LOCUS NC_014226 15593 bp DNA circular CON 12-MAR-2023
DEFINITION Waddlia chondrophila WSU 86-1044 plasmid pWc, complete sequence.
ACCESSION NC_014226
VERSION NC_014226.1
DBLINK BioProject: PRJNA224116
BioSample: SAMN02603402
Assembly: GCF_000092785.1
KEYWORDS RefSeq.
SOURCE Waddlia chondrophila WSU 86-1044
ORGANISM Waddlia chondrophila WSU 86-1044
Bacteria; Chlamydiota; Chlamydiia; Parachlamydiales; Waddliaceae;
Waddlia.
REFERENCE 1 (bases 1 to 15593)
AUTHORS Bertelli,C., Collyn,F., Croxatto,A., Ruckert,C., Polkinghorne,A.,
Kebbi-Beghdadi,C., Goesmann,A., Vaughan,L. and Greub,G.
TITLE The Waddlia genome: a window into chlamydial biology
JOURNAL PLoS One 5 (5), e10890 (2010)
PUBMED 20531937
REMARK Publication Status: Online-Only
REFERENCE 2 (bases 1 to 15593)
AUTHORS Bertelli,C. and Greub,G.
TITLE Direct Submission
JOURNAL Submitted (09-FEB-2010) Institute of Microbiology, University
Hospital Center and University of Lausanne, Bugnon 48, Lausanne VD
1011, Switzerland
COMMENT REFSEQ INFORMATION: The reference sequence is identical to
CP001929.1.
Source DNA is available from Gilbert Greub: Gilbert.Greub@chuv.ch
Bacteria is available from ATCC collection: ATCC number VR-1470.
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 :: 03/12/2023 11:24:50
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) :: 1,936
CDSs (total) :: 1,890
Genes (coding) :: 1,872
CDSs (with protein) :: 1,872
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) :: 18
CDSs (without protein) :: 18
Pseudo Genes (ambiguous residues) :: 0 of 18
Pseudo Genes (frameshifted) :: 4 of 18
Pseudo Genes (incomplete) :: 16 of 18
Pseudo Genes (internal stop) :: 1 of 18
Pseudo Genes (multiple problems) :: 2 of 18
##Genome-Annotation-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..15593
/organism="Waddlia chondrophila WSU 86-1044"
/mol_type="genomic DNA"
/strain="WSU 86-1044"
/culture_collection="ATCC:VR-1470"
/type_material="type strain of Waddlia chondrophila"
/db_xref="taxon:716544"
/plasmid="pWc"
gene 410..1372
/locus_tag="WCW_RS09490"
/old_locus_tag="wcw_p0001"
CDS 410..1372
/locus_tag="WCW_RS09490"
/old_locus_tag="wcw_p0001"
/inference="COORDINATES: protein motif:HMM:NF012798.2"
/GO_function="GO:0003677 - DNA binding [Evidence IEA]"
/GO_process="GO:0006310 - DNA recombination [Evidence
IEA]"
/GO_process="GO:0015074 - DNA integration [Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="tyrosine-type recombinase/integrase"
/protein_id="WP_143876415.1"
/translation="MTLEVVQEHKIESQAQAKSLRDKIAWQKMEMLSLDSIIVEWLET
LSERTKVNYKSGISKLTELGIINPFISLQSFSLVNHDAAIDRIKQLPDLKETTKQARA
ALYISFTRYLSRRFKGMFSKATPSREGNEKTFFRVHEKVVTEAMNLQQWTAFFEELEK
