LOCUS JAGRMD010000182 6035 bp DNA linear ENV 12-OCT-2021 DEFINITION MAG: Rhodobacteraceae bacterium isolate HKST-UBA82 2010_90503, whole genome shotgun sequence. ACCESSION JAGRMD010000182 JAGRMD010000000 VERSION JAGRMD010000182.1 DBLINK BioProject: PRJNA432264 BioSample: SAMN14564392 KEYWORDS WGS; Metagenome Assembled Genome; MAG. SOURCE Rhodobacteraceae bacterium (activated sludge metagenome) ORGANISM Rhodobacteraceae bacterium Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae. REFERENCE 1 (bases 1 to 6035) AUTHORS Wang,Y., Ye,J., Ju,F., Liu,L., Boyd,J.A., Deng,Y., Parks,D.H., Jiang,X., Yin,X., Woodcroft,B.J., Tyson,G.W., Hugenholtz,P., Polz,M.F. and Zhang,T. TITLE Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years JOURNAL Microbiome 9 (1), 199 (2021) PUBMED 34615557 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 6035) AUTHORS Zhang,T. TITLE Direct Submission JOURNAL Submitted (09-APR-2020) Civil Engineering, The University Hong Kong, Pokfulam Road, Hong Kong 999077, Hong Kong COMMENT 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-Assembly-Data-START## Assembly Method :: CLC de novo assembler v. 6.04 Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 106x Sequencing Technology :: Illumina HiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 04/20/2021 10:34:47 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision :: 5.1 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total) :: 3,272 CDSs (total) :: 3,241 Genes (coding) :: 2,819 CDSs (with protein) :: 2,819 Genes (RNA) :: 31 tRNAs :: 29 ncRNAs :: 2 Pseudo Genes (total) :: 422 CDSs (without protein) :: 422 Pseudo Genes (ambiguous residues) :: 348 of 422 Pseudo Genes (frameshifted) :: 273 of 422 Pseudo Genes (incomplete) :: 7 of 422 Pseudo Genes (internal stop) :: 2 of 422 Pseudo Genes (multiple problems) :: 208 of 422 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..6035 /organism="Rhodobacteraceae bacterium" /mol_type="genomic DNA" /submitter_seqid="2010_90503" /isolate="HKST-UBA82" /isolation_source="activated sludge from Shatin waste water treatment plant collected monthly from 2007 through 2015" /db_xref="taxon:1904441" /environmental_sample /geo_loc_name="China:Hong Kong SAR, Shatin waste water treatment plant" /lat_lon="22.406236 N 114.213394 E" /metagenome_source="activated sludge metagenome" /note="metagenomic" gene 119..541 /gene="dksA" /locus_tag="KDJ82_07790" CDS 119..541 /gene="dksA" /locus_tag="KDJ82_07790" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_017998592.