Pseudomonas Genome Database - Annotation for PA1056

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PA1056

Key to diagram

View in GBrowse:

15 putative orthologs

View metabolic pathways using PseudoCyc

Acknowledgements for this annotation

Overview
Functional Data
Sequence Data
Operons/Regulons
Polymorphisms
References

Gene Information
Strain	Pseudomonas aeruginosa PAO1 (Tax ID: 208964)	Replicon	Chromosome(5651 genes, 6264404 bp) [ RefSeq ]
Gene name		Alternate Gene Names	phaD
Locus tag	PA1056 (View 9 updates) Submit an Update	GenBank Identifier (GI)	15596253 (Precomputed BLAST results at BLINK )
Genomic location	1145197 - 1146696 (+)	Feature type	CDS
Transposon Mutant Available?	No transposon mutant available yet	Pseudomonas Ortholog Group	POG001018
Product Information
Product Name	probable NADH dehydrogenase (Class 3 )
Alternate Product Names
Subcellular localization	Cytoplasmic Membrane (Class 3)
Alternate Annotations and Cross-References
TIGR	NTL03PA01057
Systomonas	PA1056
RefSeq	NP_249747.1
GI	15596253
KEGG	PA1056
GBrowse	Click here for a GBrowse View of this and other annotations.
PseudoCyc	Click here to view metabolic pathways in PseudoCyc.

Operons/Regulons

Type

operon

Genes

Gene	Product
PA1054	probable NADH dehydrogenase
PA1055	conserved hypothetical protein
PA1056	probable NADH dehydrogenase
PA1057	conserved hypothetical protein
PA1058	conserved hypothetical protein
PA1059	conserved hypothetical protein

Evidence

Computationally Predicted

PubMed

18988623

Cross-Reference

DOOR-13331

Genomic Context

Genomic context

- This is in a cluster of genes homologous to the phaABCDEFG locus of Rhizobium meliloti.

Function Classification / Gene Ontology (GO)

PseudoCAP Function Class

Membrane proteins
Putative enzymes

GO Accession

GO Term

Evidence

Molecular Function

GO:0005451

monovalent cation:proton antiporter activity

IEA

Biological Process

GO:0015672	monovalent inorganic cation transport	IEA
GO:0015992	proton transport	IEA

Cellular Component

COG Prediction

Accession	Description	Category
COG0651	HyfB, Formate hydrogenlyase subunit 3/Multisubunit Na+/H+ antiporter, MnhD subunit [Energy production and conversion / Inorganic ion transport and metabolism].	Energy production and conversion / Inorganic ion transport and metabolism

Homology

BLINK

Precomputed BLAST results at BLINK

Homologs

58% similar to phaD [Sinorhizobium meliloti]

Structure Features

14 predicted transmembrane helices
PF00361: NADH-Ubiquinone/plastoquinone (complex I), various chains
14 predicted transmembrane helices (TMHMM v.2.0)
At least one transmembrane helix predicted by Phobius

PFAM predictions

Accession	Domain	Start	Stop	E-value	Release No.
PF00361	Oxidored_q1, NADH-Ubiquinone/plastoquinone (complex I), various chains.	124	402	3e-20	23.0

Microarray Expression Data

NCBI GEO

Link

Upstream 500 BP Region

CGGCCACTTCGAGTTGCCGCTGATCGGCGAGATCGAGCTGGCCACGGCGATGCTGTTCGACCTCGGCGTGTACCTCACCGTGGTCGGTGCCGCGCTGCTG ATCCTGTCCTACCTCGGCAAGCTCAGCCTGATGCCTGAACCCGTCGCACAAGAGGAGGCGCTCTGATGGAAGCCCTGTTCGCCATCACCCTCGGCCTGCT CACCGCCAGCGGCGTCTACCTGCTGCTGCGGGCGAGGACTTTCCCGGTGGTGCTCGGTCTCACGCTGATCTCCTACGCGGTCAACCTGTTCCTGTTCGCC ATGGGCCGACTCGGCGGCAGCGTCGCGGTGATCGGCACTCCCGGGGAGTATGGTGATCCGTTGCCGCAGGCGCTGGTGCTGACCGCCATCGTCATCGGCT TCGCCATGACCGCCTTTGTCGTTGTCCTGGCCCTGCGTGGCCTCGGTGACCTCGGCAGCGACCACGTAGATGGACGCCCGGACGAGGAGGAGCCGCGCCC

Need more than 500 BP? Try our sequence retrieval tool or view intergenic regions in GBrowse.

