ID M10316; SV 1; linear; genomic DNA; STD; UNC; 4207 BP. XX AC M10316; M13764; XX DT 02-JUL-1986 (Rel. 09, Created) DT 15-JAN-2007 (Rel. 90, Last updated, Version 5) XX DE Plasmid pJD1 from Neisseria gonorrheae DNA, complete genome. XX KW circular; complete genome; cryptic plasmid protein cppA; KW cryptic plasmid protein cppB; cryptic plasmid protein cppC; KW unidentified reading frame. XX OS Plasmid pJD1 OC other sequences; plasmids. OG Plasmid pJD1 XX RN [1] RP 1-4207 RX PUBMED; 2991186. RA Korch C., Hagblom P., Ohman H., Goransson M., Normark S.; RT "Cryptic plasmid of Neisseria gonorrhoeae: complete nucleotide sequence and RT genetic organization"; RL J. Bacteriol. 163(2):430-438(1985). XX RN [2] RP 3049-3146 RX PUBMED; 3087954. RA Hagblom P., Korch C., Jonsson A.B., Normark S.; RT "Intragenic variation by site-specific recombination in the cryptic plasmid RT of Neisseria gonorrhoeae"; RL J. Bacteriol. 167(1):231-237(1986). XX CC [2] deletion region. CC Draft entry and sequence in computer readable form for [1] kindly CC provided by C.Korch, 11/14/1985; and for [2] 12/02/86. Plasmid pJD1 CC is the smallest of the gonococcal plasmids. Its function is CC unknown. This plasmid has the ability to delete a specific segment CC of itself and can regain a segment of DNA equivalent to that which CC had been lost. It also can form cointegrates with other plasmids, CC with the fusion junction mapping at the deletion site, and it CC contains the sequences needed for its uptake by transformation. CC There are two identical short repeats (positions 3071-3078 and CC 3125-3132) [2]. One of these is deleted together with bases CC 3079-3124 [2]. The deletion of 54 nucleotides in the cppB gene CC does not affect the reading frame. The proposed model for the CC plasmid's genetic organization, contains two operons located on CC complementary strands, each encoding five proteins, which range in CC size from 27-289 AA. Proteins cppA and cppB were used to detect CC ORFs with similar codon usage. The ORFs located in this manner, ORF CC 1-7 and cppC, have recognizable RBS sequences at appropriate CC spacings. ORFs which were consistent with available data on CC expressed proteins are listed in the FEATURES table below. CC Both operons initiate in the same region. Their potential -35 and CC -10 regions are located at 714-719 and 737-742 for P1 and at CC 848-843 and 823-818 for P2 respectively. The potential length of CC the transcribed regions are about 1900 and 2400 nucleotides. XX FH Key Location/Qualifiers FH FT source 1..4207 FT /organism="Plasmid pJD1" FT /plasmid="pJD1" FT /host="UM01" FT /mol_type="genomic DNA" FT /clone="pUM[10,11,109]" FT /db_xref="taxon:2577" FT CDS complement(44..235) FT /codon_start=1 FT /transl_table=11 FT /product="unknown protein" FT /note="ORF7; putative" FT /db_xref="InterPro:IPR008687" FT /db_xref="UniProtKB/TrEMBL:Q50997" FT /protein_id="AAA88198.1" FT /translation="MRVLAGMGNNLNQIAKALNTAAKVGTLGNVEALKATTELAALERS FT LNSLRDFLAKEKNGWQSQ" FT CDS complement(421..525) FT /codon_start=1 FT /transl_table=11 FT /product="unknown protein" FT /note="ORF6; putative" FT /db_xref="UniProtKB/TrEMBL:Q50998" FT /protein_id="AAA88199.1" FT /translation="MFFPEFFMEYRRNAVMKCRFFEQKAVKNRGILPF" FT CDS 810..1679 FT /codon_start=1 FT /transl_table=11 FT /product="unknown protein" FT /note="ORF1" FT /db_xref="InterPro:IPR004322" FT /db_xref="InterPro:IPR014820" FT /db_xref="UniProtKB/TrEMBL:Q50999" FT /protein_id="AAA88200.1" FT /translation="MSQLYTQPDLFLQERIPHKPYCKDFKEAPMLVRSYAAAIKRRYIQ FT VNPSHLRVFMLFDLDYEGAGLAWEDNNLPMPAWAAINRENGGAHLAYALSAPVLTAEYG FT GRQKALRYLAALEAAYKAKLRGDVGFVSLITKNPEHPHWLTLRGVPDAIRGYDLEYLAD FT FVDLDKFKPYIGRSNVEAVGLSRNCTVFNLVSRWAHKNVLAFKQQGYTVQGWLKEVHYQ FT CMRVNGDFPVPMWEKEVKCISKSIANWVWYKFDIAASNRRFSELQAHRNSLRKTTINAG FT RTKIITEL" FT CDS 1683..1925 FT /codon_start=1 FT /transl_table=11 FT /product="unknown protein" FT /note="ORF2; putative" FT /db_xref="InterPro:IPR011991" FT /db_xref="InterPro:IPR013196" FT /db_xref="UniProtKB/TrEMBL:Q51000" FT /protein_id="AAA88201.1" FT /translation="MAYPKLKTTKRDVTAKELAKRFGCSTRTVFRAWSQSRADYLAENS FT ISRDKPWEHFGISRATWYRRGKPMPSETDNQSETA" FT CDS 1922..2167 FT /codon_start=1 FT /transl_table=11 FT /product="unknown protein" FT /note="ORF3; putative" FT /db_xref="UniProtKB/TrEMBL:Q51001" FT /protein_id="AAA88202.1" FT /translation="MTRYAINRDALYSAFKDFLYSEINANPALKSATVDDLADIVLAKK FT WRIFLPDGIKRTTAEKAAQRVLYMTNQPENQTQQEN" FT CDS 2170..2355 FT /codon_start=1 FT /transl_table=11 FT /product="unknown protein" FT /note="ORF4; putative" FT /db_xref="UniProtKB/TrEMBL:Q51002" FT /protein_id="AAA88203.1" FT /translation="MQTTIPTGSIRTFGDYGVMYIVGTPAEQLPDGDWLVNIELPESGE FT HTQYKLSHIVQDPKAA" FT CDS 2355..2633 FT /codon_start=1 FT /transl_table=11 FT /product="unknown protein" FT /note="ORF5; putative" FT /db_xref="GOA:Q51003" FT /db_xref="InterPro:IPR016368" FT /db_xref="InterPro:IPR019199" FT /db_xref="UniProtKB/Swiss-Prot:Q51003" FT /protein_id="AAA88204.1" FT /translation="MYAISFDLVVADTAQNHPKGISQAYADIGYTLRKFGFTRIQGSLY FT TCQNEDMANLFSAINELKALPWFPSSVRDIRAFRIEQWSDFTSLVKS" FT CDS complement(2611..2865) FT /codon_start=1 FT /transl_table=11 FT /product="protein A" FT /db_xref="UniProtKB/Swiss-Prot:P07048" FT /protein_id="AAA88205.1" FT /translation="MITENERDRRTAAWLIETYGAEAVAEAETRIAGARKPYPSNIAKV FT LGASLPEALKRTENAAARQKLAGLRRMLDGKAVKTSQDL" FT CDS complement(2912..3553) FT /codon_start=1 FT /transl_table=11 FT /product="B protein" FT /db_xref="InterPro:IPR006922" FT /db_xref="InterPro:IPR010356" FT /db_xref="UniProtKB/Swiss-Prot:P07049" FT /protein_id="AAA88206.1" FT /translation="MSKISDLAKTFEQTSRTEAASIEQQTKADLETLRKNINEALKQSE FT