RegulonDB

Gene
Name:	folD
Synonym(s):	ECK0522, EG10328, ads, b0529
Genome position(nucleotides):	556875 <-- 557741 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.33
External database links:

ASAP:	ABE-0001818
CGSC:	31127
ECHOBASE:	EB0324
ECOLIHUB:	folD
NCBI-GENE:	945221
OU-MICROARRAY:	b0529
STRING:	511145.b0529
COLOMBOS:	folD

Gene

Name:

folD

Synonym(s):

ECK0522, EG10328, ads, b0529

Genome position(nucleotides):

556875 <-- 557741 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

54.33

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

NCBI-GENE:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

166 -> 168

GAS

2 -> 288

AAKIIDGKTIAQQVRSEVAQKVQARIAAGLRAPGLAVVLVGSNPASQIYVASKRKACEEVGFVSRSYDLPETTSEAELLELIDTLNADNTIDGILVQLPLPAGIDNVKVLERIHPDKDVDGFHPYNVGRLCQRAPRLRPCTPRGIVTLLERYNIDTFGLNAVVIGASNIVGRPMSMELLLAGCTTTVTHRFTKNLRHHVENADLLIVAVGKPGFIPGDWIKEGAIVIDVGINRLENGKVVGDVVFEDAAKRASYITPVPGGVGPMTVATLIENTLQACVEYHDPQDE

124 -> 279

HPYNVGRLCQRAPRLRPCTPRGIVTLLERYNIDTFGLNAVVIGASNIVGRPMSMELLLAGCTTTVTHRFTKNLRHHVENADLLIVAVGKPGFIPGDWIKEGAIVIDVGINRLENGKVVGDVVFEDAAKRASYITPVPGGVGPMTVATLIENTLQAC

200 -> 200

5 -> 121

IIDGKTIAQQVRSEVAQKVQARIAAGLRAPGLAVVLVGSNPASQIYVASKRKACEEVGFVSRSYDLPETTSEAELLELIDTLNADNTIDGILVQLPLPAGIDNVKVLERIHPDKDVD

Type

Positions

Sequence

166 -> 168

GAS

2 -> 288

124 -> 279

HPYNVGRLCQRAPRLRPCTPRGIVTLLERYNIDTFGLNAVVIGASNIVGRPMSMELLLAGCTTTVTHRFTKNLRHHVENADLLIVAVGKPGFIPGDWIKEGAIVIDVGINRLENGKVVGDVVFEDAAKRASYITPVPGGVGPMTVATLIENTLQAC

200 -> 200

5 -> 121

IIDGKTIAQQVRSEVAQKVQARIAAGLRAPGLAVVLVGSNPASQIYVASKRKACEEVGFVSRSYDLPETTSEAELLELIDTLNADNTIDGILVQLPLPAGIDNVKVLERIHPDKDVD

47 -> 47

Multifun Terms (GenProtEC)

1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.2 - folic acid

1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.17 - formyl-THF biosynthesis

Gene Ontology Terms (GO)

cellular_component

GO:0005829 - cytosol

molecular_function

GO:0004486 - methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity
GO:0003824 - catalytic activity
GO:0016787 - hydrolase activity
GO:0016491 - oxidoreductase activity
GO:0004477 - methenyltetrahydrofolate cyclohydrolase activity
GO:0004488 - methylenetetrahydrofolate dehydrogenase (NADP+) activity
GO:0042803 - protein homodimerization activity

biological_process

GO:0008152 - metabolic process
GO:0000105 - histidine biosynthetic process
GO:0006164 - purine nucleotide biosynthetic process
GO:0006730 - one-carbon metabolic process
GO:0008652 - cellular amino acid biosynthetic process
GO:0009086 - methionine biosynthetic process
GO:0055114 - oxidation-reduction process
GO:0035999 - tetrahydrofolate interconversion

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	ybcJp4	556891	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.934. P-value: 6.144e-6 Read more >	[ICWHO]	[8]
promoter	ybcJp3	556967	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.804. P-value: 3.908e-5 Read more >	[ICWHO]	[8]
promoter	ybcJp5	557006	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.329. P-value: 2.699e-5 Read more >	[ICWHO]	[8]
promoter	ybcJp7	557025	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.746. P-value: 9.516e-5 Read more >	[ICWHO]	[8]
promoter	TSS_679	557596	reverse	nd	[RS-EPT-CBR]	[9]
promoter	sfmAp4	558062	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.973. P-value: 1.980e-5 Read more >	[ICWHO]	[8]
promoter	sfmAp6	558166	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.176. P-value: 5.275e-5 Read more >	[ICWHO]	[8]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

ybcJp4

556891

reverse

Similarity to the consensus
Read more >

[ICWHO]

