Chlamydia gallinacea 08-1274/3 plasmid p1274, complete sequence.
type: Entry
definition: Chlamydia gallinacea 08-1274/3 plasmid p1274, complete sequence.
sequence version: NZ_CP015841.1
sequence date: 2023-06-05
sequence: sequence
division: CON
label: NZ_CP015841.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02435823
keyword: RefSeq
source: Chlamydia gallinacea 08-1274/3
organism: Chlamydia gallinacea 08-1274/3
taxonomy: Bacteria; Chlamydiota; Chlamydiia; Chlamydiales; Chlamydiaceae; Chlamydia/Chlamydophila group; Chlamydia.
reference: 1
references: 24461712
reference: 2
reference: 3
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP015841.1.\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 :: SPAdes v. 3.7.0\nGenome Coverage :: 1795\nSequencing Technology :: Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/23/2023 04:56:17\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 962\nCDSs (total) :: 916\nGenes (coding) :: 911\nCDSs (with protein) :: 911\nGenes (RNA) :: 46\nrRNAs :: 2, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 1, 1 (5S, 16S, 23S)\ntRNAs :: 39\nncRNAs :: 3\nPseudo Genes (total) :: 5\nCDSs (without protein) :: 5\nPseudo Genes (ambiguous residues) :: 0 of 5\nPseudo Genes (frameshifted) :: 0 of 5\nPseudo Genes (incomplete) :: 5 of 5\nPseudo Genes (internal stop) :: 0 of 5\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7619
topology: circular
so has quality: SO_0000988
location: 1..7619
location: region:1-7619:1
RO_0002162: 1143323

NZ_CP015841
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02435823
type: BioSample
SIO_000068: biosample

1
title: Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov
author: Sachse, K.
author: Laroucau, K.
author: Riege, K.
author: Wehner, S.
author: Dilcher, M.
author: Creasy, H.H.
author: Weidmann, M.
author: Myers, G.
author: Vorimore, F.
author: Vicari, N.
author: Magnino, S.
author: Liebler-Tenorio, E.
author: Ruettger, A.
author: Bavoil, P.M.
author: Hufert, F.T.
author: Rossello-Mora, R.
author: Marz, M.
journal: Syst Appl Microbiol
volume: 37
issue: 2
pages: 79-88
year: 2014
pubmed: 24461712

24461712
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Holzer, M.
author: Laroucau, K.
author: Huot Creasy, H.
author: Ott, S.
author: Vorimore, F.
author: Bavoil, P.M.
author: Marz, M.
author: Sachse, K.
journal: Submitted (23-MAY-2016) RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Leutragraben 1, Jena 07743, Germany

3
title: Direct Submission
author: Sachse, K.
author: Laroucau, K.
author: Riege, K.
author: Wehner, S.
author: Dilcher, M.
author: Huot Creasy, H.
author: Weidmann, M.
author: Myers, G.
author: Vorimore, F.
author: Vicari, N.
author: Magnino, S.
author: Liebler-Tenorio, E.
author: Ruettger, A.
author: Bavoil, P.M.
author: Hufert, F.T.
author: Rossello-Mora, R.
author: Marz, M.
journal: Submitted (13-SEP-2013) Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD 21201, USA

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

position:7619:1
position: 7619
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7619:1:source
so part of: sequence
organism: Chlamydia gallinacea 08-1274/3
mol type: genomic DNA
strain: 08-1274/3
isolation source: cloacal swab
host: Gallus gallus
culture collection: CSUR:P3509
type material: type strain of Chlamydia gallinacea
plasmid: p1274
country: France
collection date: 2008

1143323
type: Taxonomy
SIO_000068: taxonomy

M787_RS04740
type: Gene
subclass of: SO_0000704
RO_0002162: 1143323
locus tag: M787_RS04740
old locus tag: M787_004740
pseudo: true
so part of: sequence
location: <3..362
location: region:3-362:1
so has part: feature:3-362:1:exon
subclass of: SO_0000010

