Borreliella valaisiana VS116 plasmid VS116_cp9, complete sequence.
type: Entry
definition: Borreliella valaisiana VS116 plasmid VS116_cp9, complete sequence.
sequence version: NC_012130.1
sequence date: 2023-04-24
sequence: sequence
division: CON
label: NC_012130.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02436326
keyword: RefSeq
source: Borreliella valaisiana VS116
organism: Borreliella valaisiana VS116
taxonomy: Bacteria; Spirochaetota; Spirochaetia; Spirochaetales; Borreliaceae; Borreliella.
reference: 1
references: 22207749
reference: 2
reference: 3
reference: 4
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP001438.1.\nThe chromosome for this strain has been deposited under the Whole\nGenome Shotgun project accession ABCY00000000. The DNA or cells for\nthis strains can be obtained from Sherwood Casjens (Univ. of Utah,\nsherwood.casjens@path.utah.edu) or Benjamin J. Luft (SUNY at Stony\nBrook, bluft@notes.cc.sunysb.edu).\nThe DNA or cells for this strains can be obtained from Sherwood\nCasjens (Univ. of Utah, sherwood.casjens@path.utah.edu) or Benjamin\nJ. Luft (SUNY at Stony Brook, bluft@notes.cc.sunysb.edu)\nThis WGS record is a draft assembly, and may contain collapsed\nrepeats, missassemblies and/or low quality consensus bases. The\nplasmids were deposited in GenBank Accession Numbers\nCP001432-CP001442.\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 :: 04/24/2023 01:26:40\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 1,249\nCDSs (total) :: 1,209\nGenes (coding) :: 1,142\nCDSs (with protein) :: 1,142\nGenes (RNA) :: 40\nrRNAs :: 2, 1, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 1, 2 (5S, 16S, 23S)\ntRNAs :: 32\nncRNAs :: 3\nPseudo Genes (total) :: 67\nCDSs (without protein) :: 67\nPseudo Genes (ambiguous residues) :: 0 of 67\nPseudo Genes (frameshifted) :: 49 of 67\nPseudo Genes (incomplete) :: 16 of 67\nPseudo Genes (internal stop) :: 41 of 67\nPseudo Genes (multiple problems) :: 33 of 67\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 9474
topology: circular
so has quality: SO_0000988
location: 1..9474
location: region:1-9474:1
RO_0002162: 445987

NC_012130
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02436326
type: BioSample
SIO_000068: biosample

1
title: Whole-genome sequences of Borrelia bissettii, Borrelia valaisiana, and Borrelia spielmanii
author: Schutzer, S.E.
author: Fraser-Liggett, C.M.
author: Qiu, W.G.
author: Kraiczy, P.
author: Mongodin, E.F.
author: Dunn, J.J.
author: Luft, B.J.
author: Casjens, S.R.
journal: J Bacteriol
volume: 194
issue: 2
pages: 545-546
year: 2012
pubmed: 22207749

22207749
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Fraser-Liggett, C.M.
author: Mongodin, E.F.
author: Casjens, B.
author: Dunn, J.
author: Luft, B.
author: Qiu, W.
author: Schutzer, S.
author: Sebastian, Y.
journal: Submitted (12-FEB-2009) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

3
title: Direct Submission
author: Fraser-Liggett, C.M.
author: Mongodin, E.F.
author: Casjens, B.
author: Dunn, J.
author: Luft, B.
author: Qiu, W.
author: Schutzer, S.
author: Sebastian, Y.
journal: Submitted (06-JAN-2009) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

4
title: Direct Submission
author: Fraser-Liggett, C.M.
author: Mongodin, E.F.
author: Casjens, S.
author: Dunn, J.
author: Luft, B.
author: Qiu, W.
author: Schutzer, S.
journal: Submitted (12-JUN-2007) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

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

position:9474:1
position: 9474
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9474:1:source
so part of: sequence
organism: Borreliella valaisiana VS116
mol type: genomic DNA
strain: VS116
type material: type strain of Borreliella valaisiana
plasmid: VS116_cp9

