Gordonia hongkongensis strain JCM 31934 plasmid pGo-1.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Gordoniaceae; Gordonia.
Gordonia hongkongensis type strain genome analysis
Submitted (12-APR-2022) Bio Health Science, Changwon National University, Changwondaero, Changwon, Gyeongnam 51140, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP095553.1.\nBacteria and source DNA available from JCM 31934.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: Miniasm v. 0.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 45.8x\nSequencing Technology :: Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 20:43:49\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,891\nCDSs (total) :: 4,832\nGenes (coding) :: 4,569\nCDSs (with protein) :: 4,569\nGenes (RNA) :: 59\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 263\nCDSs (without protein) :: 263\nPseudo Genes (ambiguous residues) :: 0 of 263\nPseudo Genes (frameshifted) :: 182 of 263\nPseudo Genes (incomplete) :: 85 of 263\nPseudo Genes (internal stop) :: 15 of 263\nPseudo Genes (multiple problems) :: 17 of 263\n##Genome-Annotation-Data-END##
the blood culture and the peritoneal dialysis effluent of two patients
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024359.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014786.2
COORDINATES: protein motif:HMM:NF025200.2
COORDINATES: similar to AA sequence:RefSeq:WP_012880131.1
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: similar to AA sequence:RefSeq:WP_003882612.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016888812.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003891612.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611184.1
GO:0004803 - transposase activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_019359429.1
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003943380.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005456631.1
glutathione-dependent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_005180118.1
COORDINATES: similar to AA sequence:RefSeq:WP_005180121.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005183308.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011896162.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006358896.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562805.1
COORDINATES: similar to AA sequence:RefSeq:WP_006900210.1
COORDINATES: protein motif:HMM:NF019151.2
COORDINATES: protein motif:HMM:NF013265.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012836523.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007319862.1
COORDINATES: protein motif:HMM:NF024056.2
COORDINATES: protein motif:HMM:NF013727.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014928868.1
COORDINATES: similar to AA sequence:RefSeq:WP_017828989.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007736268.1
COORDINATES: protein motif:HMM:TIGR00027.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014520.2
COORDINATES: similar to AA sequence:RefSeq:WP_005056596.1
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: similar to AA sequence:RefSeq:WP_006900548.1
COORDINATES: protein motif:HMM:NF012975.2
ribonuclease catalytic domain-containing protein
COORDINATES: protein motif:HMM:NF016557.2
COORDINATES: protein motif:HMM:NF022355.2
COORDINATES: protein motif:HMM:NF027484.2
COORDINATES: similar to AA sequence:RefSeq:WP_011691690.1
COORDINATES: similar to AA sequence:RefSeq:WP_019311173.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006947560.1
COORDINATES: similar to AA sequence:RefSeq:WP_019311171.1
COORDINATES: protein motif:HMM:NF015216.2
GO:0018836 - alkylmercury lyase activity [Evidence IEA]
GO:0046413 - organomercury catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016463647.1
COORDINATES: similar to AA sequence:RefSeq:WP_014928774.1
COORDINATES: protein motif:HMM:NF019886.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma factor-like helix-turn-helix DNA-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014668657.1
COORDINATES: similar to AA sequence:RefSeq:WP_007618847.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562839.1
COORDINATES: similar to AA sequence:RefSeq:WP_006368754.1
COORDINATES: protein motif:HMM:NF019913.2
COORDINATES: similar to AA sequence:RefSeq:WP_014928968.1
excalibur calcium-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014926787.1
PLD nuclease N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014928220.1
COORDINATES: similar to AA sequence:RefSeq:WP_006359781.1
COORDINATES: similar to AA sequence:RefSeq:WP_006359780.1
COORDINATES: protein motif:HMM:NF037930.2
COORDINATES: similar to AA sequence:RefSeq:WP_009778347.1
COORDINATES: similar to AA sequence:RefSeq:WP_005103269.1
COORDINATES: similar to AA sequence:RefSeq:WP_016889202.1
COORDINATES: similar to AA sequence:RefSeq:WP_005100175.1
COORDINATES: similar to AA sequence:RefSeq:WP_009481393.1
COORDINATES: similar to AA sequence:RefSeq:WP_006593495.1