81478613
type: Gene
SIO_000068: ncbigene

position:3:1
position: 3
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

position:362:1
position: 362
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3-362:1:exon

M787_RS04740
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1143323
locus tag: M787_RS04740
old locus tag: M787_004740
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010231981.1
note: incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: site-specific integrase
SIO_010081: M787_RS04740
subclass of: SO_0000673
so part of: M787_RS04740
location: <3..362
location: region:3-362:1
so has part: feature:3-362:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:3-362:1:exon

M787_RS04745
type: Gene
subclass of: SO_0000704
RO_0002162: 1143323
locus tag: M787_RS04745
old locus tag: M787_004745
so part of: sequence
location: complement(403..1323)
location: region:403-1323:-1
so has part: feature:403-1323:-1:exon
subclass of: SO_0000010

81478614
type: Gene
SIO_000068: ncbigene

position:403:-1
position: 403
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1323:-1
position: 1323
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:403-1323:-1:exon

M787_RS04745
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1143323
locus tag: M787_RS04745
old locus tag: M787_004745
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011109752.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: site-specific integrase
translation: MSNLSHYHKSRLFLTVSEAANVWLATLSPTTKKNYASGIRFLMANKILDGSMRLESLIYIDHWDLLNKIKTLTYSCSGKPVSEASKQARAACYISFTKFLYRLTKGVIKQAIPSRDFGNSTFYKIRDKVKTEFISKQEWLLFFDSLKRISFRDYLIGKLIIQGVRKLSEVISLRIEDLSFSLNQITFKIKKRHSRYSEVRVIYPNFLMEELRDYIGNRTGWVFISGNGRQVAINQVYYYFKLAENDMNLSIKVTPHVLRASALAYLKKIGCADEAIMRVSCFSSTQMLSAYDTSIDNLTSQLPLIF
SIO_010081: M787_RS04745
subclass of: SO_0000673
so part of: M787_RS04745
location: complement(403..1323)
location: region:403-1323:-1
so has part: feature:403-1323:-1:exon

WP_021828979.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:403-1323:-1:exon

M787_RS04750
type: Gene
subclass of: SO_0000704
RO_0002162: 1143323
locus tag: M787_RS04750
old locus tag: M787_004750
so part of: sequence
location: complement(1543..2268)
location: region:1543-2268:-1
so has part: feature:1543-2268:-1:exon
subclass of: SO_0000010

81478615
type: Gene
SIO_000068: ncbigene

position:1543:-1
position: 1543
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2268:-1
position: 2268
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1543-2268:-1:exon

M787_RS04750
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1143323
locus tag: M787_RS04750
old locus tag: M787_004750
inference: COORDINATES: similar to AA sequence:RefSeq:WP_020358463.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: CT583 family protein
translation: MNKLSKEASIFFQKNQENTAKEFQKKELSLDIFSVTLSDEEHEKINNLVINEDEKLDVNHNLAAIKLLTIQIKSIQKQHVLLIGEKIYKVREILREMRSPETTFSSWINLVFHTKSSAYNALGYYELFISLPDKHTKSLFQSIPYKTAYLLASRKGSIKEKITVLGKIRGMSNTLAISVLNQFLPSLRSNDELQVNDVEKKNKFLSSKLIEVLEIINSGINISEYNKNLIHQLIESISYRC
SIO_010081: M787_RS04750
subclass of: SO_0000673
so part of: M787_RS04750
location: complement(1543..2268)
location: region:1543-2268:-1
so has part: feature:1543-2268:-1:exon

WP_064317837.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1543-2268:-1:exon

M787_RS04755
type: Gene
subclass of: SO_0000704
RO_0002162: 1143323
locus tag: M787_RS04755
old locus tag: M787_004755
so part of: sequence
location: complement(2261..3043)
location: region:2261-3043:-1
so has part: feature:2261-3043:-1:exon
subclass of: SO_0000010

81478616
type: Gene
SIO_000068: ncbigene

position:2261:-1
position: 2261
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3043:-1
position: 3043
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2261-3043:-1:exon

