Neisseria musculi strain NW831 plasmid unnamed, complete sequence.
type: Entry
definition: Neisseria musculi strain NW831 plasmid unnamed, complete sequence.
sequence version: NZ_CP060415.1
sequence date: 2023-05-06
sequence: sequence
division: CON
label: NZ_CP060415.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN15791842
keyword: RefSeq
source: Neisseria musculi
organism: Neisseria musculi
taxonomy: Bacteria; Pseudomonadota; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria.
reference: 1
reference: 2
reference: 3
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP060415.1.\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 :: SMRT v. 8.0, HGAP v. 4.0, SPAdes v. 3.11.1\nGenome Coverage :: 1297.52x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 04:24:52\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) :: 2,982\nCDSs (total) :: 2,912\nGenes (coding) :: 2,747\nCDSs (with protein) :: 2,747\nGenes (RNA) :: 70\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 54\nncRNAs :: 4\nPseudo Genes (total) :: 165\nCDSs (without protein) :: 165\nPseudo Genes (ambiguous residues) :: 0 of 165\nPseudo Genes (frameshifted) :: 114 of 165\nPseudo Genes (incomplete) :: 67 of 165\nPseudo Genes (internal stop) :: 59 of 165\nPseudo Genes (multiple problems) :: 67 of 165\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4650
topology: circular
so has quality: SO_0000988
location: 1..4650
location: region:1-4650:1
RO_0002162: 1815583

NZ_CP060415
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN15791842
type: BioSample
SIO_000068: biosample

1
title: Complete Genome Sequence of mouse commensal type strain Neisseria musculi
author: Thapa, E.
author: Aluvathingal, J.
author: Nadendla, S.
author: Mehta, A.
author: Tettelin, H.
author: Weyand, N.J.
journal: Unpublished

2
title: Direct Submission
author: Thapa, E.
author: Aluvathingal, J.
author: Nadendla, S.
author: Mehta, A.
author: Tettelin, H.
author: Weyand, N.J.
journal: Submitted (21-SEP-2020) Department of Biological Sciences, Ohio University, 7 Depot Street, Life Sciences Building 233, Athens, OH 45701, USA
comments: Annotation update by submitter

3
title: Direct Submission
author: Thapa, E.
author: Aluvathingal, J.
author: Nadendla, S.
author: Mehta, A.
author: Tettelin, H.
author: Weyand, N.J.
journal: Submitted (19-AUG-2020) Department of Biological Sciences, Ohio University, 7 Depot Street, Life Sciences Building 233, Athens, OH 45701, USA

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

position:4650:1
position: 4650
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4650:1:source
so part of: sequence
organism: Neisseria musculi
mol type: genomic DNA
strain: NW831
isolation source: oral cavity
host: Mus musculus subsp. domesticus
plasmid: unnamed
country: USA: Arizona, Pima County, Tucson
lat lon: 32.208800 N 110.9207 W
collection date: 2012-10
collected by: Nathan Weyand

1815583
type: Taxonomy
SIO_000068: taxonomy

H7A79_RS14580
type: Gene
subclass of: SO_0000704
RO_0002162: 1815583
locus tag: H7A79_RS14580
so part of: sequence
location: join(4506..4650,1..623)
location: region:1-4650:1
so has part: feature:4506-4650:1:exon
so has part: feature:1-623:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:4506-4650:1:exon

position:4506:1
position: 4506
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-623:1:exon

position:623:1
position: 623
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

H7A79_RS14580
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1815583
locus tag: H7A79_RS14580
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: MobA/MobL family protein
translation: MATAHLSVKVGKAGKGTPHAEYISRTGKYAKKLEQGEKLEATESGNMPAWAEENPLTFWQAADQYERANGTVYREHEIALPRELTAEQRAELVREWVHHELGDCHAYIWAIHNKTALDGKPQPHVHLMYSERMNDGIERDPEQYFRRYNPKYPERGGAKKHRSGETPTERKAALTAQRERWEKLHNAHIDRHLPKTTLLEASRNHRAKISMKSLAEQGIDRQAAAKMTPSESAAMHRKAAADRAAQQAIDSIRAF
SIO_010081: H7A79_RS14580
subclass of: SO_0000673
so part of: H7A79_RS14580
location: join(4506..4650,1..623)
location: region:1-4650:1
so has part: feature:4506-4650:1:exon
so has part: feature:1-623:1:exon