DNA Sequence

ATGAGCCATTGGCTGATCCTGCCGATCCTGCTCCCCCTGTTTGCCGGCAGCCTGCTGCTGTTGCCGCTGGCCGAGCGCTGGCAGCGCGGCCTGTCGTTGC TCGCGGCGCTGGCACTGATCCCCCTGAGCCTACTGCTGATACGTACGGCCGCCAGCGGCGACCTGAGCGTCTATGCCCTGGGCAACTGGGCCGCGCCGTT CGGCATCGTGCTCATGCTCGATCGTCTCGCCGCCCTGATGCTGCTGGCCACCGCGGTGCTCGGCAGCGCCGCGCTGATCTACGCGCTGCGTGGCGAGGAC CGCCTGGGCAAGCATTTCCACGCGTTGTTCCAGTTCCAGCTGCTCGGTATCAACGGCGCCTTCCTGACCGGCGACCTGTTCAACCTGTTCGTGTTCTTCG AGATACTCCTGATCGCCTCCTACGCGTTGCTCCTGCATGGCGGCGGCGCGGAGCGGGTGCGCTCGGGCTTGCACTACGTGATCCTAAACCTGGTCGGCTC GGCGTTCTTCCTGATCGCCGTGGGTACCCTGTATGGCCTCACCGGCACCCTGAACATGGCCGACATGGCGCAGAAGATCGCCATGGCAGATGCCGAGCGC GCGCCGCTGCTGGCGGCAGCCGGGCTCCTGCTGCTGGTGGTGTTCGCCCTGAAGGCGGCGCTGTTGCCGCTGTACTTCTGGCTGCCGCGCGCCTATGCCA CGGCCAGCGCGCCGGTGGCGGCGCTGTTCGCGATCATGACCAAGGTCGGCATCTACTCGATCCTGCGGGTCTACACGCTGGTCTTCGGCGATGCCGCCGG CGAGCTGGCCAACCTGGCGCAGGCCTGGCTCTGGCCGCTGGCCCTGGCGACCCTCGGCCTGGGCGCGATCGGTGCCTTGGCGGCGCGGACCCTGCAAGGC CTGCTGGCCTACCTGGTGGTGGTCTCCGCCGGAACCCTCCTGGCTGGCGTGGCGTTGGGCAGCGAGCGGGCGCTGGCGGCGTCGCTGTACTACCTGCTGC ACAGTACCTGGATCGCCGGTGGCCTGTTCCTGCTCGCCGACCTGGTCGCCCGCCAGCGCGGCGACAAGGCCGGCGACCTGGTCCAGGGCCCGGCGTTGCA GAATCCTCGGTTGCTCGGCGGGGCTTTCTTCATCGGCGCCATCGCCGTTGCCGGTCTGCCGCCATTGTCGGGGTTCTTCGGCAAGGTCATGCTTTTGCAG TCGGTCGCTCCCGGCAGCCAGGCGCTGGCCCTGTGGAGCGTGGTACTGGGCAGCGGCCTGGTGGCGCTGGTGGCGTTGAGCCGGGCCGGCAGCACGCTGT TCTGGCGCACCGGGCATACCGTGCTCGGTAGCGCCGAACTGGACCACGGCCGCTTGTTCGCCTGCATCCTGTTGCTCTCCGCCGGCCCGTTGCTGGTGTT CGCCGCGAAGCCGCTGCTGGCCTACGTCCAGGCCACCGCGGCGCAGTTGCACGACCTCGACCTGTATCGCCAGATCATCACCCGCGGAGGTGCCGCATGA

Downstream 500 BP region

Click here to view the nucleotide sequence of the region 500 BP downstream of this gene.

Protein Sequence

MSHWLILPILLPLFAGSLLLLPLAERWQRGLSLLAALALIPLSLLLIRTAASGDLSVYALGNWAAPFGIVLMLDRLAALMLLATAVLGSAALIYALRGED RLGKHFHALFQFQLLGINGAFLTGDLFNLFVFFEILLIASYALLLHGGGAERVRSGLHYVILNLVGSAFFLIAVGTLYGLTGTLNMADMAQKIAMADAER APLLAAAGLLLLVVFALKAALLPLYFWLPRAYATASAPVAALFAIMTKVGIYSILRVYTLVFGDAAGELANLAQAWLWPLALATLGLGAIGALAARTLQG LLAYLVVVSAGTLLAGVALGSERALAASLYYLLHSTWIAGGLFLLADLVARQRGDKAGDLVQGPALQNPRLLGGAFFIGAIAVAGLPPLSGFFGKVMLLQ SVAPGSQALALWSVVLGSGLVALVALSRAGSTLFWRTGHTVLGSAELDHGRLFACILLLSAGPLLVFAAKPLLAYVQATAAQLHDLDLYRQIITRGGAA

BLAST search against this genome or other genomes in database
View precomputed BLAST results against all genomes at NCBI BLINK

SNPs

NOTE: This feature is currently open to beta-testing. We welcome feedback on how to improve this new resource. Please send any comments to pseudocap-mail@sfu.ca.

Showing SNPs occurring in PA1056 gene of Pseudomonas aeruginosa PAO1, Chromosome (1145197 to 1146696 bp)

Displaying the first five SNPs out of a total of 167 found in all isolate strains ( View all 167 )

Strain	Type	Mutation Description		Effect	Details	GBrowse
		DNA	Protein
Pseudomonas aeruginosa PA7	Transition	g.1145202C>T		Silent AGC(Ser) -> AGT(Ser)	SNP-417749	View
Pseudomonas aeruginosa PA7	Transition	g.1145205T>C		Silent CAT(His) -> CAC(His)	SNP-417750	View
Pseudomonas aeruginosa PA7	Transversion	g.1145227C>G	p.Leu11Val	Missense CTC(Leu) -> GTC(Val)	SNP-417751	View
Pseudomonas aeruginosa PA7	Transversion	g.1145232C>G		Silent CCC(Pro) -> CCG(Pro)	SNP-417752	View
Pseudomonas aeruginosa PA7	Transition	g.1145238T>C		Silent TTT(Phe) -> TTC(Phe)	SNP-417753	View

Select to view SNPs in a specific strain

SNP Map

PubMed

Genome-wide identification of Pseudomonas aeruginosa exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen.
Lewenza S, Gardy JL, Brinkman FS, Hancock RE.
Genome Res. 2005 Feb;15(2):321-9.
PMID: 15687295
The pha gene cluster of Rhizobium meliloti involved in pH adaptation and symbiosis encodes a novel type of K+ efflux system.
Putnoky P, Kereszt A, Nakamura T, Endre G, Grosskopf E, Kiss P, Kondorosi A.
Mol Microbiol. 1998 Jun;28(6):1091-101.
PMID: 9680201