LOCUS LZYH01000514 4735 bp DNA linear BCT 11-OCT-2016 DEFINITION Acidithiobacillus caldus strain S1 Contig0514, whole genome shotgun sequence. ACCESSION LZYH01000514 LZYH01000000 VERSION LZYH01000514.1 DBLINK BioProject: PRJNA325710 BioSample: SAMN05250861 KEYWORDS WGS. SOURCE Acidithiobacillus caldus ORGANISM Acidithiobacillus caldus Bacteria; Proteobacteria; Acidithiobacillia; Acidithiobacillales; Acidithiobacillaceae; Acidithiobacillus. REFERENCE 1 (bases 1 to 4735) AUTHORS Zhang,X., Liu,X., He,Q., Dong,W., Zhang,X., Fan,F., Peng,D., Huang,W. and Yin,H. TITLE Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics JOURNAL Front Microbiol 7, 1960 (2016) PUBMED 27999570 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 4735) AUTHORS Zhang,X. TITLE Direct Submission JOURNAL Submitted (15-JUN-2016) School of Minerals Processing and Bioengineering, Central South University, No. 932, South Lushan Road, Changsha, Hunan 410083, China COMMENT Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Assembly-Data-START## Assembly Method :: SOAPdenovo v. 2.0 Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 92.0x Sequencing Technology :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 06/15/2016 20:00:30 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set; GeneMarkS+ Annotation Software revision :: 3.3 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total) :: 3,387 CDS (total) :: 3,341 Genes (coding) :: 2,396 CDS (coding) :: 2,396 Genes (RNA) :: 46 rRNAs :: 1, 1, 2 (5S, 16S, 23S) complete rRNAs :: 1, 1 (5S, 16S) partial rRNAs :: 2 (23S) tRNAs :: 38 ncRNAs :: 4 Pseudo Genes (total) :: 945 Pseudo Genes (ambiguous residues) :: 0 of 945 Pseudo Genes (frameshifted) :: 9 of 945 Pseudo Genes (incomplete) :: 935 of 945 Pseudo Genes (internal stop) :: 4 of 945 Pseudo Genes (multiple problems) :: 3 of 945 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..4735 /organism="Acidithiobacillus caldus" /mol_type="genomic DNA" /strain="S1" /isolation_source="copper mine" /db_xref="taxon:33059" /geo_loc_name="China: Jiangxi" /collection_date="22-Apr-2015" gene complement(1..434) /locus_tag="BAE30_07785" /pseudo CDS complement(1..434) /locus_tag="BAE30_07785" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_004869328.1" /note="incomplete; too short partial abutting assembly gap; missing stop; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="hypothetical protein" gene 330..1067 /locus_tag="BAE30_07790" CDS 330..1067 /locus_tag="BAE30_07790" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_019303260.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="short-chain dehydrogenase" /protein_id="OFC60618.1" /db_xref="GI:1078539849" /translation="MSEDAKCILVTGAARRVGAEIARHLASAGCDIALHYRHSQDDAE SLAHELRALGRRVQLLQGDLLEPDYPRQLVRQTMAAFGRLDGIVHNASLYRPKAFAEV DLRHWQEMEGIHLHAPFFLAQAAAAELRLRRGAIVHITDIYAERPLLGYLPYSVSKAA LVSLTRALAKELGPEIRVNSVAPGVVLWAETQQPAEGSRAVILDRTALKRAGNPADIA RAVRFLLLEADYVSGQNVVVDGGRMIY" gene 1072..1464 /locus_tag="BAE30_07795" CDS 1072..1464 /locus_tag="BAE30_07795" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_004869332.