Phage P1 lydD:On One Page

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

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Standard Name

lydD

Gene Synonym(s)
Product Desc.

putative holin;

Product Synonyms(s)

gp014

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression
Regulation/Activity
Quick Links

porteco.png

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

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Notes

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References

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Gene

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

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Nomenclature

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

Standard name

lydD

Mnemonic
Synonyms


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Notes

Location(s) and DNA Sequence

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<protect> <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

NC_005856: 19570..20840
<gbrowseImage> name=NC_005856:19570..20840 source=bacteriophage_P1 preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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

Resource Resource Type Source Notes/Reference
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Notes

Accessions in Other Databases

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

Database Accession Notes
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Notes

Links

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References

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Categories

Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

LydD

Synonyms

gp014

Product description

putative holin;

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology <protect> 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:0034290

holin activity

PMID:15489417

ISM: Inferred from Sequence Model

F

Table 3, Text on 7062

Missing: with/from

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Interactions <protect> 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

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

Name
Sequence 
MNKLRQLRRL STMKLSLAAI VFDSIFMAVY VLNETWPLEP LLYAGLRLCL TFLSMAARLM
QQKETASDCP RRAVRKYMAR RRRR
Length

84

Mol. Wt

9.937 kDa

pI

12.0 (calculated)

Extinction coefficient

9,970 - 10,220 (calc based on 3 Y, 1 W, and 2 C residues)

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Domains/Motifs/Modification Sites

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

Type Residues Description Notes References

Domain

13 - 32

Predicted membrane-spanning helix.

TMD predicted by TMHMM[1]

Domain

42 - 59

Predicted membrane-spanning helix.

TMD predicted by TMHMM[1]


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<motif_map/>

tmhmm.php?gene=Phage_P1_lydD&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=Phage_P1_lydD taxon=10678 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

Database Accession Notes
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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. ↑ 1.0 1.1 Krogh, A et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305 567-80 PubMed

Categories

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Expression

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Overview Transcription Translation Turnover Experimental Links References Suggestions

Overview

Cellular Levels

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Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)
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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)
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Notes

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_005856:20312..20352 source=bacteriophage_P1 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

Turnover and Regulation of Turnover

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Notes

Experimental

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

Type Reference Notes
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Expression Resources <protect> 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 Phage_P1_lydD Expression

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

Database Accession Notes
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Notes

Links

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References

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Categories

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Evolution

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Homologs Families Links References Suggestions

Homologs in Other Organisms

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Organism Homologs (Statistics) Comments
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Do-It-Yourself Web Tools

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Notes

Families

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Database Accession Notes
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Notes

Links

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References

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Categories

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