Mycolicibacterium fluoranthenivorans strain 2A plasmid unnamed1.
Mycolicibacterium fluoranthenivorans (Mycobacterium fluoranthenivorans)
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae; Mycolicibacterium.
Draft genome sequence of four isobutane-metabolizing strains capable of cometabolically degrading diverse ether contaminants
Submitted (10-JUL-2020) Plant and Microbial Biology, North Carolina State University, 4545 Thomas Hall, North Carolina State University, Raleigh, NC 27695, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP059895.1.\nBacteria and source DNA available from Michael Hyman, Thomas Hall\n4545, North carolina state university.\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 :: PacBio De Novo Assembly Pipeline on CLC\n Genomics Workbench v. 20.0.2\nAssembly Name :: Isobutane_Mycolici_2A\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 47.47x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/15/2022 02:11:41\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 6,864\nCDSs (total) :: 6,808\nGenes (coding) :: 6,733\nCDSs (with protein) :: 6,733\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 75\nCDSs (without protein) :: 75\nPseudo Genes (ambiguous residues) :: 0 of 75\nPseudo Genes (frameshifted) :: 17 of 75\nPseudo Genes (incomplete) :: 63 of 75\nPseudo Genes (internal stop) :: 3 of 75\nPseudo Genes (multiple problems) :: 7 of 75\n##Genome-Annotation-Data-END##
COORDINATES: similar to AA sequence:RefSeq:WP_011437349.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006947312.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014805362.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012835503.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805363.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014805364.1
COORDINATES: similar to AA sequence:RefSeq:WP_006947302.1
aromatic/alkene monooxygenase hydroxylase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_014805366.1
aromatic/alkene/methane monooxygenase hydroxylase/oxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_014805735.1
COORDINATES: similar to AA sequence:RefSeq:WP_006947296.1
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805310.1
COORDINATES: similar to AA sequence:RefSeq:WP_019873300.1
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_014211310.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211311.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019205 - nucleobase-containing compound kinase activity [Evidence IEA]
GO:0006139 - nucleobase-containing compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005311948.1
COORDINATES: similar to AA sequence:RefSeq:WP_013874664.1
COORDINATES: similar to AA sequence:RefSeq:WP_012392389.1
COORDINATES: similar to AA sequence:RefSeq:NP_214682.1
COORDINATES: similar to AA sequence:RefSeq:WP_010908975.1
COORDINATES: similar to AA sequence:RefSeq:WP_015354180.1
COORDINATES: similar to AA sequence:RefSeq:WP_015574895.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211317.1
COORDINATES: similar to AA sequence:RefSeq:WP_003879093.1
COORDINATES: similar to AA sequence:RefSeq:WP_019695602.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211320.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211321.1
COORDINATES: similar to AA sequence:RefSeq:WP_009955421.1
COORDINATES: similar to AA sequence:RefSeq:WP_003874122.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805776.1
COORDINATES: similar to AA sequence:RefSeq:WP_014352786.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011895825.1
zinc-dependent alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014805778.1
COORDINATES: similar to AA sequence:RefSeq:WP_003889413.1
COORDINATES: similar to AA sequence:RefSeq:WP_005138667.1
GO:0003987 - acetate-CoA ligase activity [Evidence IEA]
GO:0019427 - acetyl-CoA biosynthetic process from acetate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805779.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014211334.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805772.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211336.1
COORDINATES: similar to AA sequence:RefSeq:WP_014711089.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211338.1
enoyl-CoA hydratase/isomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020120460.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211340.1
COORDINATES: similar to AA sequence:RefSeq:WP_017984505.1
COORDINATES: similar to AA sequence:RefSeq:WP_007240716.1
COORDINATES: similar to AA sequence:RefSeq:WP_018332348.1
GO:0050661 - NADP binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GO:0046170 - methanol catabolic process [Evidence IEA]
This methanol dehydrogenase is considered a nicotinoprotein, since its NADP cofactor remains is not dissociable, but instead remains permanently bound. A member of this family has been shown to act as a formaldehyde dismutase, able to convert two molecules of formaldehyde (plus one water molecule) into one of methanol and one of formate, with no net change in its redox state. More recently, it was shown in Mycobacterium smegmatis that this enzyme is critical to ethanol utilization, for which the biosynthesis of the cofactor-like electron carrier mycofactocin is also required; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014211344.1
COORDINATES: similar to AA sequence:RefSeq:WP_007236615.1
COORDINATES: similar to AA sequence:RefSeq:WP_012948208.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211348.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211353.1
methane monooxygenase/ammonia monooxygenase subunit C
COORDINATES: similar to AA sequence:RefSeq:WP_014211354.1
methane monooxygenase/ammonia monooxygenase subunit A
COORDINATES: similar to AA sequence:RefSeq:WP_014211355.1
methane monooxygenase/ammonia monooxygenase subunit B
COORDINATES: similar to AA sequence:RefSeq:WP_011209513.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805753.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211362.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805751.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211364.1
GO:0004497 - monooxygenase activity [Evidence IEA]
GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014211366.1
2Fe-2S iron-sulfur cluster binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014805748.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805747.1
COORDINATES: protein motif:HMM:NF024881.2
COORDINATES: similar to AA sequence:RefSeq:WP_014211371.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016705627.1
frameshifted; internal stop; 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:NF024109.2
COORDINATES: protein motif:HMM:NF012770.2
COORDINATES: similar to AA sequence:RefSeq:WP_015441116.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_016910398.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005248630.1
biotin carboxylase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006247325.1
3-oxoacyl-[acyl-carrier-protein] synthase III C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012948528.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562186.1
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_014805744.1
GO:0140604 - mycofactocin biosynthetic process [Evidence IEA]
Members of this protein family, MftF, are glycosyltransferases, members of PF00535 (glycosyl transferase family 2). The encoding gene is found as part of the mycofactocin cassette, in Mycobacterium tuberculosis, many other Actinobacteria, and occasional members of other lineages. Mycofactocin itself, a putative redox carrier, is a heavily modified derivative of the C-terminal Val-Tyr dipeptide of the mycofactocin precursor MftA (TIGR03969); Derived by automated computational analysis using gene prediction method: Protein Homology.