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="RNA polymerase-binding protein DksA" /protein_id="MCB1399798.1" /translation="MKPETFLPEDYKPAETEPFMNDRQLEYFRRKLLAWKHELLEQSA ETLEGLAESARNVPDIADRASEETDRALELRTRDRQRKLVSKIDAALRRIDNGEYGYC EMTGEPISLRRLDARPIATMTLEAQERHERRERVHRDD" gene 631..1802 /locus_tag="KDJ82_07795" /pseudo CDS 631..1802 /locus_tag="KDJ82_07795" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_013068139.1" /note="frameshifted; too many ambiguous residues; Derived by automated computational analysis using gene prediction method: Protein Homology." /pseudo /codon_start=1 /transl_table=11 /product="FAD-dependent monooxygenase" assembly_gap 832..883 /estimated_length=52 /gap_type="within scaffold" /linkage_evidence="paired-ends" assembly_gap 1143..1238 /estimated_length=96 /gap_type="within scaffold" /linkage_evidence="paired-ends" gene complement(1815..2594) /gene="xth" /locus_tag="KDJ82_07800" CDS complement(1815..2594) /gene="xth" /locus_tag="KDJ82_07800" /EC_number="3.1.11.2" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_011908233.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="exodeoxyribonuclease III" /protein_id="MCB1399799.1" /translation="MKIATFNINGVKARLNALIEWLDEDKADVVLLQEIKSVDEGFPR EVLEDRGWRVETHGQKSFNGVAILSKLPLEDITRGLPGDAADEQARWIEATVMGDRAV RVCGLYLPNGNPAPGPKYDYKLSWMARMRERAAALLATEEPVVMAGDYNIIPQDEDAA RPEAWREDALALPESRAAFRRILNLGFTEAFRTRVAGPGHYSFWDYQAGAWEKNNGIR IDHLLLSPQAADLLRDVQIDKEVRGRDKPSDHVPVWIELAA" gene complement(2623..3342) /locus_tag="KDJ82_07805" CDS complement(2623..3342) /locus_tag="KDJ82_07805" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_008028056.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="MCB1399800.1" /translation="MTNVLILGSGPEVVQARDWSRDGIDVIVAINHAWQVRADWDVQI HPWDFPADRLPPADSPARIVTEAEFVPAQNAHGGFVYAGATMAFTAGYWALNEYKPRC IAYFGCNMIYPSKGRTHFYGRGHPDPLRRDITLQSLEAKSARLRILAAQRGTAVVNLS HEDSRLMLPRARIGALPGTPAPYDTTAATLARRREAVLDYYVPSGRYWEEIERFDPAQ LARLDALWLRAGALGKAAVAA" gene complement(3444..3776) /locus_tag="KDJ82_07810" CDS complement(3444..3776) /locus_tag="KDJ82_07810" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_017929416.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="iron-sulfur cluster assembly accessory protein" /protein_id="MCB1399801.1" /translation="MLNIPPKVTPRAFSRLAQINEAAEAPRALRVAVEGGGCSGFQYE ITLEDAPAPEDLVLEGEGQRVLIDPVSLPFLENAVIDFSDELIGARFVVENPNATSSC GCGISFSI" gene 3852..4997 /locus_tag="KDJ82_07815" CDS 3852..4997 /locus_tag="KDJ82_07815" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_007205039.