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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR185 IGR182 IGR184 IGR188 IGR186 IGR187 IGR183 IGR181 argR, - HD0262 lpp, - HD0266 HD0267 spoU,trmH, - HD0270 yrbF, - HD0259 yfcH, - HD0261 mdh, - HD0264 obg, - HD0269 htrA, - HD0260 argS, - HD0268 argR, - HD0262 lpp, - HD0266 HD0267 spoU,trmH, - HD0270 yrbF, - HD0259 yfcH, - HD0261 mdh, - HD0264 obg, - HD0269 htrA, - HD0260 argS, - HD0268 Type: tandem, Name:  - 5 Type: tandem, Name:  - 6 argR, - HD0262 lpp, - HD0266 HD0267 spoU,trmH, - HD0270 yrbF, - HD0259 yfcH, - HD0261 yrbE, - HD0258 yrbE, - HD0258 mdh, - HD0264 obg, - HD0269 htrA, - HD0260 argS, - HD0268
* Calculated from Protein Sequence

Gene ID: HD0264

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
mdh  

Definition:
malate dehydrogenase

Gene Start:
199745

Gene Stop:
200719

Gene Length:
975

Molecular Weight*:
34234

pI*:
5.50

Net Charge*:
-4.16

EC:
1.1.1.37  

Functional Class:
Energy metabolism; TCA cycle  

Pathway: pathway table
Carbon fixation
Citrate cycle (TCA cycle)
Glyoxylate and dicarboxylate metabolism
Pyruvate metabolism
Reductive carboxylate cycle (CO2 fixation)

Secondary Evidence:
McAlister-Henn,L., Blaber,M., Bradshaw,R.A. and Nisco,S.J.
Complete nucleotide sequence of the Escherichia coli gene encoding
malate dehydrogenase
Nucleic Acids Res. 15 (12), 4993 (1987)
MEDLINE: 87259981

Vogel,R.F., Entian,K.D. and Mecke,D.
Cloning and sequence of the mdh structural gene of Escherichia coli coding for malate dehydrogenase
Arch. Microbiol. 149 (1), 36-42 (1987)
MEDLINE: 88105815

Boyd,E.F., Nelson,K., Wang,F.S., Whittam,T.S. and Selander,R.K.
Molecular genetic basis of allelic polymorphism in malate
dehydrogenase (mdh) in natural populations of Escherichia coli and
Salmonella enterica
Proc. Natl. Acad. Sci. U.S.A. 91 (4), 1280-1284 (1994)
MEDLINE: 94151313

Pupo,G.M., Karaolis,D.K., Lan,R. and Reeves,P.R.
Evolutionary relationships among pathogenic and nonpathogenic
Escherichia coli strains inferred from multilocus enzyme
electrophoresis and mdh sequence studies
Infect. Immun. 65 (7), 2685-2692 (1997)
MEDLINE: 97342740

Hall,M.D., Levitt,D.G. and Banaszak,L.J.
Crystal structure of Escherichia coli malate dehydrogenase. A
complex of the apoenzyme and citrate at 1.87 A resolution
J. Mol. Biol. 226 (3), 867-882 (1992)
MEDLINE: 92373767



Comment:
0

Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to malate dehydrogenase protein; e.g. residues 1-323 are 64% similar to (U32800) malate dehydrogenase of Haemophilus influenzae Rd, residues 1-322 are 63% similar to (AE004130) malate dehydrogenase of Vibrio cholerae, residues 1-323 are 60% similar to (AE000403) malate dehydrogenase of Escherichia coli.

COGS Summary:  COGS Search
BeTs to 14 clades of COG0039
COG name: Malate/lactate dehydrogenases
Functional Class:  C
The phylogenetic pattern of COG0039 is amt-YQvceBrh--gpo-inx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB001252 (Malate dehydrogenase active site) with a combined E-value of 1.2e-16.
    IPB001252    76-106
***** IPB001557 (L-lactate dehydrogenase) with a combined E-value of 1.7e-14.
    IPB001557A    3-34
    IPB001557B    70-119
    IPB001557C    125-167
    IPB001557E    216-257


ProDom Summary:  Protein Domain Search
Residues 129-239 are 69% similar to a (DEHYDROGENASE MALATE OXIDOREDUCTASE NAD TRICARBOXYLIC) protein domain (PD393364) which is seen in MDH_HAEIN.

Residues 2-128 are 34% similar to a (DEHYDROGENASE OXIDOREDUCTASE UDP-GLUCOSE NAD COMPLETE) protein domain (PD001278) which is seen in MDH_BACTC.

