Chlamydia abortus strain 15-70d24 plasmid II, complete sequence.
type: Entry
definition: Chlamydia abortus strain 15-70d24 plasmid II, complete sequence.
sequence version: NZ_LS450959.2
sequence date: 2023-04-29
sequence: sequence
division: CON
label: NZ_LS450959.2
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMEA4663404
keyword: RefSeq
source: Chlamydia abortus
organism: Chlamydia abortus
taxonomy: Bacteria; Chlamydiota; Chlamydiia; Chlamydiales; Chlamydiaceae; Chlamydia/Chlamydophila group; Chlamydia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nLS450959.2.\n\nOn Aug 18, 2021 this sequence version replaced NZ_LS450959.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/29/2023 03:50:02\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) :: 1,027\nCDSs (total) :: 983\nGenes (coding) :: 965\nCDSs (with protein) :: 965\nGenes (RNA) :: 44\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 38\nncRNAs :: 3\nPseudo Genes (total) :: 18\nCDSs (without protein) :: 18\nPseudo Genes (ambiguous residues) :: 0 of 18\nPseudo Genes (frameshifted) :: 14 of 18\nPseudo Genes (incomplete) :: 2 of 18\nPseudo Genes (internal stop) :: 6 of 18\nPseudo Genes (multiple problems) :: 4 of 18\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7553
topology: circular
so has quality: SO_0000988
location: 1..7553
location: region:1-7553:1
RO_0002162: 83555

NZ_LS450959
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMEA4663404
type: BioSample
SIO_000068: biosample

1
title: Direct Submission
author: Szymanska-Czerwinska, M.
author: Zareba-Marchewka, K.
journal: Submitted (09-AUG-2021) NATIONAL VETERINARY RESEARCH INSTITUTE, Cattle and Sheep Diseases Department, Partyzantow Av 57, 24-100 Pulawy, Poland

2
title: Direct Submission
author: Mitura, A.
journal: Submitted (21-MAY-2018) NATIONAL VETERINARY RESEARCH INSTITUTE, Cattle and Sheep Diseases Department, Partyzanto Av 57, 24-100 Pulawy, Poland

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

position:7553:1
position: 7553
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7553:1:source
so part of: sequence
organism: Chlamydia abortus
mol type: genomic DNA
strain: 15-70d24
isolation source: cloacal swab
host: Anas crecca
plasmid: II
country: Poland
collection date: 2015-09-11

83555
type: Taxonomy
SIO_000068: taxonomy

NVRI1_RS05045
type: Gene
subclass of: SO_0000704
RO_0002162: 83555
locus tag: NVRI1_RS05045
so part of: sequence
location: join(6959..7553,1..146)
location: region:1-7553:1
so has part: feature:6959-7553:1:exon
so has part: feature:1-146:1:exon
subclass of: SO_0000010

66226166
type: Gene
SIO_000068: ncbigene

urn:…
SIO_000300: 1
SIO_000628: feature:6959-7553:1:exon

position:6959:1
position: 6959
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-146:1:exon

position:146:1
position: 146
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

NVRI1_RS05045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 83555
locus tag: NVRI1_RS05045
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006343673.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: CT583 family protein
translation: MSKLIKEASAFFQKNQENTTKEFLKKEFAMDVFSVSLSDTEKEQIENLVVSQNSKFDEEYNRGLASIKLLTGQIKSIQKQHVLLIGEKIYKVREILKSMNSPDTTFSSWINLVFRTKSSAYNALGYYELFISLPDKDTKSLFQSIPYKTAYLLASRKGSVKDKLKVLGKINGLSNALAMDILNKFLPPLKSSQTERRVDFEEKNREVSEKLMDILKIISSGLELSEYNKNLLHQLFEKTLKADIRC
SIO_010081: NVRI1_RS05045
subclass of: SO_0000673
so part of: NVRI1_RS05045
location: join(6959..7553,1..146)
location: region:1-7553:1
so has part: feature:6959-7553:1:exon
so has part: feature:1-146:1:exon

WP_139415329.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6959-7553:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-146:1:exon

NVRI1_RS05050
type: Gene
subclass of: SO_0000704
RO_0002162: 83555
locus tag: NVRI1_RS05050
so part of: sequence
location: 368..1291
location: region:368-1291:1
so has part: feature:368-1291:1:exon
subclass of: SO_0000010

66226167
type: Gene
SIO_000068: ncbigene

position:368:1
position: 368
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1291:1
position: 1291
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:368-1291:1:exon

