LOCUS NC_002180 4532 bp ss-DNA circular PHG 22-APR-2010 DEFINITION Chlamydia phage CPAR39, complete genome. ACCESSION NC_002180 VERSION NC_002180.1 GI:9791176 DBLINK Project:247 KEYWORDS . SOURCE Chlamydia phage CPAR39 ORGANISM Chlamydia phage CPAR39 Viruses; ssDNA viruses; Microviridae; Gokushovirinae; Chlamydiamicrovirus. REFERENCE 1 (bases 1 to 4532) AUTHORS Read,T.D., Brunham,R.C., Shen,C., Gill,S.R., Heidelberg,J.F., White,O., Hickey,E.K., Peterson,J., Umayam,L.A., Utterback,T., Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S.L., Eisen,J. and Fraser,C.M. TITLE Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39 JOURNAL Nucleic Acids Res. 28 (6), 1397-1406 (2000) PUBMED 10684935 REFERENCE 2 (bases 1 to 4532) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (05-MAY-2009) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA REFERENCE 3 (bases 1 to 4532) AUTHORS Read,T.D., Brunham,R.C., Shen,C., Gill,S.R., Heidelberg,J.F., White,O., Hickey,E.K., Peterson,J., Umayam,L.A., Utterback,T., Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S.L., Eisen,J. and Fraser,C.M. TITLE Direct Submission JOURNAL Submitted (29-FEB-2000) The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from AE002163. COMPLETENESS: full length. FEATURES Location/Qualifiers source 1..4532 /organism="Chlamydia phage CPAR39" /mol_type="genomic DNA" /host="Chlamydophila pneumoniae AR39" /db_xref="taxon:117575" gene join(4425..4532,1..147) /locus_tag="phiCPAR39p1" /db_xref="GeneID:1263024" CDS join(4425..4532,1..147) /locus_tag="phiCPAR39p1" /note="generated by GeneMarkS" /codon_start=1 /transl_table=11 /product="nonstructural protein" /protein_id="NP_597909.1" /db_xref="GI:19343446" /db_xref="GeneID:1263024" /translation="MKVFTVFDIKTEIYQQPFFMQATGAAIRAFSDMVNEDPSKNQFA AHPEDYILYEIGSYDDSTGTFIPLDVPKALGTGLDFKHKQ" gene 155..1816 /locus_tag="phiCPAR39p2" /db_xref="GeneID:1263019" CDS 155..1816 /locus_tag="phiCPAR39p2" /note="Similar to Microvirus protein F" /codon_start=1 /transl_table=11 /product="major capsid protein" /protein_id="NP_063895.1" /db_xref="GI:9791178" /db_xref="GeneID:1263019" /translation="MVRNRRLPSVMSHSFAQVPSARIQRSSFDRSCGLKTTFDAGYLI PIFCDEVLPGDTFSLKEAFLARMATPIFPLMDNLRLDTQYFFVPLRLIWSNFQKFCGE QDNPGDSTDFLTPVLTAPSGGFTEGSIHDYLGLPTKVAGIECVAFWHRAYNLIWNQYY RDENIQESVDVEMGDTTSNEVNNYKLLKRGKRYDYFTSCLPWPQKGPAVTIGVGGIVP VQGLGIQWGNSSAPNPITASSWINSVNPTFINSTTPTPTGTNQILNYGQAYYIKKPGE ATTDPTPRAYVDLGSTSPVTINSLREAFQLQKLYERDARGGTRYIEIIRSHFNVQSPD ARLQRAEYLGGSSTPVNISPIPQTSSTDSTSPQGNLAAYGTAIGSKRVFTKSFTEHGV ILGLASVRADLNYQQGLDRMWSRRTRWDFYWPALSHLGEQAVLNKEIYCQGPAVKDAQ NGNVVVDEQVFGYQERFAEYRYKTSKITGKFRSNATGSLDAWHLAQQFENLPTLSPEF IEENPPMDRVVAVDTEPDFLLDGWFSLRCARPMPVYSVPGLIDHF" gene 1922..2482 /locus_tag="phiCPAR39p3" /db_xref="GeneID:1263018" CDS 