Biology Reference
In-Depth Information
Table 9.4 Summary of globin distribution in fungal genomes
—
cont'd
Number
of
genomes
Globin
subfamilies
found
Taxon
Comments
Basidiomycota incertae
sedis
1
FHbs
Blastocladiomycota (BLA)
2
SSDgbs
Chytridiomycota (CHY)
3
SSDgb
TrHb1 in
Batrachochytrium
dendrobatidis
Glomeromycota
1
No globins
Fungi incertae sedis (FINS) 7
SDgbs and
SSDgbs
No globins in one
genome
Neocallimastigomycota
0
Microsporidia
12
No globins
Total number of genomes
238
Genomes with globins
203
as queries in BLASTP and TBLASTN (
Altschul et al., 1997; Schaffer et al.,
2001
) searches with pairwise alignment of the NCBI non-redundant protein
sequence and transcriptome databases (
www.ncbi.nlm.nih.gov/BLAST/
)
.
Putative sequences shorter than 100 residues were discarded and the remain-
ing sequences were subjected to a FUGUE search (
Shi, Blundell, &
Mizuguchi, 2001
;
www.cryst.bioc.cam.ac.uk
). FUGUE scans a database
of structural profiles, calculates the sequence-structure compatibility scores
for each entry, using environment-specific substitution tables and structure-
dependent gap penalties, and produces a list of potential homologs and align-
ments. FUGUE assesses the similarity between the query and a given
structure via the
Z
score, the number of standard deviations above the mean
score obtained by chance: the default threshold
Z
¼
6.0 corresponds to a
99% probability (
Shi et al., 2001
). We accepted all sequences identified as
globins, when the following three criteria were fulfilled: a FUGUE
Z
score
>
6, the occurrence of a His residue at position F8 and proper alignment of
helices BC through G. Non-globin domains in chimeric proteins were iden-
tified using CDD search (
Marchler-Bauer et al., 2005
) and InterProScan 4.8
(
Quevillon et al., 2005
).
