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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	ycjT
Gene Synonym(s)	ECK1311, b1316, JW1309^[1], JW1309
Product Desc.	predicted hydrolase^[2]^[3] Function unknown, homologous to glycosyl hydrolases^[4]
Product Synonyms(s)	predicted hydrolase^[1], YcjT^[2]^[1], B1316^[2]^[1] , ECK1311, JW1309, b1316
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ycjM^[2]
Regulation/Activity
Quick Links
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Notes

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Part of the putative ycjM-V operon, which encodes a putative transport and catabolism system for an unknown sugar.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	ycjT
Mnemonic	Systematic nomenclature
Synonyms	ECK1311, b1316, JW1309^[1], JW1309
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	29.66 minutes	MG1655: 1375908..1378175 <gbrowseImage> name=NC_000913:1375908..1378175 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1376252..1378519 <gbrowseImage> name=NC_012967:1376252..1378519 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1266757..1269024 <gbrowseImage> name=NC_012759:1266757..1269024 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1379598..1381865 <gbrowseImage> name=NC_007779:1379598..1381865 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1465304..1467571 <gbrowseImage> name=NC_010473:1465304..1467571 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability
ΔycjT (Keio:JW1309)	deletion	deletion			PMID:16738554	Shigen CGSC9173^[5]
ΔycjT::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔycjT752::kan					PMID:16738554	CGSC:104106
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW1309	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCAGGCCAGTAACGTTATC Primer 2:CCTTCATCCTCCTGATGTTTGGT
2D3	Kohara Phage	Genobase	PMID:3038334
3H8	Kohara Phage	Genobase	PMID:3038334
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[5]	est. P1 cotransduction: 78% ^[6] Synonyms:zci-233::Tn10
recT3061::Tn10	Linked marker	CAG12081 = CGSC7375^[5]	est. P1 cotransduction: 25% ^[6] Synonyms:zcj-3061::Tn10, zda-3061::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:G6654	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13917	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003249	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945895	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3676	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004418	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	YcjT
Synonyms	predicted hydrolase^[1], YcjT^[2]^[1], B1316^[2]^[1] , ECK1311, JW1309, b1316
Product description	predicted hydrolase^[2]^[3] Function unknown, homologous to glycosyl hydrolases^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005195	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005196	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008928	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011013	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012341	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005195	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005196	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011013	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0326	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016798	hydrolase activity, acting on glycosyl bonds	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0326	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030246	carbohydrate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005196	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030246	carbohydrate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011013	F	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MTRPVTLSEP HFSQHTLNKY ASLMAQGNGY LGLRASHEED YTRQTRGMYL AGLYHRAGKG EINELVNLPD VVGMEIAING EVFSLSHEAW QRELDFASGE LRRNVVWRTS NGSGYTIASR RFVSADQLPL IALEITITPL DADASVLIST GIDATQTNHG RQHLDETQVR VFGQHLMQGS YTTQDGRSDV AISCCCKVSG DVQQCYTAKE RRLLQHTSAQ LHAGETMTLQ KLVWIDWRDD RQAALDEWGS ASLRQLEMCA QQSYDQLLAA STENWRQWWQ KRRITVNGGE AHDQQALDYA LYHLRIMTPA HDERSSIAAK GLTGEGYKGH VFWDTEVFLL PFHLFSDPTV ARSLLRYRWH NLPGAQEKAR RNGWQGALFP WESARSGEEE TPEFAAINIR TGLRQKVASA QAEHHLVADI AWAVIQYWQT TGDESFIAHE GMALLLETAK FWISRAVRVN DRLEIHDVIG PDEYTEHVNN NAYTSYMARY NVQQALNIAR QFGCSDDAFI HRAEMFLKEL WMPEIQPDGV LPQDDSFMAK PAINLAKYKA AAGKQTILLD YSRAEVNEMQ ILKQADVVML NYMLPEQFSA ASCLANLQFY EPRTIHDSSL SKAIHGIVAA RCGLLTQSYQ FWREGTEIDL GADPHSCDDG IHAAATGAIW LGAIQGFAGV SVRDGELHLN PALPEQWQQL SFPLFWQGCE LQVTLDAQRI AIRTSAPVSL RLNGQLITVA EESVFCLGDF ILPFNGTATK HQEDE
Length	755
Mol. Wt	84.867 kDa
pI	5.7 (calculated)
Extinction coefficient	144,270 - 145,645 (calc based on 23 Y, 20 W, and 11 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	References
Domain	681..731	PF03633 Glycosyl hydrolase family 65, C-terminal domain	PMID:19920124
Domain	298..677	PF03632 Glycosyl hydrolase family 65 central catalytic domain	PMID:19920124
Domain	6..241	PF03636 Glycosyl hydrolase family 65, N-terminal domain	PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ycjT taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16129277	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945895	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004418	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77154	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6654	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13917	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945895	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003249	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3676	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	1^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	2^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
ycjM
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1375888..1375928 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1316 (EcoliWiki Page)	NCBI GEO profiles for ycjT
microarray	GenExpDB:b1316 (EcoliWiki Page)	Summary of data for ycjT from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to ycjT Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:G6654	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3676	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1316
EcoGene	EcoGene:EG13917	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003249	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004418	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000020774 (score: 1.000; bootstrap: 100%) ENSANGP00000020754 (score: 0.139)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0218885 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA14242-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000006728 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000020004 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000044528 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YCJT	From SHIGELLACYC
E. coli O157	YCJT	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF03633 Glycosyl hydrolase family 65, C-terminal domain
Pfam (EcoliWiki Page)	PF03632 Glycosyl hydrolase family 65 central catalytic domain
Pfam (EcoliWiki Page)	PF03636 Glycosyl hydrolase family 65, N-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:48208
Panther (EcoliWiki Page)	PTHR11051:SF4
Superfamily (EcoliWiki Page)	SUPERFAMILY:74650
EcoCyc	EcoCyc:G6654	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13917	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003249	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3676	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004418	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

ycjT:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to ycjT Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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