Paracoccus yeei strain TT13 plasmid pTT13-3, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
Complete genome sequence of Paracoccus yeei TT13 isolated from human skin
Submitted (27-OCT-2017) Bio Health Science, Changwon National University, Changwondaero, Changwon, Gyeongnam 51140, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP024425.1.\nBacteria and source DNA available from Prof Kyoung Lee, Changwon\nNational University.\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 :: SMRTpipe HGAP v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 178.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/09/2023 03:30:10\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) :: 4,573\nCDSs (total) :: 4,510\nGenes (coding) :: 4,349\nCDSs (with protein) :: 4,349\nGenes (RNA) :: 63\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 3\nPseudo Genes (total) :: 161\nCDSs (without protein) :: 161\nPseudo Genes (ambiguous residues) :: 0 of 161\nPseudo Genes (frameshifted) :: 58 of 161\nPseudo Genes (incomplete) :: 136 of 161\nPseudo Genes (internal stop) :: 18 of 161\nPseudo Genes (multiple problems) :: 46 of 161\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_012187365.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008558680.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187387.1
COORDINATES: similar to AA sequence:RefSeq:WP_020808813.1
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_028710025.1
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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_076611562.1
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_018304771.1
GO:0016759 - cellulose synthase activity [Evidence IEA]; GO:0035438 - cyclic-di-GMP binding [Evidence IEA]
GO:0030244 - cellulose biosynthetic process [Evidence IEA]; GO:0006011 - UDP-glucose metabolic process [Evidence IEA]
UDP-forming cellulose synthase catalytic subunit
COORDINATES: protein motif:HMM:NF015149.2
GO:0006011 - UDP-glucose metabolic process [Evidence IEA]
cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB
COORDINATES: similar to AA sequence:RefSeq:WP_002720497.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024583.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF013867.2
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: protein motif:HMM:NF020137.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611133.1
COORDINATES: protein motif:HMM:NF019335.2
TonB-dependent receptor plug domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007789939.1
COORDINATES: similar to AA sequence:RefSeq:WP_019998559.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328487.1
COORDINATES: similar to AA sequence:RefSeq:WP_015318238.1
COORDINATES: similar to AA sequence:RefSeq:WP_009826832.1
COORDINATES: similar to AA sequence:RefSeq:WP_003493222.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011911055.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612008.1
GO:0015074 - DNA integration [Evidence IEA]
frameshifted; 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
COORDINATES: similar to AA sequence:RefSeq:WP_008233439.1
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_076611537.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611153.1
COORDINATES: protein motif:HMM:NF016220.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF024904.2
COORDINATES: similar to AA sequence:RefSeq:WP_018391092.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012969489.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503866.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_028714619.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611656.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803278.1
antitoxin of toxin-antitoxin stability system
COORDINATES: similar to AA sequence:RefSeq:WP_010398696.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010398697.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611355.1
programmed frameshift; 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_015931502.1
COORDINATES: similar to AA sequence:RefSeq:WP_019965978.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018857907.1
COORDINATES: similar to AA sequence:RefSeq:WP_013168535.1
COORDINATES: similar to AA sequence:RefSeq:WP_012755572.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011339001.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009488662.1
COORDINATES: similar to AA sequence:RefSeq:WP_011388135.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024765.2
COORDINATES: similar to AA sequence:RefSeq:WP_019362189.1
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_010453079.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982932.1
phosphate-starvation-inducible PsiE family protein
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_007121473.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747551.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008598154.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0004076 - biotin synthase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0009102 - biotin biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009505412.1
COORDINATES: similar to AA sequence:RefSeq:WP_018964021.1
COORDINATES: similar to AA sequence:RefSeq:WP_018860313.1
COORDINATES: similar to AA sequence:RefSeq:WP_007605509.1
COORDINATES: similar to AA sequence:RefSeq:WP_018066164.1
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF039524.1
