Kingella oralis strain DSM 18271 plasmid pDSM18271, complete sequence.
type: Entry
definition: Kingella oralis strain DSM 18271 plasmid pDSM18271, complete sequence.
sequence version: NZ_CP059568.1
sequence date: 2023-05-06
sequence: sequence
division: CON
label: NZ_CP059568.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN15603182
keyword: RefSeq
source: Kingella oralis
organism: Kingella oralis
taxonomy: Bacteria; Pseudomonadota; Betaproteobacteria; Neisseriales; Neisseriaceae; Kingella.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP059568.1.\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 :: HGAP v. 4.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 155x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 02:50:13\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) :: 2,639\nCDSs (total) :: 2,567\nGenes (coding) :: 2,539\nCDSs (with protein) :: 2,539\nGenes (RNA) :: 72\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 4\nPseudo Genes (total) :: 28\nCDSs (without protein) :: 28\nPseudo Genes (ambiguous residues) :: 0 of 28\nPseudo Genes (frameshifted) :: 9 of 28\nPseudo Genes (incomplete) :: 16 of 28\nPseudo Genes (internal stop) :: 5 of 28\nPseudo Genes (multiple problems) :: 2 of 28\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 16033
topology: circular
so has quality: SO_0000988
location: 1..16033
location: region:1-16033:1
RO_0002162: 505

NZ_CP059568
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN15603182
type: BioSample
SIO_000068: biosample

1
title: Genomic diversity of species in the Neisseriaceae family
author: Vincent, A.T.
author: Bernet, E.
author: Veyrier, F.J.
journal: Unpublished

2
title: Direct Submission
author: Vincent, A.T.
author: Bernet, E.
author: Veyrier, F.J.
journal: Submitted (22-JUL-2020) Microbiology, INRS-Institut Armand-Frappier, 531 Bd des Prairies, Laval, Quebec H7V1B7, Canada

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

position:16033:1
position: 16033
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-16033:1:source
so part of: sequence
organism: Kingella oralis
mol type: genomic DNA
strain: DSM 18271
isolation source: supragingival plaque, periodontitis
culture collection: ATCC:51147
culture collection: DSM:18271
type material: type strain of Kingella oralis
plasmid: pDSM18271
country: USA
collection date: 2006

505
type: Taxonomy
SIO_000068: taxonomy

H3L93_RS00005
type: Gene
subclass of: SO_0000704
RO_0002162: 505
locus tag: H3L93_RS00005
old locus tag: H3L93_00005
so part of: sequence
location: complement(join(14257..16033,1..7883))
location: region:1-16033:-1
so has part: feature:1-7883:-1:exon
so has part: feature:14257-16033:-1:exon
subclass of: SO_0000010

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

position:16033:-1
position: 16033
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-7883:-1:exon

position:7883:-1
position: 7883
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:14257-16033:-1:exon

position:14257:-1
position: 14257
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

