Table 2

Partial phylogenetic profiling (PPP) results

Chlorobium luteolum

78186745

8

8

16

-16.124

NHLP

78186739

9

19

26

-13.212

Trans

78186738

9

22

29

-12.492

Trans-Cleave

78186736

8

16

17

12.045

Trans-Fuse

78187852

10

95

123

-7.475

(PAS domain)


Nostoc sp. PCC 7120

17229519

9

9

23

-18.140

NHLP

17229518

11

21

38

-16.662

NHLP

17229516

8

8

23

-16.124

NHLP

17233313

10

20

26

-14.927

Trans

17229512

10

20

26

-14.927

Trans

17229513

11

33

42

-13.969

Trans-Cleave

17233311

10

25

31

-13.698

Trans-Cleave

17229514

9

24

33

-12.080

Trans-Fuse

17233314

9

26

35

-11.709

Trans-Fuse

17228094

7

19

27

-9.451

(S-layer homol.)


Microscilla marina ATCC 23134

123986279

9

16

23

-14.108

Trans

123988060

9

21

28

-12.717

Trans-Cleave

123988059

7

10

14

-12.041

Trans-Fuse

123992175

8

29

54

-9.570

(HAMP domain)


Victivallis vadensis ATCC BAA-548

150259686

8

10

16

-14.479

Trans-Fuse

150259687

9

17

24

-13.784

Trans-Cleave

150259688

8

13

20

-13.033

Trans

150259679

6

6

15

-12.093

NHLP

150259681

5

6

8

-9.303

NHLP

150259680

4

4

6

-8.062

NHLP

150257768

10

88

119

-7.798

(GAF domain)


This table shows the results of PPP, where the profile contains 14 'YES' genomes having proteins recognized by TIGR03793, about 1% of genomes and 1437 'NO' genomes. PPP scores each protein by selecting a BLAST score cutoff that gives the best possible fit between YES genomes in the profile and the set of genomes in the BLAST hits list, then scoring the fit at that depth. Columns, from left to right, are gi number, number of YES genomes encountered at the optimal depth, the total number of genomes at that depth, and the number of proteins at that depth (which can differ from the total number of genomes because several proteins may come from the same genome), the PPP score (a negative logarithm from the binomial distribution), and the protein family abbreviation. As PPP scores are not corrected for taxonomic relationships between species, scores are for comparison within each genome only and are shown down to the first noise hit. Results are shown in boldface except for noise hits. Note: Microscilla marina ATCC 23134 contains the nitrile hydratase leader peptide (NHLP) protein, 123988058, which is not detected by PPP. This gene is found co-clustered with the transport proteins identified by PPP, as shown.

Haft et al. BMC Biology 2010 8:70   doi:10.1186/1741-7007-8-70

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