Sphingomonas aliaeris strain DH-S5 plasmid punnamed2, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere
Submitted (01-SEP-2020) Institute for Food Microbiology and Hygiene, University of Bonn, Endenicher Allee 19 B, Bonn 53115, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP061037.1.\nBacteria and source DNA available from Food microbiology and\nhygiene, University of Bonn, Endenicher Allee 19B, 53115 Bonn.\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 :: MAR-2020\nAssembly Method :: flye assembly tool v. 2.7b\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 56.0x\nSequencing Technology :: Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/25/2022 04:38:31\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;\n repeat_region\nGenes (total) :: 4,133\nCDSs (total) :: 4,076\nGenes (coding) :: 3,792\nCDSs (with protein) :: 3,792\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 284\nCDSs (without protein) :: 284\nPseudo Genes (ambiguous residues) :: 0 of 284\nPseudo Genes (frameshifted) :: 234 of 284\nPseudo Genes (incomplete) :: 57 of 284\nPseudo Genes (internal stop) :: 12 of 284\nPseudo Genes (multiple problems) :: 17 of 284\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: similar to AA sequence:RefSeq:WP_007404999.1
GO:0003824 - catalytic activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017670014.1
COORDINATES: similar to AA sequence:RefSeq:WP_012030270.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007014249.1
COORDINATES: similar to AA sequence:RefSeq:WP_013269517.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019368676.1
COORDINATES: similar to AA sequence:RefSeq:WP_013078715.1
GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017977736.1
GO:0008927 - mannonate dehydratase activity [Evidence IEA]
GO:0006064 - glucuronate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001370723.1
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_016193176.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR01439.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006457507.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007686596.1
COORDINATES: similar to AA sequence:RefSeq:WP_015951488.1
GO:0016791 - phosphatase activity [Evidence IEA]
ATP-binding protein/SpoIIE family protein phosphatase
COORDINATES: similar to AA sequence:RefSeq:WP_012605601.1
COORDINATES: similar to AA sequence:RefSeq:WP_013730959.1
COORDINATES: similar to AA sequence:RefSeq:WP_005666382.1
COORDINATES: protein motif:HMM:NF013736.2
COORDINATES: similar to AA sequence:RefSeq:WP_012455796.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012257.2
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011950548.1
COORDINATES: similar to AA sequence:RefSeq:WP_010186214.1
COORDINATES: similar to AA sequence:RefSeq:WP_019517848.1
COORDINATES: similar to AA sequence:RefSeq:WP_012590629.1
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010215279.1
COORDINATES: similar to AA sequence:RefSeq:WP_010162462.1
COORDINATES: similar to AA sequence:RefSeq:WP_019516394.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004107.1
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020095762.1
COORDINATES: similar to AA sequence:RefSeq:WP_003604608.1
COORDINATES: protein motif:HMM:NF023431.2
COORDINATES: similar to AA sequence:RefSeq:WP_008129174.1
COORDINATES: similar to AA sequence:RefSeq:WP_009280290.1
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_008828908.1
COORDINATES: similar to AA sequence:RefSeq:WP_008575709.1
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_010339751.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251293.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008603814.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339748.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188931.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188930.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251298.1
COORDINATES: similar to AA sequence:RefSeq:WP_020493513.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188890.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980864.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251301.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251303.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980735.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_010188878.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: similar to AA sequence:RefSeq:WP_017980732.1
COORDINATES: similar to AA sequence:RefSeq:WP_017500361.1
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017980856.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980855.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_010188868.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219621.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017980852.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007405901.1
COORDINATES: similar to AA sequence:RefSeq:WP_011241460.1
GO:0022627 - cytosolic small ribosomal subunit [Evidence IEA]; GO:0000314 - organellar small ribosomal subunit [Evidence IEA]
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006953131.1
COORDINATES: similar to AA sequence:RefSeq:WP_017505071.1
COORDINATES: similar to AA sequence:RefSeq:WP_007681566.1
COORDINATES: similar to AA sequence:RefSeq:WP_020008005.1
PLP-dependent aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017268586.1
COORDINATES: similar to AA sequence:RefSeq:WP_008065746.1
LysR family transcriptional regulator ArgP
COORDINATES: similar to AA sequence:RefSeq:WP_004750589.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
quaternary ammonium compound efflux SMR transporter SugE
COORDINATES: similar to AA sequence:RefSeq:WP_018238513.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092732.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012590325.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018250476.1
glutathione-dependent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_019516245.1
COORDINATES: similar to AA sequence:RefSeq:WP_015656343.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219486.1
COORDINATES: similar to AA sequence:RefSeq:WP_014076289.1
COORDINATES: similar to AA sequence:RefSeq:WP_019718197.1
COORDINATES: protein motif:HMM:NF024867.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011269851.1
COORDINATES: similar to AA sequence:RefSeq:WP_017500308.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017980904.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013836229.1
COORDINATES: protein motif:HMM:NF024676.2
COORDINATES: similar to AA sequence:RefSeq:WP_018904726.1
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251310.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188793.1
COORDINATES: protein motif:HMM:NF014626.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013849896.1
COORDINATES: similar to AA sequence:RefSeq:WP_009632969.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020493507.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849894.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188780.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251150.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339720.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165182.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165183.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165184.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165185.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010188938.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010165188.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010188936.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831578.1
COORDINATES: protein motif:HMM:NF040974.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165195.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251166.1
COORDINATES: protein motif:HMM:NF036578.2
COORDINATES: similar to AA sequence:RefSeq:WP_016745447.1
GO:0018738 - S-formylglutathione hydrolase activity [Evidence IEA]
GO:0046292 - formaldehyde metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010162575.1
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_000842106.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_007706152.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013836638.1
COORDINATES: similar to AA sequence:RefSeq:WP_013836639.1
COORDINATES: similar to AA sequence:RefSeq:WP_013836641.1
GO:0030246 - carbohydrate binding [Evidence IEA]
malectin domain-containing carbohydrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017670022.1