Methylocystis bryophila strain S285 plasmid p1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Methylocystaceae; Methylocystis.
Submitted (23-FEB-2017) Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch 10, Marburg 35043, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP019949.1.\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 :: HGAP v. 2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 34.7x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/01/2023 01:47:32\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) :: 4,318\nCDSs (total) :: 4,261\nGenes (coding) :: 4,202\nCDSs (with protein) :: 4,202\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 59\nCDSs (without protein) :: 59\nPseudo Genes (ambiguous residues) :: 0 of 59\nPseudo Genes (frameshifted) :: 22 of 59\nPseudo Genes (incomplete) :: 45 of 59\nPseudo Genes (internal stop) :: 8 of 59\nPseudo Genes (multiple problems) :: 16 of 59\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: protein motif:HMM:NF003417.0
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
amino acid adenylation domain-containing protein
COORDINATES: protein motif:HMM:TIGR01733.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012873.2
COORDINATES: similar to AA sequence:RefSeq:WP_008006586.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020157078.1
COORDINATES: similar to AA sequence:RefSeq:WP_018268006.1
diaminobutyrate--2-oxoglutarate transaminase
COORDINATES: protein motif:HMM:NF013698.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF014430.2
COORDINATES: protein motif:HMM:NF013786.2
GO:0008897 - holo-[acyl-carrier-protein] synthase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
4'-phosphopantetheinyl transferase superfamily protein
COORDINATES: protein motif:HMM:NF013069.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003610856.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_003610964.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01783.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0015343 - siderophore-iron transmembrane transporter activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF015863.2
PepSY-associated TM helix domain-containing protein
COORDINATES: protein motif:HMM:NF027890.2
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_020085290.1
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: protein motif:HMM:NF024116.2
COORDINATES: similar to AA sequence:RefSeq:WP_018264448.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: protein motif:HMM:NF024091.2
COORDINATES: similar to AA sequence:RefSeq:WP_012043473.1
COORDINATES: similar to AA sequence:RefSeq:WP_013542561.1
COORDINATES: protein motif:HMM:NF033550.5
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008389590.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_006611557.1
GO:0015074 - DNA integration [Evidence IEA]
phage integrase N-terminal SAM-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008513229.1
COORDINATES: protein motif:HMM:NF013867.2
GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0008984 - protein-glutamate methylesterase activity [Evidence IEA]
GO:0006935 - chemotaxis [Evidence IEA]; GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF033572.1
COORDINATES: similar to AA sequence:RefSeq:WP_015314323.1
type II toxin-antitoxin system MqsA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011505292.1
type II toxin-antitoxin system MqsR family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018409461.1
COORDINATES: protein motif:HMM:NF018841.2
COORDINATES: similar to AA sequence:RefSeq:WP_011578806.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011992915.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004448190.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018268287.1
COORDINATES: similar to AA sequence:RefSeq:WP_018071683.1
COORDINATES: similar to AA sequence:RefSeq:WP_017265752.1
COORDINATES: similar to AA sequence:RefSeq:WP_016919157.1
COORDINATES: similar to AA sequence:RefSeq:WP_013654326.1
COORDINATES: similar to AA sequence:RefSeq:WP_019016376.1
COORDINATES: similar to AA sequence:RefSeq:WP_018427896.1
DUF2161 family putative PD-(D/E)XK-type phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_016921271.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018264162.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018264633.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]; GO:0001072 - transcription antitermination factor activity, RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016919160.1
COORDINATES: similar to AA sequence:RefSeq:WP_016919161.1
COORDINATES: similar to AA sequence:RefSeq:WP_020084884.1
COORDINATES: similar to AA sequence:RefSeq:WP_016919163.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_013639369.1
COORDINATES: protein motif:HMM:NF024754.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF022840.2
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: similar to AA sequence:RefSeq:WP_009762575.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016919179.1
COORDINATES: similar to AA sequence:RefSeq:WP_016919180.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_016919181.1
VirB4 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_016919183.1
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: similar to AA sequence:RefSeq:WP_016919184.1
COORDINATES: similar to AA sequence:RefSeq:WP_016919185.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_004129402.1
COORDINATES: similar to AA sequence:RefSeq:WP_009762565.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011505068.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578847.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011578846.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505071.1
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009734077.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578843.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011578842.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014786595.1
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_016919205.1
COORDINATES: protein motif:HMM:NF012442.2
COORDINATES: protein motif:HMM:NF014074.2
COORDINATES: protein motif:HMM:NF039808.1
COORDINATES: protein motif:HMM:NF013094.2
COORDINATES: protein motif:HMM:NF025817.2
COORDINATES: protein motif:HMM:NF025808.2
multiubiquitin domain-containing protein
COORDINATES: protein motif:HMM:NF039402.1
COORDINATES: similar to AA sequence:RefSeq:WP_003039637.1
COORDINATES: similar to AA sequence:RefSeq:WP_003614971.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016919211.1
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611382.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012427.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013927.2
GO:0016811 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01194.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:1904680 - peptide transmembrane transporter activity [Evidence IEA]
GO:0015833 - peptide transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018408667.1
COORDINATES: similar to AA sequence:RefSeq:WP_004207353.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013166.2
COORDINATES: similar to AA sequence:RefSeq:WP_018267992.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011970797.1
COORDINATES: similar to AA sequence:RefSeq:WP_011316098.1
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