Succinivibrio dextrinosolvens strain ASCUSBF53 chromosome 2, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Aeromonadales; Succinivibrionaceae; Succinivibrio.
Submitted (13-JAN-2021) R&D, Ascus Biosciences, 6450 Lusk Blvd E209, San Diego, CA 92121, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP068346.1.\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 Date :: 20-MAR-2020\nAssembly Method :: Unicycler v. 0.4.7\nAssembly Name :: ASCUSBF53\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/11/2023 06:36:55\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,476\nCDSs (total) :: 2,382\nGenes (coding) :: 2,373\nCDSs (with protein) :: 2,373\nGenes (RNA) :: 94\nrRNAs :: 7, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 7, 7 (5S, 16S, 23S)\ntRNAs :: 69\nncRNAs :: 4\nPseudo Genes (total) :: 9\nCDSs (without protein) :: 9\nPseudo Genes (ambiguous residues) :: 0 of 9\nPseudo Genes (frameshifted) :: 2 of 9\nPseudo Genes (incomplete) :: 9 of 9\nPseudo Genes (internal stop) :: 0 of 9\nPseudo Genes (multiple problems) :: 2 of 9\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:NF024811.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR01056.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF019843.2
COORDINATES: similar to AA sequence:RefSeq:WP_007055981.1
RNA-guided endonuclease TnpB family protein
COORDINATES: protein motif:HMM:NF019153.2
COORDINATES: protein motif:HMM:TIGR03743.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: protein motif:HMM:NF018836.2
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: protein motif:HMM:NF041281.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:TIGR02746.1
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF018536.2
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF005560.0
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013226.2
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: similar to AA sequence:RefSeq:WP_009142543.1
GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015776.2
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00180.1
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF033551.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: similar to AA sequence:RefSeq:WP_019933388.1
COORDINATES: protein motif:HMM:TIGR03033.1
COORDINATES: protein motif:HMM:NF024676.2
COORDINATES: protein motif:HMM:NF012570.2
COORDINATES: protein motif:HMM:NF014044.2
COORDINATES: protein motif:HMM:NF025768.2
COORDINATES: protein motif:HMM:NF025919.2
COORDINATES: similar to AA sequence:RefSeq:WP_009144302.1
COORDINATES: protein motif:HMM:NF013122.2
GO:0004527 - exonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013714.2
COORDINATES: protein motif:HMM:NF012534.2
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012334.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: protein motif:HMM:TIGR02384.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_019003545.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009142966.1
COORDINATES: similar to AA sequence:RefSeq:WP_009144196.1
GO:0009368 - endopeptidase Clp complex [Evidence IEA]
GO:0004176 - ATP-dependent peptidase activity [Evidence IEA]; GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
ATP-dependent Clp endopeptidase proteolytic subunit ClpP
COORDINATES: protein motif:HMM:NF024258.2
COORDINATES: protein motif:HMM:NF012234.2
COORDINATES: similar to AA sequence:RefSeq:WP_009144203.1
GO:0006166 - purine ribonucleoside salvage [Evidence IEA]
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:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004242485.1
COORDINATES: protein motif:HMM:NF040907.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
sugar ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012245.2
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF025477.2
COORDINATES: protein motif:HMM:NF013793.2