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Open Access Research article

Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major

V S Gowri12, Indira Ghosh2, Amit Sharma3 and Rentala Madhubala1*

Author Affiliations

1 School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India

2 School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India

3 Structural and Computational biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India

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BMC Genomics 2012, 13:621  doi:10.1186/1471-2164-13-621

Published: 14 November 2012

Additional files

Additional file 1:

Table S1. Alternative splicing of aaRSs, aaRS paralogs, editing domains and other associated proteins in Promastigote stages in Leishmania major.

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Additional file 2:

Table S2. Distribution of aaRSs, aaRS paralogs, editing domains and other associated proteins in Leishmania and Trypanosoma. Organisms are Lm: L. major; Lbr: L. braziliensis; Lta: L. tarentolae; Lmx: L. mexicana; Lin: L. infantum; Tb427: T.brucei brucei427; Tb927: T. brucei brucei (TREU927); Tbg: T. brucei gambiense; TcEs: T.cruzi Esmeraldo; TcNEs: T. cruzi Non-Esmeraldo; Tcon: T. congolense; Tv: T. vivax.

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Additional file 3:

Figure S1. Secondary structure prediction of LmLeuRS showing the first 300 residues which includes the CP1 domain. The 35 residue N-terminal insertion in the CP1 domain is highlighted in yellow. The numerical values corresponds to the confidence levels (ranging from 0–9). H refers to Helix; C refers to Coil and E refers to Sheet.

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Additional file 4:

Figure S2. Sequence based phylogeny of tRNA_SAD domains (cis/trans) of alanyl tRNA synthetases constructed using MEGA v5.0 using Maximum Likelihood method based on JTT matrix model. Bootstrap values are indicated at the inner nodes.

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Additional file 5:

Figure S3. Sequence based phylogeny of prolyl tRNA synthetase editing domains (Ybak/ProX) constructed using MEGA v5.0 using Maximum Likelihood method based on JTT matrix model. Bootstrap values indicated at the inner nodes indicate the similarity of tethered editing domains of LmProRS to AlatRNAPro type editing domains (ProX) and the standalone editing domains of LmProRS to CystRNAPro type (Ybak).

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Additional file 6:

Figure S4. Sequence based phylogeny of D-tyrosine deacylases (Dtdas) from DTDA2_HUMAN (sp|Q96FN9); DTD2_MOUSE (sp|Q8BHA3); DTD2_DANRE (sp|Q68EL2); DTD1_ECOLI (1JKE); DTD2_HINF (1J7G); DTD1_AAQU (2DBO); DTD1_PFAL (3K05); DTD1_BOVIN (sp|Q2T9V8); DTD1_HUMAN (2OKV);GEK1_ARATH (sp|Q9ZPQ3); DTDA_PYRFU (sp|P58852); DTDA_PYRHO (sp|O57774); DTDA_PYRAB (sp|Q9V2R8) constructed using MEGA v5.0 using Maximum Likelihood method based on JTT matrix model. Bootstrap values are indicated at the nodes.

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Additional file 7:

Table S3. Distribution of aaRS sequences used for generation of HMMs for all the 21 aaRS from the Swissprot database in Bacteria, Archea, Eukaryotes and Virus is given in the table.

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