WP_187001768.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4506-4650:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-623:1:exon

H7A79_RS14585
type: Gene
subclass of: SO_0000704
RO_0002162: 1815583
locus tag: H7A79_RS14585
old locus tag: H7A79_2794
so part of: sequence
location: complement(961..1365)
location: region:961-1365:-1
so has part: feature:961-1365:-1:exon
subclass of: SO_0000010

position:961:-1
position: 961
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1365:-1
position: 1365
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:961-1365:-1:exon

H7A79_RS14585
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1815583
locus tag: H7A79_RS14585
old locus tag: H7A79_2794
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: MAQQTADIKFLISGIIDGIWGKGIIANNTPENINDDVINVVNDVVERIKTCSKKMVRVDMTYNLLYSAPGTIWEVLAGLVADMAANGIKDPNNNVLATYFGWFDALRGNRQYRTCIVSAALYNRSRLEMAFLGI
SIO_010081: H7A79_RS14585
subclass of: SO_0000673
so part of: H7A79_RS14585
location: complement(961..1365)
location: region:961-1365:-1
so has part: feature:961-1365:-1:exon

WP_187001769.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:961-1365:-1:exon

H7A79_RS14590
type: Gene
subclass of: SO_0000704
RO_0002162: 1815583
locus tag: H7A79_RS14590
old locus tag: H7A79_2795
so part of: sequence
location: complement(1403..1555)
location: region:1403-1555:-1
so has part: feature:1403-1555:-1:exon
subclass of: SO_0000010

position:1403:-1
position: 1403
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1555:-1
position: 1555
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1403-1555:-1:exon

H7A79_RS14590
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1815583
locus tag: H7A79_RS14590
old locus tag: H7A79_2795
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: MKQKIKIIVSIVVGILTTGSLVAGCSSFKNGGDVHFQVDNPQVNATVSKQ
SIO_010081: H7A79_RS14590
subclass of: SO_0000673
so part of: H7A79_RS14590
location: complement(1403..1555)
location: region:1403-1555:-1
so has part: feature:1403-1555:-1:exon

WP_187001770.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1403-1555:-1:exon

H7A79_RS14595
type: Gene
subclass of: SO_0000704
RO_0002162: 1815583
locus tag: H7A79_RS14595
old locus tag: H7A79_2796
so part of: sequence
location: complement(1991..2269)
location: region:1991-2269:-1
so has part: feature:1991-2269:-1:exon
subclass of: SO_0000010

position:1991:-1
position: 1991
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2269:-1
position: 2269
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1991-2269:-1:exon

H7A79_RS14595
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1815583
locus tag: H7A79_RS14595
old locus tag: H7A79_2796
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013789853.1
GO function: GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO process: GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system RelE/ParE family toxin
translation: MLPVEWKLAARLDLIEIIDYIAQENPQAAEKMKRLLDDTAERLGEMPYINRRGRVAGTREKIAHRNYIIVYRITSDKVEILNIVHSRKNYPD
SIO_010081: H7A79_RS14595
subclass of: SO_0000673
so part of: H7A79_RS14595
location: complement(1991..2269)
location: region:1991-2269:-1
so has part: feature:1991-2269:-1:exon

WP_187001771.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1991-2269:-1:exon

H7A79_RS14600
type: Gene
subclass of: SO_0000704
RO_0002162: 1815583
locus tag: H7A79_RS14600
old locus tag: H7A79_2797
so part of: sequence
location: complement(2256..2450)
location: region:2256-2450:-1
so has part: feature:2256-2450:-1:exon
subclass of: SO_0000010

position:2256:-1
position: 2256
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2450:-1
position: 2450
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2256-2450:-1:exon

H7A79_RS14600
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1815583
locus tag: H7A79_RS14600
old locus tag: H7A79_2797
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010100874.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MNTAFLDPLIYEFDTVEEAESYDAWFRAKVEKSIADPTPSMPHDEAMAFVDAELERRRAARAAR
SIO_010081: H7A79_RS14600
subclass of: SO_0000673
so part of: H7A79_RS14600
location: complement(2256..2450)
location: region:2256-2450:-1
so has part: feature:2256-2450:-1:exon

