Chlamydia pecorum strain DBDeUG_2018 plasmid pCpecDBDeUG_2018, complete sequence.
type: Entry
definition: Chlamydia pecorum strain DBDeUG_2018 plasmid pCpecDBDeUG_2018, complete sequence.
sequence version: NZ_CP080402.1
sequence date: 2022-12-16
sequence: sequence
division: CON
label: NZ_CP080402.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN20256222
keyword: RefSeq
source: Chlamydia pecorum (Chlamydophila pecorum)
organism: Chlamydia pecorum
taxonomy: Bacteria; Chlamydiota; Chlamydiia; Chlamydiales; Chlamydiaceae; Chlamydia/Chlamydophila group; Chlamydia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP080402.1.\nBacteria and source DNA available from Chlamydia pecorum.\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 Date :: 11-JUL-2021\nAssembly Method :: Velvet v. 1.2.10\nAssembly Name :: DBDeUG_2018_F_ST69\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 3703.1x\nSequencing Technology :: Illumina NextSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/15/2022 04:45:00\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\nGenes (total) :: 992\nCDSs (total) :: 948\nGenes (coding) :: 947\nCDSs (with protein) :: 947\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) :: 1\nCDSs (without protein) :: 1\nPseudo Genes (ambiguous residues) :: 0 of 1\nPseudo Genes (frameshifted) :: 1 of 1\nPseudo Genes (incomplete) :: 0 of 1\nPseudo Genes (internal stop) :: 0 of 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7547
topology: circular
so has quality: SO_0000988
location: 1..7547
location: region:1-7547:1
RO_0002162: 85991

NZ_CP080402
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN20256222
type: BioSample
SIO_000068: biosample

1
title: Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala (Phascolarctos cinereus) Pathogen
author: White, R.T.
author: Legione, A.R.
author: Taylor-Brown, A.
author: Fernandez, C.M.
author: Higgins, D.P.
author: Timms, P.
author: Jelocnik, M.
journal: Pathogens 10 (12), 1543 (2021)
comments: DOI: 10.3390/pathogens10121543

2
title: Direct Submission
author: White, R.T.
author: Timms, P.
author: Jelocnik, M.
journal: Submitted (26-JUL-2021) Chlamydia Research Group, University of the Sunshine Coast, Sippy Downs Drive, Sippy Downs, QLD 4556, Australia

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

position:7547:1
position: 7547
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7547:1:source
so part of: sequence
organism: Chlamydia pecorum
mol type: genomic DNA
strain: DBDeUG_2018
isolation source: Urogenital tract
host: Phascolarctos cinereus
plasmid: pCpecDBDeUG_2018
country: Australia: Queensland
collection date: 2010

85991
type: Taxonomy
SIO_000068: taxonomy

DBDeUG_RS04915
type: Gene
subclass of: SO_0000704
RO_0002162: 85991
locus tag: DBDeUG_RS04915
old locus tag: DBDeUG_p0001
so part of: sequence
location: 51..935
location: region:51-935:1
so has part: feature:51-935:1:exon
subclass of: SO_0000010

70086856
type: Gene
SIO_000068: ncbigene

position:51:1
position: 51
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:935:1
position: 935
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:51-935:1:exon

DBDeUG_RS04915
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 85991
locus tag: DBDeUG_RS04915
old locus tag: DBDeUG_p0001
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: site-specific integrase
translation: MTLSEAVDIWLTTLSPLTRKNYASGIRFLSAHNILMLSMPIGDMVNVDHSDVLYKIKSLKYSLSGRLVSEASKQARAACYISLTKFLYRLTKGSITPAVPSRDFGSATFYKIRDKVKTAFLSKKEWLIFFDALKRVSFRDYLIGKLIIQGVRKLSEVISLKTEDILFSHNQICFRVKKRQNRVCEIKVTYPNFLMEELREYIGLREGLVFVSCRGKQVIKNQIYHYFRLAEHDAQLSIKVTPHVLRASALAYLKQTGFSNEDIMRVSCLSSHEMISAYDSCSVENITSRLPLIF
SIO_010081: DBDeUG_RS04915
subclass of: SO_0000673
so part of: DBDeUG_RS04915
location: 51..935
location: region:51-935:1
so has part: feature:51-935:1:exon

WP_232366983.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:51-935:1:exon

DBDeUG_RS04920
type: Gene
subclass of: SO_0000704
RO_0002162: 85991
locus tag: DBDeUG_RS04920
old locus tag: DBDeUG_p0002
so part of: sequence
location: complement(1015..1953)
location: region:1015-1953:-1
so has part: feature:1015-1953:-1:exon
subclass of: SO_0000010

70086857
type: Gene
SIO_000068: ncbigene

position:1015:-1
position: 1015
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1953:-1
position: 1953
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1015-1953:-1:exon

