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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR24 IGR25 IGR23 IGR27 IGR21 IGR19 IGR28 IGR26 IGR20 IGR22 genX, - HD0029 dcuB, - HD0025 HD0035 frdD, - HD0034 crcB, - HD0024 frdC, - HD0033 frdB, - HD0032 dapF, - HD0026 lysA, - HD0036 frdA, - HD0030 hemN, - HD0037 genX, - HD0029 dcuB, - HD0025 HD0035 frdD, - HD0034 crcB, - HD0024 frdC, - HD0033 frdB, - HD0032 dapF, - HD0026 lysA, - HD0036 frdA, - HD0030 hemN, - HD0037 genX, - HD0029 dcuB, - HD0025 HD0035 crcB, - HD0024 frdC, - HD0033 frdB, - HD0032 dapF, - HD0026 lysA, - HD0036 frdA, - HD0030 hemN, - HD0037 frdD, - HD0034
* Calculated from Protein Sequence

Gene ID: HD0030

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
frdA  

Definition:
fumarate reductase flavoprotein subunit A

Gene Start:
28572

Gene Stop:
30383

Gene Length:
1812

Molecular Weight*:
66653

pI*:
6.50

Net Charge*:
-5.32

EC:
1.3.99.1  

Functional Class:
Energy metabolism; Anaerobic respiration  

Pathway: pathway table
Butanoate metabolism
Citrate cycle (TCA cycle)
Oxidative phosphorylation
Reductive carboxylate cycle (CO2 fixation)

Secondary Evidence:
Cole,S.T.
Nucleotide sequence coding for the flavoprotein subunit the fumarate reductase of Escherichia coli.
Eur. J. Biochem. 122 (3), 479-484 (1982)
Medline: 82138876.

Blaut,M., Whittaker,K., Valdovinos,A., Ackrell,B.A., Gunsalus,R.P. and Cecchini,G.
Fumarate reductase mutants of Escherichia coli that lack covalently bound flavin.
J. Biol. Chem. 264 (23), 13599-13604 (1989)
Medline: 89340438.

Schroder,I., Gunsalus,R.P., Ackrell,B.A., Cochran,B. and Cecchini,G.
Identification of active site residues of Escherichia coli fumarate reductase by site-directed mutagenesis.
J. Biol. Chem. 266 (21), 13572-13579 (1991)
Medline: 91310624.

Iverson,T.M., Luna-Chavez,C., Cecchini,G. and Rees,D.C.
Structure of the Escherichia coli fumarate reductase respiratory complex.
Science 284 (5422), 1961-1966 (1999)
Medline: 99301923


Comment:
From GenBank (gi:120489): In E. coli, two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; the fumarate reductase is used in anaerobic growth and the succinate dehydrogenase is used in aerobic growth. Catalytic activity of this protein in E. coli is: succinate + acceptor = fumarate + reduced acceptor, requiring FAD (covalently linked) as a cofactor. Fumerate dehydrogenase forms part of an enzyme complex containing four subunits: a flavoprotein (HD0030), an iron-sulfur protein (see HD0032), and two hydrophobic anchor proteins (see HD0033 and HD0034).

Check start codon. Residue 5, a methionine, may be a more accurate start. No hits in gapped BLAST to residues 1-4 of this protein.

Blast Summary:  PSI-Blast Search
Many very strong hits in gapped BLAST to fumarate reductase, flavoprotein subunit, proteins; e.g., residues 5-585 are 80% similar to FRDA_HAEIN [1169737], residues 5-585 are 74% similar to FRDA_PROVU [120490], and residues 5-585 are 71% similar to FRDA_ECOLI [120489].

