Pseudomonas shirazica strain A28 plasmid unnamed.
Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas.
Genome sequence of Pseudomonas Shirazica A28
Submitted (20-OCT-2020) Pathogeny Microbiology, Southwest Medical University, Jiangyang, Luzhou, Sichuan 646000, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP063457.1.\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 :: Canu v. 1.5\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 150.0x\nSequencing Technology :: Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/01/2023 03:46:28\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) :: 5,591\nCDSs (total) :: 5,491\nGenes (coding) :: 5,423\nCDSs (with protein) :: 5,423\nGenes (RNA) :: 100\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 74\nncRNAs :: 4\nPseudo Genes (total) :: 68\nCDSs (without protein) :: 68\nPseudo Genes (ambiguous residues) :: 0 of 68\nPseudo Genes (frameshifted) :: 14 of 68\nPseudo Genes (incomplete) :: 59 of 68\nPseudo Genes (internal stop) :: 2 of 68\nPseudo Genes (multiple problems) :: 6 of 68\n##Genome-Annotation-Data-END##
China: No. 319, Zhongshan Road, Luzhou, Sichuan
COORDINATES: similar to AA sequence:RefSeq:YP_005221021.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:YP_005220837.1
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_001138014.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003150544.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007162521.1
COORDINATES: similar to AA sequence:RefSeq:WP_011078031.1
COORDINATES: similar to AA sequence:RefSeq:WP_011600753.1
COORDINATES: similar to AA sequence:RefSeq:WP_011600754.1
COORDINATES: protein motif:HMM:NF017300.2
GO:0006274 - DNA replication termination [Evidence IEA]
DNA replication terminus site-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_016974327.1
COORDINATES: similar to AA sequence:RefSeq:WP_016974330.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016974331.1
COORDINATES: protein motif:HMM:TIGR00180.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011077924.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
histone-like nucleoid-structuring protein, MvaT/MvaU family
COORDINATES: similar to AA sequence:RefSeq:WP_011077927.1
COORDINATES: protein motif:HMM:NF025054.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020190234.1
COORDINATES: similar to AA sequence:RefSeq:WP_016502330.1
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_011077933.1
COORDINATES: similar to AA sequence:RefSeq:WP_011077934.1
COORDINATES: similar to AA sequence:RefSeq:WP_011077935.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_076612095.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016974350.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024642.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015026477.1
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016971292.1
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: similar to AA sequence:RefSeq:WP_016971286.1
COORDINATES: similar to AA sequence:RefSeq:WP_011077967.1
COORDINATES: protein motif:HMM:NF011458.0
conjugal transfer mating pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_016971282.1
GO:0006109 - regulation of carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011077970.1
COORDINATES: similar to AA sequence:RefSeq:WP_016971279.1
COORDINATES: similar to AA sequence:RefSeq:WP_011077974.1
COORDINATES: protein motif:HMM:NF015776.2
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017848001.1
COORDINATES: similar to AA sequence:RefSeq:WP_016502347.1
COORDINATES: protein motif:HMM:NF041494.1
COORDINATES: similar to AA sequence:RefSeq:WP_011077981.1
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: similar to AA sequence:RefSeq:WP_011077984.1
COORDINATES: similar to AA sequence:RefSeq:WP_013100901.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_013100902.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_011077987.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_016969578.1
COORDINATES: protein motif:HMM:TIGR02747.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: protein motif:HMM:NF012211.1
COORDINATES: similar to AA sequence:RefSeq:WP_011077993.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: similar to AA sequence:RefSeq:WP_011077995.1
COORDINATES: similar to AA sequence:RefSeq:WP_016969580.1
COORDINATES: similar to AA sequence:RefSeq:WP_016969581.1
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_016969582.1
COORDINATES: similar to AA sequence:RefSeq:WP_011077999.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