H3L93_RS00005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 505
locus tag: H3L93_RS00005
old locus tag: H3L93_00005
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: hemagglutinin repeat-containing protein
translation: MPSTTVKKHKQRSQRFALRPLAVSLLGILTSASVWADGIVADPNAPRGQQPTVLQSNNGLPVVNIQTPTRAGVSVNQYRQFDVGEKGAVLNNSHRNVQTQLGGWIQGNPWLARGEARVIVNQVNSADPSRLNGYVEIGGRRADLVIANSAGINVNGGGFINANQVTLGVGNAAIQDGQYAGIVGGSGSLNIAAGGLDASRSDYTNLIANAVNVNGGIWANRLSVQAGGSSADTAAQPNTFAIDTGALGGMYAGTIHLMVNGAEQNSIRNAGQIFARAGEVRLDAAGNVVNSGSMVATGEAGSANLSAVRIQSQHLDNSGSIAANQLALNQTRITNSGHLLSAGEAQIQTGALHNSGQISGARLAVDTPFLHNSGTLQQTGLQGLALHSAQLTNSGKIGYPEPESSDATGNSGGQNGNAQISPAPSTAQGGGSVATHATTPIALAEGKINVQRLDNTGNITANGGIDLSNTAQLSNQGQLHLKQLTATGETLNNAGGKISAQNAAVSVAQFHNRQGQLAAEQIRVDSQRLDNTHGSLDAQALQLSAHTLDNSNGAIRSDKNTQLALSGSLKNQQGQISSAGAVSIQGQATASPTLNNDQGSILAGEQLSIQAQSLTGKGEIASGKDAEIAVRNDFTTENNLTAGRKLTLRTEGNLTNRHQLHADEAVVVAARQIDNQASGVIQSGQSTQLSADNITNRGLINSNGLTHLSSLNTLTNTGTGRIYGDHVALSAQDVVNREETVNGETKAGVIAARQRLDIGAKTVTNQEDALLFSDGGLFVGRQLNERHQAEGTAERVHNGSATIESIGDMVIDAKNLANRNNHFSIRHVPINDPTADIQPFQVGAVEKHHEIAAKGDPQRLPFSRFKVVGFSRATKLVDKAANEYSDADYELGRTPIPDSKMDYSPNSKLWRYFGIEPPKGEPKIPSVEKAEKPAALPEGTCDSAHASYNAAACQSYQQAWQKYETDKAEIEAYTQWEEQNAALFNALNDKVAAYNSQFHREIKDYTDFVFERRRYRDQIASSKPGNIRVGGNAQFTGAMTNDQSNILIGKQLFGGLERIHNVSMPAFEYVKDNGTRQYTYTRWRGGFKRYHTREWGNKDPYNPPAERHQINLNVSDVQENVSVTPNKPTDLYGSGGGQVSPINVPNARSDQNQNRIQLPNSSLYSTQPNHPDYLIETDPAFTNYRRWLGSDYLLAAFDPVNKHKRLGDGYYEQKLVNEQIARLTGYRRLDGYDNDEAQLKALMDAGITFARSQQLVPGVALSAAQVAQLTSDIVWLENQTVTLKDGSQQTVLVPKVYVVARKGDLNSTGSLISANVLQLNADEIRNGGTIAGRKVVDLRAQNIEHSGQIRGEKVWVEAQNQINLQGGDIAAGKLLSLTADQINASSTTATSGDKQNGNTVVDRVARLSVGEDGSEGGILSIQSKHDTHLNGAVVRNTSQGGKTQIVSEHGNVDLGTVATERHESYGRLSDKNHRHVHQTAEVGTDIQSQGDLLVKAGNDIKIRQGNLDSEKGLTALQAGHNIQISEGRSTLDFDESVYTQSKGVLSKRSSLDTYQRQHDEAQGSSVTGKTVYMNGDNIRAVGSSIVSDELTVLDARKDIDVQAATSRYHDIETSERKKSGFAVSVSHAKLNVGYNKSRSNVGHDADLQVAEAAQIGSLKGHTVLTAGNHVQVTGSNLLAGKDIDIQAKTVDIDAASLLQQENLTQSSKSSGFNVGINLKPGEVRQFSRYWDGIKATRKRQGTVRDKAHTWEKNHLAGALEPLTPSSGLSITRNTSSHSINETRTEATGSKVQAGGVVRINATDGDINIKGSNVFGKGGLQLQAANGEIHNLAAQEKSDVESSGFNRTSGLMGGGSIASRFIGSKTETTHEHNRSIQEVASTIGDGSPLGSVFEAQGYTQIGSNLLSGGHVDIYAKNIQIKAGEATQSNNRHYNFTQKGITVGVNAPITQAIDSAQSAVRSLEQAEQSGKQRTQAMAVANAGMQAYQASQAINKIGSGSKG…
SIO_010081: H3L93_RS00005
subclass of: SO_0000673
so part of: H3L93_RS00005
location: complement(join(14257..16033,1..7883))
location: region:1-16033:-1
so has part: feature:1-7883:-1:exon
so has part: feature:14257-16033:-1:exon

WP_182077681.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-7883:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:14257-16033:-1:exon

H3L93_RS00010
type: Gene
subclass of: SO_0000704
RO_0002162: 505
locus tag: H3L93_RS00010
old locus tag: H3L93_00010
so part of: sequence
location: 8079..9872
location: region:8079-9872:1
so has part: feature:8079-9872:1:exon
subclass of: SO_0000010

position:8079:1
position: 8079
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9872:1
position: 9872
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8079-9872:1:exon

