15671160, Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):3906-12. doi: 10.1073/pnas.0409188102. Epub 2005 Jan 25.

Characterization method

sequence homology analysis

Genomic accession number


Nucelotide position range







Lactobacillus acidophilus/1579

Degradation or Biosynthesis


Cluster number


Gene name

Gene position

Gene type

Found by CGCFinder?

epsI 1 - 1434 (-) TC: gnl|TC-DB|Q8KUK6|2.A.66.2.16 Yes
epsJ 1440 - 1952 (-) other Yes
- 2151 - 2552 (-) STP: STP|Pyr_redox Yes
- 2549 - 3844 (-) other Yes
- 3869 - 4909 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 4906 - 5562 (-) other Yes
- 5531 - 6052 (-) other Yes
- 6065 - 6946 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
epsF 6963 - 7736 (-) other Yes
epsE 7745 - 8398 (-) TC: gnl|TC-DB|H8E4X1|9.B.18.1.2 Yes
epsD 8488 - 9258 (-) other Yes
epsC 9261 - 10043 (-) TC: gnl|TC-DB|P39851|8.A.3.2.1 Yes
epsB 10059 - 10934 (-) TC: gnl|TC-DB|P72367|8.A.3.2.4 Yes
epsA 10956 - 12011 (-) CDS No




15671160, Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):3906-12. doi: 10.1073/pnas.0409188102. Epub 2005 Jan 25.


Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM.


Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, McAuliffe O, Souther N, Dobson A, Duong T, Callanan M, Lick S, Hamrick A, Cano R, Klaenhammer TR


Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism. In silico analyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus- and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota.