LOCUS       NC_001741               4877 bp ss-DNA     circular PHG 13-AUG-2018
DEFINITION  Chlamydia phage Chp1, complete genome.
ACCESSION   NC_001741
VERSION     NC_001741.1
DBLINK      BioProject: PRJNA485481
KEYWORDS    RefSeq.
SOURCE      Chlamydia virus Chp1 (Bacteriophage chp1)
  ORGANISM  Chlamydia virus Chp1
            Viruses; ssDNA viruses; Microviridae; Gokushovirinae;
            Chlamydiamicrovirus.
REFERENCE   1  (bases 1 to 4877)
  AUTHORS   Storey,C.C., Lusher,M. and Richmond,S.J.
  TITLE     Analysis of the complete nucleotide sequence of Chp1, a phage which
            infects avian Chlamydia psittaci
  JOURNAL   J. Gen. Virol. 70 (Pt 12), 3381-3390 (1989)
   PUBMED   2607341
REFERENCE   2  (bases 1 to 4877)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (05-OCT-2007) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from D00624.
            The N-terminal amino acid sequences of the three structural
            proteins VP1,VP2 and VP3 were determined and it was found that they
            were encoded by ORFs 1, 2 and 3 respectively.
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4877
                     /organism="Chlamydia virus Chp1"
                     /mol_type="genomic DNA"
                     /host="Chlamydia psittaci"
                     /db_xref="taxon:2003327"
                     /synonym="Bacteriophage chp1"
                     /note="2 bp upstream of AccI site"
     gene            join(4460..4877,1..1373)
                     /locus_tag="chp1p01"
                     /db_xref="GeneID:1261207"
     CDS             join(4460..4877,1..1373)
                     /locus_tag="chp1p01"
                     /note="ORF 1; Similar to Microvirus protein F"
                     /codon_start=1
                     /transl_table=11
                     /product="major capsid protein"
                     /protein_id="NP_044312.1"
                     /db_xref="GeneID:1261207"
                     /translation="MAKGRKLPSVMKNRFSEVPTATIRRSSFDRSHGYKTTFDMDYLV
                     PFFVDEVLPGDTFSLSETHLCRLTTLVQPIMDNIQLTTQFFFVPNRLLWDNWESFITG
                     GDEPVAWTSTNPANEYFVPQVTSPDGGYAENSIYDYFGLPTKVANYRHQVLPLRAYNL
                     IFNEYYRDENLQESLPVWTGDADPKVDPTTGEESQEDDAVPYVYKLMRRNKRYDYFTS
                     ALPGLQKGPSVGIGITGGDSGRLPVHGLAIRSYLDDSSDDQFSFGVSYVNASQKWFTA
                     DGRLTSGMGSVPVGTTGNFPIDNVVYPSYFGTTVAQTGSPSSSSTPPFVKGDFPVYVD
                     LAASSSVTINSLRNAITLQQWFEKSARYGSRYVESVQGHFGVHLGDYRAQRPIYLGGS
                     KSYVSVNPVVQNSSTDSVSPQGNLSAYALSTDTKHLFTKSFVEHGFVIGLLSATADLT
                     YQQGLERQWSRFSRYDYYWPTFAHLGEQPVYNKEIYCQSDTVMDPSGSAVNDVPFGYQ
                     ERYAEYRYKPSKVTGLFRSNATGTLDSWHLSQNFANLPTLNETFIQSNTPIDRALAVP
                     DQPDFICDFYFNYRCIRPMPVYSVPGLRRI"
     regulatory      1079..1081
                     /regulatory_class="ribosome_binding_site"
                     /locus_tag="chp1p01"
                     /note="putative"
     gene            1087..1182
                     /locus_tag="chp1p02"
                     /db_xref="GeneID:1261206"
     CDS             1087..1182
                     /locus_tag="chp1p02"
                     /note="ORF 7"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="NP_044313.1"
                     /db_xref="GeneID:1261206"
                     /translation="MCLLVIKSVMLSIVISLRRLLDYLDLTLQVL"
     repeat_region   1386..1434
                     /note="hairpin-like structure h1"
     repeat_region   1448..1492
                     /note="hairpin-like structure h1"
     repeat_region   1500..1506
                     /note="hairpin-like structure h2"
     regulatory      1510..1513
                     /regulatory_class="ribosome_binding_site"