COGS Summary:  COGS Search
BeTs to 13 clades of COG1053
COG name: Succinate dehydrogenase/fumarate reductase, flavoprotein subunits
Functional Class:  C
The phylogenetic pattern of COG1053 is Amt-YqvcEbRhuj----inx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB003952 (Fumarate reductase / succinate dehydrogenase FAD-binding site) with a combined E-value of 1.5e-208.
    IPB003952A    11-25
    IPB003952B    34-63
    IPB003952C    65-80
    IPB003952D    95-123
    IPB003952E    128-145
    IPB003952F    214-264
    IPB003952G    319-370
    IPB003952H    379-410
    IPB003952I    441-493
    IPB003952J    508-548
***** PR00368 (FAD-dependent pyridine nucleotide reductase signature) with a combined E-value of 5.7e-10.
    PR00368A    11-33
    PR00368B    193-202
    PR00368E    380-387
***** IPB000103 (Pyridine nucleotide-disulphide oxidoreductase class-II) with a combined E-value of 1.9e-06.
    IPB000103A    11-31
    IPB000103E    375-412


ProDom Summary:  Protein Domain Search
Residues 110-435 are 88% similar to a (FLAVOPROTEIN SUBUNIT OXIDOREDUCTASE FAD DEHYDROGENASE) protein domain (PD001219) which is seen in Q9CP56_PASMU.

Residues 48-109 are 82% similar to a (FLAVOPROTEIN OXIDOREDUCTASE SUBUNIT FAD DEHYDROGENASE) protein domain (PD237037) which is seen in Q9KNS5_VIBCH.

Residues 441-493 are 75% similar to a (FLAVOPROTEIN SUBUNIT OXIDOREDUCTASE) protein domain (PD001222) which is seen in Q9CP56_PASMU.

Residues 48-109 are 46% similar to a (FLAVOPROTEIN SUBUNIT SUCCINATE) protein domain (PD149640) which is seen in O68002_BRAJA.

Residues 497-574 are 76% similar to a (FLAVOPROTEIN SUBUNIT DEHYDROGENASE) protein domain (PD149830) which is seen in FRDA_HAEIN.



Paralogs:  Local Blast Search


HD0030 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 110 to 438 (E-value = 8.6e-191) place HD0030 in the FAD_binding_2 family which is described as FAD binding domain (PF00890)
Residues 458 to 584 (E-value = 2.3e-65) place HD0030 in the Succ_DH_flav_C family which is described as Fumarate reductase/succinate dehydrogenase flavoprotein C-terminal domain (PF02910)

PDB Hit:
pdb|1FUM|A Chain A, Structure Of The E. Coli Fumarate Reductase... 856 0.0
pdb|1QLA|A Chain A, Respiratory Complex Ii-Like Fumarate Reduct... 335 1e-092
pdb|1CHU|A Chain A, Structure Of L-Aspartate Oxidase: Implicati... 227 3e-060

Gene Protein Sequence:
LECIMQSVNFDVAIIGAGGGGLRAAIATAEANPNLKIALISKVYPMRSHT
VAAEGGSAAVIKDSDSFDNHFNDTVGGGDWLCEQDIVEYFVEHSPLEMTQ
LERWGCPWSRRADGEVNVRRFGGMKIERTWFAADKTGFHLLHTLFQTSIK
YPNIIRFDEHFVLDILTDNGEARGCVAMNMMEGNIVQINANAVVIATGGG
CRTYRFNTNGGIVTGDGLSMAYRHGVALRDMEFVQYHPTGLPNTGILMTE
GCRGEGGILVNKDGYRYLQDYGLGPETPIGKPENKYMELGPRDKVSQAFW
QEWRKGNTLKTEKGVDVVHLDLRHLGEKHLTERLPFICELARAYEGVDPV
KAAIPVRPVVHYTMGGIEVDMQAETSIKGLFAVGECASSGLHGANRLGSN
SLAELVVFGKVAGENAARRAQEIGARHQTQINAQAQDVVDRLHMLARQEG
NESWADIRNQMGDAMEEGCGIYRTQASMEGAVNKIEELKERYKNISIKDK
SSVFNTDLLYKIELGFILDAAQSIACSAVERKESRGAHQRLDYTERDDVN
YLKHTRAYYNAEGKPTIKYSDVKITKSQPAKRVYGAEAEAQEKVKKAAEQ
AQK$

