Table 3

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

aWhen available, EC numbers assigned to the putative enzymatic reactions are provided.

bThe column indicates the microorganism of the best hit from BLASTX search.

cMax identity and E-value from the best hit of BLASTX search are provided.

dPathway assignment was performed according to COG functional categories and KEGG pathway database.

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.

Lazzi et al.

Lazzi et al. BMC Microbiology 2014 14:28   doi:10.1186/1471-2180-14-28

Open Data