LNIRDALIGKIALQGGKRIREVLSLHSEQIDWKKREITFHQSKTRGVSKQTIITYSES
IMKQLKDLLGEGEGYLFITTTGNVVMLTQISRNFARAGKAAKIPFKVTPHVLRASAVT
YLKQQGFSDSDIMKITGHSSGEMIRAYDKSERADNPTKRVNLVM"
gene 1775..2104
/locus_tag="WCW_RS09500"
/old_locus_tag="wcw_p0003"
CDS 1775..2104
/locus_tag="WCW_RS09500"
/old_locus_tag="wcw_p0003"
/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="hypothetical protein"
/protein_id="WP_013183007.1"
/translation="MGKIKTSSKHQTYLENLSKVDLDRVSGLHKAEPLKDLTDDRQIS
MAVFECLLNNDPEGAMEVIEIYLEAMNKAKMRRKTKLPKSTMYSALKHRNPTIKTLAK
IMYSSTH"
gene 2374..2682
/locus_tag="WCW_RS09505"
CDS 2374..2682
/locus_tag="WCW_RS09505"
/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="hypothetical protein"
/protein_id="WP_041941967.1"
/translation="MKKFILITFLLIKSSFVFATIIDYKEKSIPLSVFDYKLDKFNDR
HFEKYNKYRKSNSKNNELSKALSYVNYVEANNGNCASKIVLSIELTPLFHLLDVNEKR
"
gene complement(2685..3415)
/locus_tag="WCW_RS09510"
/old_locus_tag="wcw_p0005"
CDS complement(join(2685..2926,2926..3415))
/locus_tag="WCW_RS09510"
/old_locus_tag="wcw_p0005"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_076611815.1"
/ribosomal_slippage
/GO_function="GO:0004803 - transposase activity [Evidence
IEA]"
/note="programmed frameshift; Derived by automated
computational analysis using gene prediction method:
Protein Homology."
/codon_start=1
/transl_table=11
/product="IS1 family transposase"
/protein_id="WP_227738806.1"
/translation="MNPSCPKCESTAVKKNGHIHNGKQNHRCLVCGRQFVLDPQQKII
TDQTKSEVRQALLERVSLEGICRIFSVSMPWLLSFIQQIIYELPDDLNATVVKDYKDF
EVAIIELDEQWSYVGNKKNQQWLWLAFHSASRQVLAMHVGKRDKRAAEALLAKLPEDL
KKKPFFYSDKFSVYYEVLPWKQHQAVGKNSGKTSYIERFNNTLRQRCSRLVRKTLSFS
KKLANHIGMIQYFICDYNKRMALLV"
gene 3434..3799
/locus_tag="WCW_RS09515"
/old_locus_tag="wcw_p0006"
CDS 3434..3799
/locus_tag="WCW_RS09515"
/old_locus_tag="wcw_p0006"
/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="hypothetical protein"
/protein_id="WP_013183008.1"
/translation="MAEYETLNFHQCQTNFDLSITCLGLPEKTKFTDIIINDIFRDLQ
RDVSIEIEKKHLFGKITWMAFSNTLRKSYDIEVTVEKGRITDAKQNTSDYTENMIKKE
LIDLHGHIMIQCQFKKSVE"
gene complement(3834..4070)
/locus_tag="WCW_RS09520"
/old_locus_tag="wcw_p0007"
CDS complement(3834..4070)
/locus_tag="WCW_RS09520"
/old_locus_tag="wcw_p0007"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_006342651.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="helix-turn-helix transcriptional regulator"
/protein_id="WP_013183009.1"
/translation="MSKETHNRKKTPIRKAFGLKVRMRRFEIGITQEELAEKADLHPT
YVGSVERGERNIALENIVAIAKGLGCSPKDLMPE"
gene 4222..5112
/locus_tag="WCW_RS09525"
/old_locus_tag="wcw_p0008"
CDS 4222..5112
/locus_tag="WCW_RS09525"
/old_locus_tag="wcw_p0008"