DBDeUG_RS04920
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 85991
locus tag: DBDeUG_RS04920
old locus tag: DBDeUG_p0002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012718315.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: site-specific integrase
translation: MSFQKAQQLKMECLWNDLKNFTLQEAVIVWLSSLNTHTARSYKGSILALSKIGLLSLNMTLQEFSFINHNIVIDTIKMLPQKIVSWSEGTKQVRAACYISLTKFLNRTTLGVISVAQPSRQESCKTFFKTRDLVKTNAMNYQETALFLEALKKLNYRDWLIAQTILQGAKRVSEVLSLSTKDISIQNGVISFKQKKTRGTETTTIITYPQKFMNALKEYIGNRSGIVFITRNGKHVTLRQVAGSFSRAGEIIKLPFKVTPHVLRATAVTEYKRLGCSDSDIMKVTGHVSSKMIYAYDKSSKFDNASKKVTLI
SIO_010081: DBDeUG_RS04920
subclass of: SO_0000673
so part of: DBDeUG_RS04920
location: complement(1015..1953)
location: region:1015-1953:-1
so has part: feature:1015-1953:-1:exon

WP_226328604.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1015-1953:-1:exon

DBDeUG_RS04925
type: Gene
subclass of: SO_0000704
RO_0002162: 85991
locus tag: DBDeUG_RS04925
old locus tag: DBDeUG_p0003
so part of: sequence
location: 2151..3491
location: region:2151-3491:1
so has part: feature:2151-3491:1:exon
subclass of: SO_0000010

70086858
type: Gene
SIO_000068: ncbigene

position:2151:1
position: 2151
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3491:1
position: 3491
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2151-3491:1:exon

DBDeUG_RS04925
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 85991
locus tag: DBDeUG_RS04925
old locus tag: DBDeUG_p0003
inference: COORDINATES: similar to AA sequence:RefSeq:WP_020358470.1
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: MDVEFFVLGQAINFIDAAKLVVSRLSEEHFSFYHHKKIYFFIKTIVNCRNIISIGLVWEEIKKSNYDSKLDVSYLIQMSQNADISVEIDYYIDYLHEKFTDHQLRDFLDNAYKEIHRYPNRRSPYTLVDQFKESLDSIHSKSFVSRRSFLGKTIFNLLNGNSETPGVLKQIQDRHLYRLKFNKDYINGLPTGYSEIDEQGIILSRGSFVIIAARPAMGKTAFAIDIALHLALQEKKSVGFISLEMPPHQIVERILSNLSGESCERLKRGRFSSETLLKIESISREIQNSRFFICDNKCSELNSLIDQAKALKESFDIDVLFIDYLQLLETDRRIENRQNEIAQISRKLRALAVELDIPIVCLSQLSRKVEDRGDKRPLLSDLRDSGQIEQDADAILLLYRKDYYSQESTKGLTEVIIGKNRHGAIFSTYLNFDSSTGKFFTHKEAW
SIO_010081: DBDeUG_RS04925
subclass of: SO_0000673
so part of: DBDeUG_RS04925
location: 2151..3491
location: region:2151-3491:1
so has part: feature:2151-3491:1:exon

WP_232366981.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2151-3491:1:exon

DBDeUG_RS04930
type: Gene
subclass of: SO_0000704
RO_0002162: 85991
locus tag: DBDeUG_RS04930
old locus tag: DBDeUG_p0004
so part of: sequence
location: 3485..4510
location: region:3485-4510:1
so has part: feature:3485-4510:1:exon
subclass of: SO_0000010

70086859
type: Gene
SIO_000068: ncbigene

position:3485:1
position: 3485
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4510:1
position: 4510
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3485-4510:1:exon

DBDeUG_RS04930
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 85991
locus tag: DBDeUG_RS04930
old locus tag: DBDeUG_p0004
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: MVKSENQIIKSSLHLENQKFGRKPQSSNKQLELFSTNIGSKVEVIGLDLQPSHYHALAAIQKLLSATNYRGNAEGSYLSRETNTFKFEGVIPRIKFSKSEYLDAYGVKKYKTARNKNEFGGKEALTALEALYHLGNKPYLIVATRKRWNKGEEVVDRYQTFSPILRICEGWEGLTPKENKALDEEPFYSLVSTKHKGFIIEPCPIIVDQIDSYFMLKPANMYQEIKLRFPNASKFTYTFLDWIVSTATRKKMNNNVTKAWPEKLEIGFENLSYTLRMNRYINSRNWKKIETAINRCIEIAIELKWLTKHERIQGTTISKKEVFYLNKVKFNQISTNKNLIS
SIO_010081: DBDeUG_RS04930
subclass of: SO_0000673
so part of: DBDeUG_RS04930
location: 3485..4510
location: region:3485-4510:1
so has part: feature:3485-4510:1:exon

WP_172686083.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3485-4510:1:exon

DBDeUG_RS04935
type: Gene
subclass of: SO_0000704
RO_0002162: 85991
gene: pgp3
locus tag: DBDeUG_RS04935
old locus tag: DBDeUG_p0005
so part of: sequence
location: 4571..5365
location: region:4571-5365:1
so has part: feature:4571-5365:1:exon
subclass of: SO_0000010

70086860
type: Gene
SIO_000068: ncbigene

position:4571:1
position: 4571
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5365:1
position: 5365
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4571-5365:1:exon

