LOCUS NC_017433 7493 bp DNA circular CON 12-FEB-2023
DEFINITION Chlamydia trachomatis D-LC plasmid pCTDLC1, complete sequence.
ACCESSION NC_017433
VERSION NC_017433.1
DBLINK BioProject: PRJNA224116
BioSample: SAMN00014120
Assembly: GCF_000093005.1
KEYWORDS RefSeq.
SOURCE Chlamydia trachomatis D-LC
ORGANISM Chlamydia trachomatis D-LC
Bacteria; Chlamydiota; Chlamydiia; Chlamydiales; Chlamydiaceae;
Chlamydia/Chlamydophila group; Chlamydia.
REFERENCE 1 (bases 1 to 7493)
AUTHORS Sturdevant,G.L., Kari,L., Gardner,D.J., Olivares-Zavaleta,N.,
Randall,L.B., Whitmire,W.M., Carlson,J.H., Goheen,M.M.,
Selleck,E.M., Martens,C. and Caldwell,H.D.
TITLE Frameshift mutations in a single novel virulence factor alter the
in vivo pathogenicity of Chlamydia trachomatis for the female
murine genital tract
JOURNAL Infect Immun 78 (9), 3660-3668 (2010)
PUBMED 20547745
REFERENCE 2 (bases 1 to 7493)
AUTHORS Sturdevant,G.L., Kari,L., Gardner,D.J., Olivares-Zavaleta,N.,
Randall,L.B., Whitmire,W.M., Carlson,J.H., Goheen,M.M.,
Selleck,E.M., Martens,C. and Caldwell,H.D.
TITLE Direct Submission
JOURNAL Submitted (26-MAY-2010) Research Technologies Branch of the Rocky
Mountain Laboratories, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, 903 South 4th Street,
Hamilton, MT 59840, USA
COMMENT REFSEQ INFORMATION: The reference sequence is identical to
CP002055.1.
Sequencing Center: Integrated Genomics, Inc., 2355 S. Arlington
Heights Road, Suite 270, Arlington Heights, IL 60005, USA
Source DNA and bacteria available from Harlan D. Caldwell at
hcaldwell@niaid.nih.gov<mailto:hcaldwell@niaid.nih.gov>.
The annotation was added by the NCBI Prokaryotic Genome Annotation
Pipeline (PGAP). Information about PGAP can be found here:
https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI RefSeq
Annotation Date :: 02/12/2023 16:33:19
Annotation Pipeline :: NCBI Prokaryotic Genome
Annotation Pipeline (PGAP)
Annotation Method :: Best-placed reference protein
set; GeneMarkS-2+
Annotation Software revision :: 6.4
Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA
Genes (total) :: 954
CDSs (total) :: 908
Genes (coding) :: 906
CDSs (with protein) :: 906
Genes (RNA) :: 46
rRNAs :: 2, 2, 2 (5S, 16S, 23S)
complete rRNAs :: 2, 2, 2 (5S, 16S, 23S)
tRNAs :: 37
ncRNAs :: 3
Pseudo Genes (total) :: 2
CDSs (without protein) :: 2
Pseudo Genes (ambiguous residues) :: 0 of 2
Pseudo Genes (frameshifted) :: 1 of 2
Pseudo Genes (incomplete) :: 0 of 2
Pseudo Genes (internal stop) :: 1 of 2
##Genome-Annotation-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..7493
/organism="Chlamydia trachomatis D-LC"
/mol_type="genomic DNA"
/strain="D-LC"
/db_xref="taxon:759364"
/plasmid="pCTDLC1"
gene complement(25..942)
/locus_tag="CTDLC_RS04765"
/old_locus_tag="CTDLC_p001"
CDS complement(25..942)
/locus_tag="CTDLC_RS04765"
/old_locus_tag="CTDLC_p001"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_012209813.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="integrase pGP7-D"
/protein_id="WP_011324918.1"
/translation="MGSMAFHKSRLFLTFGDASEIWLSTLSHLTRKNYASGINFLVSL
EILDLSETLIKAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFLYRLT
KGYIKPAIPLKDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGKLIVQ
GIRKLDEILSLRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTCGRNG
RVFVSKIGIPVTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDEEIMR
ISCLSSRQSVCSYCSGEEVSPLVQTPTIL"
gene complement(1176..1919)
/locus_tag="CTDLC_RS04770"
/old_locus_tag="CTDLC_p002"
CDS complement(1176..1919)
/locus_tag="CTDLC_RS04770"
/old_locus_tag="CTDLC_p002"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_010231991.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="CT583 family protein"
/protein_id="WP_014541318.1"
/translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQS
LDRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDH
FSSTTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKG
DLKTKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDLEKNRQLSDFLIEI
