Chlamydia caviae GPIC plasmid pCpGP1, complete sequence.
type: Entry
definition: Chlamydia caviae GPIC plasmid pCpGP1, complete sequence.
sequence version: NC_004720.1
sequence date: 2023-02-22
sequence: sequence
division: CON
label: NC_004720.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02603993
keyword: RefSeq
source: Chlamydia caviae GPIC
organism: Chlamydia caviae GPIC
taxonomy: Bacteria; Chlamydiota; Chlamydiia; Chlamydiales; Chlamydiaceae; Chlamydia/Chlamydophila group; Chlamydia.
reference: 1
references: 12682364
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nAE015926.1.\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 :: 02/22/2023 13:24:20\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) :: 1,041\nCDSs (total) :: 997\nGenes (coding) :: 992\nCDSs (with protein) :: 992\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) :: 1 of 5\nPseudo Genes (internal stop) :: 1 of 5\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7966
topology: circular
so has quality: SO_0000988
location: 1..7966
location: region:1-7966:1
RO_0002162: 227941

NC_004720
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02603993
type: BioSample
SIO_000068: biosample

1
title: Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae
author: Read, T.D.
author: Myers, G.S.
author: Brunham, R.C.
author: Nelson, W.C.
author: Paulsen, I.T.
author: Heidelberg, J.
author: Holtzapple, E.
author: Khouri, H.
author: Federova, N.B.
author: Carty, H.A.
author: Umayam, L.A.
author: Haft, D.H.
author: Peterson, J.
author: Beanan, M.J.
author: White, O.
author: Salzberg, S.L.
author: Hsia, R.C.
author: McClarty, G.
author: Rank, R.G.
author: Bavoil, P.M.
author: Fraser, C.M.
journal: Nucleic Acids Res
volume: 31
issue: 8
pages: 2134-2147
year: 2003
pubmed: 12682364

12682364
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Read, T.
author: Myers, G.
author: Brunham, R.
author: Nelson, W.
author: Paulsen, I.
author: Heidelberg, J.
author: Holtzapple, E.
author: Khouri, H.
author: Fedorova, N.
author: Carty, H.
author: Umayam, L.
author: Haft, D.
author: Peterson, J.
author: Beanan, M.
author: White, O.
author: Salzberg, S.
author: Hsia, R.-C.
author: McClarty, G.
author: Rank, R.
author: Bavoil, P.
author: Fraser, C.
journal: Submitted (29-OCT-2002) The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA

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

position:7966:1
position: 7966
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7966:1:source
so part of: sequence
organism: Chlamydia caviae GPIC
mol type: genomic DNA
isolate: GPIC
type material: type strain of Chlamydophila caviae
plasmid: pCpGP1

227941
type: Taxonomy
SIO_000068: taxonomy

CCA_RS05150
type: Gene
subclass of: SO_0000704
RO_0002162: 227941
locus tag: CCA_RS05150
so part of: sequence
location: join(7432..7966,1..62)
location: region:1-7966:1
so has part: feature:7432-7966:1:exon
so has part: feature:1-62:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:7432-7966:1:exon

position:7432:1
position: 7432
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-62:1:exon

position:62:1
position: 62
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

CCA_RS05150
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 227941
locus tag: CCA_RS05150
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: AAA family ATPase
translation: MKTLAFCSFKGGTGKTTLSLNIGSNLAQISKKKVLLVDLDPQANLTTGLGIQIRDEHSLNEILRSSNDVRQTIHKTKIENLDIIPSSVLVEDFRGLNKDVSLSVNHLCLALQSIQNQYDVCILDTPPSLGILTQEAFLASQYLVVCLTPEPFSILGLQKIKEFCSTIANDLDVLGIVFFACGSRSTSKPNYRSWNSDS
SIO_010081: CCA_RS05150
subclass of: SO_0000673
so part of: CCA_RS05150
location: join(7432..7966,1..62)
location: region:1-7966:1
so has part: feature:7432-7966:1:exon
so has part: feature:1-62:1:exon

