Basic Search | Intermediate Search | Advanced SQL Search | Gene Image Map |  Home

Treponema pallidum Search Results

Record: 1 of 1  
MiniMap IGR298 IGR296 IGR297 IGR302 IGR301 IGR300 IGR299 IGR303 TP0405 TP0404 TP0409 fliJ, - TP0403 TP0407 murI, - TP0406 fliH, - TP0401 fliI, - TP0402 secD, - TP0410 TP0408 TP0405 TP0404 TP0409 fliJ, - TP0403 TP0407 murI, - TP0406 fliH, - TP0401 fliI, - TP0402 secD, - TP0410 TP0408 Type: tandem, Name:  - 97 TP0404 TP0405 TP0409 fliJ, - TP0403 TP0407 murI, - TP0406 fliH, - TP0401 fliI, - TP0402 secD, - TP0410 TP0408
* Calculated from Protein Sequence

Gene ID: TP0407

DNA Molecule Name:
1  

Genbank ID:
3322689

Gene Name:


Definition:
possible halo acid dehalogenase

Gene Start:
430960

Gene Stop:
431631

Gene Length:
672

Molecular Weight*:
25501

pI*:
11.58

Net Charge*:
17.44

EC:
3.-.-.-  

Functional Class:
Uncategorized  

Pathway: pathway table
Miscellaneous Enzymes

Comment:
TP0407 was assigned the EC number, 3.-.-.- during our initial annotation of the Treponema genome. Comparison of our annotation with the annotation done by KEGGs leads us to re-examine this protein.

Looking at the results of gapped BLAST, focusing only on Swiss-Prot sequences, we observed several significant hits to DEH proteins, HAD proteins, and GPH proteins.

DEH (heloacetate dehalogenase) entries in Swiss-Prot are gaven the EC numbers 3.8.1.3. HAD (2-haloacid dehalogenase) entries in Swiss-Prot are gaven the EC numbers 3.8.1.2. GPH (phosphoglycolate phosphatase) entries in Swiss-Prot are gaven the EC numbers 3.1.3.18.

COGs analysis indicates TP407 belongs to a family of predicted phosphatases. The clustalw guide tree and phylogenetic tree didn't clearly indicate which group TP0407 belongs to.

The difference in annotation between the STD database and the KEGG database for TP0407 will remain unresolved until further data is available.


Blast Summary:  PSI-Blast Search
Gapped BLAST revealed the middle and C-terminal region has several
significant hits to hypothetical proteins and to a few haloacid
dehalogenases and phosphoglycolate phosphatases. For example residues
89-191 are 31% similar to L-2-halo acid dehalogenase of Pseudomonas sp.,
(S74078) and residues 95-187 are 35% similar to phosphoglycolate
phosphatase of Rhodobacter sphaeroides,(U67781). Four iterations of
PSI-BLAST brought many more 2-haloacid dehalogenase into the list and
showed they were the top 10 hits. For example residues 1-223 are 24%
similar to L-2-halo acid dehalogenase of Pseudomonas sp.,(S74078).

COGS Summary:  COGS Search
BeTs to 8 clades of COG0546
COG name: Predicted phosphatases
Functional Class:  R
The phylogenetic pattern of COG0546 is a-TkyQ-CEBRhuj--oL---
Number of proteins in this genome belonging to this COG is 2

Blocks Summary:  Blocks Search
None.

ProDom Summary:  Protein Domain Search
Residues 1-192 are 28% similar to YIGB_ECOLI, a hypothetical protein
of E. coli.

Paralogs:  Local Blast Search
This protein is paralogously related to TP0554, a predicted
phosphoglycolate phosphatase. Residues 95-185 are 32% similar to
TP0554.

Pfam Summary:  Pfam Search
Residues 1 to 192 (E-value = 2.7e-24) place TP0407 in the Hydrolase family which is described as haloacid dehalogenase-like hydrolase (PF00702)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
1  
90

PDB Hit:
gi|1942967|pdb|1JUD| L-2-Haloacid Dehalogenase Dehalogenase, Hydrolase Mol_id: 1; Molecule: L-2-Haloacid Dehalgenase; Chain: Null; Ec: 3.8.1.2; Engineered: Yes

Gene Protein Sequence:
MAFDIDGTLYPGWRLALRVMPFMIRNARLMRAFRAVRQELRREQRTALIP
FEDFFFAQATRIAPRVGLSAEEVRAFLDTALYRGWRRHFLHIKPFPHVLS
SVLELRRHGLKIALLSDFPPSQKGCLWGVRALCDVTLGTEEIGSLKPSPR
AFYALAQRLNLRCEEILYVGNSVHDVEGAHAAGMRIACVRRPFTSLRVRR
TRGLALFRLSHIVRICDSMSAGAG

Gene Nucleotide Sequence:  Sequence Viewer
GTGGCCTTTGACATTGATGGGACACTGTACCCTGGATGGCGCCTTGCACT
GCGTGTTATGCCCTTTATGATTCGCAATGCGCGCTTGATGCGTGCGTTCC
GTGCGGTGCGTCAGGAGYTACGTCGTGAGCAACGTACGGCACTTATTCCT
TTTGAAGACTTTTTTTTTGCGCAAGCTACGCGCATCGCGCCGCGCGTGGG
TTTATCTGCAGAAGAAGTGCGAGCCTTCCTCGACACAGCGCTGTATCGGG
GGTGGAGGCGTCACTTTTTACATATAAAGCCATTTCCTCACGTGCTTTCC
TCGGTGTTGGAGCTGAGGCGGCATGGGCTGAAGATAGCGCTTTTGTCGGA
TTTTCCTCCGAGTCAGAAAGGCTGTCTATGGGGGGTGCGCGCGTTGTGCG
ATGTAACGTTGGGCACAGAGGAGATTGGGTCCCTCAAGCCTTCTCCCCGG
GCCTTTTACGCGCTGGCGCAGAGACTGAATCTGCGCTGTGAAGAAATTCT
TTACGTGGGGAACAGTGTTCATGACGTGGAAGGCGCGCACGCAGCAGGTA
TGAGGATTGCCTGTGTGCGCAGGCCCTTTACGAGTCTTCGCGTTCGGCGC
ACGCGCGGACTGGCTCTTTTCCGACTATCGCACATTGTGCGCATATGTGA
TAGCATGAGCGCCGGCGCAGGG


Los Alamos National Laboratory     
Operated by the University of California for the National Nuclear Security Administration,
of the US Department of Energy.     Copyright © 2001 UC | Disclaimer/Privacy