Methanomethylovorans hollandica DSM 15978 plasmid pMETHO01, complete sequence.
Methanomethylovorans hollandica DSM 15978
Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia; Methanosarcinales; Methanosarcinaceae; Methanomethylovorans.
Complete sequence of plasmid of Methanomethylovorans hollandica DSM 15978
Submitted (29-FEB-2012) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003363.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4086496\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Methanomethylovorans hollandica DSM 15978\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Fresh water, Fresh water, Sediment\nnum_replicons :: 2\nref_biomaterial :: DSM 15978\nbiotic_relationship :: Free living\ntrophic_level :: Methylotroph\nrel_to_oxygen :: Obligate anaerobe\nisol_growth_condt :: 10427061\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi02921\nType Strain :: Yes\nGreengenes ID :: 431\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: Prodigal, GenePRIMP\nIsolation Site :: Anaerobic top layer (5 to 10 cm) of sediment\n (depth, 50 cm) in a eutrophic freshwater\n pond at the Dekkerswald Institute, Nijmegen,\n The Netherlands\nCell Shape :: Disc-shaped\nMotility :: Nonmotile\nTemperature Range :: Mesophile\nTemperature Optimum :: 37C\npH :: 6.5 - 7.0\nGram Staining :: Gram-\nDiseases :: None\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: Newbler v. 2.3\nGenome Coverage :: 30x\nSequencing Technology :: 454/Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/03/2023 00:59:23\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) :: 2,694\nCDSs (total) :: 2,634\nGenes (coding) :: 2,587\nCDSs (with protein) :: 2,587\nGenes (RNA) :: 60\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 2\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 19 of 47\nPseudo Genes (incomplete) :: 28 of 47\nPseudo Genes (internal stop) :: 12 of 47\nPseudo Genes (multiple problems) :: 10 of 47\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Anaerobic top layer (5 to 10 cm) of sediment (depth, 50 cm) in a eutrophic freshwater pond at the Dekkerswald Institute, Nijmegen, The Netherlands
type strain of Methanomethylovorans hollandica
Netherlands: The Dekkerswald Institute, Nijmegen
COORDINATES: protein motif:HMM:TIGR02928.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012492.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF018601.2
COORDINATES: protein motif:HMM:TIGR00716.1
GO:0004523 - RNA-DNA hybrid ribonuclease activity [Evidence IEA]
GO:0006401 - RNA catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015313749.1
GO:0004803 - transposase activity [Evidence IEA]
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015313747.1
COORDINATES: similar to AA sequence:RefSeq:WP_015054120.1
GO:0008998 - ribonucleoside-triphosphate reductase activity [Evidence IEA]
GO:0009265 - 2'-deoxyribonucleotide biosynthetic process [Evidence IEA]
anaerobic ribonucleoside-triphosphate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_015324210.1
COORDINATES: protein motif:HMM:NF020645.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF013311.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF025006.2
carboxypeptidase-like regulatory domain-containing protein
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: protein motif:HMM:NF033580.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF014044.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: similar to AA sequence:RefSeq:WP_011020315.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011306035.1
IS200/IS605 family element RNA-guided endonuclease TnpB
COORDINATES: protein motif:HMM:NF014244.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015054076.1
COORDINATES: similar to AA sequence:RefSeq:WP_015051957.1
COORDINATES: similar to AA sequence:RefSeq:WP_015054188.1
COORDINATES: similar to AA sequence:RefSeq:WP_011033708.1
COORDINATES: similar to AA sequence:RefSeq:WP_013194902.1
COORDINATES: similar to AA sequence:RefSeq:WP_011499862.1
COORDINATES: protein motif:HMM:NF024091.2
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013194920.1
COORDINATES: similar to AA sequence:RefSeq:WP_015313810.1
COORDINATES: protein motif:HMM:NF014052.2
COORDINATES: similar to AA sequence:RefSeq:WP_015313828.1
COORDINATES: similar to AA sequence:RefSeq:WP_015313827.1
COORDINATES: similar to AA sequence:RefSeq:WP_011011455.1
COORDINATES: protein motif:HMM:NF016764.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611659.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011307350.1
COORDINATES: similar to AA sequence:RefSeq:WP_011307351.1
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_011307352.1
COORDINATES: protein motif:HMM:NF038283.1
viperin family antiviral radical SAM protein
COORDINATES: protein motif:HMM:NF014825.2
COORDINATES: similar to AA sequence:RefSeq:WP_011033905.1
COORDINATES: similar to AA sequence:RefSeq:WP_013898930.1
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_011498605.1
COORDINATES: similar to AA sequence:RefSeq:WP_011367680.1
COORDINATES: protein motif:HMM:NF025693.2
COORDINATES: similar to AA sequence:RefSeq:WP_001568525.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006963956.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016362.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR02385.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF012403.2
COORDINATES: similar to AA sequence:RefSeq:WP_013037508.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024299.2
COORDINATES: similar to AA sequence:RefSeq:WP_011032516.1
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015313887.1
disaggregatase related repeat-containing protein
COORDINATES: protein motif:HMM:NF033857.1
COORDINATES: protein motif:HMM:NF015722.2
formylglycine-generating enzyme family protein
COORDINATES: protein motif:HMM:NF019912.2
COORDINATES: similar to AA sequence:RefSeq:WP_015325374.1
COORDINATES: similar to AA sequence:RefSeq:WP_015589644.1
COORDINATES: similar to AA sequence:RefSeq:WP_015052634.1
COORDINATES: similar to AA sequence:RefSeq:WP_011468307.1
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_076612386.1
COORDINATES: similar to AA sequence:RefSeq:WP_015313985.1
COORDINATES: similar to AA sequence:RefSeq:WP_011500310.1
COORDINATES: protein motif:HMM:TIGR04213.1
COORDINATES: protein motif:HMM:NF024824.2
COORDINATES: protein motif:HMM:NF024573.2
COORDINATES: similar to AA sequence:RefSeq:WP_015053243.1
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_011306721.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
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_015313870.1
COORDINATES: similar to AA sequence:RefSeq:WP_014585683.1
COORDINATES: protein motif:HMM:NF024804.2
winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011499857.1
COORDINATES: protein motif:HMM:NF013078.2
zinc dependent phospholipase C family protein
COORDINATES: protein motif:HMM:NF013499.2
GO:0003676 - nucleic acid binding [Evidence IEA]
OB-fold nucleic acid binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011498400.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036585.1
COORDINATES: similar to AA sequence:RefSeq:WP_011034691.1
catalyzes the formation of 3-phospho-D-glycerol phosphate from D-glyceraldehyde 3-phosphate in glycolysis; 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.
glyceraldehyde-3-phosphate dehydrogenase
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: protein motif:HMM:NF025030.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011696435.1
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014654.2
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: similar to AA sequence:RefSeq:WP_011020867.1
COORDINATES: protein motif:HMM:NF019949.2
COORDINATES: protein motif:HMM:NF002654.0
COORDINATES: protein motif:HMM:NF019616.2
COORDINATES: similar to AA sequence:RefSeq:WP_011499725.1
COORDINATES: protein motif:HMM:NF016906.2
COORDINATES: similar to AA sequence:RefSeq:WP_015313806.1
COORDINATES: protein motif:HMM:NF020939.2
COORDINATES: protein motif:HMM:NF013788.2
GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013897802.1
COORDINATES: protein motif:HMM:NF012372.2
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF013704.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015313977.1
COORDINATES: similar to AA sequence:RefSeq:WP_015313976.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_015325752.1