Horizontal Transfer of Archaeal Genes into the Deinococcaceae: Detection by Molecular and Computer-Based Approaches
Lorraine Olendzenski, Lei Liu, Olga Zhaxybayeva, Ryan Murphey, Dong-Guk Shin, and J. Peter Gogarten
This page is a supplement to the article published in
J.Mol.Evol
(2000)
51
: 587-599
[PubMed]
Table 1.
ORFs ranked according to the difference
max(HSP Eukaryotes, HSP Archaea) -max(HSP Bacteria).
ORF_ID
Aligned homologs (1)
NJ tree of (1)
Pruned dataset (2)
NJ tree of (2)
PUZZLE tree
PUZZLE outfile
gdr_66_ORF1.17
X
X
-
-
-
-
gdr_66_ORF0.13
X
X
-
-
-
-
gdr_80_ORF3.7
X
-
-
-
X
X
gdr_12_ORF1.14
X
X
-
-
X
X
gdr_240_ORF4.3
X
X
-
-
X
X
gdr_36_ORF2.6
X
X
-
-
X
X
gdr_95_ORF4.11
X
X
-
-
X
X
gdr_125_ORF3.8
X
X
-
-
X
X
gdr_19_ORF3.57
X
X
-
-
X
X
gdr_23_ORF4.32
X
X
-
-
X
X
gdr_66_ORF2.12
X
X
-
-
-
-
gdr_31_ORF4.25
X
X
-
-
X
X
gdr_114_ORF1.2
X
X
-
-
-
-
gdr_39_ORF4.40
X
X
-
-
X
X
gdr_121_ORF0.7
X
X
-
-
X
X
gdr_21_ORF4.16
X
X
-
-
X
X
gdr_18_ORF3.4
X
X
X
X
X
X
gdr_95_ORF3.11
X
X
-
-
X
X
gdr_119_ORF5.16
X
X
X
X
X
X
gdr_85_ORF1.8
X
X
X
X
X
X
gdr_66_ORF5.7
X
X
-
-
X
X
gdr_104_ORF0.3
X
X
X
X
X
X
gdr_104_ORF2.2
-
-
-
-
-
-
gdr_66_ORF0.17
X
X
-
-
X
X
gdr_122_ORF4.1
X
X
-
-
X
X
gdr_209_ORF3.4
X
X
X
X
X
X
gdr_54_ORF0.15
X
X
X
-
X
X
gdr_218_ORF0.5
X
X
-
-
X
X
gdr_6_ORF5.20
X
-
-
-
-
-
gdr_19_ORF4.49
X
X
-
-
X
X
gdr_171_ORF4.5
X
X
X
-
X
X
gdr_189_ORF2.5
X
X
-
-
X
X
gdr_129_ORF4.3
X
X
-
-
-
-
gdr_44_ORF2.20
X
X
-
-
X
X
gdr_125_ORF4.4
X
X
-
-
X
X
gdr_240_ORF5.1
X
X
-
-
X
X
gdr_50_ORF4.4
X
-
-
-
-
-
gdr_282_ORF3.1
X
X
-
-
X
X
gdr_7_ORF4.17
X
X
-
-
X
X
gdr_5_ORF2.46
X
-
-
-
-
-
gdr_159_ORF3.2
X
X
-
-
X
X
gdr_70_ORF2.13
X
X
-
-
X
X
gdr_164_ORF4.3
X
X
-
-
X
X
gdr_39_ORF5.22
X
X
X
X
X
X
gdr_66_ORF2.10
X
X
-
-
X
X
Table 2. Putative frequently transferred ORFs.
ORF_ID
Aligned homologs (1)
NJ tree of (1)
Pruned dataset (2)
NJ tree of (2)
PUZZLE tree
PhyloWin tree with pairwise gap removal
PhyloWin tree with global gap removal
gdr_49_ORF2.1
X
X
-
-
X
X
X
gdr_164_ORF3.2
X
X
X
X
X
X
X
gdr_121_ORF0.9
X
X
-
-
-
-
-
gdr_5_ORF0.3
X
X
-
-
X
X
X
gdr_118_ORF3.15
X
X
-
-
X
-
-
gdr_12_ORF4.6
X
X
-
-
X
X
X
gdr_170_ORF1.15
X
X
-
-
-
-
-
gdr_191_ORF2.25
X
X
-
-
-
-
-
gdr_22_ORF0.11
X
X
-
-
-
-
-
gdr_136_ORF3.8
X
X
-
-
-
X
X
gdr_83_ORF2.9
X
X
-
-
X
X
X
gdr_43_ORF2.11
X
X
-
-
X
X
X
gdr_204_ORF0.1
X
X
-
-
-
X
X
gdr_46_ORF0.9
X
X
-
-
-
X
X
gdr_165_ORF2.3
X
X
-
-
-
X
X
gdr_225_ORF5.1
X
X
-
-
-
X
X
gdr_63_ORF2.15
X
-
-
-
-
X
X
The alignments and the trees might be viewed with the following freeware programs:
ClustalX
TreeView