RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

syd gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	syd
Synonym(s):	ECK2788, G7451, b2793, ydr
Genome position(nucleotides):	2924735 <-- 2925280 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	47.8
External database links:

ASAP:	ABE-0009154
ECHOBASE:	EB2792
ECOLIHUB:	syd
OU-MICROARRAY:	b2793
STRING:	511145.b2793
COLOMBOS:	syd

Product

Name:

SecY-interacting protein

Synonym(s):

Syd, Ydr

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane,cytosol

Molecular weight:

20.708

Isoelectric point:

4.647

Motif(s):

Type	Positions	Sequence
	7 -> 179	QALKDFTARYCDAWHEEHKSWPLSEELYGVPSPCIISTTEDAVYWQPQPFTGEQNVNAVERAFDIVIQPTIHTFYTTQFAGDMHAQFGDIKLTLLQTWSEDDFRRVQENLIGHLVTQKRLKLPPTLFIATLEEELEVISVCNLSGEVCKETLGTRKRTHLASNLAEFLNQLKP

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0005737 - cytoplasm GO:0005829 - cytosol GO:0016020 - membrane GO:0005886 - plasma membrane GO:0009898 - cytoplasmic side of plasma membrane GO:0031234 - extrinsic component of cytoplasmic side of plasma membrane
	molecular_function	GO:0005515 - protein binding
	biological_process	GO:0043254 - regulation of protein-containing complex assembly

Note(s):

Note(s): ...[more].

Evidence:

[APPH] Assay of protein purified to homogeneity

Reference(s):

[1] Dalal K., et al., 2009

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PDB:

PFAM:

PRIDE:

PRODB:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

syd

Operon arrangement:

Transcription unit	Promoter
syd

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_3091	2924349	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3092	2924385	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3093	2924391	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3094	2924394	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3095	2924415	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3096 (cluster)	2924424	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924423 to 2924424, where the highest frequency is at position 2922446. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3097	2924436	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3098 (cluster)	2924452	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924451 to 2924452, where the highest frequency is at position 2922474. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3099	2924464	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3100	2924466	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3101	2924468	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3102 (cluster)	2924473	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924472 to 2924473, where the highest frequency is at position 2922494. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3103 (cluster)	2924477	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924476 to 2924477, where the highest frequency is at position 2922498. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3104	2924484	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3105	2924496	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3106	2924507	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3107	2924509	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3108 (cluster)	2924522	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924521 to 2924522, where the highest frequency is at position 2922544. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3110	2924528	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3111	2925313	reverse	nd	[RS-EPT-CBR]	[2]
promoter	sydp2	2925369	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.335. P-value: 5.068e-5 Read more >	[ICWHO]	[3]

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

Reference(s)
[1] Dalal K., Nguyen N., Alami M., Tan J., Moraes TF., Lee WC., Maurus R., Sligar SS., Brayer GD., Duong F., 2009, Structure, binding, and activity of Syd, a SecY-interacting protein., J Biol Chem 284(12):7897-902
[2] 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.
[3] 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

RegulonDB