[8]

promoter

ybcJp3

556967

reverse

Similarity to the consensus
Read more >

[ICWHO]

[8]

promoter

ybcJp5

557006

reverse

Similarity to the consensus
Read more >

[ICWHO]

[8]

promoter

ybcJp7

557025

reverse

Similarity to the consensus
Read more >

[ICWHO]

[8]

promoter

TSS_679

557596

reverse

[RS-EPT-CBR]

[9]

promoter

sfmAp4

558062

forward

Similarity to the consensus
Read more >

[ICWHO]

[8]

promoter

sfmAp6

558166

forward

Similarity to the consensus
Read more >

[ICWHO]

[8]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[ICWHO] Inferred computationally without human oversight

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Aluri S., Sah S., Miryala S., Varshney U., 2016, Physiological role of FolD (methylenetetrahydrofolate dehydrogenase), FchA (methenyltetrahydrofolate cyclohydrolase) and Fhs (formyltetrahydrofolate synthetase) from Clostridium perfringens in a heterologous model of Escherichia coli., Microbiology (Reading) 162(1):145-155
[2] Cheung E., D'Ari L., Rabinowitz JC., Dyer DH., Huang JY., Stoddard BL., 1997, Purification, crystallization, and preliminary x-ray studies of a bifunctional 5,10-methenyl/methylene-tetrahydrofolate cyclohydrolase/dehydrogenase from Escherichia coli., Proteins 27(2):322-4
[3] Dev IK., Harvey RJ., 1978, A complex of N5,N10-methylenetetrahydrofolate dehydrogenase and N5,N10-methenyltetrahydrofolate cyclohydrolase in Escherichia coli. Purification, subunit structure, and allosteric inhibition by N10-formyltetrahydrofolate., J Biol Chem 253(12):4245-53
[4] Donaldson KO., Scott VF., Scott W., 1965, Purification and properties of 5,10-methylenetetrahydrofolate dehydrogenase from Escherichia coli., J Biol Chem 240(11):4444-8
[5] Ravcheev DA., Gel'fand MS., Mironov AA., Rakhmaninova AB., 2002, [Purine regulon of gamma-proteobacteria: a detailed description], Genetika 38(9):1203-14
[6] Sah S., Aluri S., Rex K., Varshney U., 2015, One-carbon metabolic pathway rewiring in Escherichia coli reveals an evolutionary advantage of 10-formyltetrahydrofolate synthetase (Fhs) in survival under hypoxia., J Bacteriol 197(4):717-26
[7] Wahls WP., Song JM., Smith GR., 1993, Single-stranded DNA binding activity of C1-tetrahydrofolate synthase enzymes., J Biol Chem 268(32):23792-8
[8] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[9] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] Aluri S., Sah S., Miryala S., Varshney U., 2016, Physiological role of FolD (methylenetetrahydrofolate dehydrogenase), FchA (methenyltetrahydrofolate cyclohydrolase) and Fhs (formyltetrahydrofolate synthetase) from Clostridium perfringens in a heterologous model of Escherichia coli., Microbiology (Reading) 162(1):145-155

[2] Cheung E., D'Ari L., Rabinowitz JC., Dyer DH., Huang JY., Stoddard BL., 1997, Purification, crystallization, and preliminary x-ray studies of a bifunctional 5,10-methenyl/methylene-tetrahydrofolate cyclohydrolase/dehydrogenase from Escherichia coli., Proteins 27(2):322-4

[3] Dev IK., Harvey RJ., 1978, A complex of N5,N10-methylenetetrahydrofolate dehydrogenase and N5,N10-methenyltetrahydrofolate cyclohydrolase in Escherichia coli. Purification, subunit structure, and allosteric inhibition by N10-formyltetrahydrofolate., J Biol Chem 253(12):4245-53

[4] Donaldson KO., Scott VF., Scott W., 1965, Purification and properties of 5,10-methylenetetrahydrofolate dehydrogenase from Escherichia coli., J Biol Chem 240(11):4444-8

[5] Ravcheev DA., Gel'fand MS., Mironov AA., Rakhmaninova AB., 2002, [Purine regulon of gamma-proteobacteria: a detailed description], Genetika 38(9):1203-14

[6] Sah S., Aluri S., Rex K., Varshney U., 2015, One-carbon metabolic pathway rewiring in Escherichia coli reveals an evolutionary advantage of 10-formyltetrahydrofolate synthetase (Fhs) in survival under hypoxia., J Bacteriol 197(4):717-26

[7] Wahls WP., Song JM., Smith GR., 1993, Single-stranded DNA binding activity of C1-tetrahydrofolate synthase enzymes., J Biol Chem 268(32):23792-8

[8] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

[9] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.