Microbacterium sediminis strain YLB-01 plasmid unnamed, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Microbacteriaceae; Microbacterium.
Genomic analysis of Microbacterium sediminis YLB-01 reveals backgrounds related to its deep sea enviroment adaptation
Submitted (22-MAR-2019) Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, No. 184, University Road, Siming District, Xiamen, Xiamen, Simin 361000, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP038257.1.\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 :: SMRT Link v. 5.0.1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 500x\nSequencing Technology :: Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 12:34:21\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,830\nCDSs (total) :: 2,775\nGenes (coding) :: 2,757\nCDSs (with protein) :: 2,757\nGenes (RNA) :: 55\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 3\nPseudo Genes (total) :: 18\nCDSs (without protein) :: 18\nPseudo Genes (ambiguous residues) :: 0 of 18\nPseudo Genes (frameshifted) :: 9 of 18\nPseudo Genes (incomplete) :: 12 of 18\nPseudo Genes (internal stop) :: 0 of 18\nPseudo Genes (multiple problems) :: 3 of 18\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011928008.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005054880.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_006841231.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005054886.1
COORDINATES: similar to AA sequence:RefSeq:WP_018173541.1
COORDINATES: similar to AA sequence:RefSeq:WP_005054894.1
GO:0020037 - heme binding [Evidence IEA]
GO:0017004 - cytochrome complex assembly [Evidence IEA]
c-type cytochrome biogenesis protein CcsB
COORDINATES: similar to AA sequence:RefSeq:WP_017828916.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005054898.1
COORDINATES: similar to AA sequence:RefSeq:WP_005054900.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005054902.1
COORDINATES: similar to AA sequence:RefSeq:WP_005054905.1
COORDINATES: similar to AA sequence:RefSeq:WP_016463496.1
cytochrome c biogenesis CcdA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018172928.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005054911.1
COORDINATES: similar to AA sequence:RefSeq:WP_005054913.1
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016463494.1
COORDINATES: protein motif:HMM:NF016149.2
COORDINATES: similar to AA sequence:RefSeq:WP_005054917.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005054919.1
COORDINATES: similar to AA sequence:RefSeq:WP_005525963.1
COORDINATES: similar to AA sequence:RefSeq:WP_019763252.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005525777.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016697630.1
COORDINATES: protein motif:HMM:NF014533.2
GO:0009294 - DNA-mediated transformation [Evidence IEA]
COORDINATES: protein motif:HMM:NF012610.2
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005255867.1
COORDINATES: similar to AA sequence:RefSeq:WP_005052778.1
COORDINATES: similar to AA sequence:RefSeq:WP_019174038.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946610.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720936.1
COORDINATES: similar to AA sequence:RefSeq:WP_012300404.1
COORDINATES: similar to AA sequence:RefSeq:WP_012300403.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013700.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024254.2
COORDINATES: protein motif:HMM:NF024056.2
COORDINATES: similar to AA sequence:RefSeq:WP_012300392.1
COORDINATES: similar to AA sequence:RefSeq:WP_010080078.1
COORDINATES: protein motif:HMM:NF024248.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF020250.2
COORDINATES: similar to AA sequence:RefSeq:WP_017831605.1
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: similar to AA sequence:RefSeq:WP_017831603.1
COORDINATES: similar to AA sequence:RefSeq:WP_012300385.1
COORDINATES: similar to AA sequence:RefSeq:WP_012300382.1
COORDINATES: similar to AA sequence:RefSeq:WP_012300378.1
LysM peptidoglycan-binding domain-containing protein
COORDINATES: protein motif:HMM:NF013632.2
COORDINATES: similar to AA sequence:RefSeq:WP_019180296.1
COORDINATES: similar to AA sequence:RefSeq:WP_013839171.1
COORDINATES: protein motif:HMM:NF013577.2
MurR/RpiR family transcriptional regulator
COORDINATES: protein motif:HMM:NF013539.2
GO:0097367 - carbohydrate derivative binding [Evidence IEA]
GO:1901135 - carbohydrate derivative metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007515455.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018022994.1
COORDINATES: similar to AA sequence:RefSeq:WP_018022993.1
GO:0004721 - phosphoprotein phosphatase activity [Evidence IEA]; GO:0004725 - protein tyrosine phosphatase activity [Evidence IEA]
GO:0006470 - protein dephosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005052799.1
COORDINATES: similar to AA sequence:RefSeq:WP_009476914.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018022990.1
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005050776.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020388485.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017831587.1
COORDINATES: similar to AA sequence:RefSeq:WP_005050763.1
COORDINATES: similar to AA sequence:RefSeq:WP_017831575.1
COORDINATES: similar to AA sequence:RefSeq:WP_017831573.1
COORDINATES: similar to AA sequence:RefSeq:WP_005050753.1
COORDINATES: protein motif:HMM:NF019291.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
Eco57I restriction-modification methylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005052802.1
COORDINATES: similar to AA sequence:RefSeq:WP_013474031.1
COORDINATES: similar to AA sequence:RefSeq:WP_019175589.1
COORDINATES: protein motif:HMM:NF024591.2
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011559028.1
COORDINATES: similar to AA sequence:RefSeq:WP_005050739.1
COORDINATES: similar to AA sequence:RefSeq:WP_005054949.1
COORDINATES: similar to AA sequence:RefSeq:WP_020540911.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006897056.1
COORDINATES: similar to AA sequence:RefSeq:WP_013603012.1
GO:0019380 - 3-phenylpropionate catabolic process [Evidence IEA]
3-phenylpropionate/cinnamic acid dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_011689783.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020497489.1
COORDINATES: similar to AA sequence:RefSeq:WP_003875328.1
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_005444922.1
COORDINATES: similar to AA sequence:RefSeq:WP_006867081.1
COORDINATES: similar to AA sequence:RefSeq:WP_020540908.1
GO:0008695 - 3-phenylpropionate dioxygenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005050729.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612118.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020667427.1
polysaccharide deacetylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005566457.1
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558200.1
GO:0015074 - DNA integration [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006244415.1
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_013583720.1
endonuclease/exonuclease/phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005448007.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009078290.1
class II aldolase/adducin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010223651.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005444919.1
3-(cis-5,6-dihydroxycyclohexa-1, 3-dien-1-yl)propanoate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_005444924.1
COORDINATES: similar to AA sequence:RefSeq:WP_005448002.1
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_011891555.1
COORDINATES: similar to AA sequence:RefSeq:WP_005054953.1
COORDINATES: similar to AA sequence:RefSeq:WP_005050730.1
COORDINATES: similar to AA sequence:RefSeq:WP_011873077.1