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Table 3 Unique genes in Hif KR494 in relative to Hib 10810, Rd Kw20 and NTHi 3655

From: Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f

Locusa

Function

G + Cb(%)

Homologue species

Similarity/Identityc(%)

USSd

Mobile elemente

RgDF/GifKR494

Capsule

  HifGL_000665- HifGL_000673

Serotype-f capsule biosynthesis locus

25.5

H. influenzae 700222 (type f)

100/99.0-100

-

-

RgDF1

Iron transport and metabolism

  HifGL_000676- HifGL_000685*

sap 2ABCDF

38.3

H. parainfluenzae ATCC 33392

94.0-100/87.0-96.0

4

Two class-LINE transposons (overlap with sap 2C and transposase HifGL_000684); two transposase (HifGL_000683, HifGL_000684); phage island at downstream

RgDF1

  HifGL_001444*

Iron Fe3+ ABC superfamily ATP binding cassette transporter

39.7

H. haemolyticus M21639

98.0/98.0

3

A class LINE/CR1 Transposon

-

  HifGL_001664*

Heme-binding protein HutZ

38.5

P. multocida HN06

98.0/99.0

-

-

-

Motility

       

  HifGL_000989- HifGL_000994*

Fimbriae aef 3abcdef

39.5

H. aegyptius ATCC 11116

62.0/52.0 (aef 3a), 89.0-99.0/84.0-99.0 (aef 3bcdef)

4

Flanked by two class LTR-Gypsy transposon (overlaps HifGL_000986) and transposase (HifGL_000996); phage island at downstream

RgDF3

Energy production and conversion

  HifGL_001349- HifGL_001358*

Rnf electron transport complex (soh B-rnf ABD)

39.8

H. haemolyticus M19501

91.0-100/85.0-100.0

12

Two identical direct repeats (41 bp) at HifGL_001351 and HifGL_001357; phage island at downstream

RgDF4

Glycerol transport and metabolism of glycerophospholipid f

  HifGL_000396- HifGL_000397 (subunit gene duplication in glp KFQT operon)

Glycerol kinase GlpK

41.6

H. influenzae PittGGf

99.0/99.0

-

-

-

Glycerol facilitator protein GlpF

43.6

H. influenzae PittGGf

99.0/99.0

-

-

-

Posttranslational modification, protein turnover, chaperones f

  HifGL_000630-HifGL_000632 (duplication of three-gene cluster)

Phosphoethanolamine transferase

31.6

H. influenzae NT127f

99.0/99.0

-

-

-

tRNA modification GTPase TrmE

39.7

H. influenzae NT127f

99.0/97.0

-

-

-

Peptidylprolyl isomerase

34.3

H. influenzae R3021f

99.0/99.0

-

-

-

Sugar and amino acid transport and metabolism f

  HifGL_000838- HifGL_000849 (a duplication of five-genes cluster)

Methyltransferase

37.4

H. influenzae R2866f

100/99.0

8

-

RgDF2

Glycerol-3-phosphate regulon repressor GlpR

29.3

Mannheimia succiniciproducens MBEL55E

83.0/60.0

 

Glycerol-3-phosphate regulon repressor GlpR

33.2

Aggregatibacter actinomycetemcomitans D11S-1

93.0/85.0

 

Putative carbohydrate diacid regulator

37.1

H. influenzae R3021f

99.0/99.0

 

Gluconate proton symporter

44.1

H. influenzae NT127f

100/100

 

Kanamycin resistance (KNTase protein)

  HifGL_000799*

DNA polymerase beta domain protein region

32.4

M. haemolytica PHL213

77.0/63.0

-

-

-

  HifGL_000800*

Nucleotidyltransferase substrate binding protein

30.7

M. haemolytica PHL213

81.0/64.0

-

-

-

Replication, recombination and repair

  HifGL000956

DNA-damage-inducible protein J, negative regulator of translation

35.1

H. influenzae biogroup aegytptius F3031 (BPF)

98.0/97.0

-

-

-

  HifGL001635*

Type II restriction enzyme HinfI

27.4

H. influenzae Rf (type f)

100/100

-

-

RgDF6

  HifGL001636*

Adenine-specific methyltransferase HinfI

32.5

H. influenzae Rf (type f)

100/100

-

-

RgDF6

Unknown function hydrolase

  HifGL_000176*;

