Exiguobacterium sibiricum 255-15 plasmid pEXIG01, complete sequence.
type: Entry
definition: Exiguobacterium sibiricum 255-15 plasmid pEXIG01, complete sequence.
sequence version: NC_010549.1
sequence date: 2022-12-12
sequence: sequence
division: CON
label: NC_010549.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN00120225
keyword: RefSeq
source: Exiguobacterium sibiricum 255-15
organism: Exiguobacterium sibiricum 255-15
taxonomy: Bacteria; Firmicutes; Bacilli; Bacillales; Bacillales Family XII. Incertae Sedis; Exiguobacterium.
reference: 1
references: 16489412
reference: 2
reference: 3
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP001023.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 2662203\nSource DNA and bacteria available from James Tiedje\n(tiedjej@msu.edu)\nContacts: James Tiedje (tiedjej@msu.edu)\n Paul Richardson (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. it is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/12/2022 13:46:57\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,155\nCDSs (total) :: 3,055\nGenes (coding) :: 3,024\nCDSs (with protein) :: 3,024\nGenes (RNA) :: 100\nrRNAs :: 9, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 9, 9 (5S, 16S, 23S)\ntRNAs :: 69\nncRNAs :: 4\nPseudo Genes (total) :: 31\nCDSs (without protein) :: 31\nPseudo Genes (ambiguous residues) :: 0 of 31\nPseudo Genes (frameshifted) :: 12 of 31\nPseudo Genes (incomplete) :: 14 of 31\nPseudo Genes (int…

sequence
subclass of: SO_0000155
sequence length: 4885
topology: circular
so has quality: SO_0000988
location: 1..4885
location: region:1-4885:1
RO_0002162: 262543

NC_010549
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN00120225
type: BioSample
SIO_000068: biosample

1
title: Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov
author: Rodrigues, D.F.
author: Goris, J.
author: Vishnivetskaya, T.
author: Gilichinsky, D.
author: Thomashow, M.F.
author: Tiedje, J.M.
journal: Extremophiles
volume: 10
issue: 4
pages: 285-294
year: 2006
pubmed: 16489412

16489412
type: PubMed
SIO_000068: pubmed

2
title: Complete sequence of plasmid1 of Exiguobacterium sibiricum 255-15
author: Copeland, A.
author: Lucas, S.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Kiss, H.
author: Chertkov, O.
author: Monk, C.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Kuske, C.R.
author: Schmutz, J.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Mikhailova, N.
author: Vishnivetskaya, T.
author: Rodrigues, D.F.
author: Gilichinsky, D.
author: Tiedje, J.
author: Richardson, P.
journal: Unpublished

3
title: Direct Submission
author: Copeland, A.
author: Lucas, S.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Kiss, H.
author: Chertkov, O.
author: Monk, C.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Kuske, C.R.
author: Schmutz, J.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Mikhailova, N.
author: Vishnivetskaya, T.
author: Rodrigues, D.F.
author: Gilichinsky, D.
author: Tiedje, J.
author: Richardson, P.
journal: Submitted (02-APR-2008) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA

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

position:4885:1
position: 4885
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4885:1:source
so part of: sequence
organism: Exiguobacterium sibiricum 255-15
mol type: genomic DNA
strain: 255-15
type material: type strain of Exiguobacterium sibiricum
plasmid: pEXIG01

262543
type: Taxonomy
SIO_000068: taxonomy

EXIG_RS15515
type: Gene
subclass of: SO_0000704
RO_0002162: 262543
locus tag: EXIG_RS15515
old locus tag: Exig_3051
so part of: sequence
location: 240..707
location: region:240-707:1
so has part: feature:240-707:1:exon
subclass of: SO_0000010

position:240:1
position: 240
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:707:1
position: 707
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:240-707:1:exon

EXIG_RS15515
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 262543
locus tag: EXIG_RS15515
old locus tag: Exig_3051
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016510962.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKNMDLTILDVIEFNKQMKFLDVAKTHAPVGREKLREAMKLAGATFDQQTKRWHIQEGHPNEKKRVLDFVQSSRITKPNQEKAQDPLRVDPVTGQSQLDDGYFEIETKPEKIIRKKVSLDLDVTLHKRLKHTALEKDVKLYELIEGILRNYIEKK
SIO_010081: EXIG_RS15515
subclass of: SO_0000673
so part of: EXIG_RS15515
location: 240..707
location: region:240-707:1
so has part: feature:240-707:1:exon

WP_012362680.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:240-707:1:exon

EXIG_RS15520
type: Gene
subclass of: SO_0000704
RO_0002162: 262543
locus tag: EXIG_RS15520
old locus tag: Exig_3052
so part of: sequence
location: complement(758..1009)
location: region:758-1009:-1
so has part: feature:758-1009:-1:exon
subclass of: SO_0000010

position:758:-1
position: 758
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1009:-1
position: 1009
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:758-1009:-1:exon