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="OFC60619.1" /db_xref="GI:1078539850" /translation="MNGEPSKPVQPIRFYSEAELDAIEAEDPILAAKIEHVQNMAKRQ IGRKKEFSEHDPLPDPEAVAEAMAVVRRILQRDGGDIELVEIAQRDVRVRMKGACAGC PNAVLDLQQVVERIVGAVPGVARVSNTF" gene 1461..2825 /gene="rimO" /locus_tag="BAE30_07800" CDS 1461..2825 /gene="rimO" /locus_tag="BAE30_07800" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_004869334.1" /note="catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="ribosomal protein S12 methylthiotransferase" /protein_id="OFC60620.1" /db_xref="GI:1078539851" /translation="MSAAEGVGTQPPRIGMVSLGCPKAGSDTERLLTRLRAEGYLLVA DYAEADLVLVNTCGFIDAAVQESLDAIAEAIDENGRVVVTGCLGAREQGEFIRRAQPK VLAVTGPQQDGATLAAIHRVLPPRHDPLQDLVPPQGLRLTPRHYAYLKIAEGCNQSCS FCVIPSMRGKLQSREPGDILREAEALVAAGCRELLIISQDTAAYGSDRRYRTAFADGR PTRAHITDLCTSLAALGAWVRLHYVYPYPHVDALVDLMADGKILPYLDIPLQHGSPAV LKAMRRPAASDKTLDRIARWRRQLPDLTLRSTFIVGFPGESEADFRLLLDFLHAAELD RVGCFSYSPVEGAAANALADPVPEVVKEERRQRFMEVQAEISAARLRRRVGQECLVVV DGFTESGHLMARSAAEAPEIDGIIQLDPPTGGRPAAGQRLWARITGSTTHDLHGTVLA TKAE" gene complement(2779..3276) /locus_tag="BAE30_07805" CDS complement(2779..3276) /locus_tag="BAE30_07805" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_014003589.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="OFC60621.1" /db_xref="GI:1078539852" /translation="MWEYALPGDGVPTELGPAPESPWVVLGLGSNVEAERTLPWALTR LCQSFAPLYIAQPCQSVDHTGGARAYVNWVVAFPSDWEDQRLHAFAKTLEAQWGARVD GRVPLDVDLLYHAATDTWHRQAGCSYWRSGILQLFPHWRTRLPPGDALPIQPWLPEPS RADRG" gene complement(3236..3580) /locus_tag="BAE30_07810" CDS complement(3236..3580) /locus_tag="BAE30_07810" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_004869337.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="dihydroneopterin aldolase" /protein_id="OFC60624.1" /db_xref="GI:1078539855" /translation="MKALKVETRIGIYDWERQVRQRVEIDLEMGAAAAQAAAADRVEA TIDYQAVCRRVVDYVEGSEVQLVETLAEGIAEILRREFGVGWMQITIHKPGAVRGAED VGVRITRGRRAD" gene 3706..4308 /locus_tag="BAE30_07815" CDS 3706..4308 /locus_tag="BAE30_07815" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_014003590.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="glycerol-3-phosphate acyltransferase" /protein_id="OFC60622.1" /db_xref="GI:1078539853" /translation="MAAPLWKSILLVLFAYLLGSIASAVLVARALRLPDPRQHGSGNP GATNILRLGGKRAAALTLLGDMLKGLVPVLVARGLGLDGWPLASVALAAFLGHLFPLY FGFRGGKGVATALGILLAYVPLLGLCVLLTWIVVFAWRRVSSLAALVATLIAPLLAWA FALPLPAKSLVLTLAILVLWRHRSNLSRLLRGEESGFRPS" gene complement(4335..>4735) /locus_tag="BAE30_07820" CDS complement(4335..>4735) /locus_tag="BAE30_07820" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_004869343.