                     /note="putative"
     repeat_region   1514..1520
                     /note="hairpin-like structure h2"
     gene            1518..2309
                     /locus_tag="chp1p03"
                     /db_xref="GeneID:1261205"
     CDS             1518..2309
                     /locus_tag="chp1p03"
                     /note="ORF 2; 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_044314.1"
                     /db_xref="GeneID:1261205"
                     /translation="MSFAENVGRFIGNSVNSVGSVIGDGLKGFNSTQSISSAKQANLL
                     NNLPLPSLDNVLNIGMFGGLASGLLSYRAAKKQNKVMQDIANRQMAFQERMSSTAVRR
                     HVEDLKKAGLNPLLALGGSASTPQGAFYSPVNPMESGLNSAISVADKVFDYQRLAHAD
                     FQGRLNSAMSVVQLASAVQDYKRNYGKFGEVAYWFDRYAGKLLPAMLFYLFRKHPVGR
                     AVSAANSGYAVAKGAKGVNFKFSNMSSTAVQRHNSRYNVSKGWRR"
     regulatory      1776..1778
                     /regulatory_class="ribosome_binding_site"
                     /locus_tag="chp1p03"
                     /note="putative"
     gene            1782..2309
                     /locus_tag="chp1p04"
                     /db_xref="GeneID:1261204"
     CDS             1782..2309
                     /locus_tag="chp1p04"
                     /note="ORF 2a"
                     /codon_start=1
                     /transl_table=11
                     /product="structural protein"
                     /protein_id="NP_044315.1"
                     /db_xref="GeneID:1261204"
                     /translation="MAFQERMSSTAVRRHVEDLKKAGLNPLLALGGSASTPQGAFYSP
                     VNPMESGLNSAISVADKVFDYQRLAHADFQGRLNSAMSVVQLASAVQDYKRNYGKFGE
                     VAYWFDRYAGKLLPAMLFYLFRKHPVGRAVSAANSGYAVAKGAKGVNFKFSNMSSTAV
                     QRHNSRYNVSKGWRR"
     regulatory      1792..1796
                     /regulatory_class="ribosome_binding_site"
                     /locus_tag="chp1p04"
                     /note="putative"
     gene            1800..2309
                     /locus_tag="chp1p05"
                     /db_xref="GeneID:1261203"
     CDS             1800..2309
                     /locus_tag="chp1p05"
                     /note="ORF 2b"
                     /codon_start=1
                     /transl_table=11
                     /product="structural protein"
                     /protein_id="NP_044316.1"
                     /db_xref="GeneID:1261203"
                     /translation="MSSTAVRRHVEDLKKAGLNPLLALGGSASTPQGAFYSPVNPMES
                     GLNSAISVADKVFDYQRLAHADFQGRLNSAMSVVQLASAVQDYKRNYGKFGEVAYWFD
                     RYAGKLLPAMLFYLFRKHPVGRAVSAANSGYAVAKGAKGVNFKFSNMSSTAVQRHNSR
                     YNVSKGWRR"
     regulatory      2064..2067
                     /regulatory_class="ribosome_binding_site"
                     /locus_tag="chp1p05"
                     /note="putative"
     gene            2071..2319
                     /locus_tag="chp1p06"
                     /db_xref="GeneID:1261214"
     CDS             2071..2319
                     /locus_tag="chp1p06"
                     /note="ORF 6"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="NP_044317.1"
                     /db_xref="GeneID:1261214"
                     /translation="MESLVKLHIGLIDMLASCCLLCFSICLESIQLEERFLLLILVML
                     LLRVLKVLILSFRICLVRLFSVIILDIMFRKDGEGNEV"
     regulatory      2299..2302
                     /regulatory_class="ribosome_binding_site"
                     /locus_tag="chp1p06"
                     /note="putative"
     gene            2309..2746
                     /locus_tag="chp1p07"
                     /db_xref="GeneID:1261213"
     CDS             2309..2746
                     /locus_tag="chp1p07"