DBDeUG_RS04935
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 85991
gene: pgp3
locus tag: DBDeUG_RS04935
old locus tag: DBDeUG_p0005
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: MGNSGFYLNNNQNCVFADNIRLGQMTNELQDKQIIIGTPTTPTVTSLSSSNNGIIINQNTATTPATIEFSLDTPKIAQAVLESVTNDIMQEIVSNLSQELIEDVLEKIDTDSSFSFSRAFKAIEIKDCIQCNGLFTSENIGNLLGGTEIAKFTVTPENANSAFLIDANIIASRMEGAVVLALVKEGNSSPSAISYGFSSGLPNVCSLKAVIENTTTTPATFSLRIGGMESGVVWVNAMPNGNKILNAETTSTISVLEVIPQTNG
SIO_010081: DBDeUG_RS04935
subclass of: SO_0000673
so part of: DBDeUG_RS04935
location: 4571..5365
location: region:4571-5365:1
so has part: feature:4571-5365:1:exon

WP_172686084.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4571-5365:1:exon

DBDeUG_RS04940
type: Gene
subclass of: SO_0000704
RO_0002162: 85991
locus tag: DBDeUG_RS04940
old locus tag: DBDeUG_p0006
so part of: sequence
location: 5479..5787
location: region:5479-5787:1
so has part: feature:5479-5787:1:exon
subclass of: SO_0000010

70086861
type: Gene
SIO_000068: ncbigene

position:5479:1
position: 5479
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5787:1
position: 5787
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5479-5787:1:exon

DBDeUG_RS04940
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 85991
locus tag: DBDeUG_RS04940
old locus tag: DBDeUG_p0006
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: hypothetical protein
translation: MNNKQNIKNDFIKIVKNVEKDFPELDIKVKVQKEKVTFLHSPTELYHKSITIILNLLNRIESSLSLFPDSPIIDELENNNLKLKKALIMLLFSKKDMFSKNE
SIO_010081: DBDeUG_RS04940
subclass of: SO_0000673
so part of: DBDeUG_RS04940
location: 5479..5787
location: region:5479-5787:1
so has part: feature:5479-5787:1:exon

WP_058787389.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5479-5787:1:exon

DBDeUG_RS04945
type: Gene
subclass of: SO_0000704
RO_0002162: 85991
locus tag: DBDeUG_RS04945
old locus tag: DBDeUG_p0007
so part of: sequence
location: 5817..6599
location: region:5817-6599:1
so has part: feature:5817-6599:1:exon
subclass of: SO_0000010

70086862
type: Gene
SIO_000068: ncbigene

position:5817:1
position: 5817
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6599:1
position: 6599
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5817-6599:1:exon

DBDeUG_RS04945
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 85991
locus tag: DBDeUG_RS04945
old locus tag: DBDeUG_p0007
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014518306.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ParA family protein
translation: MKTITFCSFKGGTGKTTLSLNVGSNLVQYRGKKVLLVDLDPQANLTSSLGVQVKQKSLNDVFRHPQCIQEAIYKTKIENLEIIPSNTLIEDFREINFDFQIFGKHLSHCLQEVKDIYDICILDTPPSLGLLTKEAFIASNYLIICLTPEPFSILGLQKIKEFCLSLNLDQSLEVLGIVFSFWDERNSTNSTYLNIIESIYENKIFSSKVRRDVALSRSLLKETSVINAYPNSRAAQDILKLSKEIEEKLFNKLLFSQETL
SIO_010081: DBDeUG_RS04945
subclass of: SO_0000673
so part of: DBDeUG_RS04945
location: 5817..6599
location: region:5817-6599:1
so has part: feature:5817-6599:1:exon

WP_172686085.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5817-6599:1:exon

DBDeUG_RS04950
type: Gene
subclass of: SO_0000704
RO_0002162: 85991
locus tag: DBDeUG_RS04950
old locus tag: DBDeUG_p0008
so part of: sequence
location: 6596..7339
location: region:6596-7339:1
so has part: feature:6596-7339:1:exon
subclass of: SO_0000010

70086863
type: Gene
SIO_000068: ncbigene

position:6596:1
position: 6596
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7339:1
position: 7339
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6596-7339:1:exon

DBDeUG_RS04950
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 85991
locus tag: DBDeUG_RS04950
old locus tag: DBDeUG_p0008
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: MNKLNKEASIFFQKNQKHVKEEFKKKDALEAVFQTSLTQAESEQLDCLILDGNIDLEEQASEVLLEIKSITSQIKAIQKHHVLLIGEKIYRVREILNKSGSSSTTFSSWIGLVFHTKSSAYNALAYYELFLKLPSQSWRVIFQSIPYKTAYLLASRKGEIEDKMTVIEKIQGLPNSAAICILNKYLPSSRDTVISAVSSEEDINKVISDKLLELLKIVCLNPKISQYNMNLLQQLLESTLGNFNDTD
SIO_010081: DBDeUG_RS04950
subclass of: SO_0000673
so part of: DBDeUG_RS04950
location: 6596..7339
location: region:6596-7339:1
so has part: feature:6596-7339:1:exon

WP_172686086.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6596-7339:1:exon