Chlamydia crocodili strain No. 12 plasmid unnamed1, complete sequence.
type: Entry
definition: Chlamydia crocodili strain No. 12 plasmid unnamed1, complete sequence.
sequence version: NZ_CP060792.1
sequence date: 2022-11-06
sequence: sequence
division: CON
label: NZ_CP060792.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN15897673
keyword: RefSeq
source: Chlamydia crocodili
organism: Chlamydia crocodili
taxonomy: Bacteria; Chlamydiota; Chlamydiia; Chlamydiales; Chlamydiaceae; Chlamydia/Chlamydophila group; Chlamydia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP060792.1.\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 :: 11/06/2022 09:04:12\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 1,073\nCDSs (total) :: 1,029\nGenes (coding) :: 1,024\nCDSs (with protein) :: 1,024\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) :: 5\nCDSs (without protein) :: 5\nPseudo Genes (ambiguous residues) :: 0 of 5\nPseudo Genes (frameshifted) :: 3 of 5\nPseudo Genes (incomplete) :: 3 of 5\nPseudo Genes (internal stop) :: 0 of 5\nPseudo Genes (multiple problems) :: 1 of 5\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7728
topology: circular
so has quality: SO_0000988
location: 1..7728
location: region:1-7728:1
RO_0002162: 2766982

NZ_CP060792
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN15897673
type: BioSample
SIO_000068: biosample

1
title: Isolation and characterization of novel Chlamydia from Siamese crocodiles (Crocodylus siamensis)
author: Sariya, L.
journal: Unpublished

2
title: Direct Submission
author: Sariya, L.
journal: Submitted (27-AUG-2020) MoZWE, Mahidol University, Phutthamonthon 4, Phutthamonthon, Nakhon Pathom 73170, Thailand

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

position:7728:1
position: 7728
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7728:1:source
so part of: sequence
organism: Chlamydia crocodili
mol type: genomic DNA
strain: No. 12
isolation source: liver
host: Crocodylus siamensis
type material: reference strain of Chlamydia crocodili
plasmid: unnamed1
country: Thailand
collection date: 2018

2766982
type: Taxonomy
SIO_000068: taxonomy

H9Q19_RS05360
type: Gene
subclass of: SO_0000704
RO_0002162: 2766982
locus tag: H9Q19_RS05360
old locus tag: H9Q19_05325
so part of: sequence
location: join(7332..7728,1..11)
location: region:1-7728:1
so has part: feature:7332-7728:1:exon
so has part: feature:1-11:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:7332-7728:1:exon

position:7332:1
position: 7332
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-11:1:exon

position:11:1
position: 11
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

H9Q19_RS05360
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2766982
locus tag: H9Q19_RS05360
old locus tag: H9Q19_05325
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: MGNSGFYLNNNQNCVFADNIKIGQMQNPLQDQQLILGTSSTPTAAKINAKEGLKVDITTTNGAETSINLSIDPDALSKLILDQIQKDLVDAIIKNITNSLIQEVIDKIVSDPTLALTKAFKNFSISDKIQCNDLN
SIO_010081: H9Q19_RS05360
subclass of: SO_0000673
so part of: H9Q19_RS05360
location: join(7332..7728,1..11)
location: region:1-7728:1
so has part: feature:7332-7728:1:exon
so has part: feature:1-11:1:exon

WP_249324542.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7332-7728:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-11:1:exon

H9Q19_RS05320
type: Gene
subclass of: SO_0000704
RO_0002162: 2766982
gene: pgp3
locus tag: H9Q19_RS05320
old locus tag: H9Q19_05330
so part of: sequence
location: 71..568
location: region:71-568:1
so has part: feature:71-568:1:exon
subclass of: SO_0000010

position:71:1
position: 71
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:568:1
position: 568
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:71-568:1:exon

H9Q19_RS05320
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2766982
gene: pgp3
locus tag: H9Q19_RS05320
old locus tag: H9Q19_05330
inference: COORDINATES: protein motif:HMM:NF017303.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: virulence factor Pgp3
translation: MIQEVIDKIVSDPTLALTKAFKNFSISDKIQCNGLFTKTNIGTLLGGTEIGSFTITPDNTDSMFLISADIIASRMEGNVVLALVREGDSSPCAISYGYSSGVPNVCSLRTAVSNSGTTPVTFSLRVGGMESGVVWVNALANGDSILGTTTTSNISFLEVKQQTNG
SIO_010081: H9Q19_RS05320
subclass of: SO_0000673
so part of: H9Q19_RS05320
location: 71..568
location: region:71-568:1
so has part: feature:71-568:1:exon

WP_249324543.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:71-568:1:exon

H9Q19_RS05325
type: Gene
subclass of: SO_0000704
RO_0002162: 2766982
locus tag: H9Q19_RS05325
old locus tag: H9Q19_05335
so part of: sequence
location: 665..973
location: region:665-973:1
so has part: feature:665-973:1:exon
subclass of: SO_0000010

position:665:1
position: 665
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:973:1
position: 973
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:665-973:1:exon

H9Q19_RS05325
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2766982
locus tag: H9Q19_RS05325
old locus tag: H9Q19_05335
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 factor
translation: MNDKQNMTNDFIKIVKDVEKDFPELDIKMKVHKEKITFLNSPLELYHKSISVILNLLNQIQTSLGLFPDSPIVEQMEHNNLKLKKALIMLILSRKDMFSKAE
SIO_010081: H9Q19_RS05325
subclass of: SO_0000673
so part of: H9Q19_RS05325
location: 665..973
location: region:665-973:1
so has part: feature:665-973:1:exon

WP_213242108.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:665-973:1:exon

H9Q19_RS05330
type: Gene
subclass of: SO_0000704
RO_0002162: 2766982
locus tag: H9Q19_RS05330
old locus tag: H9Q19_05340
so part of: sequence
location: 1004..1783
location: region:1004-1783:1
so has part: feature:1004-1783:1:exon
subclass of: SO_0000010

position:1004:1
position: 1004
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1783:1
position: 1783
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1004-1783:1:exon

H9Q19_RS05330
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2766982
locus tag: H9Q19_RS05330
old locus tag: H9Q19_05340
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014951469.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ParA family protein
translation: MKTLAFCSFKGGTGKTTLSLNIGSNLAQISKKRVLLVDLDPQANLTTGLGIQIRDEYGLNEVLRSSNDIRQTIHKTKIENLDIIPSSVLVEDFRGLNKDVGLSVNHLYLALQSVQSQYDICILDTPPSLGILTQEAFLASQYLVVCLTPEPFSILGLQKIKEFCSTIANDLDILGIVFSFWDERNSTNSTYTDIIENICEGKILSNKVRRDITVSRSLLKESPVINVYPNSRASQDILNLTKEIENKLFFNKKLVQETL
SIO_010081: H9Q19_RS05330
subclass of: SO_0000673
so part of: H9Q19_RS05330
location: 1004..1783
location: region:1004-1783:1
so has part: feature:1004-1783:1:exon

WP_213242100.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1004-1783:1:exon

H9Q19_RS05335
type: Gene
subclass of: SO_0000704
RO_0002162: 2766982
locus tag: H9Q19_RS05335
old locus tag: H9Q19_05345
so part of: sequence
location: 1780..2520
location: region:1780-2520:1
so has part: feature:1780-2520:1:exon
subclass of: SO_0000010

position:1780:1
position: 1780
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2520:1
position: 2520
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1780-2520:1:exon

H9Q19_RS05335
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2766982
locus tag: H9Q19_RS05335
old locus tag: H9Q19_05345
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: MSKLVKEASAFFRKNQENTVKEFHKKEFAMDVFSVSLSEDEKEQLESLIISKHRDFDDTCSRGLDSIKLLTGQIKSIQKQHVLLIGEKIYKVRDILRGMNSPETTFSAWINLVFHTKSSAYNALGYYELFISLPDKDTKSLFQSIPYKTAYLLASRKGSVQDKVKVLGKIYGMSNTSAIDVLNKFLPSLRTSQIERLTDCEDRNKELSEKLMEILKTVCSGLELSEYNKNLLQQLFEKTLQIDSRC
SIO_010081: H9Q19_RS05335
subclass of: SO_0000673
so part of: H9Q19_RS05335
location: 1780..2520
location: region:1780-2520:1
so has part: feature:1780-2520:1:exon

WP_213242102.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1780-2520:1:exon

H9Q19_RS05340
type: Gene
subclass of: SO_0000704
RO_0002162: 2766982
locus tag: H9Q19_RS05340
old locus tag: H9Q19_05350
so part of: sequence
location: 2743..3666
location: region:2743-3666:1
so has part: feature:2743-3666:1:exon
subclass of: SO_0000010

position:2743:1
position: 2743
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3666:1
position: 3666
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2743-3666:1:exon

H9Q19_RS05340
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2766982
locus tag: H9Q19_RS05340
old locus tag: H9Q19_05350
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: MSGLNHYHKSRLFLTVLEAANVWLATLSPITKKNYASGIKFLISNNILDGSMKLESLVCFDHCDALNKIKSLTYTYTGKTVSEASKQARAACYISFTKFLYRLTKGLIKQASPSRDFGNSTFYKIRDKVKTEFISKKEWLVFFDSLKKISFRDYLIGKLIIQGVRKLNEVISLRTDDISFVQNQVTFKIKKRQNRYQEVKVSYPNFLMQELRDYLGNREGWVFVSGEGQQVAINQVYYYFKLAENDINSPIKVTPHVLRASALAYLKKMGFADQEIMRVSCLSSTQMLSAYDTGKTDNLTSQLPLIF
SIO_010081: H9Q19_RS05340
subclass of: SO_0000673
so part of: H9Q19_RS05340
location: 2743..3666
location: region:2743-3666:1
so has part: feature:2743-3666:1:exon

WP_213242104.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2743-3666:1:exon

