GenomeNet

Database: RefSeq
Entry: NC_017433
LinkDB: NC_017433
Original site: NC_017433 
LOCUS       NC_017433               7493 bp    DNA     circular CON 08-JUN-2013
DEFINITION  Chlamydia trachomatis D-LC plasmid pCTDLC1, complete sequence.
ACCESSION   NC_017433
VERSION     NC_017433.1  GI:385244958
DBLINK      Project: 159879
            BioProject: PRJNA159879
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)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (06-APR-2012) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (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     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence is identical to 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>.
            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..954)
                     /locus_tag="CTDLC_p001"
                     /db_xref="GeneID:12339899"
     CDS             complement(25..954)
                     /locus_tag="CTDLC_p001"
                     /codon_start=1
                     /transl_table=11
                     /product="Virulence plasmid integrase pGP7-D"
                     /protein_id="YP_005811046.1"
                     /db_xref="GI:385244959"
                     /db_xref="GeneID:12339899"
                     /translation="MVKKMGSMAFHKSRLFLTFGDASEIWLSTLSHLTRKNYASGINF
                     LVSLEILDLSETLIKAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFL
                     YRLTKGYIKPAIPLKDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGK
                     LIVQGIRKLDEILSLRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTC
                     GRNGRVFVSKIGIPVTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDE
                     EIMRISCLSSRQSVCSYCSGEEVSPLVQTPTIL"
     misc_feature    complement(130..930)
                     /locus_tag="CTDLC_p001"
                     /note="Integrase [DNA replication, recombination, and
                     repair]; Region: XerC; COG0582"
                     /db_xref="CDD:223655"
     misc_feature    complement(88..537)
                     /locus_tag="CTDLC_p001"
                     /note="DNA breaking-rejoining enzymes,
                     intergrase/recombinases, C-terminal catalytic domain. The
                     tyrosine recombinase/integrase family share the same
                     catalytic domain containing six conserved active site
                     residues. The best-studied members of this diverse
                     family...; Region: INT_REC_C; cd01182"
                     /db_xref="CDD:238587"
     misc_feature    complement(order(103..105,172..174,181..183,376..378,
                     454..456))
                     /locus_tag="CTDLC_p001"
                     /note="Int/Topo IB signature motif; other site"
                     /db_xref="CDD:238587"
     misc_feature    complement(order(103..105,172..174,181..183,454..456))
                     /locus_tag="CTDLC_p001"
                     /note="active site"
                     /db_xref="CDD:238587"
     misc_feature    complement(order(172..174,454..456))
                     /locus_tag="CTDLC_p001"
                     /note="catalytic residues [active]"
                     /db_xref="CDD:238587"
     misc_feature    complement(order(181..186,376..378,448..450,454..456))
                     /locus_tag="CTDLC_p001"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238587"
     gene            complement(1176..1919)
                     /locus_tag="CTDLC_p002"
                     /db_xref="GeneID:12339900"
     CDS             complement(1176..1919)
                     /locus_tag="CTDLC_p002"
                     /codon_start=1
                     /transl_table=11
                     /product="Virulence plasmid protein pGP6-D"
                     /protein_id="YP_005811047.1"
                     /db_xref="GI:385244960"
                     /db_xref="GeneID:12339900"
                     /translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQS
                     LDRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDH
                     FSSTTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKG
                     DLKTKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDLEKNRQLSDFLIEI
                     LRIICSGVSLSSYNENLLQQLFELFKQKS"
     misc_feature    complement(1188..1919)
                     /locus_tag="CTDLC_p002"
                     /note="Uncharacterized protein family (UPF0137); Region:
                     UPF0137; pfam03677"
                     /db_xref="CDD:146355"
     gene            complement(1916..2710)
                     /locus_tag="CTDLC_p003"
                     /db_xref="GeneID:12339901"
     CDS             complement(1916..2710)
                     /locus_tag="CTDLC_p003"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="YP_005811048.1"
                     /db_xref="GI:385244961"
                     /db_xref="GeneID:12339901"
                     /translation="MHTLVFCSFKGGTGKTTLSLNVGCNLAQFLGKKVLLADLDPQSN