H3L93_RS00010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 505
locus tag: H3L93_RS00010
old locus tag: H3L93_00010
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009426180.1
GO component: GO:0046930 - pore complex [Evidence IEA]
GO function: GO:0015288 - porin activity [Evidence IEA]
GO process: GO:0006811 - monoatomic ion transport [Evidence IEA]; GO:0015031 - protein transport [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ShlB/FhaC/HecB family hemolysin secretion/activation protein
translation: MPRKIQTHCTLSALLCTVSLSLPTTTLAQTPNEQLIQQQQQRDQFWQQQRMPQPDGRIENPSIPLPNPSISNTKSTASADANQAQCFAIQSVHLTGVNDTVSSADIAHFQPALRRALRQVGFVAGNCWGEQHINQLMVTMQNDVIGRGYTTTRILAAPQNLSEGTLVLAVLPGKVRSVRFEQKDAQEHTERITAFHNEFPIRAGELLNLRKIEQGLENLKRVPTAQTDIQIVPTEQLGESDIVVSWQQRTVPFRLTLSADDSGSKSTGRYQGNVTFSADNPLGLSDLFYISYGRALGHVPSQKGTDERREKGASQNFALHYSVPFGNWLWSFNHQNYRYHQAVAGNYTVYDYNGKSRSSDLGVSRLLYRDAKRKTHVGFKLWQRENSSYIDDAEIEVQHRKTAGWAASLSHKEYWGKATLDAQIHYKRGTGMQDALPAPEEVFNEGTSRMKIWTADIGLNLPMGKQGKWTLDSRWHGQWNKTPLTPLDRLAIGGRYTVRGFDGEMSLSAERGWYWRNELAWQYRAGHQIYAALDAGHVSGASAQYLLGQSLIGAAIGVRGQFQKGLSYDVFAAKPVHKPKYFTTAQKVYGFNVSWTF
SIO_010081: H3L93_RS00010
subclass of: SO_0000673
so part of: H3L93_RS00010
location: 8079..9872
location: region:8079-9872:1
so has part: feature:8079-9872:1:exon

WP_040559187.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8079-9872:1:exon

H3L93_RS00015
type: Gene
subclass of: SO_0000704
RO_0002162: 505
locus tag: H3L93_RS00015
old locus tag: H3L93_00015
so part of: sequence
location: 9930..10325
location: region:9930-10325:1
so has part: feature:9930-10325:1:exon
subclass of: SO_0000010

position:9930:1
position: 9930
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10325:1
position: 10325
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9930-10325:1:exon

H3L93_RS00015
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 505
locus tag: H3L93_RS00015
old locus tag: H3L93_00015
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009310048.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DNA-binding protein
translation: MAIVSVSEAARLVGKSRRTIQRDIAAGKLSKCDNGKKLDTSELIRVYGSLLNAPNDADKNAHMTQDVAPHISPDVAEMRIRLAALEAENAALKDHLGSLKQAMLLLEYKEHQATEATQQRKWWQFFKKSAD
SIO_010081: H3L93_RS00015
subclass of: SO_0000673
so part of: H3L93_RS00015
location: 9930..10325
location: region:9930-10325:1
so has part: feature:9930-10325:1:exon

WP_003799052.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:9930-10325:1:exon

H3L93_RS00020
type: Gene
subclass of: SO_0000704
RO_0002162: 505
locus tag: H3L93_RS00020
old locus tag: H3L93_00020
so part of: sequence
location: 10761..10955
location: region:10761-10955:1
so has part: feature:10761-10955:1:exon
subclass of: SO_0000010

position:10761:1
position: 10761
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10955:1
position: 10955
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10761-10955:1:exon

H3L93_RS00020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 505
locus tag: H3L93_RS00020
old locus tag: H3L93_00020
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003690223.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF5397 domain-containing protein
translation: MQPTVNTIPTGSIRTFGDYGVKYIVGTPAKQLPDGDWLVNIELPESGEHTQYKLSHIVQDPKAA
SIO_010081: H3L93_RS00020
subclass of: SO_0000673
so part of: H3L93_RS00020
location: 10761..10955
location: region:10761-10955:1
so has part: feature:10761-10955:1:exon

WP_003799054.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:10761-10955:1:exon

H3L93_RS00025
type: Gene
subclass of: SO_0000704
RO_0002162: 505
locus tag: H3L93_RS00025
old locus tag: H3L93_00025
so part of: sequence
location: 10955..11233
location: region:10955-11233:1
so has part: feature:10955-11233:1:exon
subclass of: SO_0000010

position:11233:1
position: 11233
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10955-11233:1:exon

