Data from: Comparative genomics of type VI secretion systems in strains of Pantoea ananatis from different environments

Shyntum DY, Venter SN, Moleleki LN, Toth IK, Coutinho TA

Date Published: February 28, 2014

DOI: http://dx.doi.org/10.5061/dryad.vd7k7

 

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Title Figure 11a. Alignment of representative Hcp proteins of Pantoea ananatis
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Description Alignment of all representative Hcp proteins encoded by strains of Pantoea ananatis. Hcp amino acid sequences were aligned in MEGA5 using ClustalW with default settings.
Download hcp alignment.meg (1.167 Kb)
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Title Additional file 12. Phylogenetic analysis of orphan Hcp proteins found in the genome sequence of sequenced strains of Pantoea ananatis
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Description This figure shows the evolutionary history of the Hcp proteins of Pantoea ananatis. Evolutionary history was inferred using the Maximum likelihood method based on the rtRev amino acid substitution model. The analysis includes mostly “orphan” Hcp proteins and some T6SS-related Hcp proteins from strains shown in the above figure. The different Hcp Groups (1 to 4) are shown in rectangles. The green and blue rectangles correspond to orphan Hcp proteins and type VI secretion system - associated Hcp proteins of Pantoea ananatis, respectively.
Download Additional file 12. Hcp phylogenetic tree.doc (46.59 Kb)
Download README.txt (802 bytes)
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Title Alignment of concatenated TssB and TssC sequences from different bacteria species
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Description TssBC alignment file contains alignments of the concatenated amino acid sequences of TssB and TssC proteins of bacteria whose genome sequences contain at least one type six secretion system gene cluster. The alignments were done in Mega5 using ClastalW.
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Title Figure 6. Evolutionary relationships of the different type VI secretion systems of Pantoea ananatis using concatenated TssB and TssC amino acid sequences.
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Description This figure shows the evolutionary history of the type VI secretion systems (T6SS) found in strains of Pantoea ananatis. Evolutionary history was inferred by using the Maximum Likelihood Method using the LG amino acid substitution model. The TssB/C homologs used in this study are indicated next to the name of the bacteria. Blue octagons represent T6SS phylogenetic Groups A-D proposed by Bingle et al. (2008). Representative position of PA T6SS-1 and PA T6SS-2 are shown in blue and green rectangles, respectively.
Download Fig 6. TssBC phylogenetic tree_2.doc (244.2 Kb)
Download README.txt (715 bytes)
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Title Additional file 8a. Alignment of the C-terminal amino acid sequences of RhsD proteins of Pantoea ananatis
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Description Additional file 8a contains an alignment of the amino acid sequences found on the C-terminal domain of RhsD proteins of Pantoea ananatis. The rhsD genes are found in the viscinity of vgrG genes located in the type VI secretion system-1 gene cluster of different strains of Pantoea ananatis. The Amino acid sequences from the DPIGL peptide motif which is conserved in Rhs homologs of other bacteria was used for the alignment. Alignments were done in MEGA5 using ClastalW with the default settings.
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Title Additional file 8b. Alignment of RhsI amino acid sequence of Pantoea ananatis.
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Description Additional file 8b: Alignment of the amino acid sequences of RhsI proteins located downstream of the the rhsD genes found in the viscinity of the type VI secretion system-1 gene cluster of different strains of Pantoea ananatis.
Download README.txt (376 bytes)
Download RhsI aligment.meg (1.799 Kb)
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When using this data, please cite the original publication:

Shyntum DY, Venter SN, Moleleki LN, Toth IK, Coutinho TA (2014) Comparative genomics of type VI secretion systems in strains of Pantoea ananatis from different environments. BMC Genomics 15:163. http://dx.doi.org/10.1186/1471-2164-15-163

Additionally, please cite the Dryad data package:

Shyntum DY, Venter SN, Moleleki LN, Toth IK, Coutinho TA (2014) Data from: Comparative genomics of type VI secretion systems in strains of Pantoea ananatis from different environments. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.vd7k7
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