                     LSSGLGASVRNNQKGLHDIVYKSNDLKSIICETKKDSVDLIPASFLSEQFRELDIHRG
                     PSNNLKLFLNEYCAPFYDICIIDTPPSLGGLTKEAFVAGDKLIACLTPEPFSILGLQK
                     IREFLSSVGKPEEEHILGIALSFWDDRNSTNQMYIDIIESIYKNKLFSTKIRRDISLS
                     RSLLKEDSVANVYPNSRAAEDILKLTHEIANILHIEYERDYSQRTT"
     misc_feature    complement(1943..2710)
                     /locus_tag="CTDLC_p003"
                     /note="ATPases involved in chromosome partitioning [Cell
                     division and chromosome partitioning]; Region: Soj;
                     COG1192"
                     /db_xref="CDD:224113"
     misc_feature    complement(2216..2704)
                     /locus_tag="CTDLC_p003"
                     /note="ParA and ParB of Caulobacter crescentus belong to a
                     conserved family of bacterial proteins implicated in
                     chromosome segregation. ParB binds to DNA sequences
                     adjacent to the origin of replication and localizes to
                     opposite cell poles shortly following the...; Region:
                     ParA; cd02042"
                     /db_xref="CDD:238997"
     misc_feature    complement(2663..2683)
                     /locus_tag="CTDLC_p003"
                     /note="P-loop; other site"
                     /db_xref="CDD:238997"
     misc_feature    complement(order(2336..2338,2663..2665))
                     /locus_tag="CTDLC_p003"
                     /note="Magnesium ion binding site [ion binding]; other
                     site"
                     /db_xref="CDD:238997"
     gene            complement(2738..3046)
                     /locus_tag="CTDLC_p004"
                     /db_xref="GeneID:12339902"
     CDS             complement(2738..3046)
                     /locus_tag="CTDLC_p004"
                     /codon_start=1
                     /transl_table=11
                     /product="Virulence plasmid protein pGP4-D"
                     /protein_id="YP_005811049.1"
                     /db_xref="GI:385244962"
                     /db_xref="GeneID:12339902"
                     /translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLE
                     LYHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE
                     "
     gene            complement(3116..3910)
                     /locus_tag="CTDLC_p005"
                     /db_xref="GeneID:12339903"
     CDS             complement(3116..3910)
                     /locus_tag="CTDLC_p005"
                     /codon_start=1
                     /transl_table=11
                     /product="Virulence plasmid protein pGP3-D"
                     /protein_id="YP_005811050.1"
                     /db_xref="GI:385244963"
                     /db_xref="GeneID:12339903"
                     /translation="MGNSGFYLYNTENCVFADNIKVGQMTEPLKDQQIILGTKSTPVA
                     AKMTASDGISLTVSNNSSTNASITIGLDAEKAYQLILEKLGNQILDGIADTIVDSTVQ
                     DILDKITTDPSLGLLKAFNNFPITNKIQCNGLFTPSNIETLLGGTEIGKFTVTPKSSG
                     SMFLVSADIIASRMEGGVVLALVREGDSKPCAISYGYSSGVPNLCSLRTSITNTGLTP
                     TTYSLRVGGLESGVVWVNALSNGNDILGITNTSNVSFLEVIPQTNA"
     misc_feature    complement(3119..3910)
                     /locus_tag="CTDLC_p005"
                     /note="Chlamydia virulence protein PGP3-D; Region:
                     Chlam_vir; pfam05475"
                     /db_xref="CDD:147581"
     gene            complement(3972..5027)
                     /locus_tag="CTDLC_p006"
                     /db_xref="GeneID:12339904"
     CDS             complement(3972..5027)
                     /locus_tag="CTDLC_p006"
                     /codon_start=1
                     /transl_table=11
                     /product="Virulence plasmid protein pGP2-D"
                     /protein_id="YP_005811051.1"
                     /db_xref="GI:385244964"
                     /db_xref="GeneID:12339904"
                     /translation="MVNYSNCHFIKSPIHLENQKFGRRPGQSIKISPKLAQNGMVEVI
                     GLDFLSSHYHALAAIQRLLTATNYKGNTKGVVLSRESNSFQFEGWIPRIRFTKTEFLE
                     AYGVKRYKTSRNKYEFSGKEAETALEALYHLGHQPFLIVATRTRWTNGTQIVDRYQTL
                     SPIIRIYEGWEGLTDEENIDIDLTPFNSPSTRKHKGFVVEPCPILVDQIESYFVIKPA
                     NVYQEIKMRFPNASKYAYTFIDWVITAAAKKRRKLTKDNSWPENLLLNVNVKSLAYIL
                     RMNRYICTRNWKKIELAIDKCIEIAIQLGWLSRRKRIEFLDSSKLSKKEILYLNKERF
                     EEITKKSKEQMEQESIN"
     gene            complement(5021..6376)
                     /locus_tag="CTDLC_p007"
                     /db_xref="GeneID:12339905"
     CDS             complement(5021..6376)
                     /locus_tag="CTDLC_p007"
                     /EC_number="3.6.1.-"
                     /codon_start=1
                     /transl_table=11
                     /product="Replicative DNA helicase"
                     /protein_id="YP_005811052.1"
                     /db_xref="GI:385244965"
                     /db_xref="GeneID:12339905"
                     /translation="MKTRSEIENRMQDIEYALLGKALIFEDSTEYILRQLANYEFKCS