H3L93_RS00025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 505
locus tag: H3L93_RS00025
old locus tag: H3L93_00025
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013448818.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: virulence factor
translation: MYAISFDLVVADTAEKHPKGVSQAYADIGATLRKFGFERVQGSLYTCQDENMANLFSAISALKLLPWFPDSVRDIRAFRIEQWSDFTGFVKS
SIO_010081: H3L93_RS00025
subclass of: SO_0000673
so part of: H3L93_RS00025
location: 10955..11233
location: region:10955-11233:1
so has part: feature:10955-11233:1:exon

WP_003799055.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:10955-11233:1:exon

H3L93_RS00030
type: Gene
subclass of: SO_0000704
RO_0002162: 505
locus tag: H3L93_RS00030
old locus tag: H3L93_00030
so part of: sequence
location: 11492..11995
location: region:11492-11995:1
so has part: feature:11492-11995:1:exon
subclass of: SO_0000010

position:11492:1
position: 11492
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:11995:1
position: 11995
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:11492-11995:1:exon

H3L93_RS00030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 505
locus tag: H3L93_RS00030
old locus tag: H3L93_00030
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: MENLPPPYPSRKNGWILPFKDKILMLRSKGYPFYQIAEILQPEAQKQGRKVSASIVSYWVTTWRQQEKKAEAKNPTPTPQLGEYGYNPFFADWLIGECQNLHRFGDFDENGAYFIQIDDLLDAYRKHPEIEKNGWDYQEIPTILERWASHRMAWDGLDFLKKHEKNG
SIO_010081: H3L93_RS00030
subclass of: SO_0000673
so part of: H3L93_RS00030
location: 11492..11995
location: region:11492-11995:1
so has part: feature:11492-11995:1:exon

WP_003799057.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:11492-11995:1:exon

H3L93_RS00035
type: Gene
subclass of: SO_0000704
RO_0002162: 505
locus tag: H3L93_RS00035
old locus tag: H3L93_00035
so part of: sequence
location: 12818..13798
location: region:12818-13798:1
so has part: feature:12818-13798:1:exon
subclass of: SO_0000010

position:12818:1
position: 12818
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:13798:1
position: 13798
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:12818-13798:1:exon

H3L93_RS00035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 505
locus tag: H3L93_RS00035
old locus tag: H3L93_00035
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008855174.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiator protein A
translation: MTHSKQSAQDILAARMAEIAKKNPRNVQRQPENEQQSKFQQSSNKAVVQSHLSPKRHPNADFFVIDVFDASLKDDLASMEHPIFALKNGDTRNRFYEHNGNTVTIMPSSFGCATIYDKDVWIYCISALINAQNNNEPINRVVRFTAYDFLVSTNRNTSGRYYQLLREALFRLAGTRIITNVKTGNYRLESNFGLLDKVDIIYKDETDENSPIIAIEVTLPDWLFRSIEAKQVKTISADYFRLRKPLDRRIYELCAKHCGKQKEWHISLEILHRKSGSMATLRRFRQAIKELVASNDLPDYRLSYDDKRDVLKVQNRDLSKFLSLKN
SIO_010081: H3L93_RS00035
subclass of: SO_0000673
so part of: H3L93_RS00035
location: 12818..13798
location: region:12818-13798:1
so has part: feature:12818-13798:1:exon

WP_003799062.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:12818-13798:1:exon

H3L93_RS00040
type: Gene
subclass of: SO_0000704
RO_0002162: 505
locus tag: H3L93_RS00040
old locus tag: H3L93_00040
so part of: sequence
location: complement(13815..14267)
location: region:13815-14267:-1
so has part: feature:13815-14267:-1:exon
subclass of: SO_0000010

position:13815:-1
position: 13815
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:14267:-1
position: 14267
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:13815-14267:-1:exon

H3L93_RS00040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 505
locus tag: H3L93_RS00040
old locus tag: H3L93_00040
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: MLNNSIFEKQLNQIQIDLIELALEYAKYTVDTVYIYGSNERNSVFFNAFFKEGGVITEKHKLKVFGSNFAPIELQMKFLDLGMEDFKDLCKLFEIYQGKTLTQLKLVYDVVNKKAHANYSYDSFLSDKIIADHIFNQWIENERNINKIDT
SIO_010081: H3L93_RS00040
subclass of: SO_0000673
so part of: H3L93_RS00040
location: complement(13815..14267)
location: region:13815-14267:-1
so has part: feature:13815-14267:-1:exon

WP_003799064.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:13815-14267:-1:exon