/inference="COORDINATES: protein motif:HMM:NF024206.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="ankyrin repeat domain-containing protein"
/protein_id="WP_013183010.1"
/translation="MKKLFLIFAIGIMSLTLNLKANQIDYETIQKIEEYMSNEKGWHP
LNYAIEMDDYKTALIICEYSEKVNTVDDGFNPINRIFHRTCRKINLSTPIKNRPKLSE
EALELVWAILDKGINVNYVPLNCGLPPSGNSSSSFIYICFLGLEDLFYEFIHRRVDIN
QRKGSPLATAIRAGHMNIVQSLIEEGANANWWALHQAVSSKNFEAINILLQAGADINE
IDLLMSAIFHHKKIGHYLDGLPMLRFLLEMGANPNAIAMGKKDPILKVVLTMPADTVE
QQNYKTDVINTLIEYGAVLY"
gene complement(5113..5613)
/locus_tag="WCW_RS09530"
/old_locus_tag="wcw_p0009"
CDS complement(5113..5613)
/locus_tag="WCW_RS09530"
/old_locus_tag="wcw_p0009"
/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="hypothetical protein"
/protein_id="WP_041941968.1"
/translation="MNIHAELSAFNNLRSQTEESAGQILWIEFKMRYLAERSQKIVFE
LEKITESKKEDQKYYWNCKLDDLLKAIRIAFHDQLSEKETDNLQQYQMVRNRFLHSNF
VDALKKLNLSTGGRQMLRNGERVPLDRSEIGESLKALHTNRGVRAIRDLTNSVEELLD
RLLKIE"
gene complement(5649..5867)
/locus_tag="WCW_RS09535"
/old_locus_tag="wcw_p0010"
CDS complement(5649..5867)
/locus_tag="WCW_RS09535"
/old_locus_tag="wcw_p0010"
/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="hypothetical protein"
/protein_id="WP_013183012.1"
/translation="MNRTNKNRISKLESGITEVGRHKSALVIYDPNVDYEKDLAKIDA
DVVLALPDNGRKDLKNGVVIGSCVVSYC"
gene complement(5864..6301)
/locus_tag="WCW_RS09540"
/old_locus_tag="wcw_p0011"
CDS complement(5864..6301)
/locus_tag="WCW_RS09540"
/old_locus_tag="wcw_p0011"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_006340683.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="DUF5681 domain-containing protein"
/protein_id="WP_041941969.1"
/translation="MPENAGKKQGNTRFRKGQSGNPCGKAKGTKNKATLAAEVLLEGE
LEGICRSLIAQAREGNIQAIKLVLDRVLPPKRNPTVSIELPQLKSSSDALEAITSITQ
AVGNGEISPAEGETLSRIVDVYVKALEAHDFENRLNILEEKGK"
gene complement(6724..8682)
/locus_tag="WCW_RS09545"
/old_locus_tag="wcw_p0013"
CDS complement(6724..8682)
/locus_tag="WCW_RS09545"
/old_locus_tag="wcw_p0013"
/inference="COORDINATES: protein motif:HMM:TIGR01613.1"
/GO_function="GO:0003896 - DNA primase activity [Evidence
IEA]"
/GO_process="GO:0006260 - DNA replication [Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="DNA primase family protein"
/protein_id="WP_143876416.1"
/translation="MNNNNLKTEDNQEAKEEISLEKNAFKIKSKGKSKLKFTPSIKKE
LKDVIGCQYVDILSAYVCPLGSKTEVSNLLEKNKINADLVEFHNPLPKKSKKINGMET
RLHILEKEVHKEDMELLVEAHKMKDEEGRHKSIQDFKDPPKEPGKDEKSGDLRYRIEL
DLHERFKANDEKRKEAEELRRYVEQHEKEKTENEKVLERLNKNESGDAEIFVELFEKK
YLFDPTEGKNGAFYLWDGCQWTLDIHKERYKDFEKVSDTYLIATSDESIDESVSKELF
KRSQQLRTSRRRSNVLETVSAYLSFKHSWDYCPNKLPCSNGIINLKTGDLETAQRENY
IKKVCPTSYEKNANCPKFLKFLDDITLGDKELSSFIGRVIGYALLGVPKEEKIFYFYG
NGRNGKGTLMHVIQHVLGALSKTFPSEMLLSQRNPPSSSSPNPELANLEGVRMAVFSE