1922..2482 /locus_tag="phiCPAR39p3" /note="Proteins from this cluster may be analogous to the Microvirus DNA pilot protein (protein H). This is based on (1) the number of VP2 molecules per virion and (2) the glycine rich sequence of VP2. However, no sequence similarity was detected. This protein may not be part of the mature virion in SpV4." /codon_start=1 /transl_table=11 /product="minor capsid protein" /protein_id="NP_063896.1" /db_xref="GI:9791177" /db_xref="GeneID:1263018" /translation="MNPEQLTSTLGSAVSGVAQGLSFLPGIASGVLGYLGAQKQNATA KQIAREQMAFQERMSNTAYQRAMEDMKKAGLNPMLAFSKGGASSPAGASWSPNNPVES AMNSGLAVQRLTYERKKMQAELQNLREQNRLIRNQAIREGYLAERDKYMRVAGVPVAT EMLDRTSGLLSSSAKAFKNLFSRKGR" gene 2483..2929 /locus_tag="phiCPAR39p4" /db_xref="GeneID:1263023" CDS 2483..2929 /locus_tag="phiCPAR39p4" /note="This protein may be analogous to the internal scaffolding protein of Microviruses (protein B), based on the amounts present in virions and some weak sequence similarity. However, unlike protein B, proteins in this family may remain associated with mature virions." /codon_start=1 /transl_table=11 /product="minor capsid protein" /protein_id="NP_063897.1" /db_xref="GI:9791182" /db_xref="GeneID:1263023" /translation="MFKSAYSEKKSVKMKFTQKSLTQQHNKDECDINNIVAKLNATGV LEHVERRSPRYMDCMDPMEYSEALNVVIEAQEQFDSLPAKVRERFGNDPEAMLDFLSR EENYEEAKALGFVYEDGTSGAPQTFFEADPKDDQNVANQEPGLAQK" gene 2937..3044 /locus_tag="phiCPAR39p5" /db_xref="GeneID:1263022" CDS 2937..3044 /locus_tag="phiCPAR39p5" /note="hypothetical protein; identified by Glimmer2; putative" /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="NP_063898.1" /db_xref="GI:9791181" /db_xref="GeneID:1263022" /translation="MCKKVCKKCPKKGPKNAPKIGAFYERKTPRLKQST" gene complement(3122..3217) /locus_tag="phiCPAR39p6" /db_xref="GeneID:1263021" CDS complement(3122..3217) /locus_tag="phiCPAR39p6" /note="hypothetical protein; identified by Glimmer2; putative" /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="NP_063899.1" /db_xref="GI:9791180" /db_xref="GeneID:1263021" /translation="MDASLMQFLKKVFDFYVAEVCIFFVPFLTSF" gene 3412..4395 /locus_tag="phiCPAR39p7" /db_xref="GeneID:1263020" CDS 3412..4395 /locus_tag="phiCPAR39p7" /note="Weak sequence similarity to Microvirus protein A which is involved in DNA replication initiation and termination." /codon_start=1 /transl_table=11 /product="putative replication initiation protein" /protein_id="NP_063900.1" /db_xref="GI:9791179" /db_xref="GeneID:1263020" /translation="MVCCNFNLIQAFMACVSPFVCFIDSYNQLWFPKGKKSPKPWDKV RELNSFEQTQPEEYRKRWVVMPCLKCRFCRVRNAKIWSYRCMHEASLYSQNCFLTLTY EDRYLPENGSLVRNHPRLFLMRLRKEIYPHKIRYFGCGEYGSKLQRPHYHLLIYNYDF PDKKLLSKKRGNPLFVSEKLMRLWPFGFSTVGSVTRQSAGYVARYSLKKVNGDISQDH