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=3 /transl_table=11 /product="hypothetical protein" /protein_id="OFC60623.1" /db_xref="GI:1078539854" /translation="IDAGEESALLWSFYAWALSEAGDPHAAIAACRKAIALDPEWGVA WNDLGEYLMETGRIEEALFPIRRALRSRHFDRPHLAQMNLARYYLHTGSLVRARRAAE EAARLAPGFRPAQDLSRWIRERQEEWGLKD" BASE COUNT 785 a 1651 c 1480 g 819 t ORIGIN 1 ccgtccccta gattccgata gtcctcgagc cagcgcgcga gcaccgtggc cagtacgggc 61 cccatttccg gcgccgtgac aaaatcgccg tcgggaccaa aacgccgctg ccccgccatg 121 tagtatccca gacccggggt atagaggacc gcttccaggt agtcggcaaa ggagatgctg 181 ccaccggcgg cagcgatacg agccaagatc cgcccgcgca gggccgccga gtgcgccgcc 241 gcttcgaggt cgggcggcgg caggctgaac ttgcgccgat ccgggctatg ggttacaaat 301 cctggaccag tgtcgcgcat gggttccttt tgtccgaaga cgccaaatgt atcctcgtta 361 ccggcgccgc acgccgcgtg ggtgcagaga tcgcccgcca cctggccagc gccggttgtg 421 acatcgccct gcattatagg cactcccagg acgacgctga aagccttgcc catgagttac 481 gggctctggg gcggcgggtg cagctcctgc agggggatct gctggagccc gattatcccc 541 gccaactcgt acggcagacc atggctgcct tcggtcgtct cgatggcatc gtccacaacg 601 cctccctgta tcgccccaag gcctttgccg aggtagatct gcggcactgg caggagatgg 661 aaggcataca tctgcacgct cccttctttc tcgcccaggc ggcggcggcg gaattgcgat 721 tgcggcgcgg tgccatcgtc cacatcaccg acatctatgc cgaacgtccc ttgctgggct 781 atcttcccta cagcgtcagc aaggcggccc tggtcagcct cacccgcgcc ctggccaagg 841 agctcggtcc agagatccgc gtcaatagtg tggcccccgg ggtcgtactc tgggccgaaa 901 cccagcaacc ggcggagggc tcccgcgctg tcatcctcga ccgcacagcc ctcaagcgcg 961 cgggtaaccc cgccgatatc gcccgcgccg tgcggtttct gctcctggaa gccgattatg 1021 tgagcggcca gaatgtcgtg gtggacggcg gccgcatgat atactgagcc catgaatgga 1081 gagcctagca aaccggtcca gcccatccgc ttttacagcg aggctgagct ggacgccatc 1141 gaggccgaag acccgatctt ggcggccaag atcgagcacg tccagaacat ggccaagcgc 1201 cagatcggac gaaaaaaaga gttctcggag catgaccccc tgccggatcc cgaggcggtg 1261 gccgaggcca tggccgtcgt ccgtcgaatt ctgcagaggg acggcggcga catcgagctg 1321 gtggagatcg cccagcggga tgtacgggtg cgcatgaagg gtgcctgtgc cggctgtccc 1381 aatgccgtgc tggacctgca gcaggtggtg gagcgcattg ttggcgccgt gcccggcgtc 1441 gcccgtgtga gcaatacctt ttgagcgctg ccgagggtgt ggggacgcag ccgccgcgca 1501 tcggcatggt cagcttgggt tgtcccaagg ctggcagcga taccgagcgc ctgctgacac 1561 ggctgagggc tgaaggctac ctgctggtgg cggactatgc cgaggccgat ctcgttttgg 1621 tcaatacctg cggcttcatc gatgccgccg tccaggagtc cttggacgcc attgccgagg 1681 ccatcgacga gaatggtcgg gtggtggtta cgggctgcct tggcgcccgc gagcaaggcg 1741 agttcattcg ccgagcccag cccaaggtgc tggcggtaac gggcccgcag caggatggtg 1801 ccaccctggc cgccatccat cgcgttctcc cgccccggca cgacccgctg caggacctgg 1861 tgccgccaca gggcctgcgc ctgaccccgc gtcactacgc ctacctcaag attgccgagg 1921 gctgcaatca gtcctgcagc ttctgcgtca tccccagcat gcgcggcaag ctccagagtc 1981 gggagcccgg cgatatcctg cgcgaggccg aggccttggt cgccgccggc tgccgcgaac 2041 tgctcatcat ttcccaggat acggcggcct acggcagcga ccgacgctat cgcaccgcct 2101 ttgccgacgg ccgtcccacg cgcgcgcaca ttaccgatct ttgcaccagc cttgcggcac 2161 tgggagcctg ggtccgtctc cactacgtct acccctaccc ccacgtggac gccctcgtcg 2221 acttgatggc cgacgggaag atcctgccct acctggatat tcccctgcag cacggcagcc 