EXIG_RS15520
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 262543
locus tag: EXIG_RS15520
old locus tag: Exig_3052
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: MKNAKNILIANSIVLIIILIAQLISPSIGSYLLDSKIEFLDENSTYWIAKLIETSSVQGFCLLVGLLNISLIAVSVNHLLKQK
SIO_010081: EXIG_RS15520
subclass of: SO_0000673
so part of: EXIG_RS15520
location: complement(758..1009)
location: region:758-1009:-1
so has part: feature:758-1009:-1:exon

WP_012362681.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:758-1009:-1:exon

EXIG_RS15525
type: Gene
subclass of: SO_0000704
RO_0002162: 262543
locus tag: EXIG_RS15525
old locus tag: Exig_3053
so part of: sequence
location: complement(1030..1737)
location: region:1030-1737:-1
so has part: feature:1030-1737:-1:exon
subclass of: SO_0000010

position:1030:-1
position: 1030
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1737:-1
position: 1737
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1030-1737:-1:exon

EXIG_RS15525
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 262543
locus tag: EXIG_RS15525
old locus tag: Exig_3053
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: MKKYKFLFPALLMTTFISSNVIHAEEPSIDPDLIEEVDSIGVNEDTSELVEGIDYDIEEATVYSEESSDLENSNFESSAPLQSSSNNDRITPSMVLMPGPEYKFSGVKYIKETIGKSILWKTSGVPGVTIGLDFTKSRNASVSTTYGASYHDISQSLSFTIGKSYSVSSSGSYKVPKSRGGKAIKRTEVTGQPIYKKYSVKVSKRNDILFRYDYKGLLYAYKPIGVHIKYKHYYK
SIO_010081: EXIG_RS15525
subclass of: SO_0000673
so part of: EXIG_RS15525
location: complement(1030..1737)
location: region:1030-1737:-1
so has part: feature:1030-1737:-1:exon

WP_012362682.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1030-1737:-1:exon

EXIG_RS15530
type: Gene
subclass of: SO_0000704
RO_0002162: 262543
locus tag: EXIG_RS15530
old locus tag: Exig_3054
so part of: sequence
location: complement(2550..2891)
location: region:2550-2891:-1
so has part: feature:2550-2891:-1:exon
subclass of: SO_0000010

position:2550:-1
position: 2550
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2891:-1
position: 2891
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2550-2891:-1:exon

EXIG_RS15530
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 262543
locus tag: EXIG_RS15530
old locus tag: Exig_3054
inference: COORDINATES: protein motif:HMM:NF022781.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF3139 domain-containing protein
translation: MKNKTIIYFMVILFLGIGLIGAWGYKTLYYDEKQSTSENIDGFLKENNYMQNVSTKEIVMDTTTDEYFAKVTFKDEPNNEYEIYQTGSNHFKIVGYKDGVQITNKKEGKYIKR
SIO_010081: EXIG_RS15530
subclass of: SO_0000673
so part of: EXIG_RS15530
location: complement(2550..2891)
location: region:2550-2891:-1
so has part: feature:2550-2891:-1:exon

WP_012362683.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2550-2891:-1:exon

EXIG_RS15650
type: Gene
subclass of: SO_0000704
RO_0002162: 262543
locus tag: EXIG_RS15650
old locus tag: Exig_3055
so part of: sequence
location: 2961..3755
location: region:2961-3755:1
so has part: feature:2961-3755:1:exon
subclass of: SO_0000010

position:2961:1
position: 2961
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3755:1
position: 3755
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2961-3755:1:exon

EXIG_RS15650
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 262543
locus tag: EXIG_RS15650
old locus tag: Exig_3055
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016425717.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: YiiX/YebB-like N1pC/P60 family cysteine hydrolase
translation: MIKKSFGIATLVLSLALTSPNLSYAEDLSQSKNDLSKSTYSNFIGEGVVSETVSYNSWVDINTNDSFEELEEEFPVPDRLMEVDPSNEKDKSYSIPSVSYSIMAATSSKGPVLKKGDILVSNATSSYGLTGHAGIAISSSQVLHISGAGAHPKVISSKTWQDRYGIVKGQKEGSNIKTNVYRIKSTTNASKAANWAVKNYKGKKYDYIITPTISSKNPTYCSKIVWQAYRSIKAVNYPAGDIPTPYGLPKYFKKAQNLKGMGYL
SIO_010081: EXIG_RS15650
subclass of: SO_0000673
so part of: EXIG_RS15650
location: 2961..3755
location: region:2961-3755:1
so has part: feature:2961-3755:1:exon

WP_012362684.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2961-3755:1:exon