Systematic search for putative new domain families in Mycoplasma gallisepticum genome.
BACKGROUND
Protein domains are the fundamental units of protein structure, function and evolution. The delineation of different domains in proteins is important for classification, understanding of structure, function and evolution. The delineation of protein domains within a polypeptide chain, namely at the genome scale, can be achieved in several ways but may remain problematic in many instances. Difficulties in identifying the domain content of a given sequence arise when the query sequence has no homologues with experimentally determined structure and searching against sequence domain databases also results in insignificant matches. Identification of domains under low sequence identity conditions and lack of structural homologues acquire a crucial importance especially at the genomic scale.


RESULTS
We have developed a new method for the identification of domains in unassigned regions through indirect connections and scaled up its application to the analysis of 434 unassigned regions in 726 protein sequences of Mycoplasma gallisepticum genome. We could establish 71 new domain relationships and probable 63 putative new domain families through intermediate sequences in the unassigned regions, which importantly represent an overall 10% increase in PfamA domain annotation over the direct assignment in this genome.


CONCLUSIONS
The systematic analysis of the unassigned regions in the Mycoplasma gallisepticum genome has provided some insight into the possible new domain relationships and putative new domain families. Further investigation of these predicted new domains may prove beneficial in improving the existing domain prediction algorithms.
Reddy
Chilamakuri Cs
CC
Université de La Réunion, Equipe de Bioinformatique, Laboratoire de Biochimie et Génétique Moléculaire, 15 ave René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France. bernard.offmann@univ-reunion.fr.
Rani
Sane Sudha
SS
Offmann
Bernard
B
Sowdhamini
R
R
J Mol Biol. 1995 Apr 7;247(4):536-40
7723011
Science. 1991 May 24;252(5009):1162-4
2031185
Protein Sci. 1995 Mar;4(3):506-20
7795532
Microbiology (Reading). 2003 Sep;149(Pt 9):2307-2316
12949158
Bioinformatics. 2000 Apr;16(4):404-5
10869041
Bioinformatics. 2001 Sep;17(9):849-50
11590105
Mol Biol Evol. 1987 Jul;4(4):406-25
3447015
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D173-80
16381840
Nucleic Acids Res. 2002 Jan 1;30(1):281-3
11752315
In Silico Biol. 2006;6(5):351-62
17274764
Bioinformatics. 1998;14(9):755-63
9918945
Mol Biol Evol. 2007 Aug;24(8):1596-9
17488738
Structure. 1997 Aug 15;5(8):1093-108
9309224
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
7984417
Trends Biochem Sci. 1996 Nov;21(11):425-6
8987397
BMC Bioinformatics. 2008 Jun 14;9:281
18554415
Nat Struct Biol. 1998 Jan;5(1):15-9
9437423
Nat Struct Biol. 2001 Nov;8(11):953-7
11685241
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51
16381856
J Mol Biol. 1994 Jan 7;235(1):13-26
8289237
J Mol Biol. 1997 Oct 17;273(1):349-54
9367767
Nucleic Acids Res. 1998 Jan 1;26(1):320-2
9399864
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694