Paracoccus yeei strain TT13 plasmid pTT13-5, 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\nCP024427.1.\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_014538280.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009804006.1
COORDINATES: protein motif:HMM:NF040974.1
COORDINATES: similar to AA sequence:RefSeq:WP_018234692.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014527419.1
COORDINATES: similar to AA sequence:RefSeq:WP_009849604.1
GO:0008725 - DNA-3-methyladenine glycosylase activity [Evidence IEA]
GO:0006284 - base-excision repair [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018634435.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018634434.1
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018634433.1
GO:0018850 - chloromuconate cycloisomerase activity [Evidence IEA]; GO:0018849 - muconate cycloisomerase activity [Evidence IEA]
muconate/chloromuconate family cycloisomerase
COORDINATES: similar to AA sequence:RefSeq:WP_008281990.1
GO:0018576 - catechol 1,2-dioxygenase activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
GO:0009712 - catechol-containing compound metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013757.2
IclR family transcriptional regulator C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020039323.1
4-hydroxyphenylacetate 3-hydroxylase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018634430.1
COORDINATES: similar to AA sequence:RefSeq:WP_020039321.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012072082.1
COORDINATES: similar to AA sequence:RefSeq:WP_020040785.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011336755.1
COORDINATES: similar to AA sequence:RefSeq:WP_011388787.1
COORDINATES: similar to AA sequence:RefSeq:WP_014741972.1
GO:0008851 - ethanolamine ammonia-lyase activity [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014857614.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019516656.1
Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C-terminal domain
COORDINATES: similar to AA sequence:RefSeq:WP_007687232.1
polysaccharide pyruvyl transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019370261.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489846.1
COORDINATES: similar to AA sequence:RefSeq:WP_008970810.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039558.1
COORDINATES: similar to AA sequence:RefSeq:WP_018261711.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012318299.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019370255.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818400.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012522641.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007684636.1
COORDINATES: similar to AA sequence:RefSeq:WP_019461922.1
COORDINATES: similar to AA sequence:RefSeq:WP_012605344.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039567.1
COORDINATES: similar to AA sequence:RefSeq:WP_008600882.1
COORDINATES: similar to AA sequence:RefSeq:WP_007687230.1
COORDINATES: similar to AA sequence:RefSeq:WP_015917198.1
COORDINATES: similar to AA sequence:RefSeq:WP_019997361.1
COORDINATES: similar to AA sequence:RefSeq:WP_019997360.1
COORDINATES: similar to AA sequence:RefSeq:WP_019997359.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006310925.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019997357.1
COORDINATES: similar to AA sequence:RefSeq:WP_003581982.1
COORDINATES: similar to AA sequence:RefSeq:WP_003581983.1
isocitrate lyase/PEP mutase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019997354.1
COORDINATES: similar to AA sequence:RefSeq:WP_017998877.1
COORDINATES: similar to AA sequence:RefSeq:WP_018302369.1
COORDINATES: similar to AA sequence:RefSeq:WP_010324809.1
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749819.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019751085.1
COORDINATES: similar to AA sequence:RefSeq:WP_014860019.1
GO:0003885 - D-arabinono-1,4-lactone oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749822.1
COORDINATES: similar to AA sequence:RefSeq:WP_011047828.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0016992 - lipoate synthase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0009107 - lipoate biosynthetic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_008146637.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
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_002725081.1
COORDINATES: similar to AA sequence:RefSeq:WP_012568689.1
COORDINATES: similar to AA sequence:RefSeq:WP_012605225.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018066201.1
COORDINATES: similar to AA sequence:RefSeq:WP_013418554.1
COORDINATES: similar to AA sequence:RefSeq:WP_007596484.1
COORDINATES: similar to AA sequence:RefSeq:WP_007606540.1
COORDINATES: similar to AA sequence:RefSeq:WP_018260916.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018260917.1
COORDINATES: similar to AA sequence:RefSeq:WP_004634622.1
COORDINATES: similar to AA sequence:RefSeq:WP_011926433.1
FAD-dependent tricarballylate dehydrogenase TcuA
COORDINATES: similar to AA sequence:RefSeq:WP_015435545.1
tricarballylate utilization 4Fe-4S protein TcuB
COORDINATES: similar to AA sequence:RefSeq:WP_008945084.1
GO:0046421 - methylisocitrate lyase activity [Evidence IEA]
GO:0019629 - propionate catabolic process, 2-methylcitrate cycle [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011747672.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
short-chain fatty acyl-CoA regulator family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009488937.1
COORDINATES: similar to AA sequence:RefSeq:WP_019397296.1
GO:0003871 - 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0008652 - amino acid biosynthetic process [Evidence IEA]; GO:0009086 - methionine biosynthetic process [Evidence IEA]
5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase
COORDINATES: protein motif:HMM:TIGR03173.1
nucleobase:cation symporter-2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008723656.1
COORDINATES: protein motif:HMM:NF012354.2
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_011569765.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018857982.1
COORDINATES: similar to AA sequence:RefSeq:WP_018857983.1
COORDINATES: similar to AA sequence:RefSeq:WP_008833993.1
COORDINATES: protein motif:HMM:NF016999.2
COORDINATES: similar to AA sequence:RefSeq:WP_009467409.1
COORDINATES: similar to AA sequence:RefSeq:WP_011842470.1
COORDINATES: similar to AA sequence:RefSeq:WP_009572277.1
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015923158.1
COORDINATES: similar to AA sequence:RefSeq:WP_009563570.1
COORDINATES: similar to AA sequence:RefSeq:WP_019013191.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011842475.1
COORDINATES: similar to AA sequence:RefSeq:WP_015923162.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015837 - amine transport [Evidence IEA]
The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc.; The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011425180.1
amino acid ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003458258.1
GO:0004121 - cystathionine beta-lyase activity [Evidence IEA]
GO:0009086 - methionine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009563562.1
COORDINATES: similar to AA sequence:RefSeq:WP_008891352.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887214.1
bifunctional protein tyrosine phosphatase family protein/NAD(P)/FAD-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013165815.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019461545.1
COORDINATES: protein motif:HMM:NF012706.2
COORDINATES: similar to AA sequence:RefSeq:WP_009563561.1
COORDINATES: protein motif:HMM:NF017760.2
COORDINATES: protein motif:HMM:NF015905.2
COORDINATES: similar to AA sequence:RefSeq:WP_008944296.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007003253.1
hydantoinase/oxoprolinase family protein
COORDINATES: protein motif:HMM:NF036686.2
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005861769.1
COORDINATES: similar to AA sequence:RefSeq:WP_012321501.1
COORDINATES: similar to AA sequence:RefSeq:WP_014749140.1
COORDINATES: similar to AA sequence:RefSeq:WP_012417238.1
COORDINATES: similar to AA sequence:RefSeq:WP_017998420.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007812573.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0001558 - regulation of cell growth [Evidence IEA]
type II toxin-antitoxin system PrlF family antitoxin