Methylorubrum extorquens DM4 plasmid p1METDI, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Methylobacteriaceae; Methylorubrum.
Submitted (09-OCT-2017) Genoscope - CEA (Commissariat a l'energie atomique et aux energies alternatives) : BP 191 91006 EVRY cedex - FRANCE (E-mail : seqref@genoscope.cns.fr - Web : www.genoscope.cns.fr)
REFSEQ INFORMATION: The reference sequence is identical to\nFP103043.1.\nAnnotation results relative to BLAST similarities, COG\nassignations, enzymatic function prediction (PRIAM software), TMHMM\nand SignalP predictions, and synteny conservation (Syntonizer\nsoftware) are available in the MicroScope annotation system\nhttp://www.genoscope.cns.fr/agc/microscope.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/16/2023 02:38:24\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) :: 5,821\nCDSs (total) :: 5,744\nGenes (coding) :: 5,561\nCDSs (with protein) :: 5,561\nGenes (RNA) :: 77\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 58\nncRNAs :: 4\nPseudo Genes (total) :: 183\nCDSs (without protein) :: 183\nPseudo Genes (ambiguous residues) :: 0 of 183\nPseudo Genes (frameshifted) :: 56 of 183\nPseudo Genes (incomplete) :: 147 of 183\nPseudo Genes (internal stop) :: 34 of 183\nPseudo Genes (multiple problems) :: 46 of 183\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Methylobacterium dichloromethanicum
COORDINATES: similar to AA sequence:RefSeq:WP_012606235.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012606236.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778762.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778763.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606239.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606240.1
COORDINATES: similar to AA sequence:RefSeq:WP_043766018.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
leucine zipper domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606242.1
COORDINATES: protein motif:HMM:TIGR03454.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778768.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF014060.2
COORDINATES: similar to AA sequence:RefSeq:WP_012778770.1
IS21-like element ISMdi7 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_003596510.1
IS21-like element ISMdi7 family helper ATPase IstB
COORDINATES: protein motif:HMM:NF017437.2
COORDINATES: similar to AA sequence:RefSeq:WP_012778771.1
ISL3-like element ISMdi2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_012319572.1
IS256-like element ISMex3 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_076611761.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS3-like element ISMex5 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_015822921.1
GO:0003987 - acetate-CoA ligase activity [Evidence IEA]
GO:0019427 - acetyl-CoA biosynthetic process from acetate [Evidence IEA]
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_003597382.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822922.1
GO:0015293 - symporter activity [Evidence IEA]
GO:0006847 - plasma membrane acetate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007558573.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012453725.1
FIST N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017486118.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012454852.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012606252.1
IS5-like element ISMdi24 family transposase
COORDINATES: protein motif:HMM:NF024180.2
COORDINATES: similar to AA sequence:RefSeq:WP_012330561.1
14.3 : Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides
COORDINATES: similar to AA sequence:RefSeq:WP_003605844.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
2.6 : Sugar-nucleotide biosynthesis and conversions
COORDINATES: similar to AA sequence:RefSeq:WP_012752845.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012254904.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: protein motif:HMM:NF021616.2
COORDINATES: protein motif:HMM:NF014686.2
COORDINATES: protein motif:HMM:NF024811.2
COORDINATES: protein motif:HMM:NF017345.2
FdtA/QdtA family cupin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019898928.1
GO:0008483 - transaminase activity [Evidence IEA]
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_076612221.1
frameshifted; internal stop; 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_076611490.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611110.1
IS701-like element ISMdi28 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_012606012.1
internal stop; 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_012778787.1
IS21-like element ISMdi27 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_012778788.1
IS21-like element ISMdi27 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_076611771.1
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_076611367.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611868.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612078.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF012888.2
GO:0050656 - 3'-phosphoadenosine 5'-phosphosulfate binding [Evidence IEA]; GO:0008146 - sulfotransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013752.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611470.1
COORDINATES: similar to AA sequence:RefSeq:WP_010875294.1
GO:0003953 - NAD+ nucleosidase activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012778790.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01439.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018264113.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_076611304.1
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.
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF033564.0
COORDINATES: similar to AA sequence:RefSeq:WP_008113808.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_009803737.1
GO:0030554 - adenyl nucleotide binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020678122.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014744322.1
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_011654176.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0015803 - branched-chain amino acid transport [Evidence IEA]
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_011654177.1
COORDINATES: similar to AA sequence:RefSeq:WP_009459234.1
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF013757.2
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: protein motif:HMM:NF015692.2
GO:0016799 - hydrolase activity, hydrolyzing N-glycosyl compounds [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
ADP-ribosylglycohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611158.1
IS3-like element ISMdi5 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_012334433.1
COORDINATES: similar to AA sequence:RefSeq:WP_003597379.1
COORDINATES: similar to AA sequence:RefSeq:WP_019400199.1
class I poly(R)-hydroxyalkanoic acid synthase
COORDINATES: similar to AA sequence:RefSeq:WP_076611370.1
IS3-like element ISMdi16 family transposase
COORDINATES: protein motif:HMM:NF012245.2
COORDINATES: similar to AA sequence:RefSeq:WP_041359162.1
IS5-like element ISMdi26 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_012253262.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015822258.1
GO:0005215 - transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015950581.1
zinc-binding alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611539.1
IS3-like element ISMex16 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_009867760.1
COORDINATES: similar to AA sequence:RefSeq:WP_015857281.1
COORDINATES: protein motif:HMM:NF037406.2
COORDINATES: similar to AA sequence:RefSeq:WP_012778812.1
IS110-like element ISMex29 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_020493507.1
COORDINATES: similar to AA sequence:RefSeq:WP_018264137.1
COORDINATES: similar to AA sequence:RefSeq:WP_012456582.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655065.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606181.1
COORDINATES: similar to AA sequence:RefSeq:WP_008838806.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015931593.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606184.1
COORDINATES: similar to AA sequence:RefSeq:WP_007692751.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012318852.1
COORDINATES: similar to AA sequence:RefSeq:WP_006022612.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606167.1
COORDINATES: similar to AA sequence:RefSeq:WP_013368621.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606195.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606196.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606199.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606200.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606201.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606202.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606203.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606204.1
COORDINATES: similar to AA sequence:RefSeq:WP_012329822.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606206.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606207.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_012606210.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606211.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606212.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606218.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606219.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606220.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606221.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606222.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606223.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606224.1
DotI/IcmL family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606225.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606227.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606228.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606229.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606230.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606231.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606232.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778862.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606234.1