Mycolicibacterium frederiksbergense strain LB 501T plasmid unnamed2.
Mycolicibacterium frederiksbergense (Mycobacterium frederiksbergense)
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae; Mycolicibacterium.
Draft, Whole-Genome Sequence of the Anthracene-degrading Mycobacterium frederiksbergense LB501T, Isolated from a Polycyclic Aromatic Hydrocarbon (PAH)-Contaminated Soil
Submitted (03-APR-2019) Laboratory of Bioengineering, Catholic University of Louvain, Place Croix du Sud, 2/19, L7.05.19, Louvain-la-Neuve 1348, Belgium
REFSEQ INFORMATION: The reference sequence is identical to\nCP038798.1.\nBacteria and source DNA available from Catholic University of\nLouvain Earth & Life Institute Laboratory of Bioengineering Place\nCroix du Sud, 2/19, L7.05.19 1348 Louvain-la-Neuve Belgium.\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 :: HGAP v. 3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 194.0x\nSequencing Technology :: PacBio RSII; Illumina NextSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/16/2023 12:10:51\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) :: 6,537\nCDSs (total) :: 6,482\nGenes (coding) :: 6,281\nCDSs (with protein) :: 6,281\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) :: 201\nCDSs (without protein) :: 201\nPseudo Genes (ambiguous residues) :: 0 of 201\nPseudo Genes (frameshifted) :: 118 of 201\nPseudo Genes (incomplete) :: 115 of 201\nPseudo Genes (internal stop) :: 14 of 201\nPseudo Genes (multiple problems) :: 40 of 201\n##Genome-Annotation-Data-END##
polycyclic aromatic hydrocarbon (PAH)-contaminated soil
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF014898.2
GO:0015074 - DNA integration [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:NP_218155.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014817212.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011726865.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [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_011781139.1
COORDINATES: similar to AA sequence:RefSeq:WP_003872487.1
COORDINATES: similar to AA sequence:RefSeq:WP_011559062.1
COORDINATES: similar to AA sequence:RefSeq:WP_015308793.1
COORDINATES: similar to AA sequence:RefSeq:WP_011726870.1
COORDINATES: similar to AA sequence:RefSeq:WP_011781751.1
GO:0015914 - phospholipid transport [Evidence IEA]
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012398.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558018.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011599025.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016895001.1
GO:0008774 - acetaldehyde dehydrogenase (acetylating) activity [Evidence IEA]
acetaldehyde dehydrogenase (acetylating)
COORDINATES: similar to AA sequence:RefSeq:WP_010360540.1
GO:0003824 - catalytic activity [Evidence IEA]
fumarylacetoacetate hydrolase family protein
COORDINATES: protein motif:HMM:NF014899.2
COORDINATES: similar to AA sequence:RefSeq:WP_020631358.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
bifunctional 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin subunit
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF024966.2
GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
aromatic-ring-hydroxylating dioxygenase subunit beta
COORDINATES: protein motif:HMM:NF013044.2
COORDINATES: protein motif:HMM:NF014795.2
COORDINATES: similar to AA sequence:RefSeq:WP_011730987.1
mycofactocin-coupled SDR family oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013472535.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024788.2
PLDc N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_005176048.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_076611738.1
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_016705911.1
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_003944213.1
COORDINATES: similar to AA sequence:RefSeq:WP_003890979.1
COORDINATES: protein motif:HMM:NF025398.2
COORDINATES: similar to AA sequence:RefSeq:WP_011599022.1
COORDINATES: similar to AA sequence:RefSeq:WP_013423713.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003893958.1
GO:0047472 - 3-carboxy-cis,cis-muconate cycloisomerase activity [Evidence IEA]
3-carboxy-cis,cis-muconate cycloisomerase
COORDINATES: similar to AA sequence:RefSeq:WP_011559101.1
GO:0018578 - protocatechuate 3,4-dioxygenase activity [Evidence IEA]
GO:0046278 - 3,4-dihydroxybenzoate metabolic process [Evidence IEA]
protocatechuate 3,4-dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_014360281.1
protocatechuate 3,4-dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_006369656.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019735209.1
COORDINATES: similar to AA sequence:RefSeq:WP_009977821.1
class II aldolase/adducin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005054949.1
COORDINATES: similar to AA sequence:RefSeq:WP_005256000.1
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_011855194.1
3-(cis-5,6-dihydroxycyclohexa-1, 3-dien-1-yl)propanoate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013470350.1
COORDINATES: similar to AA sequence:RefSeq:WP_011599101.1
GO:0008695 - 3-phenylpropionate dioxygenase activity [Evidence IEA]
GO:0019380 - 3-phenylpropionate catabolic process [Evidence IEA]
3-phenylpropionate/cinnamic acid dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_014211435.1
COORDINATES: protein motif:HMM:NF037625.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011739028.1
COORDINATES: similar to AA sequence:RefSeq:WP_018599405.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611204.1
COORDINATES: protein motif:HMM:NF013698.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_005142312.1
COORDINATES: similar to AA sequence:RefSeq:WP_014941576.1
COORDINATES: similar to AA sequence:RefSeq:WP_007237543.1
COORDINATES: similar to AA sequence:RefSeq:WP_007170749.1
COORDINATES: similar to AA sequence:RefSeq:WP_007172498.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016881265.1
COORDINATES: similar to AA sequence:RefSeq:WP_086557958.1
frameshifted; 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_014211470.1
COORDINATES: similar to AA sequence:RefSeq:WP_011559036.1
GO:0016829 - lyase activity [Evidence IEA]
dihydrodipicolinate synthase family protein
COORDINATES: protein motif:HMM:NF019498.2
COORDINATES: similar to AA sequence:RefSeq:NP_217321.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891592.1
COORDINATES: similar to AA sequence:RefSeq:WP_015288385.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_032488867.1
COORDINATES: similar to AA sequence:RefSeq:WP_006867087.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211433.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891522.1
COORDINATES: similar to AA sequence:RefSeq:WP_011777851.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011559104.1
COORDINATES: similar to AA sequence:RefSeq:WP_019736229.1
GO:0047575 - 4-carboxymuconolactone decarboxylase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003929145.1
COORDINATES: similar to AA sequence:RefSeq:WP_011855201.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470385.1