nuclease-related domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016969585.1
COORDINATES: similar to AA sequence:RefSeq:WP_016969586.1
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:TIGR02740.1
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016969791.1
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: similar to AA sequence:RefSeq:WP_011078018.1
GO:0008855 - exodeoxyribonuclease VII activity [Evidence IEA]; GO:0004527 - exonuclease activity [Evidence IEA]
GO:0006308 - DNA catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016502355.1
GO:0009318 - exodeoxyribonuclease VII complex [Evidence IEA]
GO:0008855 - exodeoxyribonuclease VII activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005782454.1
COORDINATES: similar to AA sequence:RefSeq:WP_011078025.1
COORDINATES: similar to AA sequence:RefSeq:WP_011078026.1
COORDINATES: protein motif:HMM:NF023227.2
COORDINATES: similar to AA sequence:RefSeq:WP_003152694.1
multidrug efflux transporter outer membrane subunit TOprJ1
COORDINATES: similar to AA sequence:RefSeq:WP_118842627.1
multidrug efflux RND transporter permease subunit TMexD3
COORDINATES: similar to AA sequence:RefSeq:WP_118842626.1
multidrug efflux RND transporter periplasmic adaptor subunit TMexC3
COORDINATES: similar to AA sequence:RefSeq:WP_004665563.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012075821.1
COORDINATES: similar to AA sequence:RefSeq:WP_020191571.1
COORDINATES: similar to AA sequence:RefSeq:WP_001568731.1
COORDINATES: similar to AA sequence:RefSeq:WP_003422414.1
COORDINATES: similar to AA sequence:RefSeq:WP_009051461.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014852982.1
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_017685227.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: protein motif:HMM:TIGR02779.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003910 - DNA ligase (ATP) activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003175058.1
COORDINATES: similar to AA sequence:RefSeq:WP_003284021.1
COORDINATES: similar to AA sequence:RefSeq:WP_016974345.1
COORDINATES: similar to AA sequence:RefSeq:WP_007250645.1
COORDINATES: protein motif:HMM:NF014273.2
COORDINATES: similar to AA sequence:RefSeq:WP_009397337.1
COORDINATES: protein motif:HMM:NF013658.2
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019584489.1
COORDINATES: similar to AA sequence:RefSeq:WP_017335987.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003150546.1
GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
putative toxin-antitoxin system toxin component, PIN family
COORDINATES: similar to AA sequence:RefSeq:WP_004574519.1
COORDINATES: similar to AA sequence:RefSeq:WP_005413391.1
COORDINATES: similar to AA sequence:RefSeq:WP_004574521.1
COORDINATES: similar to AA sequence:RefSeq:WP_020795286.1
mercuric resistance transcriptional repressor protein MerD
COORDINATES: similar to AA sequence:RefSeq:WP_008567175.1
COORDINATES: similar to AA sequence:RefSeq:WP_020795287.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004574525.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229640.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:YP_005229639.1
COORDINATES: similar to AA sequence:RefSeq:WP_004574528.1
GO:0001228 - DNA-binding transcription activator activity, RNA polymerase II-specific [Evidence IEA]
Hg(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004574529.1
co-regulatory protein PtrA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005005993.1
GO:0045282 - plasma membrane succinate dehydrogenase complex [Evidence IEA]
GO:0000104 - succinate dehydrogenase activity [Evidence IEA]
GO:0006099 - tricarboxylic acid cycle [Evidence IEA]
succinate dehydrogenase, cytochrome b556 subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003464988.1
Uncharacterized protein conserved in bacteria
COORDINATES: similar to AA sequence:RefSeq:WP_003464986.1
COORDINATES: similar to AA sequence:RefSeq:WP_005005995.1
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002118292.1
COORDINATES: similar to AA sequence:RefSeq:WP_003464980.1
Thiol-disulfide isomerase and thioredoxins
COORDINATES: similar to AA sequence:RefSeq:WP_003464979.1
COORDINATES: similar to AA sequence:RefSeq:WP_003464978.1
COORDINATES: similar to AA sequence:RefSeq:WP_005006001.1
COORDINATES: similar to AA sequence:RefSeq:WP_003044989.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]
zinc-binding alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016487060.1
COORDINATES: similar to AA sequence:RefSeq:WP_002118270.1