WP_238374168.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7432-7966:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-62:1:exon

CCA_RS05385
type: Gene
subclass of: SO_0000704
RO_0002162: 227941
locus tag: CCA_RS05385
so part of: sequence
location: 7..678
location: region:7-678:1
so has part: feature:7-678:1:exon
subclass of: SO_0000010

position:7:1
position: 7
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:678:1
position: 678
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7-678:1:exon

CCA_RS05385
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 227941
locus tag: CCA_RS05385
inference: COORDINATES: similar to AA sequence:RefSeq:WP_020358465.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ParA family protein
translation: MDLDPQANLTTGLGIQIRDEHSLNEILRSSNDVRQTIHKTKIENLDIIPSSVLVEDFRGLNKDVSLSVNHLCLALQSIQNQYDVCILDTPPSLGILTQEAFLASQYLVVCLTPEPFSILGLQKIKEFCSTIANDLDVLGIVFSFWDERNSTNSMYTDIIETIYEGKILSSKVRRDITVSRSLLKETSVINAYPNSRASQDILNLTKEIENKLFFNQKLVQETL
SIO_010081: CCA_RS05385
subclass of: SO_0000673
so part of: CCA_RS05385
location: 7..678
location: region:7-678:1
so has part: feature:7-678:1:exon

WP_238374169.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7-678:1:exon

CCA_RS05115
type: Gene
subclass of: SO_0000704
RO_0002162: 227941
locus tag: CCA_RS05115
old locus tag: CCAA00001
so part of: sequence
location: 675..1415
location: region:675-1415:1
so has part: feature:675-1415:1:exon
subclass of: SO_0000010

position:675:1
position: 675
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1415:1
position: 1415
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:675-1415:1:exon

CCA_RS05115
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 227941
locus tag: CCA_RS05115
old locus tag: CCAA00001
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: MSKLIKEASAFFQKNQENTVKEFHKKEFAMDVFSISLSEDEKEKIENLIVSQHGNFDDECSHGLASIKLLTGQIKSIQKQHVLLIGEKIYKVREILRAMNSPDTTFSAWINLVFHTKSSAYNALGYYELFISLPDKDTKSLFQSIPYKTAYLLASRKGSVKDKVKVLGKIEGMSNTAAIDILNRFLPSLRASQTERSINFEDKNKELSEKLMEILKTVCSGLELSEYNKNLLQQLFEKTLQANSRC
SIO_010081: CCA_RS05115
subclass of: SO_0000673
so part of: CCA_RS05115
location: 675..1415
location: region:675-1415:1
so has part: feature:675-1415:1:exon

WP_011109751.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:675-1415:1:exon

CCA_RS05120
type: Gene
subclass of: SO_0000704
RO_0002162: 227941
locus tag: CCA_RS05120
old locus tag: CCAA00002
so part of: sequence
location: 1638..2561
location: region:1638-2561:1
so has part: feature:1638-2561:1:exon
subclass of: SO_0000010

position:1638:1
position: 1638
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2561:1
position: 2561
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1638-2561:1:exon

CCA_RS05120
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 227941
locus tag: CCA_RS05120
old locus tag: CCAA00002
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: MSGLSHYHKSRLFLTILEAANVWLATLSPITRKNYASGIKFLVSNNILDGSMKLESLICFDHCDVLNKIKSLTYTYTGKTVSEASKQARAACYISFTKFLYRLTKGVVKQACPSRDFGNSTFYKIRDKVKTEFISKKEWLLFFDSLKRISFRDYLIGKLIIQGVRKLSEVISLRTEDLSFAQNQVTFKVKKRQNRYQEVKVSYPNFLMQELRSYLGNREGWVFISREGEQVAINQVYYYFKLAESDINSPIKVTPHVLRASALAYLKKMGFADQEIMRISCLSSTQMLSAYDTGMTDNLTSQLPLIF
SIO_010081: CCA_RS05120
subclass of: SO_0000673
so part of: CCA_RS05120
location: 1638..2561
location: region:1638-2561:1
so has part: feature:1638-2561:1:exon