INEGRKIDSAKVKNLSGRDIIPCRRLYSNVDLQITPTHTMILQTNYKPKAPSEDKALW
SRNILIPFKARFVKEPKDGENEREIKESLKDELLEEAKGILKWMVDGCLEYQEIGLKV
PQSVIDQTEGYRKENDGIGCFLEEMCFQDPAVSTQKSKMEAAIKNYCKANEMKEPTRN
EISDYLKIRFKEGRKSQGSYWKGIKIED"
gene complement(8747..10324)
/locus_tag="WCW_RS09840"
/old_locus_tag="wcw_p0014"
CDS complement(8747..10324)
/locus_tag="WCW_RS09840"
/old_locus_tag="wcw_p0014"
/EC_number="3.6.4.-"
/inference="COORDINATES: protein motif:HMM:NF012492.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="DEAD/DEAH box helicase"
/protein_id="WP_013183016.1"
/translation="MLTLRKYQRECLDAIASNYKNGNCRQLVSLPTASGKTVVFASLI
KEFEGKSLVLAHTNELLEQAREKIQMIAPNLSVGLVNADSKEFDFPVIVSSIQSARQP
NNLVELQAQNFKLLVYDECHHAASKTSRNILNALGFGCKTDRLLCGFTATAFRQDGKG
LKEVFDTVAYQRTIKEMIEEGYLCPPKGIKVSTDIDLSKVKMGDGDFQAESLAKVMDI
PEIRQIVFDAYQKEGEGRQTICFGVNIQHAYNLSCLFNCCGISSDTIHGRMSKSERES
VLKRYRSGQIQVLCNCQVLTEGFDAPETSCVIVARPTQSKGLYQQMAGRGLRLYPNKR
DCIIIDLCAKHHGLCNTVTLLEDSEKINEVEKLEKSDQPGLVESFPANLNQKLKAALI
RFDPLGQEFTWTCNESNIYVLKGDNIRLGIVPINKDRYRVVLASEKGSQTISDDLNFE
YSFAVAEDFARSNRDVFIVSDREAKWRNFPASAKQIALIRSKGYRAGLDKLTRGQASD
IISSGTLRGGSGCYVEK"
gene complement(10318..10977)
/locus_tag="WCW_RS09555"
/old_locus_tag="wcw_p0015"
CDS complement(10318..10977)
/locus_tag="WCW_RS09555"
/old_locus_tag="wcw_p0015"
/inference="COORDINATES: protein motif:HMM:NF025107.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="helix-turn-helix domain-containing protein"
/protein_id="WP_013183017.1"
/translation="MNSTKEDIEHFKNLYPMLTPTQQKIWNYLHWFCRNYRVVKPSHK
HIAEKVGCHRDTVIQAIKKFSELGWLMTLKKAWRTCTYFISEHLLRLDPTKKDTFRRD
PPKPENPPNPTQDPTVNPTHINSSSNYNRNVRDDNVQHTGNYSEEEPIPYEIRNLPVS
QKDKRLLSKYGLHVLRLAIEDFVTYQRLYRVRNVAAFITSRCKAYVQKFRTQPKSGVA
C"
gene complement(10977..11270)
/locus_tag="WCW_RS09560"
/old_locus_tag="wcw_p0016"
CDS complement(10977..11270)
/locus_tag="WCW_RS09560"
/old_locus_tag="wcw_p0016"
/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="hypothetical protein"
/protein_id="WP_013183018.1"
/translation="MLETLSQEQNTQTTSPTEGFIAKIRKMLDAIPSEFVQPKHLHEL
GFFGSHSAATHFVQDGGIPHVRISPYRILIQKEDVLAFLKEKYRQKSKKVGGE"
gene complement(11601..12521)
/locus_tag="WCW_RS09565"
/old_locus_tag="wcw_p0017"
CDS complement(11601..12521)
/locus_tag="WCW_RS09565"
/old_locus_tag="wcw_p0017"
/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="tyrosine-type recombinase/integrase"
/protein_id="WP_162268183.1"
/translation="MVLDPVKPGKEMSTKDIGRFLEENKSGFCSSELLKCVLLNIPIT
VAVKEWLATIENPDTKRKYKKAMERIFALEPLSDVTKRNCAITTLDKNWSGAVGIYKL
MEEIEAPESAIKTCQSVFSRFCDFIRIATLGIVDPEETPKQKEDYYAVSILYENTDWE
EFISSMRTPFNLLAEMTFLAAKSCELRLRLANSKKNILSLDTSQINFQNNTISFKSEQ
SYQVTDILGHPLCIPFTESFMKKLKDYIGERKGVVFLSKKNKPLFATQVQREFKKASK
