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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR29 IGR24 IGR25 IGR23 IGR27 IGR30 IGR28 IGR31 IGR26 IGR22 genX, - HD0029 thdF, - HD0039 yidC, - HD0040 HD0035 frdD, - HD0034 frdC, - HD0033 HD0038 frdB, - HD0032 lysA, - HD0036 frdA, - HD0030 hemN, - HD0037 genX, - HD0029 thdF, - HD0039 yidC, - HD0040 HD0035 frdD, - HD0034 frdC, - HD0033 HD0038 frdB, - HD0032 lysA, - HD0036 frdA, - HD0030 hemN, - HD0037 genX, - HD0029 thdF, - HD0039 yidC, - HD0040 HD0035 frdC, - HD0033 HD0038 frdB, - HD0032 lysA, - HD0036 frdA, - HD0030 hemN, - HD0037 frdD, - HD0034
* Calculated from Protein Sequence

Gene ID: HD0036

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
lysA  

Definition:
diaminopimelate decarboxylase, lysA

Gene Start:
32171

Gene Stop:
33484

Gene Length:
1314

Molecular Weight*:
48167

pI*:
6.60

Net Charge*:
-4.17

EC:
4.1.1.20  

Functional Class:
Amino acid biosynthesis; Aspartate family  

Pathway: pathway table
Lysine biosynthesis

Secondary Evidence:
Stragier,P., Danos,O. and Patte,J.C.
Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. II. Nucleotide sequence of the lysA gene and its regulatory region.
J. Mol. Biol. 168 (2), 321-331 (1983)
Medline: 83294516.

Comment:
From GenBank (gi:1169235): In H.influenzae, this protein catalyzes the reaction: meso-2,6-diaminohelptanedioate = l-lysine + CO2, requiring a cofactor, pyridoxal phosphate. This is the last step in the biosynthesis of lysine. This protein belongs to family 2 of ornithine, DAP, and arginine decarboxylases.

Note: Check start codon. No hits to the first 20 amino acid residues of this protein. Currently exhibits a non-methionine start, but residue 21 is a methionine.

Blast Summary:  PSI-Blast Search
Residues 21 to 435 are 68% ( EScore : 1e-167 ) identical to sp|P44316|DCDA_HAEIN DIAMINOPIMELATE DECARBOXYLASE between residues 1 and 415 in [Haemophilus influenzae Rd]
Residues 21 to 437 are 57% ( EScore : 1e-140 ) identical to gb|AAF93302.1| (AE004103) diaminopimelate decarboxylase between residues 1 and 417 in [Vibrio cholerae]
Residues 21 to 435 are 55% ( EScore : 1e-133 ) identical to sp|P19572|DCDA_PSEAE between residues 1 and 413
Residues 21 to 437 are 53% ( EScore : 1e-125 ) identical to sp|O05321|DCDA_PSEFL DIAMINOPIMELATE DECARBOXYLASE between residues 1 and 416 in [Pseudomonas fluorescens]
Residues 31 to 432 are 49% ( EScore : 1e-111 ) identical to emb|CAB83764.1| (AL162753) diaminopimelate decarboxylase between residues 3 and 402 in [Neisseria meningitidis]
Residues 31 to 432 are 49% ( EScore : 1e-110 ) identical to gb|AAF42304.1| (AE002546) diaminopimelate decarboxylase between residues 3 and 402 in [Neisseria meningitidis MC58]
Residues 23 to 425 are 41% ( EScore : 5e-91 ) identical to sp|O67262|DCDA_AQUAE DIAMINOPIMELATE DECARBOXYLASE between residues 10 and 410 in [Aquifex aeolicus]
Residues 24 to 433 are 40% ( EScore : 3e-84 ) identical to gb|AAD19416.1| (AF102543) diaminopimelate decarboxylase between residues 4 and 416 in [Zymomonas mobilis]
Residues 45 to 432 are 42% ( EScore : 2e-79 ) identical to sp|Q9ZME5|DCDA_HELPJ DIAMINOPIMELATE DECARBOXYLASE between residues 11 and 398 in [Helicobacter pylori J99]
Residues 47 to 433 are 41% ( EScore : 2e-78 ) identical to sp|P56129|DCDA_HELPY DIAMINOPIMELATE DECARBOXYLASE between residues 13 and 399 in [Helicobacter pylori 26695]

COGS Summary:  COGS Search
BeTs to 11 clades of COG0019
COG name: Diaminopimelate decarboxylase
Functional Class:  E
The phylogenetic pattern of COG0019 is amt-yQVCebrhUJ-------
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB000183 (Orn/DAP/Arg decarboxylases family 2) with a combined E-value of 1.9e-72.
    IPB000183A    77-121
    IPB000183B    178-192
    IPB000183C    213-224
    IPB000183D    246-265
    IPB000183E    291-314
    IPB000183F    359-368
    IPB000183G    381-401


ProDom Summary:  Protein Domain Search
Residues 239-336 are 76% similar to a (DECARBOXYLASE DIAMINOPIMELATE LYASE) protein domain (PD312460) which is seen in Q9CL23_PASMU.

Residues 34-155 are 79% similar to a (DECARBOXYLASE ORNITHINE LYASE BIOSYNTHESIS PYRIDOXAL) protein domain (PD001258) which is seen in Q9CL23_PASMU.