mycofactocin biosynthesis glycosyltransferase MftF
COORDINATES: similar to AA sequence:RefSeq:WP_007167828.1
GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
mycofactocin system GMC family oxidoreductase MftG
COORDINATES: similar to AA sequence:RefSeq:WP_003403310.1
GO:0071768 - mycolic acid biosynthetic process [Evidence IEA]
cyclopropane mycolic acid synthase family methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014211376.1
MftD, an enzyme found in the mycofactocin biosynthesis locus, performs an oxidative deamination of 3-amino-5-[(p-hydroxyphenyl)methyl]-4, 4-dimethyl-2-pyrrolidinone (AHDP). The resulting compound, now called pre-mycofactocin (PMFT), is a biologically active redox cofactor that can oxidize the non-exchangeable NADH of TIGR03971 family SDR-type oxidoreductases.; MftD, an enzyme found in the mycofactocin biosynthesis locus, performs an oxidative deamination of 3-amino-5-[(p-hydroxyphenyl)methyl]-4, 4-dimethyl-2-pyrrolidinone (AHDP). The resulting compound, now called pre-mycofactocin (PMFT), is a biologically active redox cofactor that can oxidize the non-exchangeable NADH of TIGR03971 family SDR-type oxidoreductases.; MftD, an enzyme found in the mycofactocin biosynthesis locus, performs an oxidative deamination of 3-amino-5-[(p-hydroxyphenyl)methyl]-4, 4-dimethyl-2-pyrrolidinone (AHDP). The resulting compound, now called pre-mycofactocin (PMFT), is a biologically active redox cofactor that can oxidize the non-exchangeable NADH of TIGR03971 family SDR-type oxidoreductases; Derived by automated computational analysis using gene prediction method: Protein Homology.
mycofactocin biosynthesis FMN-dependent deaminase MftD
COORDINATES: similar to AA sequence:RefSeq:WP_014805740.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]
GO:0140604 - mycofactocin biosynthetic process [Evidence IEA]; GO:0031179 - peptide modification [Evidence IEA]
MftC is a radical SAM/SPASM enzyme that catalyzes the first two steps in biosynthesis of the electron carrier mycofactocin from the terminal Val-Tyr dipeptide of the precursor peptide MftA.; MftC is a radical SAM/SPASM enzyme that catalyzes the first two steps in biosynthesis of the electron carrier mycofactocin from the terminal Val-Tyr dipeptide of the precursor peptide MftA; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014805739.1
MftB, a small protein, is a peptide chaperone that assists the radical SAM enzyme MftC in performing two modifications to the C-terminal Val-Tyr dipeptide of the mycofactocin precursor peptide, MftA. MftB's role is analogous to the role of PqqD in the biosynthesis of PQQ, a cofactor that derives entirely from a Tyr and a Glu in the precursor PqqA; Derived by automated computational analysis using gene prediction method: Protein Homology.
mycofactocin biosynthesis chaperone MftB
COORDINATES: similar to AA sequence:RefSeq:WP_014805738.1
GO:0009055 - electron transfer activity [Evidence IEA]
Mycofactocin is a small molecule electron carrier derived from the final two amino acids, Val-Tyr, of MftA, the mycofactocin precursor. It plays a role in redox homeostasis and the metabolism of alcohols and aldehydes in Actinobacteria, including Mycobacterium tuberculosis; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014805737.1
mycofactocin oligosaccharide methyltransferase MftM
COORDINATES: similar to AA sequence:RefSeq:WP_003897657.1
COORDINATES: similar to AA sequence:RefSeq:WP_011782599.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805369.1
COORDINATES: similar to AA sequence:RefSeq:WP_014942604.1
HoxN/HupN/NixA family nickel/cobalt transporter
COORDINATES: protein motif:HMM:NF022388.2
COORDINATES: similar to AA sequence:RefSeq:WP_015304084.1
COORDINATES: similar to AA sequence:RefSeq:WP_015297574.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246597.1
COORDINATES: similar to AA sequence:RefSeq:WP_015297575.1
COORDINATES: protein motif:HMM:NF025398.2
COORDINATES: similar to AA sequence:RefSeq:WP_011562949.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298293.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298291.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243942.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243941.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562953.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298287.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243933.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298273.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298272.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562995.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562996.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298269.1