445987
type: Taxonomy
SIO_000068: taxonomy

BVAVS116_RS05350
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05350
old locus tag: BVAVS116_C0001
so part of: sequence
location: 164..1285
location: region:164-1285:1
so has part: feature:164-1285:1:exon
subclass of: SO_0000010

63641827
type: Gene
SIO_000068: ncbigene

position:164:1
position: 164
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1285:1
position: 1285
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:164-1285:1:exon

BVAVS116_RS05350
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05350
old locus tag: BVAVS116_C0001
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014540129.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid maintenance protein
translation: MKNLSNVNKTSKKTPCYNKLQHKLIVLISTLKYINTKYQKYTQKNILYYFNENLKRNGQTTTTLRTMQKYLYKLQKEIKVTTNYYKHMGVNFGTEIYYQLNFSKKECHTKINKYFQEKKHARFTSRVNNHLKDKFTKKGSVELGGCLSNKNNNIKEEKERKKKIEKFQIIKYANKCKFYCKEFLPIVLNLDISKNEKIKILKTVKRIEIKLIKGKNINLNKSCFKEKQNKLKEILENTKKQLEKKGYNAKQLKINFQKTYENYKNKPHFIIEYHKYNDLSTIKRKLEKSIELKKENPQKDYENIKTNIYNILIEQLKEKANIEFLKPIVKTYLNNKNKIEYKKVFGTYYYELLELIKDQKSLFNLKELDRKAI
SIO_010081: BVAVS116_RS05350
subclass of: SO_0000673
so part of: BVAVS116_RS05350
location: 164..1285
location: region:164-1285:1
so has part: feature:164-1285:1:exon

WP_012664768.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:164-1285:1:exon

BVAVS116_RS05355
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05355
old locus tag: BVAVS116_C0002
so part of: sequence
location: 1295..1846
location: region:1295-1846:1
so has part: feature:1295-1846:1:exon
subclass of: SO_0000010

63641828
type: Gene
SIO_000068: ncbigene

position:1295:1
position: 1295
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1846:1
position: 1846
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1295-1846:1:exon

BVAVS116_RS05355
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05355
old locus tag: BVAVS116_C0002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010890602.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF226 domain-containing protein
translation: MENLLKTTKTEERKFDFHKTSIFIMKEKKNDRNIYHTKILKEIHKVVSDKKQRCIVLFKDLFNESKIQNLYLYPIQEGDKFLGIFYGYKKPIKNILVQYKLDGVKKAYTFSKAYYIEFRFKTGSVFCYIKDIRRLLKKEKIDTQYNKALVERFLNLEKHVYEFYNKKYSSEGLIIKWILKNLK
SIO_010081: BVAVS116_RS05355
subclass of: SO_0000673
so part of: BVAVS116_RS05355
location: 1295..1846
location: region:1295-1846:1
so has part: feature:1295-1846:1:exon

WP_012664769.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1295-1846:1:exon

BVAVS116_RS05360
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05360
old locus tag: BVAVS116_C0003
so part of: sequence
location: 1822..2568
location: region:1822-2568:1
so has part: feature:1822-2568:1:exon
subclass of: SO_0000010

63641829
type: Gene
SIO_000068: ncbigene

position:1822:1
position: 1822
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2568:1
position: 2568
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1822-2568:1:exon

BVAVS116_RS05360
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05360
old locus tag: BVAVS116_C0003
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014017761.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ParA family protein
translation: MDFKKSKIITIANIKGGVGKSTSSIIFSILLAQKYKVLLIDMDTQASITSYFNKKIIENKFDLLKKNIYGVLKSNYLINDSIINVNNRLDLLPSYLSLHEFSEEILPYKTHRLKNSLKYLKFNYDYIIIDTNPHLDSTLSNALVISEHIMVPMAAEKWAIESLQLLEFFINKLKLNLKIFLFATKFKKNKTHKDLLAILQKNSRFLGIISEREDLNRRIAKNDDFDLDRDYIKEYVNILKHFNAKTRN
SIO_010081: BVAVS116_RS05360
subclass of: SO_0000673
so part of: BVAVS116_RS05360
location: 1822..2568
location: region:1822-2568:1
so has part: feature:1822-2568:1:exon

