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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR24 IGR25 IGR23 IGR16 IGR17 IGR18 IGR15 IGR21 IGR19 IGR20 IGR22 HD0020 HD0018 HD0021 HD0019 yfeU, - HD0017 genX, - HD0029 dcuB, - HD0025 frdD, - HD0034 crcB, - HD0024 frdC, - HD0033 frdB, - HD0032 dapF, - HD0026 HD0023 frdA, - HD0030 HD0020 HD0018 HD0021 HD0019 yfeU, - HD0017 genX, - HD0029 dcuB, - HD0025 frdD, - HD0034 crcB, - HD0024 frdC, - HD0033 frdB, - HD0032 dapF, - HD0026 HD0023 frdA, - HD0030 yfeU, - HD0017 genX, - HD0029 dcuB, - HD0025 HD0022 HD0021 HD0019 HD0020 HD0018 HD0022 crcB, - HD0024 frdC, - HD0033 frdB, - HD0032 dapF, - HD0026 HD0023 frdA, - HD0030 frdD, - HD0034
* Calculated from Protein Sequence

Gene ID: HD0026

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
dapF  

Definition:
diaminopimelate epimerase, dapF

Gene Start:
26333

Gene Stop:
27172

Gene Length:
840

Molecular Weight*:
31002

pI*:
6.70

Net Charge*:
-1.87

EC:
5.1.1.7  

Functional Class:
Amino acid biosynthesis; Aspartate family  

Pathway: pathway table
Lysine biosynthesis

Secondary Evidence:
Richaud,C. and Printz,C.
Nucleotide sequence of the dapF gene and flanking regions from Escherichia coli K12.
Nucleic Acids Res. 16 (21), 10367 (1988)
Medline: 89057481

Comment:
From GenBank (gi:8247918): This protein catalyzes the reaction: LL-2,6-DIAMINOHEPTANEDIOATE = MESO-DIAMINOHEPTANEDIOATE, involved in the sixth step in the biosynthesis of lysine from aspartate semialdehyde.

Check start codon. Residue 6 (methionine) may be more accurate.

For other "dap" genes, see HD1107 (dapA), HD1398 (dapB), HD0630 (dapD), HD0642 (dapE).

Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to diaminopimelate epimerase proteins; e.g., residues 6-279 are 74% similar to DAPF_HAEIN [1169225], residues 6-279 are 67% similar to DAPF_ECOLI [8247918], and residues 5-277 are 64% similar to the sequence for diaminopimelate epimerase in Vibrio cholerae [9654526].

COGS Summary:  COGS Search
BeTs to 12 clades of COG0253
COG name: Diaminopimelate epimerase
Functional Class:  E
The phylogenetic pattern of COG0253 is amt--qvcebrhuj----inx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB001653 (Diaminopimelate epimerase) with a combined E-value of 2.8e-68.
    IPB001653A    8-20
    IPB001653B    41-51
    IPB001653C    68-84
    IPB001653D    117-128
    IPB001653E    158-180
    IPB001653F    190-200
    IPB001653G    217-228


ProDom Summary:  Protein Domain Search
Residues 6-279 are 74% similar to a (EPIMERASE DIAMINOPIMELATE ISOMERASE) protein domain (PD005029) which is seen in DAPF_HAEIN.



Paralogs:  Local Blast Search

HD0026 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 8 to 129 (E-value = 1.3e-46) place HD0026 in the DAP_epimerase family which is described as Diaminopimelate epimerase (PF01678)
Residues 156 to 272 (E-value = 3.5e-48) place HD0026 in the DAP_epimerase family which is described as Diaminopimelate epimerase (PF01678)

PDB Hit:
pdb|1BWZ|A Chain A, Diaminopimelate Epimerase From Hemophilus I... 432 3e-122
pdb|1BWZ|A Chain A, Diaminopimelate Epimerase From Hemophilus I... 517 5e-148

Gene Protein Sequence:
MIGNNMQFSKMHGLGNDFMVIDGVTQNVYLTEDMIRKLADRHYGVGFDQL
LLVEPPYDPELDFHYRIFNADGSEVAQCGNGARCFARFVSLKGLINRSDM
YVSTAKGKMVLTLVDEENVRVNMGEPIWEPAKIPFIANKFEKNYILRTDL
QTVLCGVVSMGNPHCVLQVDDIEQATVHQLGALLEKHHRFPERANVGFMQ
IIDRHHIKLRVFERGVGETKACGSGACAAVAVGIMQGVLDANVQVSLPGG
TLQIEWQGKGKPLYMTGTATHIYDGFIKL$

Gene Nucleotide Sequence:  Sequence Viewer
ATGATAGGAAATAATATGCAATTTTCAAAAATGCACGGGCTGGGTAATGA
CTTTATGGTGATTGATGGGGTAACACAGAATGTTTATTTGACAGAAGATA
TGATCCGTAAATTAGCAGATCGTCATTATGGAGTCGGTTTTGATCAATTG
TTACTTGTTGAGCCACCTTACGACCCAGAGCTTGATTTTCACTACCGTAT
TTTTAATGCAGATGGCAGTGAAGTTGCTCAATGTGGAAATGGCGCGCGTT
GTTTTGCCCGCTTCGTTAGTCTAAAGGGCTTAATTAATCGATCAGATATG
TATGTCAGTACTGCTAAAGGTAAAATGGTATTAACTTTAGTGGATGAAGA
AAATGTGCGGGTAAATATGGGAGAGCCGATTTGGGAACCGGCAAAAATTC
CATTTATTGCCAATAAATTTGAGAAAAACTACATTTTGCGTACTGATTTA
CAAACGGTGTTGTGCGGTGTTGTTTCGATGGGTAATCCGCATTGTGTGTT
ACAGGTGGACGATATTGAGCAAGCCACTGTACATCAGCTTGGTGCTTTAT
TAGAGAAACATCACCGCTTTCCCGAGCGGGCGAATGTTGGCTTTATGCAA
ATCATTGATCGCCATCATATTAAATTACGCGTGTTTGAACGTGGCGTAGG
TGAAACGAAGGCTTGTGGTAGTGGCGCTTGTGCTGCGGTTGCGGTTGGTA
TTATGCAAGGTGTACTAGATGCTAATGTGCAAGTTAGTTTGCCCGGCGGT
ACACTCCAAATTGAGTGGCAAGGCAAGGGTAAACCGCTTTATATGACAGG
CACGGCGACGCATATTTATGATGGATTTATTAAACTATAG


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