Scandinavium goeteborgense strain CCUG 66741 plasmid pSg66741_1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Scandinavium.
Scandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant
Complete genome sequence of Scandinavium goeteborgense CCUG 66741T
Submitted (27-MAY-2020) Infectious Diseases, University of Gothenburg - CCUG, Guldhedsgatan 10, Box 7193, Gothenburg, Vastra Gotaland 40234, Sweden
Submitted (30-NOV-2018) Infectious Diseases, University of Gothenburg - CCUG, Guldhedsgatan 10, Box 7193, Gothenburg, Vastra Gotaland 40234, Sweden
REFSEQ INFORMATION: The reference sequence is identical to\nCP054057.1.\nBacteria and source DNA available from Culture Collection\nUniversity of Gothenburg (CCUG).\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 :: 24-MAY-2020\nAssembly Method :: SPAdes v. 3.13.1; Canu v. 1.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 1000.0x\nSequencing Technology :: Illumina NovaSeq 6000; Oxford Nanopore\n MiniION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/19/2023 19:05:08\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) :: 4,541\nCDSs (total) :: 4,420\nGenes (coding) :: 4,357\nCDSs (with protein) :: 4,357\nGenes (RNA) :: 121\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 89\nncRNAs :: 10\nPseudo Genes (total) :: 63\nCDSs (without protein) :: 63\nPseudo Genes (ambiguous residues) :: 0 of 63\nPseudo Genes (frameshifted) :: 30 of 63\nPseudo Genes (incomplete) :: 44 of 63\nPseudo Genes (internal stop) :: 10 of 63\nPseudo Genes (multiple problems) :: 17 of 63\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Scandinavium goeteborgense
Bacteriology Laboratory, Department of Clinical Bacteriology, Sahlgrenska University Hospital
COORDINATES: similar to AA sequence:RefSeq:WP_001293470.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611477.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_086558235.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611491.1
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.
COORDINATES: similar to AA sequence:RefSeq:WP_012767745.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_004966400.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_000099160.1
COORDINATES: protein motif:HMM:NF027307.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024986.2
COORDINATES: similar to AA sequence:RefSeq:WP_012477168.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611932.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_076611553.1
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_086558178.1
COORDINATES: similar to AA sequence:RefSeq:WP_004718848.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_004929604.1
GO:0015473 - fimbrial usher porin activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004244938.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0071555 - cell wall organization [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006820303.1
COORDINATES: similar to AA sequence:RefSeq:WP_004244922.1
GO:0007155 - cell adhesion [Evidence IEA]
COORDINATES: protein motif:HMM:NF012635.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611384.1
GO:0015074 - DNA integration [Evidence IEA]
frameshifted; 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: protein motif:HMM:NF016800.2
COORDINATES: similar to AA sequence:RefSeq:WP_017694167.1
COORDINATES: similar to AA sequence:RefSeq:WP_018896995.1
COORDINATES: protein motif:HMM:NF019148.2
WavE lipopolysaccharide synthesis family protein
COORDINATES: protein motif:HMM:NF013245.2
COORDINATES: similar to AA sequence:RefSeq:WP_016536028.1
COORDINATES: similar to AA sequence:RefSeq:WP_016536030.1
COORDINATES: similar to AA sequence:RefSeq:WP_001395480.1
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
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
conjugative transfer relaxase/helicase TraI
COORDINATES: similar to AA sequence:RefSeq:WP_014063902.1
COORDINATES: similar to AA sequence:RefSeq:WP_000998048.1
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_012442751.1
GO:0003725 - double-stranded RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008114374.1
COORDINATES: similar to AA sequence:RefSeq:WP_007871462.1
COORDINATES: similar to AA sequence:RefSeq:WP_006465019.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014544635.1
GO:0046417 - chorismate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013068.2
COORDINATES: similar to AA sequence:RefSeq:WP_013183349.1
COORDINATES: similar to AA sequence:RefSeq:WP_004181973.1
COORDINATES: similar to AA sequence:RefSeq:WP_006660414.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0033103 - protein secretion by the type VI secretion system [Evidence IEA]
type VI secretion system contractile sheath small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_017892320.1
GO:0033104 - type VI protein secretion system complex [Evidence IEA]
type VI secretion system contractile sheath large subunit