QKITADINARQLRMSKAVFKPYLWSLLGISAAGLIVIAGLFIAIWSVKNELDDLKQQRA FT EAERTLDLLETKTKGLTLENCPVENSKATRVCVATEKRMLDALAELESNHAAIEQRMMK FT ALTHLGERLAELEQENTSLAQQLASLAAELERQSEIRQRQSEILNQPAKR" FT CDS complement(join(3637..4207,1..47)) FT /codon_start=1 FT /transl_table=11 FT /product="protein C" FT /db_xref="InterPro:IPR005094" FT /db_xref="UniProtKB/Swiss-Prot:P07047" FT /protein_id="AAA88197.1" FT /translation="MIVQFFNRGKGGGSGPIDYLLGKDRDREEARLLRGDPEETAALIN FT SSDYAKKYTAGCLSFEESNIPAEQKHALMDSFEECIFAGLDKDQYNCLWVEHRDKGRLE FT LNFVIPNIELLSGKRLQPYYYAADRGRVDAWRTMQNLTHGYSDPDDPAKRQSMTQAKDL FT PRNTQEAAQSITEHHRRLRSPSPIRQAKKPRRRAGNAGKGRF" XX SQ Sequence 4207 BP; 894 A; 1129 C; 1039 G; 1145 T; 0 other; ggaccactcc cgccgccttt ccccctattg aaaaactgca caatcattgg gactgccatc 60 cgttcttttc tttggctaaa aaatcccgta gggaatttaa ggaacgttcc aacgctgcca 120 gctcggtcgt cgccttgagt gcttccacat tgcccaacgt gccgaccttt gcggcggtgt 180 tcagggcctt ggctatttgg ttcaggttgt tacccatgcc tgcaaggacg cgcacgactt 240 cgggcgggaa ttggaatttg acggtttttt tgtcggatgc tttgccatct tccaaaaccc 300 gctcccgaat gtagcgggct aaattcggat gggtcttctg tcgggtcaaa gtctcaaact 360 cggtcgggct gactcggatg atgagttgct ttgttcgctt ttcggcggca ctcgaacctg 420 tcaaaagggc aaaatacccc tgtttttgac tgctttctgc tcaaaaaaac ggcatttcat 480 cacggcattt cgccgatact ccatgaagaa ctccgggaag aacacgcacg ccgccctgtc 540 ggaactggtt tcatgtttcc cccaaaacgc cgccctgctg gccggcttag gtcgcgctgc 600 tgcgctccaa gctttaccgc ttcgcctgct ggcttcgcta aattgcggat tggaaaattt 660 tgaaataaga acccctatcg ggctgttatc tgattatggt tattttgaca tagttgtatc 720 atcttaaaaa caagcataca atctgcaaat cttagacaaa gcaaaacccc cgccaaacgc 780 caatctgcac gggggtttcg agatacaaca tgagccaatt atacacccaa cccgacctct 840 tcttgcaaga acgtatccca cacaagccat actgcaaaga tttcaaagaa gcgcctatgc 900 tggtgcgctc ttacgctgcc gccatcaaac gtcgctacat ccaagtcaat ccgtcgcatc 960 tgcgtgtgtt tatgctcttt gacttggatt acgaaggggc ggggttggct tgggaagaca 1020 ataatctgcc tatgcctgct tgggcggcaa tcaacaggga aaacggcggc gcacaccttg 1080 cctatgcgct ttccgcgcct gtgctgacgg cggaatacgg tgggagacaa aaagccctgc 1140 gctatcttgc tgcacttgaa gcagcatata aggcgaaatt gcgcggtgat gtgggctttg 1200 tatcgctgat tacgaaaaat cccgaacatc cgcattggct gacgctgcgc ggcgttcctg 1260 acgcaatcag gggctacgat ttggagtatc ttgcggattt cgtggattta gacaagttta 1320 agccctatat cggtcgctct aacgtggaag cggtcggatt aagcagaaat tgcacggtgt 1380 ttaaccttgt gagccgttgg gcgcacaaaa acgtgttggc gttcaaacag cagggctaca 1440 cggtgcaagg ctggctgaaa gaagtgcatt accagtgtat gcgggtaaat ggggatttcc 1500 ctgtcccgat gtgggaaaaa gaagtgaaat gtatctccaa atcaatcgct aactgggttt 1560 ggtacaagtt tgatattgca gccagcaatc gacggttttc ggaattgcag gctcatcgga 1620 atagtttgcg gaaaacaacc atcaatgcag gcagaacaaa aatcatcacg gagctttgaa 1680 atatggccta tccaaaactg aaaaccacca agcgagacgt tacggctaaa gaactggcaa 1740 aacgcttcgg ctgttccaca agaaccgttt ttcgggcatg gtcgcaatcc cgcgccgact 1800 acctagccga aaactctatc agccgcgata