GenomeNet

Database: RefSeq
Entry: NC_017433
LinkDB: NC_017433
Original site: NC_017433 
LOCUS       NC_017433               7493 bp    DNA     circular CON 12-AUG-2015
DEFINITION  Chlamydia trachomatis D-LC plasmid pCTDLC1, complete sequence.
ACCESSION   NC_017433
VERSION     NC_017433.1  GI:385244958
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN00014120
            Assembly: GCF_000093005.1
KEYWORDS    RefSeq.
SOURCE      Chlamydia trachomatis D-LC
  ORGANISM  Chlamydia trachomatis D-LC
            Bacteria; Chlamydiae; 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 was derived from
            CP002055.
            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>.
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            
            ##Genome-Annotation-Data-START##
            Annotation Provider                    :: NCBI
            Annotation Date                        :: 08/12/2015 12:17:24
            Annotation Pipeline                    :: NCBI Prokaryotic Genome
                                                      Annotation Pipeline
            Annotation Method                      :: Best-placed reference
                                                      protein set; GeneMarkS+
            Annotation Software revision           :: 3.0
            Features Annotated                     :: Gene; CDS; rRNA; tRNA;
                                                      ncRNA; repeat_region
            Genes                                  :: 959
            CDS                                       910
            Pseudo Genes                           :: 5
            rRNAs                                  :: 2, 2, 2 (5S, 16S, 23S)
            complete rRNAs                         :: 2, 2, 2 (5S, 16S, 23S)
            tRNAs                                  :: 37
            ncRNA                                  :: 1
            Frameshifted Genes                     :: 5
            Frameshifted Genes On Monomer Runs     :: 1
            Frameshifted Genes Not On Monomer Runs :: 0
            ##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..912)
                     /locus_tag="CTDLC_RS04765"
                     /old_locus_tag="CTDLC_p001"
     CDS             complement(25..912)
                     /locus_tag="CTDLC_RS04765"
                     /old_locus_tag="CTDLC_p001"
                     /inference="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_011324918.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="integrase"
                     /protein_id="WP_049749264.1"
                     /db_xref="GI:908374643"
                     /translation="MFLTFGDASEIWLSTLSHLTRKNYASGINFLVSLEILDLSETLI
                     KAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFLYRLTKGYIKPAIPL
                     KDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGKLIVQGIRKLDEILS
                     LRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTCGRNGRVFVSKIGIP
                     VTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDEEIMRISCLSSRQSV
                     CSYCSGEEVSPLVQTPTIL"
     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="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_010889889.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="virulence factor"
                     /protein_id="WP_014541318.1"
                     /db_xref="GI:504354216"
                     /translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQS
                     LDRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDH
                     FSSTTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKG
                     DLKTKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDLEKNRQLSDFLIEI
                     LRIICSGVSLSSYNENLLQQLFELFKQKS"
     gene            complement(1916..2635)
                     /locus_tag="CTDLC_RS04775"
                     /old_locus_tag="CTDLC_p003"
     CDS             complement(1916..2635)
                     /locus_tag="CTDLC_RS04775"
                     /old_locus_tag="CTDLC_p003"
                     /inference="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_011324920.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="chromosome partitioning protein ParA"
                     /protein_id="WP_041199551.1"
                     /db_xref="GI:752528032"
                     /translation="MAQFLGKKVLLADLDPQSNLSSGLGASVRNNQKGLHDIVYKSND
                     LKSIICETKKDSVDLIPASFLSEQFRELDIHRGPSNNLKLFLNEYCAPFYDICIIDTP
                     PSLGGLTKEAFVAGDKLIACLTPEPFSILGLQKIREFLSSVGKPEEEHILGIALSFWD
                     DRNSTNQMYIDIIESIYKNKLFSTKIRRDISLSRSLLKEDSVANVYPNSRAAEDILKL
                     THEIANILHIEYERDYSQRTT"
     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="EXISTENCE: similar to AA
                     sequence:SwissProt:B0BCM0.1"
                     /note="pGP4-D; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="virulence factor"
                     /protein_id="WP_010889887.1"
                     /db_xref="GI:499192347"
                     /translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLE
                     LYHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE
                     "
     gene            complement(3116..3910)
                     /locus_tag="CTDLC_RS04785"
                     /old_locus_tag="CTDLC_p005"
     CDS             complement(3116..3910)
                     /locus_tag="CTDLC_RS04785"
                     /old_locus_tag="CTDLC_p005"
                     /inference="EXISTENCE: 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"
                     /protein_id="WP_014541320.1"
                     /db_xref="GI:504354218"
                     /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="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_012718307.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="virulence factor"
                     /protein_id="WP_014541321.1"
                     /db_xref="GI:504354219"
                     /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"
                     /EC_number="3.6.1.-"
                     /inference="EXISTENCE: 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="DNA helicase"
                     /protein_id="WP_014541322.1"
                     /db_xref="GI:504354220"
                     /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="EXISTENCE: similar to AA
                     sequence:RefSeq:WP_012718315.1"
                     /note="pGP8-D; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Virulence plasmid integrase pGP8-D"
                     /protein_id="WP_010889883.1"
                     /db_xref="GI:499192343"
                     /translation="MGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWKRMKSFSLFEV
                     IMHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILDAIKKVSSAKT
                     SWTEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTREIVKTDAMNSL
                     QTASFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATISFSQLKNRQT
                     EKRIIITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQAGLQAAIPFKI
                     TPHVLRATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNASKKMALI"
CONTIG      join(CP002055.1:1..7493)
//
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