Pseudomonas hydrolytica strain KHPS2 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas.
Genome sequences of two Pseudomonas isolates that can use metformin as a sole nitrogen source
Submitted (01-JUL-2022) Plant and Microbial Biology, University of Minnesota, 1445 Gortner Avenue, St. Paul, MN 55108, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP100554.1.\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 :: unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 99x\nSequencing Technology :: Illumina NextSeq; Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/21/2023 04:21:08\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) :: 5,192\nCDSs (total) :: 5,110\nGenes (coding) :: 5,062\nCDSs (with protein) :: 5,062\nGenes (RNA) :: 82\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 66\nncRNAs :: 4\nPseudo Genes (total) :: 48\nCDSs (without protein) :: 48\nPseudo Genes (ambiguous residues) :: 0 of 48\nPseudo Genes (frameshifted) :: 13 of 48\nPseudo Genes (incomplete) :: 36 of 48\nPseudo Genes (internal stop) :: 5 of 48\nPseudo Genes (multiple problems) :: 6 of 48\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+.
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF038091.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020852263.1
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_007160867.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012216568.1
COORDINATES: protein motif:HMM:NF015431.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01728.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]; GO:0005488 - binding [Evidence IEA]
GO:0042918 - alkanesulfonate transport [Evidence IEA]
aliphatic sulfonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_015297829.1
GO:0052717 - tRNA-specific adenosine-34 deaminase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012823731.1
GO:0016787 - hydrolase activity [Evidence IEA]
isochorismatase family cysteine hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_011811489.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015277150.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004424788.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003449170.1
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: protein motif:HMM:NF041859.1
GO:0071824 - protein-DNA complex organization [Evidence IEA]
histone-like nucleoid-structuring protein, MvaT/MvaU family
COORDINATES: protein motif:HMM:NF018154.2
COORDINATES: protein motif:HMM:NF015397.2
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_002933279.1
COORDINATES: protein motif:HMM:NF019069.2
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_006762839.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019951365.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_020191957.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017113439.1
COORDINATES: similar to AA sequence:RefSeq:WP_032490160.1
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_076612041.1
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:NP_248989.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004356 - glutamate-ammonia ligase activity [Evidence IEA]
GO:0006542 - glutamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_248990.1
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008569251.1
polyamine ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014340742.1
spermidine/putrescine ABC transporter substrate-binding protein PotF
COORDINATES: protein motif:HMM:NF016819.2
COORDINATES: protein motif:HMM:NF012703.2
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013334.2
hydrogenase maturation nickel metallochaperone HypA
COORDINATES: similar to AA sequence:RefSeq:WP_002706882.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
hydrogenase nickel incorporation protein HypB
COORDINATES: protein motif:HMM:NF012655.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF014218.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF019498.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612067.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018860470.1
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_001231163.1
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: similar to AA sequence:RefSeq:WP_008293723.1
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_020750540.1
COORDINATES: similar to AA sequence:RefSeq:WP_004661680.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011117183.1
COORDINATES: similar to AA sequence:RefSeq:WP_010895249.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_013006728.1
COORDINATES: protein motif:HMM:NF023505.2
COORDINATES: similar to AA sequence:RefSeq:WP_020308962.1
COORDINATES: similar to AA sequence:RefSeq:WP_009106276.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]; GO:0006265 - DNA topological change [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005430728.1
COORDINATES: protein motif:HMM:NF015118.2
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: protein motif:HMM:NF016238.2