WP_011109752.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1638-2561:1:exon

CCA_RS05125
type: Gene
subclass of: SO_0000704
RO_0002162: 227941
locus tag: CCA_RS05125
old locus tag: CCAA00003
so part of: sequence
location: complement(2622..3611)
location: region:2622-3611:-1
so has part: feature:2622-3611:-1:exon
subclass of: SO_0000010

position:2622:-1
position: 2622
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3611:-1
position: 3611
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2622-3611:-1:exon

CCA_RS05125
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 227941
locus tag: CCA_RS05125
old locus tag: CCAA00003
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: MHKSLDTVFGNKVYQSNLSHQELLSIRNERIWEGLRDIQLSEAIFIWLSSLNNHTARSYKGSVLALEKIGLISLNISLQEFALLNHNIILDSIKQVPMKIIPWSEGTKQVRAACYISLTKFLNRATSGLISIAQPSHQESNKTFYKIRDLVKTNAMNEVERVMFLKALEKINHRDWLIAQTILQGAKRVTEALSVTVDKISFENGTISFDQSKSRGMSKTTIITYPQRFMRLMQNYVGNRLGLVFITKTGKSVGLKQLAGTFAKAGVKARIPFKVTPHVLRATAVTEYKKMGCSDSDIMKVTGHSSSKMIYAYDKSTTSENASKKVSLI
SIO_010081: CCA_RS05125
subclass of: SO_0000673
so part of: CCA_RS05125
location: complement(2622..3611)
location: region:2622-3611:-1
so has part: feature:2622-3611:-1:exon

WP_050707704.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2622-3611:-1:exon

CCA_RS05130
type: Gene
subclass of: SO_0000704
RO_0002162: 227941
locus tag: CCA_RS05130
old locus tag: CCAA00004
so part of: sequence
location: 3733..5109
location: region:3733-5109:1
so has part: feature:3733-5109:1:exon
subclass of: SO_0000010

position:3733:1
position: 3733
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5109:1
position: 5109
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3733-5109:1:exon

CCA_RS05130
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 227941
locus tag: CCA_RS05130
old locus tag: CCAA00004
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: MIKQSEEERELLDVEFFVLGQAVNYLEHAHTIVRRLSENHFKSENHKNLFILIRDILRDRDTISISLIWEEIKRRNLDKRMDVSYLIHMSQNADIPIDLDHHIDFLHEKHVNNLLKEFLDSSFQDFTRYPNRRSPFTLIDQFKERLDDIHKKTSYPRRKNIGKTVYDIFASGDDGKNSVISQIRHRYDYRSRHQIDYVDGLSTGYSSIDENSIILSKGNFVVVAARPAMGKTAFAIDIALNLVLEQEKAVGFISLEMSPNQIVERVVSNLSEISCEQLKRGNFSRDVLSKIENIGMRLKGTHFFICDNKSTDLNTLIDQARELRENQGIDALFIDYLQLIGSNKKAENRQNEIAEISRQLRKLAGELQIPIVCLSQLSRKVEDRGDKRPMLSDLRDSGQIEQDADVILFLHRKDYYSQEATKGLSEIIIGKNRHGSVFSTNLRFNSSTGKFSVQKEAW
SIO_010081: CCA_RS05130
subclass of: SO_0000673
so part of: CCA_RS05130
location: 3733..5109
location: region:3733-5109:1
so has part: feature:3733-5109:1:exon

WP_011109754.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3733-5109:1:exon