                     HHKNIFIVFKYLKDNGLPITVDSAWEELLRRRIKDMDKSYLGLMLHDALSNDKLRSVS
                     HTVFLDDLSVCSAEENLSNFIFRSFNEYNENPLRRSPFLLLERIKGRLDSAIAKTFSI
                     RSARGRSIYDIFSQSEIGVLARIKKRRAAFSENQNSFFDGFPTGYKDIDDKGVILAKG
                     NFVIIAARPSIGKTALAIDMAINLAVTQQRRVGFLSLEMSAGQIVERIVANLTGISGE
                     KLQRGDLSKEELFRVEEAGETVRESHFYICSDSQYKLNLIANQIRLLRKEDRVDVIFI
                     DYLQLINSSVGENRQNEIADISRTLRGLASELNIPIVCLSQLSRKVEDRANKVPMLSD
                     LRDSGQIEQDADVILFINRKESSSNCEITVGKNRHGSVFSSVLHFDPKISKFSAIKKV
                     W"
     misc_feature    complement(6095..6358)
                     /locus_tag="CTDLC_p007"
                     /note="DnaB-like helicase N terminal domain; Region: DnaB;
                     pfam00772"
                     /db_xref="CDD:250122"
     misc_feature    complement(5030..5779)
                     /locus_tag="CTDLC_p007"
                     /note="DnaB-like helicase C terminal domain; Region:
                     DnaB_C; pfam03796"
                     /db_xref="CDD:252168"
     misc_feature    complement(5060..5761)
                     /locus_tag="CTDLC_p007"
                     /note="DnaB helicase C terminal domain. The hexameric
                     helicase DnaB unwinds the DNA duplex at the  chromosome
                     replication fork. Although the mechanism by which DnaB
                     both couples ATP hydrolysis to translocation along DNA and
                     denatures the duplex is unknown, a...; Region: DnaB_C;
                     cd00984"
                     /db_xref="CDD:238484"
     misc_feature    complement(5681..5701)
                     /locus_tag="CTDLC_p007"
                     /note="Walker A motif; other site"
                     /db_xref="CDD:238484"
     misc_feature    complement(order(5066..5068,5099..5101,5144..5146,
                     5252..5254,5372..5374,5681..5686))
                     /locus_tag="CTDLC_p007"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:238484"
     misc_feature    complement(5372..5383)
                     /locus_tag="CTDLC_p007"
                     /note="Walker B motif; other site"
                     /db_xref="CDD:238484"
     misc_feature    complement(order(5126..5131,5144..5149,5231..5257,
                     5330..5338,5354..5359))
                     /locus_tag="CTDLC_p007"
                     /note="DNA binding loops [nucleotide binding]"
                     /db_xref="CDD:238484"
     gene            6445..7467
                     /locus_tag="CTDLC_p008"
                     /db_xref="GeneID:12339906"
     CDS             6445..7467
                     /locus_tag="CTDLC_p008"
                     /codon_start=1
                     /transl_table=11
                     /product="Virulence plasmid integrase pGP8-D"
                     /protein_id="YP_005811053.1"
                     /db_xref="GI:385244966"
                     /db_xref="GeneID:12339906"
                     /translation="MRIGYITRDFMGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWK
                     RMKSFSLFEVIMHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILD
                     AIKKVSSAKTSWTEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTRE
                     IVKTDAMNSLQTASFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATI
                     SFSQLKNRQTEKRIIITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQA
                     GLQAAIPFKITPHVLRATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNAS
                     KKMALI"
     misc_feature    6955..7422
                     /locus_tag="CTDLC_p008"
                     /note="DNA breaking-rejoining enzymes,
                     intergrase/recombinases, C-terminal catalytic domain. The
                     tyrosine recombinase/integrase family share the same
                     catalytic domain containing six conserved active site
                     residues. The best-studied members of this diverse
                     family...; Region: INT_REC_C; cd01182"
                     /db_xref="CDD:238587"
     misc_feature    order(7039..7044,7114..7116,7306..7311,7414..7416)
                     /locus_tag="CTDLC_p008"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238587"
     misc_feature    order(7039..7041,7114..7116,7309..7311,7318..7320,
                     7387..7389,7414..7416)
                     /locus_tag="CTDLC_p008"
                     /note="Int/Topo IB signature motif; other site"
                     /db_xref="CDD:238587"
     misc_feature    order(7039..7041,7309..7311,7318..7320,7387..7389,
                     7414..7416)
                     /locus_tag="CTDLC_p008"
                     /note="active site"
                     /db_xref="CDD:238587"
     misc_feature    order(7039..7041,7318..7320,7414..7416)
                     /locus_tag="CTDLC_p008"
                     /note="catalytic residues [active]"
                     /db_xref="CDD:238587"
CONTIG      join(CP002055.1:1..7493)
//
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