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="deoxyguanosinetriphosphate triphosphohydrolase" /protein_id="MCB1399802.1" /translation="MLQPYACQPEDSRGRLHAESMSTFRSPFQRDRDRIIHSSAFRRL KHKTQVFVEHEGDYYRTRLTHTIEVAQVARTIAGALGLNTDLAEAVALAHDLGHPPFG HTGEDALADLMQPFGGFDHNAQALRIVTRLEKHYAGFDGLNLTWETLEGIAKHNGPVT GDLSYALAEVNAEWDLELHTNASAEAQVAAVADDVAYNHHDLHDGLRAGLFSEEDLME LPTIGPCFEEVDRLHPGLDPTRRRHEALRRVFGVMVEDVIAVAQNRLVSLCPESADDI RAMEGPIIRFSKPLYQNLKALKGFLFTRMYRAPSVVEERRRVTGMVNALFPLFLDDPA LLPEDWQDEVARAADRTALARVVLDYVAGMTDRFAIQEYHRLLGSDS" assembly_gap 5104..5255 /estimated_length=152 /gap_type="within scaffold" /linkage_evidence="paired-ends" gene complement(<5256..5653) /locus_tag="KDJ82_07820" CDS complement(<5256..5653) /locus_tag="KDJ82_07820" /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="MCB1399803.1" /translation="MTLGFNRRHMLTLLALGGAAALAGCGGGQWQTEYQPAGPSARDW SLAGVDVTVPANLTVSEDNSVYVPKADIVWQAEAAGDRRAQVSRILQEGIAAGARGLK GPRRVRFRVTLETFHALNIKSRKSAPKGTGV" gene 5834..>6035 /locus_tag="KDJ82_07825" CDS 5834..>6035 /locus_tag="KDJ82_07825" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_005853328.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="OsmC family peroxiredoxin" /protein_id="MCB1399804.1" /translation="MIVKSGSAHWEGALKDGKGTVSTESGALAAQPYGFNTRFEGRPG TNPEELIAAAHAACFSMALSAGL" BASE COUNT 960 a 1862 c 1952 g 961 t ORIGIN 1 tgcccaagat ggaatgtggg tagtgacatc ccccaccaca tcgggtatgg cacgcggcga 61 ggagcgccag atgaccagtg acacttcaga acataccggc gccaacaagg gatcagaaat 121 gaagcctgaa acgttcctcc ccgaggatta caaacccgcc gaaaccgaac ctttcatgaa 181 tgaccgccag cttgagtatt tccgccgcaa gctgctggcc tggaaacacg agctgctgga 241 gcagtcggca gaaacgcttg aaggtctggc ggaatcggcc cgaaacgtgc ccgacatcgc 301 cgaccgcgcc tcggaagaga ccgaccgcgc gctggagctg cgcacccgcg accggcagcg 361 caagcttgtc agcaagatcg acgcggcgct gcgccggatc gacaacggcg aatacggcta 421 ttgcgagatg acgggagagc cgatcagcct caggcggctg gatgcgcgcc cgatcgcgac 481 gatgacgctt gaggcgcagg aacgccacga gcggcgcgaa cgcgtgcatc gtgacgactg 541 accggcgccc ggccggcttg atctgacgca aggacaaagg accaccgggc cgtaaggttc 601 cggtggtttt tctttcgcgg ggggtgattt gtgctgacag ccagaaaagt gaccgtgctg 661 ggcgggggcg tcgcggggtt gacggtggcg cgcgcgcttg cgctgcgcgg cgccgaggtg 721 accgtgctgg aacaggccga ggcgatccgc gaggtgggcg cgggccttca gatctcgccc 781 aacggggcgc gggtgctgcg ggcgcttggc ctgggtgatt ccctggcgcg cnnnnnnnnn 841 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnntggcgcg gctggacatg 901 gcgcgcctgc gtccgggcga ggaataccgc ttcgtgcatc gcgcccggct gatcgacctt 961 ctggccgagg gcgcgcgcgc ggccggcgtg cagatccgcc tgctgcaaca gatcgacaag 1021 gtggaactgg gcgatcatcc gccgcggctg accaatcatc ggggcgtccc gcaagaggcc 1081 gatcttctga tcggtgcgga cgggctgcat tcgcgggtgc gtcaggcgct gaacggcaag 1141 gtnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 1201 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnca tgtggtcagc tatccgcttg 1261 gcggggggct gcgcaacatc gtcgccgtcg aggaacgccg ccgctgggtc gaagagggct 1321 ggaacatgcg cgacgatgcc ctggccgtgc gcaccgcctt cgaggatttc tgcccgcagg 1381 tcacggactg gctggcgaag atcgacgaat gctggctttg ggggctgttt cgccacccgg 1441 tcgcacatcg ctggcacggc