Residues 2-62 are 62% similar to a (DEHYDROGENASE OXIDOREDUCTASE MALATE) protein domain (PD005394) which is seen in Q9VEB1_DROME.

Residues 241-323 are 52% similar to a (DEHYDROGENASE MALATE OXIDOREDUCTASE NAD ACID) protein domain (PD335525) which is seen in MDH_HAEIN.

Residues 1-128 are 68% similar to a (DEHYDROGENASE OXIDOREDUCTASE NAD L-LACTATE GLYCOLYSIS) protein domain (PD000350) which is seen in Q9XCZ8_VIBCH.



Paralogs:  Local Blast Search

HD0264 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 1 to 152 (E-value = 1.1e-58) place HD0264 in the Ldh_1_N family which is described as lactate/malate dehydrogenase, NAD binding domain (PF00056)
Residues 154 to 322 (E-value = 8.4e-42) place HD0264 in the Ldh_1_C family which is described as lactate/malate dehydrogenase, alpha/beta C-terminal domain (PF02866)

PDB Hit:
pdb|2CMD| Malate Dehydrogenase (E.C.1.1.1.37) >gi|442876|pdb... 367 1e-102
pdb|1MLD|A Chain A, Malate Dehydrogenase (E.C.1.1.1.37) >gi|999... 279 4e-076
pdb|1A5Z| Lactate Dehydrogenase From Thermotoga Maritima (Tm... 89 1e-018

Gene Protein Sequence:
MKVTVLGAAGGIGQTLSLLLKLRLPAGADLALYDISPVTPGIAVDISHIP
TSVNAIGYAGEDPSVALKDPSVALKDTNLVIITAGIARKPGMTRADLFNI
NAGIVKDLVEKVAEVCPMACIGIVTNPVNTLVPIAAEVLRKAGVYDKSKL
FGVTTLDVVRAKTFVSELKHKNVETVTVPVVGGHSGTTILPLLSQALAEG
RLLDFSQTEIESLTQRIKNAGTEVVEAKAGGGSATLSMAESGARFALAVF
KALLGEDCVRYAYVQSKEGSGYPEFFAHPVRFGLKGIEEILPIAPLNEYE
QTQFEELKPILEADIELGKKFVNP$

Gene Nucleotide Sequence:  Sequence Viewer
ATGAAAGTTACTGTATTAGGCGCTGCAGGTGGGATAGGACAAACGTTATC
TCTGTTATTAAAGCTTCGTTTACCGGCGGGGGCAGATTTAGCACTATATG
ATATTTCGCCGGTTACGCCGGGCATTGCAGTTGATATTAGCCATATTCCA
ACCTCGGTCAATGCGATAGGGTATGCGGGTGAAGATCCGTCCGTCGCACT
AAAAGATCCGTCCGTCGCACTAAAAGATACTAATTTAGTGATCATTACCG
CAGGTATTGCACGTAAACCGGGTATGACTCGTGCTGACTTATTTAATATT
AATGCCGGTATTGTGAAAGATTTAGTTGAGAAAGTTGCTGAGGTTTGCCC
AATGGCTTGCATTGGCATTGTGACTAATCCGGTTAATACATTGGTGCCGA
TTGCTGCTGAAGTATTACGTAAAGCGGGGGTATATGATAAAAGTAAATTA
TTCGGTGTAACAACGTTAGACGTTGTGCGTGCTAAAACATTTGTATCAGA
ATTAAAACACAAAAATGTTGAAACAGTCACTGTGCCAGTCGTGGGAGGGC
ATTCAGGGACAACTATTTTACCGCTTCTTTCGCAAGCCTTAGCGGAAGGT
CGGTTATTAGATTTTTCACAAACAGAAATTGAGTCGCTTACTCAGCGGAT
CAAAAATGCAGGGACGGAAGTGGTGGAGGCTAAAGCGGGTGGCGGTTCGG
CAACGCTGTCAATGGCAGAGTCAGGTGCACGTTTTGCGCTAGCTGTCTTT
AAAGCACTATTAGGAGAAGATTGCGTGCGTTATGCTTATGTCCAGAGTAA
AGAAGGCTCAGGATATCCGGAGTTTTTTGCACATCCTGTCCGCTTTGGTT
TAAAAGGTATTGAAGAAATTCTGCCGATTGCGCCATTAAATGAATATGAA
CAAACGCAGTTTGAAGAACTTAAGCCTATATTAGAGGCGGATATTGAATT
GGGTAAGAAATTCGTTAATCCATAA


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