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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0584

PubMed

23530958, BMC Microbiol. 2013 Mar 26;13:68. doi: 10.1186/1471-2180-13-68.

Characterization method

microarray

Genomic accession number

CP001834.1

Nucelotide position range

2317224-2332669

Substrate

melibiose

Loci

LLKF_2259-LLKF_2269

Species

Lactococcus lactis/1358

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

sucP LLKF_2259 ADA65829.1 0 - 1446 (-) CP001834.1:2317224-2318670 2.4.1.7
- LLKF_2260 ADA65830.1 1532 - 2360 (-) CP001834.1:2318756-2319584 -
- LLKF_2261 ADA65831.1 2372 - 3242 (-) CP001834.1:2319596-2320466 -
- LLKF_2262 ADA65832.1 3342 - 4587 (-) CP001834.1:2320566-2321811 -
- LLKF_2263 ABX75749.1 4736 - 5606 (+) CP001834.1:2321960-2322830 -
purH LLKF_2264 ABX75750.1 5677 - 7222 (-) CP001834.1:2322901-2324446 2.1.2.3, 3.5.4.10
galT LLKF_2265 ABX75751.1 7346 - 8831 (-) CP001834.1:2324570-2326055 2.7.7.10
galK LLKF_2266 ABX75752.1 8827 - 10018 (-) CP001834.1:2326051-2327242 2.7.1.6
aga LLKF_2267 ABX75753.1 10014 - 12231 (-) CP001834.1:2327238-2329455 3.2.1.22
galR LLKF_2268 ABX75754.2 12361 - 13399 (-) CP001834.1:2329585-2330623 -
fbp LLKF_2269 ABX75755.1 13523 - 15446 (-) CP001834.1:2330747-2332670 3.1.3.11

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

sucP 1 - 1446 (-) CAZyme: GH13|GH13_18 Yes
- 1533 - 2360 (-) TC: gnl|TC-DB|Q00751|3.A.1.1.28 Yes
- 2373 - 3242 (-) TC: gnl|TC-DB|Q00750|3.A.1.1.28 Yes
- 3343 - 4587 (-) TC: gnl|TC-DB|Q00749|3.A.1.1.28 Yes
- 4737 - 5606 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 Yes
purH 5678 - 7222 (-) other Yes
galT 7347 - 8831 (-) other Yes
galK 8828 - 10018 (-) other Yes
aga 10015 - 12231 (-) CAZyme: GH36 Yes
galR 12362 - 13399 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0044558 No
fbp 13524 - 15446 (-) CDS No

PUL ID

PUL0584

PubMed

23530958, BMC Microbiol. 2013 Mar 26;13:68. doi: 10.1186/1471-2180-13-68.

Title

Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.

Author

Bayjanov JR, Starrenburg MJ, van der Sijde MR, Siezen RJ, van Hijum SA

Abstract

BACKGROUND: Lactococcus lactis is used in dairy food fermentation and for the efficient production of industrially relevant enzymes. The genome content and different phenotypes have been determined for multiple L. lactis strains in order to understand intra-species genotype and phenotype diversity and annotate gene functions. In this study, we identified relations between gene presence and a collection of 207 phenotypes across 38 L. lactis strains of dairy and plant origin. Gene occurrence and phenotype data were used in an iterative gene selection procedure, based on the Random Forest algorithm, to identify genotype-phenotype relations. RESULTS: A total of 1388 gene-phenotype relations were found, of which some confirmed known gene-phenotype relations, such as the importance of arabinose utilization genes only for strains of plant origin. We also identified a gene cluster related to growth on melibiose, a plant disaccharide; this cluster is present only in melibiose-positive strains and can be used as a genetic marker in trait improvement. Additionally, several novel gene-phenotype relations were uncovered, for instance, genes related to arsenite resistance or arginine metabolism. CONCLUSIONS: Our results indicate that genotype-phenotype matching by integrating large data sets provides the possibility to identify gene-phenotype relations, possibly improve gene function annotation and identified relations can be used for screening bacterial culture collections for desired phenotypes. In addition to all gene-phenotype relations, we also provide coherent phenotype data for 38 Lactococcus strains assessed in 207 different phenotyping experiments, which to our knowledge is the largest to date for the Lactococcus lactis species.