M787_RS04755
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1143323
locus tag: M787_RS04755
old locus tag: M787_004755
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011458557.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ParA family protein
translation: MQTLSFCSFKGGTGKTTLSLNVGCNLAQEKKKRVLLVDLDPQANLTVGLGVQICEKHNLDAILRDPDKIKNAIHKTKINHLDIIPSSVLIEDFRGFNRDISLTINHLYMSLQTIRHSYDVCILDTPPSLGILTREAFLASQYLIICLTPEPFSILGLQKIKEFYSTIDNDLQVLGIVFSFWDERNSTNSTYLNIVESMYPGKILSSKIRKDITLSRSLLKETSVTNAYPNSRASQDILKLTEEIENKLFLNKKLFRTSCE
SIO_010081: M787_RS04755
subclass of: SO_0000673
so part of: M787_RS04755
location: complement(2261..3043)
location: region:2261-3043:-1
so has part: feature:2261-3043:-1:exon

WP_077974869.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2261-3043:-1:exon

M787_RS04760
type: Gene
subclass of: SO_0000704
RO_0002162: 1143323
locus tag: M787_RS04760
old locus tag: M787_004760
so part of: sequence
location: complement(3074..3382)
location: region:3074-3382:-1
so has part: feature:3074-3382:-1:exon
subclass of: SO_0000010

81478617
type: Gene
SIO_000068: ncbigene

position:3074:-1
position: 3074
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3382:-1
position: 3382
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3074-3382:-1:exon

M787_RS04760
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1143323
locus tag: M787_RS04760
old locus tag: M787_004760
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006343675.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MNNKQNMTHDFIQIVKDVEKNFPELDLKMRVHREKITFMNSPIELYNKSISVILDLLNQIQTSLSLFPDSPIVEQLENNNLKLKKALIMLILSRKDMFSKSE
SIO_010081: M787_RS04760
subclass of: SO_0000673
so part of: M787_RS04760
location: complement(3074..3382)
location: region:3074-3382:-1
so has part: feature:3074-3382:-1:exon

WP_064317838.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3074-3382:-1:exon

M787_RS04765
type: Gene
subclass of: SO_0000704
RO_0002162: 1143323
gene: pgp3
locus tag: M787_RS04765
old locus tag: M787_004765
so part of: sequence
location: complement(3483..4277)
location: region:3483-4277:-1
so has part: feature:3483-4277:-1:exon
subclass of: SO_0000010

81478618
type: Gene
SIO_000068: ncbigene

position:3483:-1
position: 3483
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4277:-1
position: 4277
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3483-4277:-1:exon

M787_RS04765
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1143323
gene: pgp3
locus tag: M787_RS04765
old locus tag: M787_004765
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: MGNSGFYLNDNQNCVFADNIKLGQMTDVLKDQQIIIGTSTTPVAAKFQATDGIKVDITNSNNQDATINVSIDPNEMTETILDKIQDELMDEIVQNVTNSLVQEVIDKITSDPTLSITKAFKHFSLSNKIQCNGLFTKYNIDTLDGGTEIGKFTITPDNTNSMFLVFADIIASRMEGTVVLSLVREGDTKPCAISYGYSSGVPNLCSLRTAIANTGSSPVTFSLRVGGMDSGVVWVNALANGESILGISATSNVSFLEVKQQSDG
SIO_010081: M787_RS04765
subclass of: SO_0000673
so part of: M787_RS04765
location: complement(3483..4277)
location: region:3483-4277:-1
so has part: feature:3483-4277:-1:exon

WP_064317839.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3483-4277:-1:exon

M787_RS04770
type: Gene
subclass of: SO_0000704
RO_0002162: 1143323
locus tag: M787_RS04770
old locus tag: M787_004770
so part of: sequence
location: complement(4335..5378)
location: region:4335-5378:-1
so has part: feature:4335-5378:-1:exon
subclass of: SO_0000010

81478619
type: Gene
SIO_000068: ncbigene

position:4335:-1
position: 4335
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5378:-1
position: 5378
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4335-5378:-1:exon