2281 ctgccgtgct caaggccatg cgtcgacctg ccgccagcga caagaccctc gatcgcatcg 2341 cccgctggcg ccgccagctg ccggatctca ccctacgcag caccttcatc gtcggcttcc 2401 ccggagagag cgaagcagac ttccgtctct tgctggactt cctgcatgcg gcggaactgg 2461 accgtgtcgg ttgcttcagc tactccccgg tggaaggggc cgccgccaac gcccttgccg 2521 atcccgtacc cgaggtcgtc aaggaagagc gccggcagcg gttcatggaa gtgcaggcag 2581 agatcagcgc cgcccgcctg cgtcggcgcg tcggtcaaga gtgtctggtg gtcgtggacg 2641 gttttaccga gtcggggcac ctaatggcac gctcggccgc ggaggctcca gagatcgacg 2701 gcatcattca actcgacccg ccgacgggcg ggcggcccgc cgcgggacaa cgcctgtggg 2761 cccgcatcac cgggagcact acccacgatc tgcacgggac ggttctggca accaaggctg 2821 aataggtagg gcgtccccgg gcgggagcct ggtgcgccag tgtggaaaaa gctgcagtat 2881 accgctgcgc cagtaactgc agcccgcctg ccggtgccag gtgtccgtgg cagcatggta 2941 cagaagatcg acatccaaag gcacgcggcc atccacccgc gcgccccact gggcctctag 3001 cgtcttggca aaggcgtgca agcgctgatc ctcccagtcc gaaggaaagg cgacgaccca 3061 attgacgtag gcgcgggcgc cacccgtgtg gtctacggac tgacagggct gcgcgatgta 3121 caggggcgca aacgactggc acaggcgcgt caacgcccag ggcaaggtcc gctcggcctc 3181 gacattgctg ccgaggccaa ggacgaccca gggagactcc ggtgcgggcc ccagctcagt 3241 cggcacgccg tccccgggta atgcgtactc ccacatcctc ggccccgcgc accgccccgg 3301 gcttgtggat ggtgatctgc atccagccaa cgccaaactc ccgccgcagg atctcggcga 3361 taccctcggc caaggtttcc accagctgta cttcggaacc ttccacgtaa tccaccacgc 3421 gtcggcaaac cgcctgataa tcgatggtgg cttcgacccg atccgctgct gctgcctgcg 3481 ccgccgctgc acccatctcg aggtcgatct ccacacgctg gcggacctgt cgttcccagt 3541 cgtagatacc gatgcgggtc tcgaccttga gggctttcac gaataagcta tccacggaat 3601 ctccctgaac cgttccgcgc ggacctcgcc cgcgtcagtg cggcacccat catagcgaag 3661 aggaggcttt ttatcagccc cgcaaacccc gtcgccgccg cggccatggc cgctccccta 3721 tggaagtcga tcctgctcgt gctgttcgcc tacctcctgg gctccatcgc cagtgccgtc 3781 ctcgtcgccc gcgccctgcg cctacccgac ccgcgtcagc acggttccgg taatcccggc 3841 gctaccaaca tcctgcgcct gggcggcaag cgggccgccg ccctgaccct actgggcgat 3901 atgctgaaag gactcgtgcc cgtgctcgtg gcgcgcggcc tgggcctgga cggctggccc 3961 cttgcctcgg tggcgcttgc cgcctttctc ggacaccttt ttccgctgta ttttggtttt 4021 cgcggaggca agggcgtagc cacagccctg ggtatactgt tggcctacgt gcccctactc 4081 ggcctgtgcg tgctgctcac ctggatcgtg gtctttgcct ggcgccgtgt ctcctccctg 4141 gctgccctcg tcgccaccct gatagcgcct ttgctggcct gggccttcgc cctgccgctt 4201 ccggcaaaga gcctggtgct gaccttggcg atactcgtgc tgtggcgcca ccgcagcaac 4261 ctcagccgcc tgctgcgcgg cgaggagtcg ggctttcgcc cttcctagac cgtcacggga 4321 accagggtac cgcctcagtc tttgaggccc cactcctcct gccgctcacg aatccagcgg 4381 gaaagatcct gcgctggacg aaaacccggg gccaaccgcg ccgcctcctc tgcagcccgc 4441 cgggcgcgca cgagactacc ggtgtgcagg tagtagcggg caaggttcat ctgcgccagg 4501 tgcggccggt cgaagtggcg cgagcgcagg gcacggcgaa tggggaaaag ggcttcctcg 4561 atgcgccccg tctccatcag gtactcaccg aggtcgttcc aggccacccc ccactcggga 4621 tccagagcga tggccttgcg gcaggcggct atggcggcgt ggggatcgcc agcctcggac 4681 agcgcccagg cataaaaact ccacagcagc gctgactcct cgccggcgtc gatgg //