                     /note="ORF 3; 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_044318.1"
                     /db_xref="GeneID:1261213"
                     /translation="MKFRTIYDEERPAPVLECKDESLCLAYQCTETSIEKLVKLANQN
                     PSYLHAFAGDPTRQPEYGECPSPLDYQDALEIVARGEEAFYSLPANIRVNFSNPMEFL
                     SWLEDPANYDEVEKLGLLDPEKVQIRKSKLQKDQKEEVSSEEK"
     repeat_region   2334..2339
                     /locus_tag="chp1p07"
                     /note="hairpin-like structure h3"
     repeat_region   2345..2350
                     /locus_tag="chp1p07"
                     /note="hairpin-like structure h3"
     regulatory      2810..2813
                     /regulatory_class="ribosome_binding_site"
                     /note="putative"
     gene            2823..2933
                     /locus_tag="chp1p08"
                     /db_xref="GeneID:1261212"
     CDS             2823..2933
                     /locus_tag="chp1p08"
                     /note="ORF 8"
                     /codon_start=1
                     /transl_table=11
                     /product="nonstructural protein"
                     /protein_id="NP_044319.1"
                     /db_xref="GeneID:1261212"
                     /translation="MVRRRRLRRRISRRIFRRTVARVGRRRRSFRGGIRF"
     repeat_region   2946..2954
                     /note="hairpin-like structure h4"
     regulatory      2946..2950
                     /regulatory_class="ribosome_binding_site"
                     /note="putative"
     gene            2960..4159
                     /locus_tag="chp1p09"
                     /db_xref="GeneID:1261211"
     CDS             2960..4159
                     /locus_tag="chp1p09"
                     /note="ORF 4; 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_044320.1"
                     /db_xref="GeneID:1261211"
                     /translation="MRYSLDSYLISVYIRLTQRKSDYMCTNPIIPIVQYKVPVKSSLD
                     VVDWSKFRSNFKANLFFFEKNVVRRAVSNVDEAFRFTEQLKQVSYLSTFDLDGYHQVK
                     QFSFPLPCRKCSECLQKRSKDLAVQATMEARSHEENSVLILTYDNDHLGDNILDYDHI
                     RVFQKRLRRYVDYHYGKKIKFLTVGEYGDKKGRMHWHMIVFGWKPKSEEQLEPYLGGK
                     YRTDVRYRSRKLKELWKFGYVDVDEATDGNIFYVARYVQKKFVVGCDLDSSKSSSRRE
                     KKTASQALGLDYFFSYLRQFLKTKRIVLNGFRYGFPRYFKDLLRKLVSEDSEFDTEYY
                     NALRKRLLSVCSYSMVNKYFTYLECLVEVLPVLNFHDLYQRALRYMDQSILKPHASDH
                     DGEYNTT"
     repeat_region   2963..2972
                     /locus_tag="chp1p09"
                     /note="hairpin-like structure h4"
     regulatory      3532..3535
                     /regulatory_class="ribosome_binding_site"
                     /locus_tag="chp1p09"
                     /note="putative"
     gene            3539..4159
                     /locus_tag="chp1p10"
                     /db_xref="GeneID:1261210"
     CDS             3539..4159
                     /locus_tag="chp1p10"
                     /note="ORF 4a"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="NP_044321.1"
                     /db_xref="GeneID:1261210"
                     /translation="MHWHMIVFGWKPKSEEQLEPYLGGKYRTDVRYRSRKLKELWKFG
                     YVDVDEATDGNIFYVARYVQKKFVVGCDLDSSKSSSRREKKTASQALGLDYFFSYLRQ
                     FLKTKRIVLNGFRYGFPRYFKDLLRKLVSEDSEFDTEYYNALRKRLLSVCSYSMVNKY
                     FTYLECLVEVLPVLNFHDLYQRALRYMDQSILKPHASDHDGEYNTT"
     regulatory      4158..4162
                     /regulatory_class="ribosome_binding_site"
                     /note="putative"
     gene            4168..4458
                     /locus_tag="chp1p11"
                     /db_xref="GeneID:1261209"
     CDS             4168..4458
                     /locus_tag="chp1p11"
                     /note="ORF 5"
                     /codon_start=1
