malS:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

malS

Gene Synonym(s)

ECK3560, b3571, JW3543[1], JW3543

Product Desc.

ALPHA-AMYL-PERI[2][3]

alpha-Amylase, periplasmic[4]

Product Synonyms(s)

alpha-amylase[1], B3571[2][1], MalS[2][1] , ECK3560, JW3543, b3571

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): malS[2], OP00184

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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MalT regulon.[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

malS

Mnemonic

Maltose

Synonyms

ECK3560, b3571, JW3543[1], JW3543

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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

80.51 minutes 

MG1655: 3735520..3737550
<gbrowseImage> name=NC_000913:3735520..3737550 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3667953..3669983
<gbrowseImage> name=NC_012967:3667953..3669983 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3623846..3625876
<gbrowseImage> name=NC_012759:3623846..3625876 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3902918..3900888
<gbrowseImage> name=NC_007779:3900888..3902918 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3833097..3835127
<gbrowseImage> name=NC_010473:3833097..3835127 source=DH10B preset=GeneLocation </gbrowseImage>

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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

Coding Start (SO:0000323)

MG1655

3735571

Edman degradation

PMID:1544897


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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 Comments

ΔmalS (Keio:JW3543)

deletion

deletion

PMID:16738554

Shigen
CGSC10615[5]

malS::Tn5KAN-I-SceI (FB21298)

Insertion at nt 1816 in Minus orientation

PMID:15262929

E. coli Genome Project:FB21298

does not contain pKD46

malS::Tn5KAN-I-SceI (FB21299)

Insertion at nt 1816 in Minus orientation

PMID:15262929

E. coli Genome Project:FB21299

contains pKD46

ΔmalS754::kan

PMID:16738554

CGSC:101744


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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

JW3543

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAACTCGCCGCCTGTTTTCT

Primer 2:CCtTGTTGCCCTGCCCAGACGAC

7C3

Kohara Phage

Genobase

PMID:3038334

10C8

Kohara Phage

Genobase

PMID:3038334

6F2

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: % [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: % [6]

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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:EG11316

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11316

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001287

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948088

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1292

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011668

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

MalS

Synonyms

alpha-amylase[1], B3571[2][1], MalS[2][1] , ECK3560, JW3543, b3571

Product description

ALPHA-AMYL-PERI[2][3]

alpha-Amylase, periplasmic[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:0016052

carbohydrate catabolic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0000272

polysaccharide catabolic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006047

F

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006589

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013781

F

Seeded from EcoCyc (v14.0)

complete

GO:0004556

alpha-amylase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.2.1.1

F

Seeded from EcoCyc (v14.0)

complete

GO:0005509

calcium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0106

F

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006047

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006589

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013781

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0119

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:0042597

periplasmic space

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0574

C

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0200

C

Seeded from EcoCyc (v14.0)

complete

GO:0043169

cation binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006047

F

Seeded from EcoCyc (v14.0)

complete

GO:0043169

cation binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006589

F

Seeded from EcoCyc (v14.0)

complete

GO:0043169

cation binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013781

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

PMID:3005273

IDA: Inferred from Direct Assay

C

complete

GO:0004556

alpha-amylase activity

PMID:3005273

IDA: Inferred from Direct Assay

F

complete

GO:0051692

cellular oligosaccharide catabolic process

PMID:3005273

IDA: Inferred from Direct Assay

P

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

Periplasm

PMID:1544897

EchoLocation:malS

periplasm


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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 

MKLAACFLTL LPGFAVAASW TSPGFPAFSE QGTGTFVSHA QLPKGTRPLT LNFDQQCWQP
ADAIKLNQML SLQPCSNTPP QWRLFRDGEY TLQIDTRSGT PTLMISIQNA AEPVASLVRE
CPKWDGLPLT VDVSATFPEG AAVRDYYSQQ IAIVKNGQIM LQPAATSNGL LLLERAETDT
SAPFDWHNAT VYFVLTDRFE NGDPSNDQSY GRHKDGMAEI GTFHGGDLRG LTNKLDYLQQ
LGVNALWISA PFEQIHGWVG GGTKGDFPHY AYHGYYTQDW TNLDANMGNE ADLRTLVDSA
HQRGIRILFD VVMNHTGYAT LADMQEYQFG ALYLSGDEVK KSLGERWSDW KPAAGQTWHS
FNDYINFSDK TGWDKWWGKN WIRTDIGDYD NPGFDDLTMS LAFLPDIKTE STTASGLPVF
YKNKMDTHAK AIDGYTPRDY LTHWLSQWVR DYGIDGFRVD TAKHVELPAW QQLKTEASAA
LREWKKANPD KALDDKPFWM TGEAWGHGVM QSDYYRHGFD AMINFDYQEQ AAKAVDCLAQ
MDTTWQQMAE KLQGFNVLSY LSSHDTRLFR EGGDKAAELL LLAPGAVQIF YGDESSRPFG
PTGSDPLQGT RSDMNWQDVS GKSAASVAHW QKISQFRARH PAIGAGKQTT LLLKQGYGFV
REHGDDKVLV VWAGQQ
Length

676

Mol. Wt

75.713 kDa

pI

5.4 (calculated)

Extinction coefficient

174,750 - 175,375 (calc based on 25 Y, 25 W, and 5 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 Notes References

motif

1-17

UniProt Manual:Signal Peptides

UniProt:P25718

Domain

226..598

PF00128 Alpha amylase, catalytic domain

PMID:19920124

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

Structures

<beststructure> gene=malS 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:16131442

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948088

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011668

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P25718

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11316

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11316

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948088

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001287

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1292

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

12

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

19

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

0a

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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<protect>

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

Transcription unit(s)

malS

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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_000913:3735500..3735540 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:b3571 (EcoliWiki Page)

NCBI GEO profiles for malS

microarray

GenExpDB:b3571 (EcoliWiki Page)

Summary of data for malS 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

GFP Fusion

Intergenic region (3734711..3735182) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ10; Well:G10[7]

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Notes

Accessions Related to malS Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11316

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1292

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3571

EcoGene

EcoGene:EG11316

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001287

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011668

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Dictyostelium discoideum

  • DDB0214924 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPCC11E109c (score: 1.000; bootstrap: 100%)
  • SPAC27E21 (score: 0.461)
  • SPAC25H19 (score: 0.242)
  • SPCC632c (score: 0.197)
  • SPAC23D34c (score: 0.192)
  • SPCC7572 (score: 0.189)

From Inparanoid:20070104

Shigella flexneri

MALS

From SHIGELLACYC

E. coli O157

MALS

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF00128 Alpha amylase, catalytic domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:51445

Panther (EcoliWiki Page)

PTHR10357:SF72

EcoCyc

EcoCyc:EG11316

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11316

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001287

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1292

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011668

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 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. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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