COORDINATES: similar to AA sequence:RefSeq:WP_011559098.1
GO:0009436 - glyoxylate catabolic process [Evidence IEA]; GO:0071704 - organic substance metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011777845.1
GO:0008677 - 2-dehydropantoate 2-reductase activity [Evidence IEA]
GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005623854.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: protein motif:HMM:NF014664.2
GO:0051920 - peroxiredoxin activity [Evidence IEA]
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003886031.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF028007.2
GO:0051219 - phosphoprotein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003900923.1
COORDINATES: similar to AA sequence:RefSeq:WP_005113543.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011599405.1
COORDINATES: similar to AA sequence:RefSeq:WP_015297882.1
COORDINATES: similar to AA sequence:RefSeq:WP_013491219.1
COORDINATES: similar to AA sequence:RefSeq:WP_016895523.1
COORDINATES: similar to AA sequence:RefSeq:WP_016895279.1
COORDINATES: similar to AA sequence:RefSeq:WP_016895278.1
COORDINATES: similar to AA sequence:RefSeq:WP_016895275.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148585.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006898598.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805373.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148583.1
COORDINATES: protein motif:HMM:NF041492.1
COORDINATES: protein motif:HMM:NF024824.2
COORDINATES: similar to AA sequence:RefSeq:WP_011562908.1
COORDINATES: protein motif:HMM:NF025447.2
COORDINATES: similar to AA sequence:RefSeq:WP_011731392.1
COORDINATES: protein motif:HMM:NF013021.2
COORDINATES: protein motif:HMM:NF022388.2
COORDINATES: protein motif:HMM:NF025577.2
COORDINATES: similar to AA sequence:RefSeq:WP_005148570.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148569.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148568.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246314.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148572.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148565.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017206310.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243945.1
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005148562.1
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005148561.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
type VII secretion-associated serine protease mycosin
COORDINATES: protein motif:HMM:TIGR03920.1
GO:0003674 - molecular_function [Evidence IEA]
type VII secretion integral membrane protein EccD
COORDINATES: similar to AA sequence:RefSeq:WP_005148559.1
COORDINATES: protein motif:HMM:NF025377.2
COORDINATES: protein motif:HMM:NF017793.2
COORDINATES: protein motif:HMM:NF013127.2
COORDINATES: protein motif:HMM:TIGR03925.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148550.1
COORDINATES: protein motif:HMM:NF013073.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF022231.2
COORDINATES: similar to AA sequence:RefSeq:WP_005148687.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896304.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246601.1
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: similar to AA sequence:RefSeq:WP_006246248.1
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015298179.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004674 - protein serine/threonine kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_217874.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
GO:0003677 - DNA binding [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0045927 - positive regulation of growth [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:NP_217875.1
COORDINATES: protein motif:HMM:NF014643.2
COORDINATES: similar to AA sequence:RefSeq:WP_005147884.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298218.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470986.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470985.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014177611.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005148496.1
COORDINATES: similar to AA sequence:RefSeq:WP_007617942.1
COORDINATES: protein motif:HMM:NF013757.2
IclR family transcriptional regulator C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006897072.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020674403.1
COORDINATES: protein motif:HMM:NF019604.2
GO:0000166 - nucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014211480.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211418.1
COORDINATES: similar to AA sequence:RefSeq:WP_010268629.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211420.1
3-methyl-2-oxobutanoate hydroxymethyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014211421.1
GO:0003864 - 3-methyl-2-oxobutanoate hydroxymethyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014211422.1
COORDINATES: similar to AA sequence:RefSeq:WP_019526845.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016698413.1
GO:0004619 - phosphoglycerate mutase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
COORDINATES: similar to AA sequence:RefSeq:WP_014211424.1
COORDINATES: similar to AA sequence:RefSeq:WP_009478481.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211426.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003893965.1
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014211428.1
GO:0047443 - 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity [Evidence IEA]
4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase
COORDINATES: similar to AA sequence:RefSeq:WP_014211429.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014211430.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014211431.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611184.1
COORDINATES: similar to AA sequence:RefSeq:WP_013161536.1
COORDINATES: similar to AA sequence:RefSeq:WP_005515436.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013732590.1
COORDINATES: protein motif:HMM:NF012464.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014814.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611099.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_083047449.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805325.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470989.1
COORDINATES: similar to AA sequence:RefSeq:WP_011777795.1
COORDINATES: similar to AA sequence:RefSeq:WP_011776848.1
COORDINATES: similar to AA sequence:RefSeq:WP_011559056.1
COORDINATES: similar to AA sequence:RefSeq:WP_019509830.1
COORDINATES: similar to AA sequence:RefSeq:WP_019511864.1
COORDINATES: similar to AA sequence:RefSeq:WP_011559061.1
COORDINATES: similar to AA sequence:RefSeq:WP_015297644.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470347.1
COORDINATES: protein motif:HMM:NF020850.2
catalyzes the formation of acetyl-CoA from acetalaldehyde; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013298.2
COORDINATES: similar to AA sequence:RefSeq:WP_014211432.1
COORDINATES: protein motif:HMM:NF007422.0