                     /transl_table=11
                     /product="nonstructural protein"
                     /protein_id="NP_044322.1"
                     /db_xref="GeneID:1261209"
                     /translation="MHMFYYSIYDRKARSYGDLISFPSGEKEAAIRWFRDVVMDSDSK
                     NILHRYPEDFDFCYIGYFDKDKGRFYPVDAGIVTIINAGEFFLDSEYRQEEV"
     regulatory      4271..4273
                     /regulatory_class="ribosome_binding_site"
                     /locus_tag="chp1p11"
                     /note="putative"
     gene            4282..4458
                     /locus_tag="chp1p12"
                     /db_xref="GeneID:1261208"
     CDS             4282..4458
                     /locus_tag="chp1p12"
                     /note="ORF 5a"
                     /codon_start=1
                     /transl_table=11
                     /product="nonstructural protein"
                     /protein_id="NP_044323.1"
                     /db_xref="GeneID:1261208"
                     /translation="MDSDSKNILHRYPEDFDFCYIGYFDKDKGRFYPVDAGIVTIINA
                     GEFFLDSEYRQEEV"
     regulatory      4450..4454
                     /regulatory_class="ribosome_binding_site"
                     /locus_tag="chp1p12"
                     /note="putative"
ORIGIN      
        1 gtctacctac taaagttgca aattatcggc atcaagtttt gccattaaga gcatataatt
       61 tgatatttaa tgagtattat cgtgatgaga atcttcagga gtctttacct gtttggacag
      121 gagatgctga tcctaaggtt gatccgacta ctggagaaga atctcaagag gatgatgcag
      181 ttccttatgt atataagtta atgcgtcgca ataagcgata tgattatttt acttctgctc
      241 ttcctggttt gcagaaaggt ccttctgttg gaataggtat tacaggtgga gattcaggac
      301 gtcttccagt tcatggttta gcgattagat cttatttgga tgattcttct gatgatcagt
      361 ttagttttgg tgtttcttat gtaaacgctt cacagaaatg gtttactgca gatggtcgtt
      421 tgacttctgg aatgggtagt gttcctgttg gtacaactgg taattttcct attgataatg
      481 ttgtgtatcc atcttatttt ggtacgactg ttgcccaaac tggtagtcca tcttcttctt
      541 ctactccgcc ttttgttaag ggtgattttc ctgtttatgt tgatttagcg gcttcatctt
      601 cagttacgat taattcgctt cgtaatgcga ttactttgca acagtggttt gagaagagtg
      661 ctcgttatgg aagtagatat gttgaatctg ttcaaggtca ttttggcgtt catcttggtg
      721 attatcgtgc tcagcgacca atctatttag gtggatctaa gtcttatgtt tctgttaatc
      781 ctgtagtaca gaattcatct acagattcag tttctcctca aggaaatctt tctgcttatg
      841 cattatctac agatactaaa catttgttta cgaagtcttt tgttgagcat ggttttgtta
      901 taggtcttct ttcagctaca gcggatttaa cttatcagca aggtttagag cgtcagtggt
      961 caagatttag tcgttatgat tattattggc ctacttttgc tcatttggga gagcagcctg
     1021 tttataataa agagatttat tgccaatcag atactgttat ggatcctagt ggttctgcgg
     1081 ttaatgatgt gccttttggt tatcaagagc gttatgctga gtatcgttat aagccttcga
     1141 aggttactgg attatttaga tctaacgcta caggtactct agattcttgg catttgtctc
     1201 agaattttgc gaatttacct actttgaatg agacttttat tcagagtaat acgccgatag
     1261 atagagcgtt agcagttcct gatcagcctg attttatttg tgacttttac tttaattatc
     1321 gttgtattag gcctatgccg gtgtattctg ttccaggttt aagaaggatt taatatccca
     1381 acgagcgtga cccagtaaat gcgagaagag cagcgtaaga aaatattagt caatgtaacg
     1441 tagtggaatt gattaatact tttctgaagc gaaaattttg cattgggtca cgtaagtgac
     1501 ataattttag aggaattatg agtttcgcgg agaatgttgg tagattcata ggaaattctg
     1561 tgaattctgt cggaagtgtt ataggagatg gtcttaaagg ttttaattcc actcagtcta
     1621 tttccagtgc taagcaggca aaccttctta ataatttgcc tttgccttct ttagataatg
     1681 ttttaaatat tggaatgttt ggcggtcttg cttcaggcct tctttcttat agagctgcta
     1741 aaaagcaaaa taaggttatg caggatattg ctaataggca aatggctttt caggagcgaa
     1801 tgtctagtac ggctgttcga cgtcatgtag aggacttaaa gaaggcaggt ttgaatccgc
     1861 ttttagcttt aggtggatct gcttctactc ctcaaggtgc tttttattct cctgttaatc