aaccgtggga acacttcggc atttcccgcg 1860 ccacttggta caggcgcggc aagcctatgc cgtctgaaac tgacaaccaa agcgaaacag 1920 catgacaaga tacgcaataa accgcgatgc tctgtactcg gcattcaaag attttctgta 1980 ttcggaaatt aacgcaaatc ctgctttgaa aagcgcaacg gttgatgatc ttgcagatat 2040 agttctagcc aaaaaatgga gaatttttct gcctgacggc atcaaacgca caacagccga 2100 aaaagctgcc caacgggttt tgtacatgac aaaccagcct gaaaaccaaa cccaacagga 2160 gaactaacca tgcaaaccac tatccccacc ggttcaatcc gcacctttgg cgattacggc 2220 gtgatgtaca tcgtcggcac gcctgccgaa cagcttccgg acggcgattg gctcgtaaat 2280 attgaactgc cggaaagcgg cgaacacacg caatacaaac tgtcccacat cgttcaagac 2340 ccaaaggctg cctaatgtac gcgatttctt ttgatttggt ggttgccgat accgctcaaa 2400 accatccgaa aggcatttcc caagcctacg cggatattgg atacaccctg cggaaattcg 2460 gctttacccg cattcaggga agtttgtaca cctgccaaaa cgaagatatg gctaacctgt 2520 tttcagccat caacgagcta aaagctctgc cttggtttcc gtcttctgtc cgcgatattc 2580 gggcgttccg cattgagcag tggtctgatt tcacaagtct tgtgaagtct taactgcctt 2640 accgtccaac atccgccgca gccctgccag tttttggcgc gctgcggcgt tttctgtgcg 2700 ttttagggct tcgggtaggc tagcccccaa tactttggcg atattgctcg gatagggctt 2760 tctcgcgccc gcaatgcggg tttctgcttc cgctacggct tctgccccgt aggtctctat 2820 cagccatgcg gctgttcgcc tgtcgcgttc gttctcggta atcatcggct cattccccat 2880 cccctgcttt gggttcgttt gtatcgttgg cttatcgttt ggctggttga ttcaagattt 2940 cgctctgccg ttgccgtatt tcgctctgcc gctctaactc ggctgccaag ctcgctagct 3000 gctgcgctaa actcgtgttt tcctgctcta gctctgccaa cctttcgccc aagtgcgtta 3060 aggctttcat cattcgctgc tcgattgctg cgtgattgct ctctaattcc gctaacgcgt 3120 ccagcattcg cttctcggtc gctacgcata cccgcgttgc tttgctgttc tcgactgggc 3180 aattttccag tgtcaaacct ttggtcttgg tttccaacag gtctagggtg cgctctgctt 3240 cggctctctg ctgtttcaag tcgtccagct cgttcttgac gctccatatc gctatgaaca 3300 gccctgctat gactatcaac cctgccgccg atatacctag caagctccac agatagggct 3360 tgaatactgc cttgctcatg cgtaactgcc gggcgtttat atcggcggtt attttctgct 3420 cgctttgctt caatgcctcg ttgatatttt tccgtaacgt ctctaagtct gctttcgttt 3480 gttgctctat gctggcggct tcggtgcgtg atgtctgctc gaaggtcttc gccaaatcgg 3540 aaatcttgct catacagtgc gcctttcagt cggatgttgc gcccttttgg gtccgggttc 3600 ttgatgctga tgctgctgat ggtcgctcgt gatatttcaa aacctacctt ttccagcgtt 3660 tccagcacgt ctgcgcggct ttttagcttg cctgataggg ctagggcttc taagccgtct 3720 gtgatgctct gtgatgctct gtgcggcttc ctgcgtgttt ctcggcaggt ctttggcttg 3780 ggtcatgctc tgccgtttgg cggggtcgtc tgggtcgctg tatccgtgcg tcaggttctg 3840 catggtgcgc catgcgtcca ctcttcctct gtcggcggcg tagtagtagg gctgtaaccg 3900 ctttccgctc aaaagctcga tgttcggtat cacgaagttg agttccaaac gccctttgtc 3960 tcggtgttct acccataggc agttgtattg gtctttgtcc aagcctgcaa aaatacactc 4020 ttcgaagctg tccatcaggg cgtgtttctg ttcggcgggg atgttgcttt cttcaaagct 4080 caggcagccg gcggtgtatt tcttggcgta atcgctgctg tttatcaggg cggcggtttc 4140 ttcggggtcg ccgcgtaata atctggcttc ttctcggtcg cggtctttgc ctagaagata 4200 gtctatc 4207 //