magnesium and cobalt transport protein CorA
COORDINATES: similar to AA sequence:RefSeq:WP_005006007.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione S-transferase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003464967.1
GO:0033744 - L-methionine:thioredoxin-disulfide S-oxidoreductase activity [Evidence IEA]; GO:0008113 - peptide-methionine (S)-S-oxide reductase activity [Evidence IEA]
GO:0030091 - protein repair [Evidence IEA]; GO:0006979 - response to oxidative stress [Evidence IEA]
peptide-methionine (S)-S-oxide reductase MsrA
Conserved domain frequently associated with peptide methionine sulfoxide reductase
COORDINATES: similar to AA sequence:RefSeq:WP_003044951.1
GO:0033743 - peptide-methionine (R)-S-oxide reductase activity [Evidence IEA]
peptide-methionine (R)-S-oxide reductase MsrB
COORDINATES: similar to AA sequence:RefSeq:WP_011911830.1
IS21-like element ISPst3 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_012080643.1
COORDINATES: similar to AA sequence:RefSeq:WP_014834018.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229646.1
COORDINATES: similar to AA sequence:RefSeq:WP_013124600.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_003155746.1
COORDINATES: similar to AA sequence:RefSeq:WP_011517528.1
COORDINATES: similar to AA sequence:RefSeq:WP_003155741.1
COORDINATES: similar to AA sequence:RefSeq:WP_032491390.1
subclass B1 metallo-beta-lactamase VIM-2
COORDINATES: similar to AA sequence:RefSeq:WP_003159191.1
AAC(6')-Ib family aminoglycoside 6'-N-acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_001247892.1
COORDINATES: similar to AA sequence:RefSeq:WP_008932165.1
Uncharacterized conserved protein, contains double-stranded beta-helix domain
COORDINATES: similar to AA sequence:RefSeq:WP_003465043.1
COORDINATES: similar to AA sequence:RefSeq:WP_011809177.1
COORDINATES: similar to AA sequence:RefSeq:WP_003100856.1
COORDINATES: similar to AA sequence:RefSeq:WP_003100853.1
COORDINATES: similar to AA sequence:RefSeq:WP_019897068.1
COORDINATES: similar to AA sequence:RefSeq:WP_008021599.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
iron chelate uptake ABC transporter family permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_017847952.1
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_016487050.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_010466151.1
COORDINATES: similar to AA sequence:RefSeq:WP_010466153.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:NP_253837.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010466156.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003465041.1
COORDINATES: similar to AA sequence:RefSeq:WP_003465039.1
COORDINATES: similar to AA sequence:RefSeq:WP_003465037.1
Spermidine/putrescine-binding periplasmic protein
COORDINATES: similar to AA sequence:RefSeq:WP_003465034.1
ABC-type spermidine/putrescine transport system, permease component I
COORDINATES: similar to AA sequence:RefSeq:WP_003465031.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
ABC-type spermidine/putrescine transport system, permease component II
COORDINATES: similar to AA sequence:RefSeq:WP_020289701.1
COORDINATES: similar to AA sequence:RefSeq:WP_001513488.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
AraC-type DNA-binding domain-containing proteins
COORDINATES: similar to AA sequence:RefSeq:WP_012080657.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003464991.1
COORDINATES: similar to AA sequence:RefSeq:WP_000414383.1
COORDINATES: similar to AA sequence:RefSeq:WP_003089120.1
COORDINATES: similar to AA sequence:RefSeq:WP_009682418.1
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003150552.1
COORDINATES: similar to AA sequence:RefSeq:WP_003089113.1
GDCCVxC domain-containing (seleno)protein
COORDINATES: similar to AA sequence:RefSeq:WP_003089110.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221000.1
IS6-like element IS26 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_032492145.1
aminoglycoside O-phosphotransferase APH(3')-Ia
COORDINATES: similar to AA sequence:RefSeq:WP_004194535.1
COORDINATES: similar to AA sequence:RefSeq:WP_000259031.1
sulfonamide-resistant dihydropteroate synthase Sul1
COORDINATES: similar to AA sequence:RefSeq:WP_000679427.1
quaternary ammonium compound efflux SMR transporter QacE delta 1
COORDINATES: similar to AA sequence:RefSeq:WP_032488483.1
oxacillin-hydrolyzing class D beta-lactamase OXA-10
incomplete; too short partial abutting assembly gap; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.