NVRI1_RS05050
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 83555
locus tag: NVRI1_RS05050
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011109752.1
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: site-specific integrase
translation: MSGLSHHHKSRLFLTVLEAANVWLATLSPITRKNYASGIKFLVANHILDGSMKLEGLVCCDHCDILNRIKSLTFTYSGKPVSEASKQARAACYISFTKFLYRLTKGVIKHASPSKDFGNPTFYKIRDKVKTEFISKREWLLFFDALKKISFRDYLIGKLIIQGVRKLTEVISLRTEDISFAKNQVTFKVKKRQNRYQEVKVSYPNFLMQELQDYLGNREGWVFVSGEGQQVAINQVYYYFKLAEGDINSPIKVTPHVLRASALAYLKKMGFADQEIMRVSCLSSTQMLSAYDTGMTDNLTSQLPLIF
SIO_010081: NVRI1_RS05050
subclass of: SO_0000673
so part of: NVRI1_RS05050
location: 368..1291
location: region:368-1291:1
so has part: feature:368-1291:1:exon

WP_010891146.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:368-1291:1:exon

NVRI1_RS05055
type: Gene
subclass of: SO_0000704
RO_0002162: 83555
locus tag: NVRI1_RS05055
so part of: sequence
location: complement(1375..2343)
location: region:1375-2343:-1
so has part: feature:1375-2343:-1:exon
subclass of: SO_0000010

66226168
type: Gene
SIO_000068: ncbigene

position:1375:-1
position: 1375
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2343:-1
position: 2343
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1375-2343:-1:exon

NVRI1_RS05055
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 83555
locus tag: NVRI1_RS05055
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006343679.1
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: site-specific integrase
translation: MFGNEVYSNNLTHQEFLSIRNQHLWEKLRDIPLYEAVHTWLSSLTNHTSRSYRGSILALERIGLISLKMPLQQFALLNHNIILDSIKQIPTSVVCWSEGTKQVRAACYISLTKFLNRVTSGIIAIAQPSHQESNKTFYKIRDLVKTNAMNQAERLLFLEELSKINYRDWLIAQTILQGAKRVTEALSLTTDRICFENGVISFNQIKSRGVFKTTIITYPQRFMKLLQDYVGERKGLVFITKKGKGVGLKQLACTFAKAGRKAHIQFKVTPHVLRATAVTEYKKMGCSDSDIMKITGHSSSKMIYAYDKSTIADNASKKVSLI
SIO_010081: NVRI1_RS05055
subclass of: SO_0000673
so part of: NVRI1_RS05055
location: complement(1375..2343)
location: region:1375-2343:-1
so has part: feature:1375-2343:-1:exon

WP_244989903.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1375-2343:-1:exon

NVRI1_RS05060
type: Gene
subclass of: SO_0000704
RO_0002162: 83555
locus tag: NVRI1_RS05060
so part of: sequence
location: 2486..3862
location: region:2486-3862:1
so has part: feature:2486-3862:1:exon
subclass of: SO_0000010

66226169
type: Gene
SIO_000068: ncbigene

position:2486:1
position: 2486
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3862:1
position: 3862
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2486-3862:1:exon

NVRI1_RS05060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 83555
locus tag: NVRI1_RS05060
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014951477.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replicative DNA helicase
translation: MIKQSEEEKDLLDVEFFVLGQAVNYLEHAHVIVRRLSEHHFKSENHKNIFLLIRDILRDRDTISISLIWEEIKRRNLDKSMDVSYLIHMSQNADIPIDLDHHIDFLHERHVDNLLKEFLDSSFQDFTRYPNRRSPYTLIDQFKERLDNIYEKTSYPRRKYVGKTVYDIFSSGENGKASVISQIRHRYDYRSRHKIDYVDGLPTGYSSIDEHSIILSKGNFVVIAARPAMGKTAFAIDIALNLVLEQGKAVGFISLEMSPNQIVERIISNLSETSCEQLKRGNFSRDVLSKIESIGTKLKGTHFFICDNKSTDINTLIDQARELRENQGIDALFIDYLQLIGSSKKAENRQNEIADISRQLRKLAVDLQIPIICLSQLSRKVEDRGDKRPMLSDLRDSGQIEQDADVILFLHRKDYYSQEATKGLSEIIVGKNRHGSVFSTTLGFNSCTGRFSIQKEAW
SIO_010081: NVRI1_RS05060
subclass of: SO_0000673
so part of: NVRI1_RS05060
location: 2486..3862
location: region:2486-3862:1
so has part: feature:2486-3862:1:exon

WP_139415333.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2486-3862:1:exon

NVRI1_RS05065
type: Gene
subclass of: SO_0000704
RO_0002162: 83555
locus tag: NVRI1_RS05065
so part of: sequence
location: 3856..4899
location: region:3856-4899:1
so has part: feature:3856-4899:1:exon
subclass of: SO_0000010

66226170
type: Gene
SIO_000068: ncbigene

position:3856:1
position: 3856
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4899:1
position: 4899
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3856-4899:1:exon

