pathway assignmentd
COGe KEGG
37 AC/AT 396 Guanylate kinase (EC 2.7.4.8) L. rhamnosus GG 98% - 1e-84 YP_003171760.1 COG0194 [F] ko00230: Purine metabolism
40 AC/AT 302 Putative phosphoketolase (EC 4.1.2.9) L. rhamnosus GG 99% - 3e-57 YP_005864692.1 COG3957 [G] ko00030: Pentose phosphate pathway
48 AC/AT 199 Monooxygenase L. rhamnosus Lc 705 95% - 6e-17 YP_003174467.1 COG2329: Conserved protein involved in polyketide biosynthesis related to monooxygenase [R] _
54 AC/AT 137 Hypothetical protein L. rhamnosus 77% - 2e-07 WP_005689523.1 _ _
72 AC/AT 340 Lipoteichoic acid synthase LtaS Type IIa (EC 3.1.6) L. rhamnosus Lc 705 100% - 5e-43 YP_003173514.1 COG1368: Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [M] _
76 AC/AT 433 Conserved hypothetical protein L. rhamnosus Lc 705 85% - 9e-27 YP_003174890.1 _ _
86 AC/AT 109 L-xylulose 5-phosphate 3-epimerase (EC 5.1.3.22) L. rhamnosus GG 94% - 9e-13 YP_003172471.1 COG3623 [G] ko00040: Pentose and glucuronate interconversions
93 AC/AT 305 Pyruvate oxidase (EC 1.2.3.3) L. rhamnosus GG 93% - 5e-40 YP_003171582.1 COG3961: Pyruvate decarboxylase and related thiamine pyrophosphate-requiring enzymes [G] ko00620: Pyruvate metabolism
95 AC/AT 229 Plasmid pNCD0151 L. casei 98% - 4e-68 Z50861.1 _ _
97 AC/AT 227 Plasmid pNCD0151 L. casei 96% - 3e-64 Z50861.1 _ _
106 AC/AT 170 Plasmid pNCD0151 L. casei 97% - 9e-48 Z50861.1 _ _
120 AC/AT 107 Hypothetical protein L. casei 96% - 4e-10 WP_003574536.1 _ _
121 AC/AT 105 Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) L. rhamnosus Lc 705 92% - 5e-08 YP_003174148.1 COG0131 [E] ko00340: Hystidine metabolism
122 AC/AT 102 Plasmid pNCD0151 L. casei 96% - 5e-23 Z50861.1 _ _
162 AT/AC 350 Calcineurin-like phosphoesterase family protein L. rhamnosus ATCC 8530 97% - 3e-70 YP_005872999.1 COG0737: 5′-nucleotidase/2′,3′-cyclic phosphodiesterase and related esterases [F] _
168 AT/AC 238 Plasmid pNCD0151 L. casei 98% - 1e-68 Z50861.1 _ _
170 AT/AC 222 Hypothetical protein L. rhamnosus GG 98% - 5e-34 YP_003171844.1 _ _
211 AT/AT 240 5S ribosomal RNA L. rhamnosus GG 98% - 2e-11 NR_103302.1 _ _
212 AT/AT 234 5S ribosomal RNA L. rhamnosus GG 98% - 4e-09 NR_103302.1 _ _
  1. aWhen available, EC numbers assigned to the putative enzymatic reactions are provided.
  2. bThe column indicates the microorganism of the best hit from BLASTX search.
  3. cMax identity and E-value from the best hit of BLASTX search are provided.
  4. dPathway assignment was performed according to COG functional categories and KEGG pathway database.
  5. eE, Amino acid transport and metabolism; F, Nucleotide transport and metabolism; G, Carbohydrate transport and metabolism; M, Cell wall/membrane/envelope biogenesis; R, General function prediction only.