CCA_RS05135
type: Gene
subclass of: SO_0000704
RO_0002162: 227941
locus tag: CCA_RS05135
old locus tag: CCAA00005
so part of: sequence
location: 5103..6146
location: region:5103-6146:1
so has part: feature:5103-6146:1:exon
subclass of: SO_0000010

position:5103:1
position: 5103
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6146:1
position: 6146
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5103-6146:1:exon

CCA_RS05135
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 227941
locus tag: CCA_RS05135
old locus tag: CCAA00005
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: MVKSENQIIKSSLHLENQKFGRKPQLSEDQLELFSSICTESKIEVIGLDLQPSHYHALAAIQKLLTATNYRGNLEGSYLSRETNTFKFEGTIPRIKFTKAEYLEAYGVKKYKTARNKNEFGGKEALIALEALYHLGNEPYLIVATRKRWNKGEEVVDRYQTFSPILRICEGWEGLTPKENKALDEEPFLNLISKKHKGFIIEPCPIIVDQIDSYFVLKPANMYQEIKLRFPNASKFTYTFIDWIVSTATRKKMNSSGLKEWPDKIEIGFETLSYTLRMNRYITSRNWKKIESAINRCIEIAIELKWLNKHERIQGKTISKKEVFYLNKSKFQQISTNKTIQNTTNNN
SIO_010081: CCA_RS05135
subclass of: SO_0000673
so part of: CCA_RS05135
location: 5103..6146
location: region:5103-6146:1
so has part: feature:5103-6146:1:exon

WP_011109755.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5103-6146:1:exon

CCA_RS05140
type: Gene
subclass of: SO_0000704
RO_0002162: 227941
gene: pgp3
locus tag: CCA_RS05140
old locus tag: CCAA00006
so part of: sequence
location: 6201..6995
location: region:6201-6995:1
so has part: feature:6201-6995:1:exon
subclass of: SO_0000010

position:6201:1
position: 6201
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6995:1
position: 6995
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6201-6995:1:exon

CCA_RS05140
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 227941
gene: pgp3
locus tag: CCA_RS05140
old locus tag: CCAA00006
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: MGNSGFYLNNNQNCVFADNIKVGQMQNPLQDQQLILGTTSTPTAAKITAKEGLKVDFETADSNNASINLSVDSDALSKLILDQIQKDLVDAIIGNITNSLIQEVIDKIISDPTLALTKAFKNFSISDKIQCNGLFTKTNIGTLLGGTEIGTFTITPDNADSMFLISADIIASRMEGNVVLALVKEGDSAPCAVSYGYSSGIPNVCSLRTAVSNSGANPVTFSLRVGGMESGVVWVNALANGDSILGTTTTSNISFLEVKQQTNG
SIO_010081: CCA_RS05140
subclass of: SO_0000673
so part of: CCA_RS05140
location: 6201..6995
location: region:6201-6995:1
so has part: feature:6201-6995:1:exon

WP_011109756.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6201-6995:1:exon

CCA_RS05145
type: Gene
subclass of: SO_0000704
RO_0002162: 227941
locus tag: CCA_RS05145
old locus tag: CCAA00007
so part of: sequence
location: 7093..7401
location: region:7093-7401:1
so has part: feature:7093-7401:1:exon
subclass of: SO_0000010

position:7093:1
position: 7093
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7401:1
position: 7401
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7093-7401:1:exon

CCA_RS05145
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 227941
locus tag: CCA_RS05145
old locus tag: CCAA00007
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: MNDKQNMTNDFIKIVKDVEKDFPELDIKMKVHKEKITFLNSPLELYHKSISVILNLLNQIQTSLGLFPDSPIVEQMEHSNLKLKKALIMLILSRKDMFSKAE
SIO_010081: CCA_RS05145
subclass of: SO_0000673
so part of: CCA_RS05145
location: 7093..7401
location: region:7093-7401:1
so has part: feature:7093-7401:1:exon

WP_011109757.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7093-7401:1:exon