NVRI1_RS05065
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 83555
locus tag: NVRI1_RS05065
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014951478.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: virulence factor
translation: MVKSENQIIKSSLHLENQKFGRKPQLSEDLFELFPNICTESKIEVIGLDLQPSHYHALAAIQKLLTATNYRGNLEGSYLSRETNTFKFEGIIPRIKFTKSEYLEAYGVKKYKTSRNKNEFGGKEALIALEALYHLGNEPYLIVATRKRWNKGEEVVDRYQTFSPILRICEGWEGLTPKENKALDEEPFLDLISKKHKGFIIEPCPIIIDQIDSYFVLKPANMYQEIKLRFPNASKFTYTFIDWIVSTATRKKMNSSGLKEWPDKIEIGFENLSYTLRMNRYITSRNWKKIESAINRCIEIAIELKWLNKHERIQGKTISKKEVFYLNKSKFQQISTNKTIQSATNKN
SIO_010081: NVRI1_RS05065
subclass of: SO_0000673
so part of: NVRI1_RS05065
location: 3856..4899
location: region:3856-4899:1
so has part: feature:3856-4899:1:exon

WP_139415335.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3856-4899:1:exon

NVRI1_RS05070
type: Gene
subclass of: SO_0000704
RO_0002162: 83555
gene: pgp3
locus tag: NVRI1_RS05070
so part of: sequence
location: 4955..5749
location: region:4955-5749:1
so has part: feature:4955-5749:1:exon
subclass of: SO_0000010

66226171
type: Gene
SIO_000068: ncbigene

position:4955:1
position: 4955
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5749:1
position: 5749
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4955-5749:1:exon

NVRI1_RS05070
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 83555
gene: pgp3
locus tag: NVRI1_RS05070
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014951470.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: virulence factor Pgp3
translation: MGNSGFYLNETQNCVFADNIKLGQMQNPLQDQQLILGTSSTPTAAKLNAKDGLKIDISNTNSQNATIDLSIDADALSKLILDQIQKSLVDAIIKDITNSLIQEVIDRIVSDPNLALTKAFKNFSLSEKIQCNGLFTKSNIGTLLGGTEIGKFTITPDNVNSMFLISADIIASRMEGNVVLALVREGDSSPCAISYGYSSGIPNVCSLRTAVNNTGTDPVTFSLRVGGMDSGVVWVNALANGESILGTTATSNISFLEVKQQTNG
SIO_010081: NVRI1_RS05070
subclass of: SO_0000673
so part of: NVRI1_RS05070
location: 4955..5749
location: region:4955-5749:1
so has part: feature:4955-5749:1:exon

WP_139415337.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4955-5749:1:exon

NVRI1_RS05075
type: Gene
subclass of: SO_0000704
RO_0002162: 83555
locus tag: NVRI1_RS05075
so part of: sequence
location: 5844..6152
location: region:5844-6152:1
so has part: feature:5844-6152:1:exon
subclass of: SO_0000010

66226172
type: Gene
SIO_000068: ncbigene

position:5844:1
position: 5844
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6152:1
position: 6152
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5844-6152:1:exon

NVRI1_RS05075
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 83555
locus tag: NVRI1_RS05075
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012209817.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Virulence plasmid protein pGP4-D
translation: MNDKQNMTNDFIKIVKDVEKDFPELDIKMKVHKEKITFLNSPLELYHKSISVILNLLNQIQTSLSLFPDSPIVEQMEHNNLKLKKALIMLILSRKDMFSKAE
SIO_010081: NVRI1_RS05075
subclass of: SO_0000673
so part of: NVRI1_RS05075
location: 5844..6152
location: region:5844-6152:1
so has part: feature:5844-6152:1:exon

WP_006343675.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5844-6152:1:exon

NVRI1_RS05080
type: Gene
subclass of: SO_0000704
RO_0002162: 83555
locus tag: NVRI1_RS05080
so part of: sequence
location: 6183..6962
location: region:6183-6962:1
so has part: feature:6183-6962:1:exon
subclass of: SO_0000010

66226173
type: Gene
SIO_000068: ncbigene

position:6183:1
position: 6183
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6962:1
position: 6962
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6183-6962:1:exon

NVRI1_RS05080
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 83555
locus tag: NVRI1_RS05080
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014951469.1
GO function: GO:0005524 - ATP binding [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ParA family protein
translation: MKTLAFCSFKGGTGKTTLSLNIGSNLAQVSRKKVLLVDLDPQANLTTGLGVQIQDDHSLNEILRHSNEIGRAIHKTKIENLDIIPSSVLVEDFRGLNKDISLSVNHLHLALQKVQDQYDVCILDTPPSLGILSQEAFLASDYLVVCLTPEPFSILGLQKIKEFCSTIGNNLDILGIVFSFWDERNSTNSTYMDIIETIYEGKILSSKIRRDITVSRSLLKESSVINAYPNSRAAKDILNLTKEIENKLFSDEKLVQETL
SIO_010081: NVRI1_RS05080
subclass of: SO_0000673
so part of: NVRI1_RS05080
location: 6183..6962
location: region:6183-6962:1
so has part: feature:6183-6962:1:exon

WP_220577991.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6183-6962:1:exon