     1921 ctatggagtc aggacttaat tctgcgatat cagttgcgga taaagttttt gattatcagc
     1981 gtttagctca tgctgatttt cagggtcgtt tgaattctgc tatgagtgtt gttcagttgg
     2041 cttctgctgt tcaggattat aaaaggaact atggaaagtt tggtgaagtt gcatattggt
     2101 ttgatcgata tgctggcaag ttgttgcctg ctatgctttt ctatttgttt agaaagcatc
     2161 cagttggaag agcggtttct gctgctaatt ctggttatgc tgttgctaag ggtgctaaag
     2221 gtgttaattt taagttttcg aatatgtcta gtacggctgt tcagcgtcat aattctagat
     2281 ataatgtttc gaaaggatgg agaaggtaat gaagtttaga acgatttatg atgaggagcg
     2341 tcctgctcct gttttggagt gtaaggatga aagtctatgt ttggcttatc aatgtactga
     2401 gacgtctatt gaaaaattgg ttaagttagc gaatcagaat ccttcttatt tacatgcatt
     2461 tgctggtgat cctactcgtc aacctgaata tggagagtgt ccttctcctt tggattatca
     2521 agatgcttta gagattgtag ctcgtggtga agaggctttt tattctttac ctgcgaatat
     2581 tcgagttaat ttttcgaatc ctatggagtt tttgtcatgg ttagaggacc ctgctaatta
     2641 tgatgaagtt gagaagttag gtttattgga tcctgagaaa gttcagataa gaaaatctaa
     2701 gttacaaaaa gatcaaaaag aagaggtttc ttctgaggaa aaatagcgag ggctatatcc
     2761 tcttggctat atagcccgag cgacacaaaa tatataaaac cttaatgaaa ggatgtattt
     2821 cgatggttcg tagaagacgt ttgagaagaa gaataagtag aagaattttt agaagaacag
     2881 tagctagagt tggtagaagg cgaaggtctt ttcgtggtgg tattagattt taaggcaaaa
     2941 aaaatggagt atctttttaa tgagatactc cttagactca tatctaatat ccgtttatat
     3001 ccgtttaaca caaaggaaat cagattatat gtgtactaat cctattatac ctatagttca
     3061 atataaagtt ccagttaaat cttcgttaga tgttgtggat tggtctaaat ttaggtctaa
     3121 ctttaaggct aatctgtttt ttttcgagaa gaatgttgtt cgtcgtgctg taagtaatgt
     3181 agatgaagct tttagattta ctgagcaact gaagcaagtt agttatttat ctacttttga
     3241 tcttgatggt tatcatcagg tgaagcagtt ttcttttcct cttccttgta ggaaatgttc
     3301 tgagtgtttg cagaagcgtt ctaaggattt agcggttcaa gctactatgg aagcgcgttc
     3361 tcatgaggag aattctgttt tgattcttac ttatgataat gatcatttag gcgataatat
     3421 tttagattat gatcatattc gagtttttca gaagcgtttg cgtcgttatg tggattatca
     3481 ctatggcaaa aagattaagt ttttgactgt aggagaatat ggtgataaga aaggtcgtat
     3541 gcattggcat atgattgttt ttggttggaa gccgaaatct gaggaacaat tagagcctta
     3601 tttaggagga aagtatcgaa cggatgttcg atatcgttct agaaagctta aggaactatg
     3661 gaaatttggt tatgttgatg tagatgaagc tacagatggt aatatttttt atgtagctcg
     3721 ttatgtgcag aaaaagtttg ttgttggatg tgatttagat tcttctaagt ctagttctag
     3781 gagagagaag aagacagctt ctcaagcttt aggtttagat tatttttttt cttatttaag
     3841 gcaatttctt aagactaaga ggatagtttt aaatggtttt agatatggat ttccgcgtta
     3901 ttttaaggat ttattgagga agttggtttc agaggattcg gagtttgata ctgagtatta
     3961 taatgcttta aggaaaaggt tacttagtgt atgtagttat tcgatggtaa ataaatattt
     4021 tacctattta gaatgcttag ttgaagtttt gccagttttg aattttcatg atttatacca
     4081 gcgtgcgctt aggtatatgg atcaatctat tcttaagccg catgctagtg atcatgatgg
     4141 agaatataat actacttagg agatctgatg catatgtttt attattcaat ttatgatcga
     4201 aaggctcggt cttatggaga tttgatctct tttccttcag gtgagaaaga ggctgctatt
     4261 cgatggttta gagatgttgt gatggattca gattctaaga atattttgca tcgatatcct
     4321 gaggattttg atttttgcta tattggttat tttgataagg ataaaggacg tttttatcct
     4381 gtggatgctg ggatagttac gattattaat gcaggagagt tttttttaga ttctgagtat
     4441 agacaagaag aggtttaata tggctaaagg acgaaagctt ccgtcggtta tgaagaatcg
     4501 tttttcagag gtaccgacag ctacgattag gcgttcaagt tttgatcggt ctcacggtta
     4561 taagactacg tttgatatgg attatttagt tccatttttt gttgatgaag ttcttcctgg
     4621 agatactttt tctttatcgg agacgcatct ttgtcgtttg actacgttag ttcaaccgat
     4681 tatggataat attcagttaa ctactcagtt tttctttgtt cccaatcgtt tgctttggga
     4741 taattgggaa tcgtttatta caggtggtga tgagcctgta gcttggacaa gcactaatcc
     4801 tgctaatgag tattttgttc ctcaagtaac ttctcctgat ggaggttacg cagagaattc
     4861 tatttatgac tattttg
//