catggcgccg cgatccttgg cgatgccgcg catccgacgt 1501 tgcccttcct ggcgcagggc gcggtcatgg cgatggagga cgcctgggtt ctggccgaat 1561 cccttgccgg gcatgacagc gacgaagccg ccttcgccgc ctatcaggcc gcccgcgcgc 1621 cgcgctgcgc ggccatcgtc gaggccgcga accgcaatgc gcgcaactat cacctgtcgg 1681 ggatcagccg cggggtggct catctggggc tgcgcgcggc ctcgcgcctg gcgccgggca 1741 agcttctgga ccggttcgac tggatctacg gccacgacgt gacggggggc gcgggccgct 1801 aggccgcgct gcgctcaggc cgcaagctcg atccagacgg gaacgtggtc cgagggcttg 1861 tcgcgcccgc gcacctcttt gtcgatctgc acgtcgcgca acaggtccgc cgcctgcggg 1921 ctgagcagca aatggtcgat gcggatgccg ttgttctttt cccaggcgcc ggcctgataa 1981 tcccagaagg aataatgccc cggccccgcg acgcgggtgc ggaaggcctc ggtgaagccc 2041 aggttgagga tgcggcggaa ggcggcgcgg ctttcgggca gggcaagcgc atcctcgcgc 2101 caggcctcgg ggcgggcggc atcctcgtcc tgcgggatga tgttgtaatc gcccgccatg 2161 accacgggtt cctcggtggc cagaagggcc gcggcgcgtt cgcgcatgcg ggccatccag 2221 gacagtttgt aatcgtattt cggccccggc gcggggttgc cgttgggcag gtaaagcccg 2281 cagacgcgca ccgcgcgatc ccccatcacc gtggcctcga tccagcgcgc ctgttcgtcg 2341 gccgcgtcgc cgggcaggcc gcgcgtgatg tcctcaagcg gcagcttcga caggatcgcc 2401 acgccgttga agcttttctg gccatgcgtt tccacccgcc agccgcgatc ttccagaacc 2461 tcgcggggga agccctcgtc gacggatttg atctcttgca gcaggacgac atcggccttg 2521 tcctcgtcca gccattcgat cagggcgttc aggcgtgcct tgacgccgtt gatgttgaac 2581 gtggcgattt tcatggggcc tccggctgcc tgcgccccct tcttaggccg cgacggccgc 2641 cttgccaagc gcaccggccc gcagccacaa cgcatcgagg cgcgcaagct gggcgggatc 2701 gaaacgctcg atctcttccc aatagcgccc ggagggaacg taatagtcca gaaccgcctc 2761 gcgccgccgt gcaagggtgg cggcggtggt gtcatagggg gcgggggtgc cgggcagcgc 2821 gccgatccgt gcgcggggca gcatcaggcg gctgtcctcg tgagagaggt tgacgacggc 2881 ggtgccgcgt tgcgcggcca gaatgcgcag ccgcgcggat ttcgcctcaa ggctttgcag 2941 cgtgatgtcg cggcgcagcg gatcggggtg gccgcgcccg tagaaatgcg tccgcccctt 3001 cgaggggtag atcatgttgc agccaaaata ggcgatgcag cgcggcttgt attcgttcag 3061 cgcccaatat cctgccgtga aggccattgt tgcgccagcg tagacaaagc cgccatgggc 3121 gttctgcgcg gggacgaatt ccgcctcggt cacgatccgg gccggactgt cggcgggagg 3181 caggcggtcg gcggggaaat cccatgggtg gatctgcacg tcccagtcgg cgcgcacctg 3241 ccaggcatgg ttgatcgcca cgatcacatc aatgccgtcg cgcgaccagt cgcgcgcctg 3301 caccacctcg gggccggagc ccagaatcag cacattggtc attttgtgat cccccgtcgc 3361 acaaagctta aacccggttt ggcagatcac caaaaccggg tggcggaaac ttgccgaaag 3421 cgggcgggcc ggggccgggg gcgctagatc gagaaggaaa tcccgcagcc gcaactactg 3481 gtcgcgttgg ggttttccac cacgaaccgc gcgccgatca gctcatccga gaaatcaatg 3541 accgcatttt ccagaaacgg cagcgagacc gggtcgatca gcacccgctg gccttcgcct 3601 tccagcacca gatcctcggg ggcgggggcg tcttccagcg tgatctcgta ttgaaagccc 3661 gagcagccgc ccccctcgac cgccacgcgc agggcgcggg gggcttcggc ggcttcgttg 3721 atctgggcca gccgggaaaa ggcgcgcggc