Residues 359-429 are 52% similar to a (DECARBOXYLASE DIAMINOPIMELATE LYASE) protein domain (PD115551) which is seen in Q9CL23_PASMU.

Residues 156-226 are 81% similar to a (DECARBOXYLASE DIAMINOPIMELATE) protein domain (PD407348) which is seen in Q9CL23_PASMU.



Paralogs:  Local Blast Search

HD0036 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 53 to 302 (E-value = 2.3e-114) place HD0036 in the Orn_Arg_deC_N family which is described as Pyridoxal-dependent decarboxylase, pyridoxal binding domain (PF02784)
Residues 305 to 412 (E-value = 9.5e-39) place HD0036 in the Orn_DAP_Arg_deC family which is described as Pyridoxal-dependent decarboxylase, C-terminal sheet domain (PF00278)

PDB Hit:
pdb|1F3T|A Chain A, Crystal Structure Of Trypanosoma Brucei Orn... 89 1e-018
pdb|7ODC|A Chain A, Crystal Structure Ornithine Decarboxylase F... 87 3e-018
pdb|2TOD|A Chain A, Ornithine Decarboxylase From Trypanosoma Br... 87 5e-018

Gene Protein Sequence:
VTKYDRFFVDFCSIKSNGLAMNHFAYKHHQLFAEKVAVKALATQYGTPAY
IYSRATLEQHWRAFDEAFGDRPHLICFAVKSNPNLAVLNVMAKLGSGFDI
VSQGELERVLAAGGDPAKIVFSGVAKSHIEIRRALAVGIHCFNVESVAEL
HRINQIAGELGKIATISLRVNPDVDAGTHPYISTGLKENKFGISVQQARA
VYQLASRLPHIQVVGLDCHIGSQLTELQPFLDAADRLIVLLEQLYRDGIR
LSHLDLGGGLGVVYHTETPPQPAEYVRALLAKFAHYPELEIILEPGRAIT
ADAGILVTKVEYLKSNEDRHFAIVDTGMNDLLRPALYDAYMHISEVDQSL
KRVEQQYEVVGPICETADFLGKARTLAIAEGDLLAVYSAGAYGASMSSTY
NSRPQAVEIMVDGATSHLIKKRSDFAELWRNEKCITD$

Gene Nucleotide Sequence:  Sequence Viewer
GTGACAAAATATGACCGCTTTTTTGTGGACTTTTGCAGTATCAAATCAAA
CGGACTTGCTATGAATCATTTTGCTTATAAACATCATCAGCTTTTTGCGG
AAAAGGTTGCAGTGAAAGCGCTTGCGACACAATATGGTACACCAGCATAT
ATCTATTCTCGTGCGACTTTAGAACAGCATTGGCGCGCGTTTGATGAAGC
TTTTGGTGATCGGCCTCACTTAATTTGTTTTGCGGTTAAATCCAACCCAA
ATTTGGCGGTTTTAAATGTTATGGCAAAACTAGGTTCAGGTTTTGATATT
GTTTCTCAAGGTGAATTAGAGCGCGTATTAGCTGCAGGGGGTGATCCAGC
CAAAATCGTTTTTTCAGGTGTTGCCAAGTCACATATAGAAATTCGCCGGG
CGTTAGCGGTCGGTATTCATTGTTTTAATGTTGAGTCGGTCGCAGAATTG
CATCGAATTAATCAAATCGCGGGCGAATTAGGCAAAATAGCGACTATTTC
GTTACGGGTGAATCCTGATGTTGATGCGGGAACTCACCCTTATATTTCAA
CCGGTCTAAAAGAAAATAAATTTGGCATTAGCGTCCAGCAGGCTCGGGCG
GTTTATCAATTAGCCAGTCGTTTACCTCATATTCAAGTCGTTGGTTTGGA
TTGCCATATCGGTTCACAATTAACGGAATTGCAACCTTTTCTCGATGCGG
CTGATCGTTTAATTGTCTTGCTTGAACAACTTTATCGCGACGGTATCCGT
TTAAGTCATTTAGATTTAGGCGGCGGTTTAGGCGTTGTATACCATACTGA
AACACCGCCTCAGCCGGCTGAATATGTACGTGCTTTATTAGCTAAATTTG
CTCATTATCCGGAGTTGGAGATTATTCTTGAGCCGGGGCGTGCCATTACT
GCTGATGCGGGTATTTTAGTGACCAAAGTTGAATATCTTAAAAGCAATGA
AGATCGCCATTTTGCGATTGTCGATACGGGTATGAATGATCTGTTACGGC
CGGCATTATATGATGCGTATATGCATATTAGTGAAGTGGATCAATCCTTA
AAGCGAGTTGAACAACAATATGAGGTAGTCGGCCCTATTTGTGAAACCGC
TGATTTTTTAGGTAAGGCAAGAACATTAGCCATTGCTGAAGGAGATTTAC
TGGCGGTATATTCAGCAGGCGCCTATGGAGCTTCAATGTCATCTACTTAT
AATTCACGACCACAAGCGGTTGAAATTATGGTGGACGGTGCAACTAGCCA
TTTGATTAAGAAGCGGTCAGATTTTGCTGAATTGTGGCGGAATGAGAAGT
GTATTACTGACTAA


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