WP_012664770.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1822-2568:1:exon

BVAVS116_RS05365
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05365
old locus tag: BVAVS116_C0004
so part of: sequence
location: 2652..3209
location: region:2652-3209:1
so has part: feature:2652-3209:1:exon
subclass of: SO_0000010

63641830
type: Gene
SIO_000068: ncbigene

position:2652:1
position: 2652
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3209:1
position: 3209
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2652-3209:1:exon

BVAVS116_RS05365
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05365
old locus tag: BVAVS116_C0004
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014017762.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: chromosome replication/partitioning protein
translation: MSLGIKINDRIIAKEETKKNLNNKEEVIEHYNTLKTQLKSNLQQGVYSKIENMKILKEIKDNEYYKLDGYKNFNSFIKDYKLAKTQTYCYLRIAQAIENGVIEEPFLLENGIKETIIFLRNSNSEKIKKSKQNLIKPLRFQLKKQESYDFYKKNAKFTSFMMDEIFENQKEFLNRLMKKYEKLKV
SIO_010081: BVAVS116_RS05365
subclass of: SO_0000673
so part of: BVAVS116_RS05365
location: 2652..3209
location: region:2652-3209:1
so has part: feature:2652-3209:1:exon

WP_012664771.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2652-3209:1:exon

BVAVS116_RS05370
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05370
old locus tag: BVAVS116_C0005
so part of: sequence
location: 3482..4411
location: region:3482-4411:1
so has part: feature:3482-4411:1:exon
subclass of: SO_0000010

63641831
type: Gene
SIO_000068: ncbigene

position:3482:1
position: 3482
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4411:1
position: 4411
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3482-4411:1:exon

BVAVS116_RS05370
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05370
old locus tag: BVAVS116_C0005
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010258286.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ERF family protein
translation: MQNLNNNPQEINQAEIHFISDMKTLRMNLSGIEKNLKGYGYKYQNFNDIVEEIYNVIEKHNLQLDFKQFPTFTYDPYGRVHIVRTTFYSTNTGYKDSFYTPILTENLKWNNENGSKNVNTTPQLVGSSITYFKRYALVAYLNIRSEVDTDAAPINNNGYKNENSTMSSKQVSVNQEQKKDINQNQIKNFNKKLKIGKSYYYEIFRNALFNIKNWVNEDTEKSNIKALIRALCVDNDDVLDNIFEKDLKLKSIEYWAKILKDYFNKTNKLDDLNKFEKFMLDKESIYETSVLKFFCMLKEERQFDYIFLL
SIO_010081: BVAVS116_RS05370
subclass of: SO_0000673
so part of: BVAVS116_RS05370
location: 3482..4411
location: region:3482-4411:1
so has part: feature:3482-4411:1:exon

WP_012664772.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3482-4411:1:exon

BVAVS116_RS05375
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05375
old locus tag: BVAVS116_C0006
so part of: sequence
location: complement(4518..4745)
location: region:4518-4745:-1
so has part: feature:4518-4745:-1:exon
subclass of: SO_0000010

63641832
type: Gene
SIO_000068: ncbigene

position:4518:-1
position: 4518
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4745:-1
position: 4745
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4518-4745:-1:exon

BVAVS116_RS05375
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05375
old locus tag: BVAVS116_C0006
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: MIDIKKKLKLLEANVENNINLALNAVNKIETLEKNINLTINIVNRKMEILEKNLNKKIDNLISRIDTLEKNFNKK
SIO_010081: BVAVS116_RS05375
subclass of: SO_0000673
so part of: BVAVS116_RS05375
location: complement(4518..4745)
location: region:4518-4745:-1
so has part: feature:4518-4745:-1:exon

WP_051008163.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4518-4745:-1:exon

BVAVS116_RS05380
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05380
old locus tag: BVAVS116_C0007
so part of: sequence
location: complement(5197..5553)
location: region:5197-5553:-1
so has part: feature:5197-5553:-1:exon
subclass of: SO_0000010