H9Q19_RS05345
type: Gene
subclass of: SO_0000704
RO_0002162: 2766982
locus tag: H9Q19_RS05345
old locus tag: H9Q19_05355
so part of: sequence
location: complement(3753..4721)
location: region:3753-4721:-1
so has part: feature:3753-4721:-1:exon
subclass of: SO_0000010

position:3753:-1
position: 3753
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4721:-1
position: 4721
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3753-4721:-1:exon

H9Q19_RS05345
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2766982
locus tag: H9Q19_RS05345
old locus tag: H9Q19_05355
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006343679.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: site-specific integrase
translation: MFGNKVYQGNLSHQEFLSIRNERIWEGLRDIPLYEAVCLWLSSLNNHTARSYKGSILALEKIGLVSLKISLQEFALLNHNVILDSIKQVPMKIVPWSEGTKQVRAACYISLTKFLNRATSGLISIAQPSHQESNKTFYKIRDLVKTNALNKIERITFLEALEKINHRDWLIAQTILQGAKRVTEALSITTDKISFENGTISFNQNKSRGVSKTTVITYPQRFMKLISDYVGNRLGLVFITKNGKGVGLKQLAGTFAKAGIKANISFKVTPHVLRATAVTEYKKMGCSDSDIMKVTGHSSSKMIYAYDKSTTSENASKKVSLI
SIO_010081: H9Q19_RS05345
subclass of: SO_0000673
so part of: H9Q19_RS05345
location: complement(3753..4721)
location: region:3753-4721:-1
so has part: feature:3753-4721:-1:exon

WP_213242106.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3753-4721:-1:exon

H9Q19_RS05350
type: Gene
subclass of: SO_0000704
RO_0002162: 2766982
locus tag: H9Q19_RS05350
old locus tag: H9Q19_05360
so part of: sequence
location: 4864..6240
location: region:4864-6240:1
so has part: feature:4864-6240:1:exon
subclass of: SO_0000010

position:4864:1
position: 4864
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6240:1
position: 6240
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4864-6240:1:exon

H9Q19_RS05350
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2766982
locus tag: H9Q19_RS05350
old locus tag: H9Q19_05360
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: DnaB-like helicase C-terminal domain-containing protein
translation: MIKQSEEEKELLDVEFFVLGQAVNYLEHAHTVVRRLSESHFKLENHKNIFLLIRDILRDRDTISISLIWEEIKRRNLDKRMDVSYLIHMSQNADIPIDLDHHIDFLHEKHVNSLLKEFLDSSFQDFTRYPNRRSPYTLIDQFKERLDNIHKKTSYPRRKNIGKTVYDIFSLGDDGKNSVISQIRHRYDYRSRHQIDYVDGLPTGYSPIDENSIILSKGNFVVVAARPAMGKTAFAIDIALNLVLEQQKAVGFISLEMSPNQIVERVVSNLSEISCEQLKRGNFSRDILSKIEDIGKRLKGTHFFICDNKSTDLNALIDQARELKENQGIDALFIDYLQLIGSNKKAENRQNEIAEISRQLRKLAGELQIPVVCLSQLSRKVEDRGDKRPMLSDLRDSGQIEQDADVILFLHRKDYYSQEAPKGLSEIIIGKNRHGSVFSTNLKFNSSTGKFSVQKEAW
SIO_010081: H9Q19_RS05350
subclass of: SO_0000673
so part of: H9Q19_RS05350
location: 4864..6240
location: region:4864-6240:1
so has part: feature:4864-6240:1:exon

WP_213242096.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4864-6240:1:exon

H9Q19_RS05355
type: Gene
subclass of: SO_0000704
RO_0002162: 2766982
locus tag: H9Q19_RS05355
old locus tag: H9Q19_05365
so part of: sequence
location: 6234..7277
location: region:6234-7277:1
so has part: feature:6234-7277:1:exon
subclass of: SO_0000010

position:6234:1
position: 6234
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7277:1
position: 7277
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6234-7277:1:exon

H9Q19_RS05355
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2766982
locus tag: H9Q19_RS05355
old locus tag: H9Q19_05365
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: MVRSENQIIKSSLHLENQKFGRKPQLTEDQLELFSSVCTESKIEVIGLDLQPSHYHALSAIQKLLTATNYRGNLEGSYLSRETNTFKFEGTIPRIKFTKAEYLEAYGVKKYKTSRNKNEFGGKEALIALEALYHLGNEPYLIVATRKRWNKGEEVVDRYQTFSPILRICEGWEGLTPKENKALDEEPFLNLVSKKHKGFIIEPCPIIVDQIDSYFVLKPANMYQEIKLRFPNASKFTYTFIDWIVSTATRKKMNSSGLKEWPDKIEIGFENLSYTLRMNRYITSRNWKKIESAINRCIEIAIELKWLNKHERIQGKTISKKEVFYLNKNKFQQISTNKTIQNTTNNN
SIO_010081: H9Q19_RS05355
subclass of: SO_0000673
so part of: H9Q19_RS05355
location: 6234..7277
location: region:6234-7277:1
so has part: feature:6234-7277:1:exon

WP_213242098.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6234-7277:1:exon