M787_RS04770
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1143323
locus tag: M787_RS04770
old locus tag: M787_004770
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: hypothetical protein
translation: MVKSENQVIKSSLHLENQKFGRKPLLSEEQLELFSNICTESKIEVIGLDLQPSHYHALAAIQKLLTATNYRGNLEGSYLSRETNTFKFEGVIPRIKFTKSEYLEAYGVKKYKTSRNKNEFGGKEALIALEALYHLGNEPYLIVATRKRWNKGEEVVDRYQTFSPILRICEGWEGLTPKENKALDEEPFLNLISKKHKGFIIEPCPIIVDQIDSYFVLKPANMYQEIKLRFPNASKFTYTFIDWIVSTATRKKMNSSGIKEWPDKIEIGLETLSYTLRMNRYITSRNWKKIETAINRCVEIAIELKWLNKHERLQGSTIAKKEVFYLNKDKFQQISKNKTIQNSSNIN
SIO_010081: M787_RS04770
subclass of: SO_0000673
so part of: M787_RS04770
location: complement(4335..5378)
location: region:4335-5378:-1
so has part: feature:4335-5378:-1:exon

WP_021828974.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4335-5378:-1:exon

M787_RS04775
type: Gene
subclass of: SO_0000704
RO_0002162: 1143323
locus tag: M787_RS04775
old locus tag: M787_004775
so part of: sequence
location: complement(5372..6742)
location: region:5372-6742:-1
so has part: feature:5372-6742:-1:exon
subclass of: SO_0000010

81478620
type: Gene
SIO_000068: ncbigene

position:5372:-1
position: 5372
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6742:-1
position: 6742
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5372-6742:-1:exon

M787_RS04775
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1143323
locus tag: M787_RS04775
old locus tag: M787_004775
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: MIEQSAEEKELLDVEFFILGQAVNYCDNARTIIQRLSEHHFLSPKHRSIFILIKDILSRRDTVSIALIWEEIKKRNMDEHMDVSYLIHMSQNADIPIDLDQHIEFLHEQHINGLLKEFLDLSFQDFTKYPNRCSPYTLIEKFKDRLDTIYSKADTKKRYGRTIYDIFSCGDDGSDSVISQIRQRYNFRLEKHIDYVDGLLTGYSSIDEHSIILSKGNFVVLAARPAMGKTAFAIDMALKIVLEQEKAIGFISLEMSPNQIVERVISNLSEISCEHLKRGNFSRDVLTKIEHLGTRLKNSPFFICDNKCTDLISLINQCKNLKNHYAVDALFIDYLQLISPKKKSENRQNEIAEISRELRKLAVELQIPIICLSQLSRKVEDRMDKRPMLSDLRDSGQIEQDADVILFIHRKDYYSQDANKGVAEIIIGKNRHGSVFSTNLKFSSSTGRFSVQKESW
SIO_010081: M787_RS04775
subclass of: SO_0000673
so part of: M787_RS04775
location: complement(5372..6742)
location: region:5372-6742:-1
so has part: feature:5372-6742:-1:exon

WP_021828975.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5372-6742:-1:exon

M787_RS04735
type: Gene
subclass of: SO_0000704
RO_0002162: 1143323
locus tag: M787_RS04735
old locus tag: M787_004735
pseudo: true
so part of: sequence
location: 6847..>7617
location: region:6847-7617:1
so has part: feature:6847-7617:1:exon
subclass of: SO_0000010

81478612
type: Gene
SIO_000068: ncbigene

position:6847:1
position: 6847
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7617:1
position: 7617
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6847-7617:1:exon

M787_RS04735
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1143323
locus tag: M787_RS04735
old locus tag: M787_004735
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006343679.1
note: incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: site-specific integrase
SIO_010081: M787_RS04735
subclass of: SO_0000673
so part of: M787_RS04735
location: 6847..>7617
location: region:6847-7617:1
so has part: feature:6847-7617:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:6847-7617:1:exon