YGQRLPEFLMCSLKPGIGADWYEKYKRDVYPQDYLVVQDKGKSFKTRPPRYYDKLHSR FDPEEMEEIKQKRVEKFMALPELTQDKAEVKQYIFNDRTKRLFRDYEEESY" ORIGIN 1 gatccttcga aaaatcaatt tgccgcgcat cctgaagatt acattctcta tgagattgga 61 tcttacgatg actctactgg aactttcatt cccttagatg tgcctaaagc cttaggaaca 121 ggcttggatt ttaagcacaa acagtaggga agatatggtt aggaatcggc gtttgccttc 181 agttatgagt cattctttcg cgcaagttcc atcagcgcga attcagagaa gttcttttga 241 tagatcttgt ggtttaaaga ctacattcga cgccggttac ctaatcccta tcttttgcga 301 tgaagttctc cctggagata ctttctcctt gaaagaggcg tttttagcac gtatggctac 361 gcctatcttt cctcttatgg ataatttgcg tttagatacg cagtatttct ttgttcctct 421 tcgacttata tggtcgaatt tccaaaagtt ctgtggagaa caagataatc ctggagattc 481 cacagatttt cttaccccag ttttaaccgc tcctagtggg ggatttactg aaggatcaat 541 ccatgattat cttggtctac ctactaaagt tgcaggaatt gaatgtgttg cgttctggca 601 cagagcttac aatttgattt ggaaccagta ctatcgtgat gagaatattc aggaatctgt 661 tgacgtggaa atgggagaca ccacctctaa tgaggtgaat aattataagc ttcttaagcg 721 tgggaagcgt tatgattact tcacttcatg tctcccttgg ccacaaaaag gtcctgcagt 781 gacaatcgga gttggaggta ttgttcctgt tcaaggttta ggaattcaat gggggaattc 841 tagtgctcca aatcctataa ctgcttctag ttggataaat tctgttaatc ctacatttat 901 aaattctaca acgccgacgc ctacaggaac gaatcagatt ttgaattatg gtcaggcgta 961 ttatattaag aagcctggag aagcaactac agatcctaca cctagggctt atgtagattt 1021 aggttctact tctcctgtga cgattaattc tcttcgtgaa gctttccaat tgcaaaagct 1081 ttatgagaga gatgctcgtg gcggaacaag gtacattgag attattcgtt cccatttcaa 1141 tgtgcagtct ccagatgcaa ggttgcaacg tgcagagtat cttggaggtt cttcaactcc 1201 tgtgaatatt tctccgattc cacagacttc ctcaacagac tccacatctc ctcaaggaaa 1261 tcttgctgct tatggtacag cgattggatc gaagcgagtc ttcacaaagt ctttcacaga 1321 acatggtgta attcttggat tagcctctgt acgcgccgat ctcaactatc agcaaggttt 1381 ggataggatg tggtcacgaa gaacgcgctg ggacttttac tggcctgctc ttagccattt 1441 aggtgagcaa gctgtgctca ataaagagat ctattgccaa ggtcctgcag ttaaggatgc 1501 tcagaatggt aatgttgttg tggatgagca agtctttgga tatcaggaga gatttgcgga 1561 gtatcgctat aagacttcga aaatcactgg gaagttccga tcaaatgcta caggttcttt 1621 agatgcatgg catttagctc agcagtttga gaatcttcca acactttctc cagagtttat 1681 cgaagaaaat cctcctatgg atcgtgttgt tgctgtagat actgagccag attttctctt 1741 agatggttgg ttttcattgc gttgtgcaag accaatgcct gtctattctg ttccaggtct 1801 tattgatcat ttctaatttc cactcagttt tccggtttga taaagcaaac tcacgttcgt 1861 agataagtga gtacggtgaa aaccaaaacg gaaagctgag gcgtaaaaat gtggagaatt 1921 tatgaatccc gaacaactca cgagtactct cggttcagca gtttctggag ttgcccaagg 1981 attatccttc ctccctggaa tagcttccgg agttttagga tatcttggcg cacagaaaca 2041 aaatgcgact gcgaagcaaa ttgctagaga gcaaatggct tttcaggagc gcatgtctaa 2101 cacggcatac caacgtgcta tggaagacat gaagaaagct ggccttaacc ctatgttagc 2161 tttttctaaa ggcggtgctt cttctcctgc aggagcgtca tggtctccga ataatcctgt 2221 agagagcgcg