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Results: 6

1.
Fig. 6

Fig. 6. From: Group-specific comparison of four lactobacilli isolated from human sources using differential blast analysis.

Differences in e-value distribution between the four lactobacilli of human origin when compared to the two custom databases dbLB and dbLAB. Based on the best BlastP hit, similarities were grouped within the assigned e-value ranges. Solid bars represent results for the custom Lactobacillus database dbLB (a) and the custom LAB database dbLAB (b). E-value ranges correspond to trust level intervals described in Table 2 (color figure online)

Eric Altermann, et al. Genes Nutr. 2011 August;6(3):319-340.
2.
Fig. 5

Fig. 5. From: Group-specific comparison of four lactobacilli isolated from human sources using differential blast analysis.

Protein similarity and genome synteny of four Lactobacillus genomes pACT were used to simultaneously analyze four complete genomes on amino acid level. Double lines featuring pointed boxes indicate predicted ORFs in their respective orientation. Red and blue lines in between the genomes represent amino acid similarities between ORFs below the selected threshold. Red lines show direct alignments, whereas blues lines depict inversions. The threshold was set to 1e-70 and only hits with a more significant e-value are indicated (reprinted from [37]) (color figure online)

Eric Altermann, et al. Genes Nutr. 2011 August;6(3):319-340.
3.
Fig. 4

Fig. 4. From: Group-specific comparison of four lactobacilli isolated from human sources using differential blast analysis.

Phylogenetic tree of cell-envelop proteinases (CEP) of selected LAB. Deduced amino acid sequences of CEPs identified in other LAB were aligned using ClustalW [42], and the phylogenetic tree was calculated and visualized using Mega3.1 [40]. The evolutionary history was inferred using the neighbor-joining method [59]. The evolutionary distances were computed using the Poisson correction method [73] and are in the units of the number of amino acid substitutions per site. Protein names and respective organisms are indicated on the phylogenetic tree (color figure online)

Eric Altermann, et al. Genes Nutr. 2011 August;6(3):319-340.
4.
Fig. 2

Fig. 2. From: Group-specific comparison of four lactobacilli isolated from human sources using differential blast analysis.

Schematic representation of a pACT analysis of two homologous genome regions in L. johnsonii NCC533 (upper panel) and L. acidophilus NCFM (lower panel). Genomes are indicated by the black horizontal lines (not to scale). Predicted ORFs are shown as red (cluster 1), green (cluster 2), and cyan (cluster 3) arrows. ORF numbers are indicated within the arrows. Gray arrows represent ORFs with no similarity to the corresponding ORFs at the respective genome location of the other genome. Alignments were created and similarity scores were calculated as described. Blue vertical bars indicate a level of similarity below an e-value of 1e-80. Predicted terminator and promoter structures between ORFs Ljo733 and Ljo732 are indicated by gray inverted triangles and a gray arrow, respectively (color figure online)

Eric Altermann, et al. Genes Nutr. 2011 August;6(3):319-340.
5.
Fig. 3

Fig. 3. From: Group-specific comparison of four lactobacilli isolated from human sources using differential blast analysis.

Potential autonomous units identified in LAB. Alignment of previously described and newly identified PAUs in L. acidophilus NCFM, L. johnsonii NCC533, Lactococcus lactis ssp. cremoris SK11, and Streptococcus agalactiae NEM316. Elements of the core region are shown as colored arrows: DNA segregation ATPase FtsK, red arrow; replication protein RepA, green arrow; Integrase IntG, pink arrow; conserved hypothetical ORFs, orange and cyan arrows, respectively. Flanking ORFs with predicted functions are displayed in light gray arrows. Different functional classes are indicated by distinct pattern. Adjacent ORFs with no functional characterization are indicated by solid gray arrows. Predicted tRNAs are displayed as vertical cyan boxes. Alignments are centered on the start position of IntG and are drawn to scale (color figure online)

Eric Altermann, et al. Genes Nutr. 2011 August;6(3):319-340.
6.

Fig. 1. From: Group-specific comparison of four lactobacilli isolated from human sources using differential blast analysis.

Comparative DBA analysis of four Lactobacillus genomes. The atlases each represent a circular view of the complete genome sequences of L. acidophilus NCFM (a), L. johnsonii NCC533 (b), L. gasseri ATCC33323 (c), and L. plantarum WCFS1 (d), respectively. The right-hand legend describes the single circles in the top-down- outermost-innermost direction. The circle was created using Genewiz and in-house developed software. Innermost circle 1, GC-Skew. Circle 2, COG classification. Predicted ORFs were analyzed using the COG database and grouped into the 4 major categories. 1, Information storage and processing; 2, Cellular processes and signaling; 3, Metabolism; 4, Poorly characterized; and 5, ORFs with uncharacterized COGs or no COG assignment. Circle 3, ORF orientation. ORFs in sense orientation (ORF +) are shown in blue; ORFs oriented in anti-sense direction (ORF −) in red. Circle 4, G+C content deviation. Deviations from the average GC content are shown in either green (low GC spike) or orange (high GC spike). A boxfilter was applied to visualize contiguous regions of low or high deviations. Circles 5 and 6, Blast similarities, using LAB and Lactobacillus custom databases, respectively. Deduced amino acid sequences compared against the respective database using gapped BlastP [7]. Regions in blue represent unique proteins in NCFM, whereas highly conserved features are shown in red. The degree of color saturation corresponds to the level of similarity. Circle 7, DBA analysis. Predicted ORFs present in at least one member of the Lactobacillus database (dbLB), but not equally conserved in any member of the LAB database (dbLAB) are highlighted in green. Geneproducts present in at least one member of the LAB database, but not equally conserved in any member of the Lactobacillus database are highlighted in red. Features described in more detail are indicated by trapezoids in the corresponded color and roman numbers. Black trapezoids represent unique genome regions, either not found in any custom database or otherwise outstanding within the genome (color figure online)

Eric Altermann, et al. Genes Nutr. 2011 August;6(3):319-340.

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