63641833
type: Gene
SIO_000068: ncbigene

position:5197:-1
position: 5197
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5553:-1
position: 5553
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5197-5553:-1:exon

BVAVS116_RS05380
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05380
old locus tag: BVAVS116_C0007
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006434156.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSNINKYNLNSYDKKNLSQINIYNNVENIKKEISNIKENIVKDTSLLDNKILNLEIQMTDLENDIKDIKKEFYKTKALINTIFQEYYTKSILVLITIIPFITTIFSSIVLWIITKFSK
SIO_010081: BVAVS116_RS05380
subclass of: SO_0000673
so part of: BVAVS116_RS05380
location: complement(5197..5553)
location: region:5197-5553:-1
so has part: feature:5197-5553:-1:exon

WP_051008164.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5197-5553:-1:exon

BVAVS116_RS05385
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05385
old locus tag: BVAVS116_C0008
so part of: sequence
location: complement(5590..5778)
location: region:5590-5778:-1
so has part: feature:5590-5778:-1:exon
subclass of: SO_0000010

63641834
type: Gene
SIO_000068: ncbigene

position:5590:-1
position: 5590
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5778:-1
position: 5778
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5590-5778:-1:exon

BVAVS116_RS05385
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05385
old locus tag: BVAVS116_C0008
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: MKNKMFIFYVFVVLINSCKMHFGTIDKQTTSCKIHKKTKNELLMSCIHRYERQGLIISNLEN
SIO_010081: BVAVS116_RS05385
subclass of: SO_0000673
so part of: BVAVS116_RS05385
location: complement(5590..5778)
location: region:5590-5778:-1
so has part: feature:5590-5778:-1:exon

WP_012664775.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5590-5778:-1:exon

BVAVS116_RS05390
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05390
old locus tag: BVAVS116_C0010
so part of: sequence
location: 7061..7846
location: region:7061-7846:1
so has part: feature:7061-7846:1:exon
subclass of: SO_0000010

63641835
type: Gene
SIO_000068: ncbigene

position:7061:1
position: 7061
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7846:1
position: 7846
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7061-7846:1:exon

BVAVS116_RS05390
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05390
old locus tag: BVAVS116_C0010
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010258297.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: tyrosine-type recombinase/integrase
translation: MEINDYLDFKKNTAQALLKIHEDYQKILQIIGKNKTLKSSIKKSTENKQENSKPPAKLYLNPKTNQLIKKCVKTLKKIDPISGWFVHLLVISGCRGAELQKVKMQDISSFLSKTGKTLYNIKVNVVKKRINTCVREFVINSKEFNAIQKVHEDYFKEKNLNTSRTYFFQKTKHRFKDNRINIDHIAKKFKKLLRRWGFRANKSLHLCRNLFIFNLKASGYNSFQIKELMKYSSTYEIDNIYGLSSASKIQAYECVKDSIGL
SIO_010081: BVAVS116_RS05390
subclass of: SO_0000673
so part of: BVAVS116_RS05390
location: 7061..7846
location: region:7061-7846:1
so has part: feature:7061-7846:1:exon

WP_012664777.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7061-7846:1:exon

BVAVS116_RS05395
type: Gene
subclass of: SO_0000704
RO_0002162: 445987
locus tag: BVAVS116_RS05395
old locus tag: BVAVS116_C0011
pseudo: true
so part of: sequence
location: complement(7897..9261)
location: region:7897-9261:-1
so has part: feature:7897-9261:-1:exon
subclass of: SO_0000010

63641836
type: Gene
SIO_000068: ncbigene

position:7897:-1
position: 7897
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9261:-1
position: 9261
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7897-9261:-1:exon

BVAVS116_RS05395
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 445987
locus tag: BVAVS116_RS05395
old locus tag: BVAVS116_C0011
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006434155.1
note: internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: DUF244 domain-containing protein
SIO_010081: BVAVS116_RS05395
subclass of: SO_0000673
so part of: BVAVS116_RS05395
location: complement(7897..9261)
location: region:7897-9261:-1
so has part: feature:7897-9261:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:7897-9261:-1:exon