Cell wall-associated hydrolase

~48.0-49.0

H. haemolyticus M21639

100/100

-

Three transposons LINE/R2, LINE/R1 and LTR/Copia

GifKR494-2

  HifGL_000233;

GifKR494-8

  HifGL_001417;

GifKR494-14

  HifGL_001593;

GifKR494-17

  HifGL_001616;

GifKR494-19

  HifGL_001665

GifKR494-22

Trimeric autotransporter of unknown function

  HifGL_000054

Putative YadA-like protein

43.3

H. haemolyticus M19107

83.0/ 77.0

-

-

-

  HifGL_000835

Hep_Hag family protein

43.5

Neisseria mucosa ATCC 25996

63.0/ 45.0

-

-

-

  HifGL_000837*

Putative target SNARE coiled-coil domain-containing protein

37.9

H. haemolyticus M19501

83.0/ 75.0

1

-

-

  HifGL_000844

Putative YadA-like protein

40.3

H. haemolyticus M19501

99.0/ 99.0

1

-

-

  HifGL_001158

Hep_Hag superfamily protein

32.9

H. aegyptius ATCC 11116

97.0/ 85.0

-

-

-

HifGL_001217

Trimeric autotransporter adhesin

37.4

H. influenzae biogroup aegytptius F3031 (BPF)

86.0/ 83.0

-

-

-

  HifGL_001431*

Trimeric autotransporter adhesin

40.7

H. influenzae biogroup aegytptius F3047

86.0/ 80.0

1

-

-

  HifGL_001626

YadA/hemagluttinin like protein

40.8

H. aegyptius ATCC 11116

88.0/84.0

-

-

RgDF6

Other metabolic genes

  HifGL000310*

Glutathione S-transferase domain-containing protein

40.8

Actinobacillus ureae ATCC 25976

98.0/99.0

-

-

-

  HifGL000957

Addiction module antitoxin/rele toxin-like protein, plasmid stabilization system

33.3

H. haemolyticus M21127

100/98.0

-

-

-

  HifGL001004

Phospholipase/carboxylesterase

33.1

A. succinogenes 130Z

89.0/79.0

-

-

-

  HifGL001672*

Putative lipoprotein

33.8

H. haemolyticus M19501

95.0/93.0

-

-

-

  1. aUnique CDS of hypothetical proteins and phage products are not included.
  2. bAverage G + C content is presented for single locus or as an average value of the indicated loci cluster or operon.
  3. cProtein sequence similarity and identity (over the complete protein length) is presented in percentage as individual value for single CDS or as range of value for clustered CDSs.
  4. dHaemophilus influenzae uptake signal sequence (USS) (AAGTGCGGT).
  5. eMobile elements include phage island, transposase, tandem repeats and transposons. Transposon sequences and transposase, respectively, were predicted based on transposon database using softwares of RepeatMasker and RepeatProteinMask (http://www.repeatmasker.org/). Tandem repeat sequences were predicted by using Tandem Repeat Finder (http://tandem.bu.edu/trf/trf.html). Prophage islands were predicted using Prohinder software and ACLAME database (http://aclame.ulb.ac.be/), thereafter we performed BLAST comparison (standalone BLAT v.34) between KR494 genome and prophage database.
  6. fThese genes that exist in the Hif KR494 genome as a two-copy number resulted in unusual allelic duplication in the Hif KR494 genome. Despite these genes were considered unique in KR494 when compared to Hib 10810, Rd Kw20 and NTHi 3655, they also shared homology with NTHi PittGG, NT127, R3021 and R3866 that were not included as reference strains in the present study.
  7. *Target single locus or contiguous loci assessed in gene distribution studies (Table 5).
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BMC Genomics

ISSN: 1471-2164

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