NLPNEITPVMLGWAGVLAYKEKSKKKFPFK"
gene complement(12586..12885)
/locus_tag="WCW_RS09570"
/old_locus_tag="wcw_p0018"
CDS complement(12586..12885)
/locus_tag="WCW_RS09570"
/old_locus_tag="wcw_p0018"
/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="hypothetical protein"
/protein_id="WP_013183020.1"
/translation="MSKKAKLSQLHKELTTLNKTESKVEAKTETRNAQKKTSIGANPL
RGERGDFLKVTITLPPGMLADLKRLGLERKLQGMKDTDVSSLIRESLTTFLESQE"
gene complement(12898..13554)
/locus_tag="WCW_RS09575"
/old_locus_tag="wcw_p0019"
CDS complement(12898..13554)
/locus_tag="WCW_RS09575"
/old_locus_tag="wcw_p0019"
/inference="COORDINATES: protein motif:HMM:NF013793.2"
/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_013183021.1"
/translation="MKTIISCLNLKGGCGKSSTIVNLGGVFSENKKKPLLIDLDEQQS
STHWARQGGDKFPFPVIPLSIETAGKVKSEIERLANEHKADTILIDTPPQLEDDALIT
ALLSDIVLIPVSPSPLDLWAAQQAVNTIKDAREERGGKLPKAILIPSRVMNRTTLAKD
IKGSLKAFGEPISPAISLRVAIAEAAIAGLPIGHYAPNSPGHKEFTNLWKFVNSQIRK
"
gene 13828..14394
/locus_tag="WCW_RS09580"
/old_locus_tag="wcw_p0020"
CDS 13828..14394
/locus_tag="WCW_RS09580"
/old_locus_tag="wcw_p0020"
/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="hypothetical protein"
/protein_id="WP_041941971.1"
/translation="MRKFLVLSAIFVLASSHSFAANKVYTIGEIFGIVADDQEWSCEV
VSVENSGLIGNDYGNLFVQGSSKNHPVSFDFFHTMHRIKNWTDNPHPHLERILKNYTN
CSNTILLNWKIKQCSWSKIIVEGDYLDNSKVGYFQLFSEFEPTAFMYDDIKKPVFNLL
IKIESEFMDEETLQFYYDSVKPLKKRLY"
gene 14489..14734
/locus_tag="WCW_RS09585"
/old_locus_tag="wcw_p0021"
CDS 14489..14734
/locus_tag="WCW_RS09585"
/old_locus_tag="wcw_p0021"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_013182277.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_013183023.1"
/translation="MAQTARISRRSDSIIQEMVSLTGYSKVEVIEHALETYRRNERMR
LMNEAYQTLKSDKSAWEEELKDREELEGTIADGFEEE"
gene 14715..15080
/locus_tag="WCW_RS09590"
/old_locus_tag="wcw_p0022"
CDS 14715..15080
/locus_tag="WCW_RS09590"
/old_locus_tag="wcw_p0022"
/EC_number="3.1.-.-"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_013182276.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="type II toxin-antitoxin system PemK/MazF family
toxin"
/protein_id="WP_013183024.1"
/translation="MALKKNNPLQGEVWLFDPDPVKGNEIGKKVRPALVVSNNLMNKG
VSGLIIIVPITSKDKKIPSHIRIEPPEGGVNLPSFAVCEQVRSISKSRLVKRLGKVQS
ATVLKEVGSWLNDLLWIDI"
gene complement(15193..15558)
/locus_tag="WCW_RS09595"
CDS complement(15193..15558)
/locus_tag="WCW_RS09595"
/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="hypothetical protein"
/protein_id="WP_041941972.1"
/translation="MNLEKGISRIGIVFGVICGCTLIFLAWKTDLYFNLLSHFDFKYE
ENHTHLYNTGEIVEISGFKILRQIRITNEDAPSKLMHIVLPKVGTVLGVSIALFLSGF
YLIKGVFETINWVIRGFRG"
CONTIG join(CP001929.1:1..15593)
//