WP_187001772.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2256-2450:-1:exon

H7A79_RS14605
type: Gene
subclass of: SO_0000704
RO_0002162: 1815583
locus tag: H7A79_RS14605
old locus tag: H7A79_2798
so part of: sequence
location: complement(2447..2683)
location: region:2447-2683:-1
so has part: feature:2447-2683:-1:exon
subclass of: SO_0000010

position:2447:-1
position: 2447
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2683:-1
position: 2683
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2447-2683:-1:exon

H7A79_RS14605
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1815583
locus tag: H7A79_RS14605
old locus tag: H7A79_2798
inference: COORDINATES: protein motif:HMM:NF019884.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: HTH domain-containing protein
translation: MPKARTDKRPFTARELAEKFKCSQVTIRKYWAQDRADYLAENSISRDKPWEHLGISRATWYRRRKPMPPETLTTGEKS
SIO_010081: H7A79_RS14605
subclass of: SO_0000673
so part of: H7A79_RS14605
location: complement(2447..2683)
location: region:2447-2683:-1
so has part: feature:2447-2683:-1:exon

WP_187001765.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2447-2683:-1:exon

H7A79_RS14610
type: Gene
subclass of: SO_0000704
RO_0002162: 1815583
locus tag: H7A79_RS14610
old locus tag: H7A79_2799
so part of: sequence
location: complement(2661..3527)
location: region:2661-3527:-1
so has part: feature:2661-3527:-1:exon
subclass of: SO_0000010

position:2661:-1
position: 2661
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3527:-1
position: 3527
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2661-3527:-1:exon

H7A79_RS14610
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1815583
locus tag: H7A79_RS14610
old locus tag: H7A79_2799
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003690219.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MQDRIPHKPYCKDFKDAPQLVRSYAYAIKRRYIQVNPPHLRVFMLHDLDYDGAALAWEDNNLPMPAWAAVNRENGHAHIAYALSAPVLTADYGGRQAALRYLAAVEAAYHAKLRCDDGFTSLITKNPEHPHWLTLRGVPDATRGYDLPYLAEFVDLDKFKPYVGRTNPEAMGLGRNCTVFNVVSRWAYRNIREFKFERGIREWKRAVLHQCLDVNSGFPCPMMLKEVQCIAKSISNWVWNRFDIAASDRRFAALQAHRNSLRKTYGAGSGREKNEFAEWLKNAKSTNR
SIO_010081: H7A79_RS14610
subclass of: SO_0000673
so part of: H7A79_RS14610
location: complement(2661..3527)
location: region:2661-3527:-1
so has part: feature:2661-3527:-1:exon

WP_246408200.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2661-3527:-1:exon

H7A79_RS14615
type: Gene
subclass of: SO_0000704
RO_0002162: 1815583
locus tag: H7A79_RS14615
old locus tag: H7A79_2800
so part of: sequence
location: complement(3834..4301)
location: region:3834-4301:-1
so has part: feature:3834-4301:-1:exon
subclass of: SO_0000010

position:3834:-1
position: 3834
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4301:-1
position: 4301
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3834-4301:-1:exon

H7A79_RS14615
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1815583
locus tag: H7A79_RS14615
old locus tag: H7A79_2800
inference: COORDINATES: protein motif:HMM:NF018152.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: conjugal transfer protein TraD
translation: MAVFSERMTAFVSSRISYLKNLKNQTEQQQMFVELGRKFLNGEELSASELRGLKTLATAEKAAEKAAEATRAAHKLVSEKNEKARKERTRNMINAAGLMGLAGLLDKKTGRPLTSPDLLLGALVELANRNPTDLEKQSWEQSGTALLAKAKADKD
SIO_010081: H7A79_RS14615
subclass of: SO_0000673
so part of: H7A79_RS14615
location: complement(3834..4301)
location: region:3834-4301:-1
so has part: feature:3834-4301:-1:exon

WP_187001767.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3834-4301:-1:exon