Gene Nucleotide Sequence:  Sequence Viewer
TTGGAGTGCATAATGCAAAGTGTTAATTTTGATGTTGCAATTATAGGTGC
TGGTGGCGGTGGTCTGCGTGCAGCAATCGCCACGGCTGAAGCTAATCCTA
ATCTGAAAATCGCCTTAATTTCAAAGGTTTATCCAATGCGTAGCCATACG
GTGGCGGCGGAGGGGGGCTCTGCTGCGGTGATTAAAGATAGCGATTCATT
TGATAATCATTTTAATGATACTGTCGGGGGTGGGGACTGGCTGTGTGAAC
AAGATATTGTGGAATATTTTGTTGAACATTCACCGCTTGAAATGACTCAA
TTAGAACGTTGGGGTTGTCCTTGGAGCCGTCGAGCAGATGGCGAAGTTAA
TGTGCGTCGTTTTGGTGGGATGAAAATTGAACGTACTTGGTTCGCTGCAG
ATAAAACAGGCTTTCACTTATTACATACCCTTTTCCAAACATCGATTAAA
TACCCTAACATTATTCGGTTTGATGAGCATTTTGTGTTAGATATTTTGAC
CGATAATGGTGAAGCGCGAGGCTGTGTTGCGATGAATATGATGGAAGGTA
ACATCGTTCAAATCAATGCTAATGCGGTCGTGATTGCGACAGGCGGTGGT
TGCCGAACTTATCGTTTTAATACCAATGGTGGCATTGTGACGGGTGATGG
CTTATCAATGGCTTATCGTCACGGCGTGGCATTACGTGATATGGAGTTTG
TTCAATATCATCCAACAGGGCTACCAAATACGGGGATCTTAATGACGGAA
GGGTGTCGTGGTGAAGGCGGTATTTTAGTGAATAAAGATGGTTACCGCTA
CTTGCAAGATTATGGGCTTGGCCCAGAAACACCGATTGGTAAACCAGAAA
ATAAATATATGGAGTTAGGCCCACGTGACAAAGTTTCCCAAGCATTCTGG
CAAGAATGGCGAAAAGGAAATACATTAAAAACAGAAAAAGGTGTTGATGT
TGTACATTTAGATTTACGTCATTTAGGTGAGAAACATTTGACTGAACGTT
TGCCATTTATCTGTGAATTAGCACGCGCTTATGAAGGTGTTGATCCTGTC
AAAGCGGCGATTCCTGTTCGCCCTGTTGTGCATTACACAATGGGGGGGAT
TGAAGTAGATATGCAAGCAGAAACCTCAATTAAAGGTCTATTTGCAGTTG
GTGAATGTGCTTCTTCAGGCTTACACGGTGCGAATCGTTTAGGATCTAAT
TCATTAGCTGAATTGGTGGTATTTGGTAAAGTAGCGGGCGAAAATGCTGC
GCGCCGTGCACAAGAAATAGGCGCTCGTCATCAAACACAAATTAATGCAC
AAGCACAAGATGTGGTGGATCGATTACATATGTTAGCACGTCAAGAAGGT
AATGAATCCTGGGCAGATATTCGTAATCAAATGGGCGATGCAATGGAAGA
AGGATGTGGTATTTATCGCACACAAGCCAGTATGGAAGGGGCGGTAAATA
AAATTGAAGAGCTTAAAGAACGTTATAAGAATATTAGTATTAAGGATAAA
TCAAGTGTGTTTAATACTGATTTACTCTATAAGATTGAATTGGGTTTTAT
TTTAGATGCTGCGCAATCTATTGCTTGTTCTGCAGTTGAACGTAAAGAGT
CGCGTGGTGCGCATCAACGGTTAGACTATACTGAACGTGATGATGTGAAT
TATTTAAAACATACTCGTGCTTATTATAACGCTGAGGGTAAACCAACGAT
TAAATATTCAGATGTGAAAATTACCAAATCACAGCCAGCAAAACGGGTAT
ACGGTGCAGAAGCTGAAGCGCAAGAAAAAGTTAAGAAAGCAGCAGAACAG
GCACAAAAATAG


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