View source for Evolution for haloacid dehalogenase-like hydrolase domain containing 2

Whole sequence alignment
                        <nowiki>                                         Score    E
Sequences producing significant alignments:                      (bits) Value

gb|AAH58177.1| Haloacid dehalogenase-like hydrolase domain conta...   462   e-128
ref|NP_084102.1| haloacid dehalogenase-like hydrolase domain con...   462   e-128
dbj|BAE28142.1| unnamed protein product [Mus musculus]                460   e-128
pdb|2HO4|A Chain A, Crystal Structure Of Protein From Mouse Mm.2...   453   e-126
ref|NP_001014173.1| hypothetical protein LOC361351 [Rattus norve...   446   e-124
ref|XP_537270.1| PREDICTED: similar to haloacid dehalogenase-lik...   437   e-121
ref|NP_001030194.1| haloacid dehalogenase-like hydrolase domain ...   426   e-118
ref|XP_001148863.1| PREDICTED: haloacid dehalogenase-like hydrol...   424   e-117
emb|CAH93402.1| hypothetical protein [Pongo pygmaeus]                 424   e-117
ref|NP_115500.1| haloacid dehalogenase-like hydrolase domain con...   421   e-116
ref|XP_001086150.1| PREDICTED: similar to haloacid dehalogenase-...   418   e-115
ref|XP_001086254.1| PREDICTED: similar to haloacid dehalogenase-...   413   e-114
dbj|BAB22395.1| unnamed protein product [Mus musculus]                410   e-113
ref|XP_414700.2| PREDICTED: hypothetical protein [Gallus gallus]      390   e-107
gb|AAS66213.1| LRRG00122 [Rattus norvegicus]                          389   e-107
ref|NP_001013491.1| hypothetical protein LOC541346 [Danio rerio]...   371   e-101</nowiki>

gi:14149777 is human version.


Phylogenetic tree from CLUSTALX


[[Image:tree.jpg]]


Phylogenetic tree from PHYLIP

[[Image:treep.jpg]]

Phylogenetic tree from PHYLIP - by species

[[Image:treetrans.jpg]]


BLAST for first 100 nucleotides

  <nowiki>  Score     E
Sequences producing significant alignments:                       (Bits)  Value

gi|114794442|pdb|2HO4|A  Chain A, Crystal Structure Of Protein...   175    8e-43 
gi|34849757|gb|AAH58177.1|  Haloacid dehalogenase-like hydrola...   174    2e-42 
gi|21313310|ref|NP_084102.1|  haloacid dehalogenase-like hydro...   172    4e-42 
gi|74190684|dbj|BAE28142.1|  unnamed protein product [Mus musculu   172    4e-42 
gi|78042510|ref|NP_001030194.1|  haloacid dehalogenase-like hy...   167    1e-40 
gi|57089151|ref|XP_537270.1|  PREDICTED: similar to haloacid d...   167    1e-40 
gi|12833114|dbj|BAB22395.1|  unnamed protein product [Mus musculu   167    2e-40 
gi|75040931|sp|Q5R4B4|HDHD2_PONPY  Haloacid dehalogenase-like ...   162    4e-39
gi|62079029|ref|NP_001014173.1|  hypothetical protein LOC36135...   162    7e-39 
gi|114673047|ref|XP_001148863.1|  PREDICTED: haloacid dehaloge...   161    9e-39 
gi|85861235|ref|NP_001034291.1|  haloacid dehalogenase-like hy...   159    4e-38 
gi|14149777|ref|NP_115500.1|  haloacid dehalogenase-like hydro...   159    6e-38 
gi|114673057|ref|XP_001148387.1|  PREDICTED: haloacid dehaloge...   158    9e-38 
gi|109122087|ref|XP_001086150.1|  PREDICTED: similar to haloac...   155    8e-37 
gi|109092050|ref|XP_001088800.1|  PREDICTED: similar to haloac...   154    1e-36</nowiki>


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BLAST search for whole sequence turns out a high number of similar matches. Top few matches were used to generate a phylogenetic tree.

Both phylogenetic trees from CLUSTALX and PHYLIP both show similar results with PHYLIP being known as the more accurate version for study. 

It is not suprising that the closest related to the human is the chimpanzee's gene and orangutan. It has long been known that these are the two closest related animals to humans and so this result is to be expected. The suprising result is for the mouse genes. There are 4 genes all closely related and branching off with 3 being off the same branch with slight differences. All the mouse genes are similar with the top one a confirmed and studied example and subsequent genes all showing very close matches. With the high degree of nucleotide match and studied and identified genes of many species it is arguable that the genes labeled as "predicted" and "hypothetical" are of that function. The mouse gene seems to be the genes closest to the ancestorial gene with the identified and yet studied forms.

BLAST search for first 100 nucleotides is run to determine the degree of conservance between strains. Values were much lower indicating less matches but the matches were still very much the same types of proteins. This suggests that the first 30 odd amino acids do vary a bit between different species.