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Prediction and analysis of paralogous proteins in Trichomonas vaginalis genome.

Singh S, Singh G, Singh AK, Gautam G, Farmer R, Lodhi SS, Wadhwa G - Bioinformation (2011)

Bottom Line: It was speculated that a significant portion of the proteome contains paralogous proteins.In the present study about 50,000 proteins were searched where 2,700 proteins were found to be paralogous under the rigid selection criteria.The Pfam database search has identified significant number of paralogous proteins which were further categorized among different 1496 paralogous protein in pfam families, 1027 paralogous protein contains domain, 60 proteins were having different repeats and 1092 paralogous protein sequences of clans.

View Article: PubMed Central - PubMed

ABSTRACT
Trichomonas vaginalis causes trichomoniasis, second most sexually transmitted disease. The genome sequence draft of T. vaginalis was published by The Institute of Genomic Research reveals an abnormally large genome size of 160 Mb. It was speculated that a significant portion of the proteome contains paralogous proteins. The present study was aimed at identification and analysis of the paralogous proteins. The all against all search approach is used to identify the paralogous proteins. The dataset of proteins was retrieved from TIGR and TrichDB FTP server. The BLAST-P program performed all against all database searches against the protein database of Trichomonas vaginalis available at NCBI genome database. In the present study about 50,000 proteins were searched where 2,700 proteins were found to be paralogous under the rigid selection criteria. The Pfam database search has identified significant number of paralogous proteins which were further categorized among different 1496 paralogous protein in pfam families, 1027 paralogous protein contains domain, 60 proteins were having different repeats and 1092 paralogous protein sequences of clans. Such identification and functional annotation of paralogous proteins will also help in removing paralogous proteins from possible drug targets in future. Presence of huge number of paralogous proteins across wide range of gene families and domains may be one of the possible mechanisms involved in the T. vaginalis genome expansion and evolution.

No MeSH data available.


Related in: MedlinePlus

Pfam Clan predicted for paralogous proteins.
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Related In: Results  -  Collection


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Figure 2: Pfam Clan predicted for paralogous proteins.

Mentions: Some of significant protein families are Adeno_E4 (362), CDO_I (71),DUF1111 (357), PAT1 (75), VirE (339) followed by domains Alpha-2-MRAP_C (213), Pox_D5 (282), RNA_helicase (193), Lipid_DES (64),Ketoacyl-synt (92), Apolipoprotein (55) and significant repeats are PT (15),Collagen (44) Figure 1. Similarly some of significant predicted clan areCL0318 (356), CL0123 (280), CL0023 (209), CL0046 (92), CL0029 (79),CL0194 (19) and CL0044 (17) Figure 2. Some other clan also present but notin significant value are CL0028 (5), CL0219 (5), CL0125 (4), CL0236 (3),CL0281 (3), CL0020 (3), CL0063 (1), CL0119 (1), CL0072 (1), CL0183 (1)and CL0295 (1). Here we can clearly see the evidences of evolutionaryrelationship among paralogous protein in the form of sequence motifs, proteinfamilies, domain and repeats [12].


Prediction and analysis of paralogous proteins in Trichomonas vaginalis genome.

Singh S, Singh G, Singh AK, Gautam G, Farmer R, Lodhi SS, Wadhwa G - Bioinformation (2011)

Pfam Clan predicted for paralogous proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3064849&req=5

Figure 2: Pfam Clan predicted for paralogous proteins.
Mentions: Some of significant protein families are Adeno_E4 (362), CDO_I (71),DUF1111 (357), PAT1 (75), VirE (339) followed by domains Alpha-2-MRAP_C (213), Pox_D5 (282), RNA_helicase (193), Lipid_DES (64),Ketoacyl-synt (92), Apolipoprotein (55) and significant repeats are PT (15),Collagen (44) Figure 1. Similarly some of significant predicted clan areCL0318 (356), CL0123 (280), CL0023 (209), CL0046 (92), CL0029 (79),CL0194 (19) and CL0044 (17) Figure 2. Some other clan also present but notin significant value are CL0028 (5), CL0219 (5), CL0125 (4), CL0236 (3),CL0281 (3), CL0020 (3), CL0063 (1), CL0119 (1), CL0072 (1), CL0183 (1)and CL0295 (1). Here we can clearly see the evidences of evolutionaryrelationship among paralogous protein in the form of sequence motifs, proteinfamilies, domain and repeats [12].

Bottom Line: It was speculated that a significant portion of the proteome contains paralogous proteins.In the present study about 50,000 proteins were searched where 2,700 proteins were found to be paralogous under the rigid selection criteria.The Pfam database search has identified significant number of paralogous proteins which were further categorized among different 1496 paralogous protein in pfam families, 1027 paralogous protein contains domain, 60 proteins were having different repeats and 1092 paralogous protein sequences of clans.

View Article: PubMed Central - PubMed

ABSTRACT
Trichomonas vaginalis causes trichomoniasis, second most sexually transmitted disease. The genome sequence draft of T. vaginalis was published by The Institute of Genomic Research reveals an abnormally large genome size of 160 Mb. It was speculated that a significant portion of the proteome contains paralogous proteins. The present study was aimed at identification and analysis of the paralogous proteins. The all against all search approach is used to identify the paralogous proteins. The dataset of proteins was retrieved from TIGR and TrichDB FTP server. The BLAST-P program performed all against all database searches against the protein database of Trichomonas vaginalis available at NCBI genome database. In the present study about 50,000 proteins were searched where 2,700 proteins were found to be paralogous under the rigid selection criteria. The Pfam database search has identified significant number of paralogous proteins which were further categorized among different 1496 paralogous protein in pfam families, 1027 paralogous protein contains domain, 60 proteins were having different repeats and 1092 paralogous protein sequences of clans. Such identification and functional annotation of paralogous proteins will also help in removing paralogous proteins from possible drug targets in future. Presence of huge number of paralogous proteins across wide range of gene families and domains may be one of the possible mechanisms involved in the T. vaginalis genome expansion and evolution.

No MeSH data available.


Related in: MedlinePlus