Edwardsiella ictaluri strain S07-698 plasmid pEI-A07-698-1, complete sequence.
type: Entry
definition: Edwardsiella ictaluri strain S07-698 plasmid pEI-A07-698-1, complete sequence.
sequence version: NZ_CP084522.1
sequence date: 2023-03-26
sequence: sequence
division: CON
label: NZ_CP084522.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN08930813
keyword: RefSeq
source: Edwardsiella ictaluri
organism: Edwardsiella ictaluri
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Hafniaceae; Edwardsiella.
reference: 1
reference: 2
reference: 3
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP084522.1.\nBacteria and source DNA available from Matt Griffin.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: Canu v. 2.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 177.0x\nSequencing Technology :: Illumina; Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/26/2023 06:53:03\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,632\nCDSs (total) :: 3,505\nGenes (coding) :: 3,272\nCDSs (with protein) :: 3,272\nGenes (RNA) :: 127\nrRNAs :: 9, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 8, 8 (5S, 16S, 23S)\ntRNAs :: 97\nncRNAs :: 5\nPseudo Genes (total) :: 233\nCDSs (without protein) :: 233\nPseudo Genes (ambiguous residues) :: 0 of 233\nPseudo Genes (frameshifted) :: 126 of 233\nPseudo Genes (incomplete) :: 155 of 233\nPseudo Genes (internal stop) :: 70 of 233\nPseudo Genes (multiple problems) :: 96 of 233\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5643
topology: circular
so has quality: SO_0000988
location: 1..5643
location: region:1-5643:1
RO_0002162: 67780

NZ_CP084522
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN08930813
type: BioSample
SIO_000068: biosample

1
title: Comparative genomics of Edwardsiella genus reveals species-based diversity
author: Tekedar, H.C.
author: Kumru, S.
author: Waldbieser, G.C.
author: Reichley, S.R.
author: Lawrence, M.L.
author: Griffin, M.J.
journal: Unpublished

2
title: Direct Submission
author: Tekedar, H.C.
author: Kumru, S.
author: Waldbieser, G.C.
author: Reichley, S.R.
author: Lawrence, M.L.
author: Griffin, M.J.
journal: Submitted (25-SEP-2021) College of Veterinary Medicine, Department of Comparative Biomedical Sciences, Mississippi State University, 127 Experiment Station Road, Stoneville, MS 38776, USA

3
title: Direct Submission
author: Tekedar, H.C.
author: Reichley, S.R.
author: Kumru, S.
author: Waldbieser, G.C.
author: Lawrence, M.L.
author: Griffin, M.J.
journal: Submitted (17-APR-2018) College of Veterinary Medicine, Mississippi State University, 127 Experiment Station Road, Stoneville, MS 38776, USA

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5643:1
position: 5643
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5643:1:source
so part of: sequence
organism: Edwardsiella ictaluri
mol type: genomic DNA
strain: S07-698
host: Ictalurus punctatus
plasmid: pEI-A07-698-1
country: USA
collection date: 2007

67780
type: Taxonomy
SIO_000068: taxonomy

DB741_RS18150
type: Gene
subclass of: SO_0000704
RO_0002162: 67780
locus tag: DB741_RS18150
old locus tag: DB741_18140
so part of: sequence
location: complement(430..1428)
location: region:430-1428:-1
so has part: feature:430-1428:-1:exon
subclass of: SO_0000010

69540753
type: Gene
SIO_000068: ncbigene

position:430:-1
position: 430
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1428:-1
position: 1428
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:430-1428:-1:exon

DB741_RS18150
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 67780
locus tag: DB741_RS18150
old locus tag: DB741_18140
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MLPINRIIATASHSTATHSVDTGATTRIGLATSANISFHEGPYTHKKQGVLYAPFASSDIVDMAIGKNMVRTKQSKPIYPLLSRNEQDKATLEQMRATLLSKWKEEYEAEILHLKEYIDQITQHGLTEKEARQHYPLGPEGFDNIQKRIVKYCALIDALTNLTIKSSNDLKSLSPDQHKLYVVGHGGAGMDILAEDPACQQGMVTAKEIAHQLAEGGLDKRFTDIRVTACWSADTCEPTSFQKSALDLASQPETQRSGFLGLFGKKEIVAEPFAQTLSNEMTREGFEQPRVSGYHGIGMTFSSFGEHNLRRLPESEESDARASTVRRVFIPA
SIO_010081: DB741_RS18150
subclass of: SO_0000673
so part of: DB741_RS18150
location: complement(430..1428)
location: region:430-1428:-1
so has part: feature:430-1428:-1:exon

WP_015396715.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:430-1428:-1:exon

DB741_RS18155
type: Gene
subclass of: SO_0000704
RO_0002162: 67780
locus tag: DB741_RS18155
old locus tag: DB741_18145
so part of: sequence
location: complement(1432..1854)
location: region:1432-1854:-1
so has part: feature:1432-1854:-1:exon
subclass of: SO_0000010

69540754
type: Gene
SIO_000068: ncbigene

position:1432:-1
position: 1432
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1854:-1
position: 1854
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1432-1854:-1:exon

