Paracoccus yeei strain TT13 plasmid pTT13-4, 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\nCP024426.1.\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_018001704.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011751253.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504821.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF014068.2
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]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018000887.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: similar to AA sequence:RefSeq:WP_018000888.1
COORDINATES: similar to AA sequence:RefSeq:WP_018000889.1
COORDINATES: similar to AA sequence:RefSeq:WP_018000890.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0015220 - choline transmembrane transporter activity [Evidence IEA]
GO:0015871 - choline transport [Evidence IEA]
choline ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012264.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF014667.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012348667.1
COORDINATES: protein motif:HMM:NF024758.2
COORDINATES: similar to AA sequence:RefSeq:WP_017140340.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001460.1
GO:0045027 - DNA end binding [Evidence IEA]
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003499405.1
COORDINATES: similar to AA sequence:RefSeq:WP_020179442.1
COORDINATES: similar to AA sequence:RefSeq:WP_015102202.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
TIGR03885 family FMN-dependent LLM class oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007879749.1
COORDINATES: similar to AA sequence:RefSeq:WP_007879747.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006726748.1
COORDINATES: protein motif:HMM:NF014234.2
COORDINATES: similar to AA sequence:RefSeq:WP_019238022.1
GO:0015926 - glucosidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017928547.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001039.1
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: similar to AA sequence:RefSeq:WP_009762824.1
COORDINATES: similar to AA sequence:RefSeq:WP_019364082.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750582.1
COORDINATES: similar to AA sequence:RefSeq:WP_011568540.1
GO:0016780 - phosphotransferase activity, for other substituted phosphate groups [Evidence IEA]
GO:0008654 - phospholipid biosynthetic process [Evidence IEA]
CDP-alcohol phosphatidyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011750584.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750585.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011750586.1
COORDINATES: similar to AA sequence:RefSeq:WP_011842546.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008232641.1
COORDINATES: similar to AA sequence:RefSeq:WP_019183534.1
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009493866.1
COORDINATES: protein motif:HMM:NF033563.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611133.1
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_002721525.1
COORDINATES: similar to AA sequence:RefSeq:WP_002721523.1
GO:0030253 - protein secretion by the type I secretion system [Evidence IEA]
HlyD family type I secretion periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011338731.1
COORDINATES: similar to AA sequence:RefSeq:WP_018098862.1
COORDINATES: similar to AA sequence:RefSeq:WP_011841881.1
COORDINATES: similar to AA sequence:RefSeq:WP_002721514.1
COORDINATES: similar to AA sequence:RefSeq:WP_011338725.1
COORDINATES: similar to AA sequence:RefSeq:WP_004673711.1
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017996258.1
GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0033286 - ATPase-coupled ectoine transmembrane transporter activity [Evidence IEA]; GO:0033288 - ATPase-coupled hydroxyectoine transmembrane transporter activity [Evidence IEA]
GO:0051470 - ectoine transport [Evidence IEA]; GO:0033308 - hydroxyectoine transport [Evidence IEA]
ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
COORDINATES: similar to AA sequence:RefSeq:WP_017277303.1
GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0033286 - ATPase-coupled ectoine transmembrane transporter activity [Evidence IEA]; GO:0033288 - ATPase-coupled hydroxyectoine transmembrane transporter activity [Evidence IEA]; GO:0033294 - ectoine binding [Evidence IEA]; GO:0033295 - hydroxyectoine binding [Evidence IEA]
ectoine/hydroxyectoine ABC transporter substrate-binding protein EhuB
COORDINATES: similar to AA sequence:RefSeq:WP_011746629.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0033286 - ATPase-coupled ectoine transmembrane transporter activity [Evidence IEA]; GO:0033288 - ATPase-coupled hydroxyectoine transmembrane transporter activity [Evidence IEA]
ectoine/hydroxyectoine ABC transporter permease subunit EhuC
COORDINATES: similar to AA sequence:RefSeq:WP_015319077.1
ectoine/hydroxyectoine ABC transporter permease subunit EhuD
COORDINATES: similar to AA sequence:RefSeq:WP_011746631.1
GO:0042400 - ectoine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016735735.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
hydroxyectoine utilization dehydratase EutB
COORDINATES: similar to AA sequence:RefSeq:WP_011746633.1
COORDINATES: similar to AA sequence:RefSeq:WP_010975302.1
DoeA (degradation of ectoine A) is also called EutD (ectoine utilization D); Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010394635.1
N(2)-acetyl-L-2,4-diaminobutanoate deacetylase DoeB
COORDINATES: similar to AA sequence:RefSeq:WP_007800917.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_011746637.1
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010394641.1
COORDINATES: similar to AA sequence:RefSeq:WP_011751135.1