atgaattctg gacttgccgt gcaaagactt acttatgaac gtaagaaaat 2281 gcaggcagag cttcagaatc ttcgtgagca gaaccgtttg attagaaacc aagcaatacg 2341 tgaaggctat ctcgcagaac gagataaata tatgcgtgtt gctggagttc ctgtggctac 2401 tgagatgtta gatagaactt caggtcttct ctcatcttca gctaaggcat ttaagaatct 2461 tttttcaaga aaaggaaggt agatgtttaa gtcggcatat tccgaaaaaa aatctgtaaa 2521 gatgaagttt acacagaaat ctttgacgca acaacacaac aaagatgagt gtgatattaa 2581 caacattgtc gcaaaactca acgctacagg cgttttagag cacgtagagc gacgatctcc 2641 acgttatatg gactgtatgg accctatgga gtattccgag gctctaaacg tcgttattga 2701 ggctcaggag caatttgact ctttaccagc gaaagttcgt gaacgttttg gaaatgatcc 2761 ggaagcgatg ctcgatttct tgagccgtga agaaaattat gaagaagcaa aggcgttagg 2821 ttttgtttat gaagatggaa cttctggagc acctcaaaca ttttttgaag ctgatcctaa 2881 agatgatcaa aatgtggcaa accaagaacc tggattagcc caaaaatgag caaattttgt 2941 gcaaaaaagt gtgcaaaaaa tgcccaaaaa aagggccaaa aaatgccccc aaaatcggag 3001 cattttacga gagaaaaaca cctagactta aacagtctac ttgatctgtt taagtctagg 3061 tgataccgat tcaaggaaat atttgaaaaa ataagcccta tttagggccc aaaatttaag 3121 cttaaaatga ggttaaaaat ggcacgaaga agatacagac ttccgcgacg tagaagtcga 3181 agactttttt caagaactgc attaaggatg catccaagaa ataggcttcg aagaattatg 3241 cgtggcggca ttaggttcta gttttggacg ttaaggaaat ctttaaggtt atgctaaatt 3301 aactgtcatg tataatttgg ctcgtgaccg aatagtcata ttcgcactga ataaattgta 3361 cacaacagtt gaaggcttgg atgttgattt ttaatgtctt agccttcatt tttggtttgt 3421 tgtaacttta atttaattca ggcatttatg gcgtgtgtct ctcctttcgt atgttttata 3481 gattcttata accagctctg gtttcccaaa ggtaagaagt ctcctaaacc ttgggataaa 3541 gtccgtgaat taaattcttt tgagcaaact caacctgaag agtatcgaaa acgatgggtt 3601 gtgatgcctt gtcttaagtg taggttttgc agagtgcgga atgcaaagat ttggtcgtat 3661 cgttgcatgc acgaagcgtc tttatattct cagaattgtt ttttaacttt gacttatgag 3721 gatcgttatc ttccagagaa tggctctttg gtgagaaatc atcctcgttt gtttcttatg 3781 cgattgagga aagagatcta tcctcataaa attcgttatt ttggatgtgg tgaatatgga 3841 tcgaaattac aaaggcctca ttatcatctt cttatttata attacgattt tcctgataag 3901 aagctcttga gtaaaaagcg tggcaatcct ctctttgttt ctgagaagtt aatgcggctt 3961 tggccttttg gattctctac agtaggatct gtaacgcggc agagtgcagg ttatgtagcg 4021 cgatattctt tgaagaaagt gaatggagat atttctcaag atcattacgg tcaaagactt 4081 ccggagtttc ttatgtgttc tcttaaacca ggaataggag cggattggta tgagaaatat 4141 aaacgcgatg tttatcctca ggattatctt gttgtgcaag ataaagggaa gtcttttaag 4201 acgcgtcctc cacgttacta tgataagtta cattctcggt ttgatccgga agagatggaa 4261 gagatcaaac aaaaacgcgt agagaaattt atggctttgc ctgagttaac tcaagataag 4321 gctgaggtga agcaatatat tttcaatgac cgtacgaaga gactctttag agactatgag 4381 gaggagagtt actaaacttt tttaaaaaat aggagctttt ttcaatgaaa gtttttacag 4441 tgtttgatat taagacggaa atttatcagc agcctttctt tatgcaggct acgggagcgg 4501 caattagagc gttttccgat atggtaaatg ag //