DB741_RS18155
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 67780
locus tag: DB741_RS18155
old locus tag: DB741_18145
inference: COORDINATES: protein motif:HMM:NF015482.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTVISTNVLQAQIGNMLTGFGLPLDTLHTLAAERTLALQLEGLPDLMLSLVEEEIWLWSMLQNLSTNRLIDCAPAVLTQLIRPVDGILGGQLTLGEGEKGYELKGQVNPRWLDQENGLLITTQGFIRLLAVFCHATETDN
SIO_010081: DB741_RS18155
subclass of: SO_0000673
so part of: DB741_RS18155
location: complement(1432..1854)
location: region:1432-1854:-1
so has part: feature:1432-1854:-1:exon

WP_020846157.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1432-1854:-1:exon

DB741_RS18160
type: Gene
subclass of: SO_0000704
RO_0002162: 67780
locus tag: DB741_RS18160
old locus tag: DB741_18150
so part of: sequence
location: complement(2396..2839)
location: region:2396-2839:-1
so has part: feature:2396-2839:-1:exon
subclass of: SO_0000010

69540755
type: Gene
SIO_000068: ncbigene

position:2396:-1
position: 2396
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2839:-1
position: 2839
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2396-2839:-1:exon

DB741_RS18160
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 67780
locus tag: DB741_RS18160
old locus tag: DB741_18150
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTTKTTTLSIRISSEMRHELEALAEKNRLSLSDFVKRTLCENMTGRRFEQAQNELTRLESSARNIDRQTAKLAGEHRELLEKTQNRGKEMLKVIAAVQRQTADLSTAIDGIRTRERWERFTTLLICAMFLLIFGFAGTCAAYWLLIS
SIO_010081: DB741_RS18160
subclass of: SO_0000673
so part of: DB741_RS18160
location: complement(2396..2839)
location: region:2396-2839:-1
so has part: feature:2396-2839:-1:exon

WP_108986482.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2396-2839:-1:exon

DB741_RS18165
type: Gene
subclass of: SO_0000704
RO_0002162: 67780
locus tag: DB741_RS18165
old locus tag: DB741_18155
so part of: sequence
location: 3645..4586
location: region:3645-4586:1
so has part: feature:3645-4586:1:exon
subclass of: SO_0000010

69540756
type: Gene
SIO_000068: ncbigene

position:3645:1
position: 3645
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4586:1
position: 4586
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3645-4586:1:exon

DB741_RS18165
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 67780
locus tag: DB741_RS18165
old locus tag: DB741_18155
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010848986.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MTSPALSLFCEHLPRKPYHTNELLHGVRIGAASRAMLARYIQHNQPHAMYWLVFDVDRLGAAIDWSDVNAPTPNLTVKNPANGHAHLLYALDTAVRTAPDNSSLKALRYAAAIERGLRDKLRADLGYSSLLCKNPLHDYWGVTEWRSEPYTLDELADYVDLSASDPRREAQAYGLGRNCQLFEKTRTWSYRAIRQGWPEYDQWLSAVIQRVEAYNAQLTVPLSLAECKAIGKSIAKWTHQRITEQGFAQYVADTHTPEIQAARGGRNTHESQAAKGRKSKRGAVEDSARSLKPWEALGISRRWYYQKKKRGLL
SIO_010081: DB741_RS18165
subclass of: SO_0000673
so part of: DB741_RS18165
location: 3645..4586
location: region:3645-4586:1
so has part: feature:3645-4586:1:exon

WP_010895416.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3645-4586:1:exon

DB741_RS18170
type: Gene
subclass of: SO_0000704
RO_0002162: 67780
locus tag: DB741_RS18170
old locus tag: DB741_18160
pseudo: true
so part of: sequence
location: <4679..>4789
location: region:4679-4789:1
so has part: feature:4679-4789:1:exon
subclass of: SO_0000010

69540757
type: Gene
SIO_000068: ncbigene

position:4679:1
position: 4679
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

position:4789:1
position: 4789
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4679-4789:1:exon

DB741_RS18170
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 67780
locus tag: DB741_RS18170
old locus tag: DB741_18160
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012477181.1
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO process: GO:0006313 - transposition, DNA-mediated [Evidence IEA]
note: internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: IS1 family transposase
SIO_010081: DB741_RS18170
subclass of: SO_0000673
so part of: DB741_RS18170
location: <4679..>4789
location: region:4679-4789:1
so has part: feature:4679-4789:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4679-4789:1:exon

DB741_RS18175
type: Gene
subclass of: SO_0000704
RO_0002162: 67780
locus tag: DB741_RS18175
old locus tag: DB741_18165
so part of: sequence
location: complement(4878..5240)
location: region:4878-5240:-1
so has part: feature:4878-5240:-1:exon
subclass of: SO_0000010

69540758
type: Gene
SIO_000068: ncbigene

position:4878:-1
position: 4878
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5240:-1
position: 5240
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4878-5240:-1:exon

DB741_RS18175
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 67780
locus tag: DB741_RS18175
old locus tag: DB741_18165
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MISNNMIKCNVFHDLHIPNDAAESDVETYKNDLSERISCEYNTDSEEVFILASPEELKDTESLSLAVSPKALHQAISCELAKMTDHELRERDMVETGKEIKPDDEVTKLHEYIIRANGYV
SIO_010081: DB741_RS18175
subclass of: SO_0000673
so part of: DB741_RS18175
location: complement(4878..5240)
location: region:4878-5240:-1
so has part: feature:4878-5240:-1:exon

WP_049640979.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4878-5240:-1:exon