LRIICSGVSLSSYNENLLQQLFELFKQKS"
gene complement(1916..2710)
/locus_tag="CTDLC_RS04775"
/old_locus_tag="CTDLC_p003"
CDS complement(1916..2710)
/locus_tag="CTDLC_RS04775"
/old_locus_tag="CTDLC_p003"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_015506340.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="ParA family protein"
/protein_id="WP_014541319.1"
/translation="MHTLVFCSFKGGTGKTTLSLNVGCNLAQFLGKKVLLADLDPQSN
LSSGLGASVRNNQKGLHDIVYKSNDLKSIICETKKDSVDLIPASFLSEQFRELDIHRG
PSNNLKLFLNEYCAPFYDICIIDTPPSLGGLTKEAFVAGDKLIACLTPEPFSILGLQK
IREFLSSVGKPEEEHILGIALSFWDDRNSTNQMYIDIIESIYKNKLFSTKIRRDISLS
RSLLKEDSVANVYPNSRAAEDILKLTHEIANILHIEYERDYSQRTT"
gene complement(2738..3046)
/locus_tag="CTDLC_RS04780"
/old_locus_tag="CTDLC_p004"
CDS complement(2738..3046)
/locus_tag="CTDLC_RS04780"
/old_locus_tag="CTDLC_p004"
/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"
/protein_id="WP_010889887.1"
/translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLE
LYHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE
"
gene complement(3116..3910)
/gene="pgp3"
/locus_tag="CTDLC_RS04785"
/old_locus_tag="CTDLC_p005"
CDS complement(3116..3910)
/gene="pgp3"
/locus_tag="CTDLC_RS04785"
/old_locus_tag="CTDLC_p005"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_014541320.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="virulence factor Pgp3"
/protein_id="WP_014541320.1"
/translation="MGNSGFYLYNTENCVFADNIKVGQMTEPLKDQQIILGTKSTPVA
AKMTASDGISLTVSNNSSTNASITIGLDAEKAYQLILEKLGNQILDGIADTIVDSTVQ
DILDKITTDPSLGLLKAFNNFPITNKIQCNGLFTPSNIETLLGGTEIGKFTVTPKSSG
SMFLVSADIIASRMEGGVVLALVREGDSKPCAISYGYSSGVPNLCSLRTSITNTGLTP
TTYSLRVGGLESGVVWVNALSNGNDILGITNTSNVSFLEVIPQTNA"
gene complement(3972..5027)
/locus_tag="CTDLC_RS04790"
/old_locus_tag="CTDLC_p006"
CDS complement(3972..5027)
/locus_tag="CTDLC_RS04790"
/old_locus_tag="CTDLC_p006"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_015506342.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="DUF5597 domain-containing protein"
/protein_id="WP_014541321.1"
/translation="MVNYSNCHFIKSPIHLENQKFGRRPGQSIKISPKLAQNGMVEVI
GLDFLSSHYHALAAIQRLLTATNYKGNTKGVVLSRESNSFQFEGWIPRIRFTKTEFLE
AYGVKRYKTSRNKYEFSGKEAETALEALYHLGHQPFLIVATRTRWTNGTQIVDRYQTL
SPIIRIYEGWEGLTDEENIDIDLTPFNSPSTRKHKGFVVEPCPILVDQIESYFVIKPA
NVYQEIKMRFPNASKYAYTFIDWVITAAAKKRRKLTKDNSWPENLLLNVNVKSLAYIL
RMNRYICTRNWKKIELAIDKCIEIAIQLGWLSRRKRIEFLDSSKLSKKEILYLNKERF
EEITKKSKEQMEQESIN"
gene complement(5021..6376)
/locus_tag="CTDLC_RS04795"
/old_locus_tag="CTDLC_p007"
CDS complement(5021..6376)
/locus_tag="CTDLC_RS04795"
/old_locus_tag="CTDLC_p007"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_012718306.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="replicative DNA helicase"
/protein_id="WP_014541322.1"
/translation="MKTRSEIENRMQDIEYALLGKALIFEDSTEYILRQLANYEFKCS
HHKNIFIVFKYLKDNGLPITVDSAWEELLRRRIKDMDKSYLGLMLHDALSNDKLRSVS
HTVFLDDLSVCSAEENLSNFIFRSFNEYNENPLRRSPFLLLERIKGRLDSAIAKTFSI
RSARGRSIYDIFSQSEIGVLARIKKRRAAFSENQNSFFDGFPTGYKDIDDKGVILAKG
NFVIIAARPSIGKTALAIDMAINLAVTQQRRVGFLSLEMSAGQIVERIVANLTGISGE
KLQRGDLSKEELFRVEEAGETVRESHFYICSDSQYKLNLIANQIRLLRKEDRVDVIFI
DYLQLINSSVGENRQNEIADISRTLRGLASELNIPIVCLSQLSRKVEDRANKVPMLSD
LRDSGQIEQDADVILFINRKESSSNCEITVGKNRHGSVFSSVLHFDPKISKFSAIKKV
W"
gene 6475..7467
/locus_tag="CTDLC_RS04800"
/old_locus_tag="CTDLC_p008"
CDS 6475..7467
/locus_tag="CTDLC_RS04800"
/old_locus_tag="CTDLC_p008"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_010231981.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="site-specific integrase"
/protein_id="WP_010889883.1"
/translation="MGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWKRMKSFSLFEV
IMHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILDAIKKVSSAKT
SWTEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTREIVKTDAMNSL
QTASFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATISFSQLKNRQT
EKRIIITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQAGLQAAIPFKI
TPHVLRATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNASKKMALI"
CONTIG join(CP002055.1:1..7493)
//