COORDINATES: similar to AA sequence:RefSeq:YP_005227577.1
type VI secretion system baseplate subunit TssK
COORDINATES: similar to AA sequence:RefSeq:WP_004851537.1
type VI secretion system protein TssL, short form
COORDINATES: similar to AA sequence:RefSeq:WP_016159832.1
COORDINATES: similar to AA sequence:RefSeq:YP_005226602.1
COORDINATES: similar to AA sequence:RefSeq:WP_010431630.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015461686.1
COORDINATES: similar to AA sequence:RefSeq:WP_000688531.1
COORDINATES: similar to AA sequence:RefSeq:WP_000059651.1
type VI secretion system Vgr family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014230196.1
COORDINATES: similar to AA sequence:RefSeq:WP_004877032.1
LysM peptidoglycan-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_005227552.1
COORDINATES: similar to AA sequence:RefSeq:WP_014839082.1
COORDINATES: similar to AA sequence:RefSeq:WP_001088844.1
COORDINATES: similar to AA sequence:RefSeq:WP_015461677.1
COORDINATES: similar to AA sequence:RefSeq:YP_005227549.1
type VI secretion system baseplate subunit TssF
COORDINATES: similar to AA sequence:RefSeq:WP_000553779.1
type VI secretion system baseplate subunit TssG
COORDINATES: similar to AA sequence:RefSeq:WP_014230185.1
type VI secretion system lipoprotein TssJ
COORDINATES: similar to AA sequence:RefSeq:WP_010431583.1
type VI secretion system baseplate subunit TssE
COORDINATES: similar to AA sequence:RefSeq:WP_004851499.1
COORDINATES: similar to AA sequence:RefSeq:WP_004851496.1
COORDINATES: similar to AA sequence:RefSeq:WP_004543218.1
COORDINATES: similar to AA sequence:RefSeq:WP_020191363.1
COORDINATES: similar to AA sequence:RefSeq:WP_003020799.1
aspartate aminotransferase family protein
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_076611760.1
COORDINATES: similar to AA sequence:RefSeq:WP_017801002.1
COORDINATES: similar to AA sequence:RefSeq:WP_016496240.1
GO:0047761 - butyrate kinase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009639305.1
GO:0016746 - acyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011764756.1
COORDINATES: similar to AA sequence:RefSeq:WP_012703589.1
frameshifted; internal stop; 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.
COORDINATES: similar to AA sequence:RefSeq:WP_076611160.1
COORDINATES: similar to AA sequence:RefSeq:WP_006812181.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015870489.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_015673692.1
GO:0055085 - transmembrane transport [Evidence IEA]
small-conductance mechanosensitive channel MscS
COORDINATES: similar to AA sequence:RefSeq:WP_076612096.1
COORDINATES: similar to AA sequence:RefSeq:WP_004264637.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611102.1
COORDINATES: similar to AA sequence:RefSeq:WP_014263773.1
COORDINATES: protein motif:HMM:NF021778.2
beta-propeller fold lactonase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008815373.1
COORDINATES: similar to AA sequence:RefSeq:WP_004883363.1
COORDINATES: similar to AA sequence:RefSeq:WP_001481272.1
COORDINATES: similar to AA sequence:RefSeq:NP_490544.1
COORDINATES: similar to AA sequence:RefSeq:WP_015870302.1
COORDINATES: similar to AA sequence:RefSeq:WP_004940523.1
COORDINATES: protein motif:HMM:NF040977.1
COORDINATES: similar to AA sequence:RefSeq:WP_019076706.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013087217.1
COORDINATES: similar to AA sequence:RefSeq:WP_011846847.1
COORDINATES: protein motif:HMM:NF017843.2
COORDINATES: protein motif:HMM:NF007279.0
COORDINATES: similar to AA sequence:RefSeq:WP_006710107.1
COORDINATES: similar to AA sequence:RefSeq:WP_013202818.1
COORDINATES: similar to AA sequence:RefSeq:WP_001044770.1
VapC toxin family PIN domain ribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_006326267.1
COORDINATES: similar to AA sequence:RefSeq:WP_016246479.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017146297.1
COORDINATES: similar to AA sequence:RefSeq:WP_001567382.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF018986.2
COORDINATES: similar to AA sequence:RefSeq:WP_001567380.1
COORDINATES: similar to AA sequence:RefSeq:WP_001567378.1
GO:0033743 - peptide-methionine (R)-S-oxide reductase activity [Evidence IEA]
GO:0030091 - protein repair [Evidence IEA]; GO:0006979 - response to oxidative stress [Evidence IEA]
peptide-methionine (R)-S-oxide reductase MsrB
COORDINATES: similar to AA sequence:RefSeq:WP_014140367.1
GO:0033744 - L-methionine:thioredoxin-disulfide S-oxidoreductase activity [Evidence IEA]; GO:0008113 - peptide-methionine (S)-S-oxide reductase activity [Evidence IEA]
peptide-methionine (S)-S-oxide reductase MsrA
COORDINATES: similar to AA sequence:RefSeq:WP_012218041.1
type I restriction-modification system subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_014063950.1
ParB/RepB/Spo0J family plasmid partition protein
COORDINATES: similar to AA sequence:RefSeq:NP_052640.1