gtgaccttcg gcggaatgtt aagcatcgtc 3781 ggacctgttc tttcctgtct ccctcgatat aggatggcgc aaaacgcgcg acaagacgag 3841 gggatcgggc cttgcttcaa ccatatgcct gtcagccgga ggacagccgg gggcggcttc 3901 atgccgaaag catgtccacc ttccgctctc cctttcagcg cgaccgtgac cggatcatcc 3961 attcctcggc cttccggcgg ctgaagcaca agacgcaggt cttcgtcgag catgagggcg 4021 attactaccg cacccgcctg acccatacga tcgaggtggc acaggtcgcg cgcaccatcg 4081 cgggcgcgct tgggctgaat accgatctgg ccgaggcggt ggcgcttgcc catgaccttg 4141 gccatccgcc cttcggccat accggagagg atgccttggc cgacctaatg cagcccttcg 4201 gcgggttcga ccacaacgcg caggccctgc gcatcgtgac ccggctggaa aagcactatg 4261 ccggctttga cgggctgaac ctgacatggg aaacgctgga aggcattgcc aagcataacg 4321 ggccggtgac gggcgatctg tcctatgccc tggccgaggt gaatgccgaa tgggatctgg 4381 agctgcacac caacgcctcg gccgaggcgc aggtggccgc ggtggccgac gatgtcgcct 4441 ataaccacca tgacctgcat gacgggctgc gcgcggggct tttcagcgaa gaggatctga 4501 tggagctgcc caccatcggc ccctgcttcg aagaggtcga ccgcctgcat ccggggcttg 4561 accccacgcg ccgccgccac gaggcgctgc gccgcgtctt cggcgtgatg gtcgaggatg 4621 tgatcgccgt ggcgcagaac cgccttgtgt cgctttgccc cgaaagcgcc gatgacatcc 4681 gcgcgatgga ggggccgatc atccgctttt ccaagccgct ctaccagaac ctcaaggcgc 4741 tcaagggctt tctgttcacg cgcatgtatc gcgcgccaag cgtggtggag gaacgccgcc 4801 gcgtgacggg gatggtcaac gcgcttttcc cgctgtttct ggacgatccc gcactgctgc 4861 ccgaggactg gcaggacgag gttgcccgcg cggcggaccg caccgcgctt gcgcgggtcg 4921 tgctggatta tgtggccggc atgacggacc gtttcgccat tcaggaatat caccggcttc 4981 tggggtccga tagctgaccg gaccccggcc cggcgctgct cagccgccca tgcgcgagaa 5041 ggtggtgcga ttgtccggcc caaggccaag ccagcccgcc gtcgtggccg caagatgtgc 5101 cacnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 5161 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 5221 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnacgcc ggtgcctttc ggggccgatt 5281 tgcgcgactt gatgttgagc gcgtggaagg tttccagcgt gacgcggaag cgcacgcgcc 5341 ggggcccttt caggccgcgc gcacccgccg cgatcccttc ttgcaagatg cgcgacactt 5401 gcgcgcgccg gtcccccgcg gcttcggcct gccagacgat atcggccttg ggaacgtaga 5461 ccgagttgtc ctcggacacg gtcaggttcg ccggaacggt aacgtccacc cccgccagcg 5521 accagtcgcg cgcggacggt ccggccggtt gatactcggt ctgccattgc ccgcctccgc 5581 agccggcaag ggcggcggcc ccccccaagg caagaagcgt aagcatgtgg cggcgattga 5641 acccaagagt catcattaaa gcacccgttt cttttattgc gcccaaggct tatcctgttc 5701 gggcgtcttt tcaaagcgcc agttccgtca ggttggcccg cgcggcgata tgtccgggcc 5761 gaaggcggca ggcgccaacc gcggaaccgc ccggccgcgg gcgcgttccg cccttgcaag 5821 acaggaggat ggcatgatcg tgaaatcagg ttccgcgcat tgggaaggtg cgctgaagga 5881 cggcaagggc accgtttcga ccgaaagcgg ggcgcttgcc gcacagccct atggcttcaa 5941 cacccgcttc gagggccgcc ccggcaccaa ccccgaagag ctgatcgccg ccgcgcatgc 6001 ggcgtgtttc tcgatggcgc tttcggccgg gcttg //