DUF883 C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018044311.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017998456.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010400456.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010400454.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012112893.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_007600987.1
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_012092589.1
COORDINATES: similar to AA sequence:RefSeq:WP_006339666.1
COORDINATES: similar to AA sequence:RefSeq:WP_012112829.1
COORDINATES: similar to AA sequence:RefSeq:WP_019905749.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327498.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007425269.1
GO:0045250 - cytosolic pyruvate dehydrogenase complex [Evidence IEA]
GO:0004738 - pyruvate dehydrogenase activity [Evidence IEA]
GO:0006086 - acetyl-CoA biosynthetic process from pyruvate [Evidence IEA]
pyruvate dehydrogenase (acetyl-transferring), homodimeric type
COORDINATES: similar to AA sequence:RefSeq:WP_012331181.1
GO:0045254 - pyruvate dehydrogenase complex [Evidence IEA]
GO:0004742 - dihydrolipoyllysine-residue acetyltransferase activity [Evidence IEA]
dihydrolipoyllysine-residue acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_005858184.1
GO:0004148 - dihydrolipoyl dehydrogenase activity [Evidence IEA]
GO:0045454 - cell redox homeostasis [Evidence IEA]; GO:0051068 - dihydrolipoamide metabolic process [Evidence IEA]; GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019994825.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749200.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749199.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820493.1
COORDINATES: similar to AA sequence:RefSeq:WP_004172336.1
COORDINATES: similar to AA sequence:RefSeq:WP_009811393.1
COORDINATES: similar to AA sequence:RefSeq:WP_028713484.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009357484.1
COORDINATES: similar to AA sequence:RefSeq:WP_012218152.1
COORDINATES: similar to AA sequence:RefSeq:WP_002857643.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606173.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612078.1
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: similar to AA sequence:RefSeq:WP_076611865.1
COORDINATES: similar to AA sequence:RefSeq:WP_018517385.1
COORDINATES: similar to AA sequence:RefSeq:WP_013275212.1
GO:0042925 - benzoate transmembrane transporter activity [Evidence IEA]
GO:0042919 - benzoate transport [Evidence IEA]
benzoate/H(+) symporter BenE family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_018647594.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012331239.1
COORDINATES: similar to AA sequence:RefSeq:WP_007422483.1
COORDINATES: similar to AA sequence:RefSeq:WP_009338705.1
COORDINATES: similar to AA sequence:RefSeq:WP_007596264.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014376.2
COORDINATES: protein motif:HMM:NF024406.2
IS66 family transposase zinc-finger binding domain-containing protein
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_008336078.1
COORDINATES: similar to AA sequence:RefSeq:WP_008208328.1
transcriptional regulator/antitoxin MazE
COORDINATES: similar to AA sequence:RefSeq:WP_019296978.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011749697.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011749696.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749695.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008281741.1
COORDINATES: similar to AA sequence:RefSeq:WP_007813111.1
COORDINATES: similar to AA sequence:RefSeq:WP_013654839.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
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.; 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.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_013654837.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001307.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749688.1
COORDINATES: similar to AA sequence:RefSeq:WP_015316928.1
COORDINATES: protein motif:HMM:NF023204.2
COORDINATES: similar to AA sequence:RefSeq:WP_003517890.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001304.1
COORDINATES: similar to AA sequence:RefSeq:WP_007164525.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612067.1
COORDINATES: protein motif:HMM:TIGR01783.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0015343 - siderophore-iron transmembrane transporter activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_015280640.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954973.1
COORDINATES: similar to AA sequence:RefSeq:WP_006402469.1
COORDINATES: similar to AA sequence:RefSeq:WP_012431170.1
GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF017045.2
COORDINATES: protein motif:HMM:NF013899.2
COORDINATES: similar to AA sequence:RefSeq:WP_006402478.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016530 - metallochaperone activity [Evidence IEA]
GO:0019627 - urea metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015823729.1
GO:0016151 - nickel cation binding [Evidence IEA]; GO:0009039 - urease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012431165.1
GO:0035550 - urease complex [Evidence IEA]
GO:0043419 - urea catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014973499.1
COORDINATES: similar to AA sequence:RefSeq:WP_013592471.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006402483.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_017958101.1
COORDINATES: similar to AA sequence:RefSeq:WP_006386256.1
COORDINATES: similar to AA sequence:RefSeq:WP_008966099.1
COORDINATES: similar to AA sequence:RefSeq:WP_015668030.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015341784.1
COORDINATES: protein motif:HMM:NF018841.2