COORDINATES: similar to AA sequence:RefSeq:WP_011751134.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505445.1
GO:0004514 - nicotinate-nucleotide diphosphorylase (carboxylating) activity [Evidence IEA]
GO:0019363 - pyridine nucleotide biosynthetic process [Evidence IEA]
carboxylating nicotinate-nucleotide diphosphorylase
COORDINATES: similar to AA sequence:RefSeq:WP_009505446.1
GO:0008734 - L-aspartate oxidase activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009505447.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0008987 - quinolinate synthetase A activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015083.2
COORDINATES: similar to AA sequence:RefSeq:WP_002725117.1
GSU2403 family nucleotidyltransferase fold protein
COORDINATES: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: protein motif:HMM:NF024860.2
COORDINATES: similar to AA sequence:RefSeq:WP_013384618.1
COORDINATES: similar to AA sequence:RefSeq:WP_013384619.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750836.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396570.1
COORDINATES: similar to AA sequence:RefSeq:WP_008291243.1
COORDINATES: similar to AA sequence:RefSeq:WP_036750437.1
GO:0052876 - methylamine dehydrogenase (amicyanin) activity [Evidence IEA]
methylamine dehydrogenase (amicyanin) large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_036750432.1
MauE/DoxX family redox-associated membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_011750952.1
methylamine dehydrogenase accessory protein MauD
COORDINATES: similar to AA sequence:RefSeq:WP_010396581.1
methylamine dehydrogenase (amicyanin) small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011750954.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396585.1
COORDINATES: similar to AA sequence:RefSeq:WP_005617919.1
COORDINATES: similar to AA sequence:RefSeq:WP_017486765.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396588.1
quinol dehydrogenase ferredoxin subunit NapH
COORDINATES: similar to AA sequence:RefSeq:WP_014249913.1
COORDINATES: similar to AA sequence:RefSeq:WP_009208343.1
GO:0004452 - isopentenyl-diphosphate delta-isomerase activity [Evidence IEA]
GO:0008299 - isoprenoid biosynthetic process [Evidence IEA]
type 2 isopentenyl-diphosphate Delta-isomerase
COORDINATES: protein motif:HMM:NF012568.2
COORDINATES: similar to AA sequence:RefSeq:WP_013027996.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0008610 - lipid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011914880.1
phytoene/squalene synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020305759.1
COORDINATES: similar to AA sequence:RefSeq:WP_020652234.1
GO:0045436 - lycopene beta cyclase activity [Evidence IEA]
GO:0016117 - carotenoid biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01426.1
COORDINATES: similar to AA sequence:RefSeq:WP_003592106.1
COORDINATES: similar to AA sequence:RefSeq:WP_009502360.1
COORDINATES: similar to AA sequence:RefSeq:WP_017140496.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001701.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750610.1
COORDINATES: similar to AA sequence:RefSeq:WP_008225504.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_010392848.1
COORDINATES: similar to AA sequence:RefSeq:WP_018329143.1
COORDINATES: similar to AA sequence:RefSeq:WP_004291839.1
COORDINATES: similar to AA sequence:RefSeq:WP_018688503.1
COORDINATES: similar to AA sequence:RefSeq:WP_009466447.1
carboxyl transferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018301902.1
acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_012061469.1
COORDINATES: similar to AA sequence:RefSeq:WP_011840852.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018455818.1
COORDINATES: similar to AA sequence:RefSeq:WP_003580141.1
COORDINATES: similar to AA sequence:RefSeq:WP_017276592.1
COORDINATES: similar to AA sequence:RefSeq:WP_004676513.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003593701.1
COORDINATES: similar to AA sequence:RefSeq:WP_012558113.1
COORDINATES: similar to AA sequence:RefSeq:WP_012558112.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005859008.1
COORDINATES: similar to AA sequence:RefSeq:WP_002719828.1
COORDINATES: protein motif:HMM:TIGR00765.1
YihY/virulence factor BrkB family protein
COORDINATES: protein motif:HMM:NF024180.2
COORDINATES: similar to AA sequence:RefSeq:WP_011569202.1
COORDINATES: similar to AA sequence:RefSeq:WP_018183764.1
COORDINATES: similar to AA sequence:RefSeq:WP_011569204.1
COORDINATES: similar to AA sequence:RefSeq:WP_007255952.1
COORDINATES: similar to AA sequence:RefSeq:WP_014761073.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017273897.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0033296 - rhamnose binding [Evidence IEA]; GO:0015153 - rhamnose transmembrane transporter activity [Evidence IEA]
GO:0015762 - rhamnose transmembrane transport [Evidence IEA]
rhamnose ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011455714.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007797217.1
bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013533596.1
GO:0008740 - L-rhamnose isomerase activity [Evidence IEA]
GO:0019301 - rhamnose catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011910499.1
GO:0030246 - carbohydrate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007067517.1
COORDINATES: similar to AA sequence:RefSeq:WP_018486335.1
COORDINATES: similar to AA sequence:RefSeq:WP_012756004.1
COORDINATES: similar to AA sequence:RefSeq:WP_020397570.1
COORDINATES: similar to AA sequence:RefSeq:WP_008877195.1
COORDINATES: similar to AA sequence:RefSeq:WP_018486334.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: similar to AA sequence:RefSeq:WP_009809145.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2