Paracoccus aminophilus JCM 7686 plasmid pAMI1, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Paracoccus.
Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids
Submitted (02-AUG-2013) Department of Bacterial Genetics, University of Warsaw, Faculty of Biology, Institute of Microbiology, Miecznikowa 1, Warsaw 02-096, Poland
REFSEQ INFORMATION: The reference sequence is identical to\nCP006651.1.\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 :: Newbler de novo assembler software\n (Roche) v. 2.6\nReference-guided Assembly :: partially based on Paracoccus\n denitrificans PD1222\nGenome Coverage :: 30-50X\nSequencing Technology :: 454\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/14/2022 12:16:24\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,704\nCDSs (total) :: 4,629\nGenes (coding) :: 4,565\nCDSs (with protein) :: 4,565\nGenes (RNA) :: 75\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 60\nncRNAs :: 3\nPseudo Genes (total) :: 64\nCDSs (without protein) :: 64\nPseudo Genes (ambiguous residues) :: 0 of 64\nPseudo Genes (frameshifted) :: 24 of 64\nPseudo Genes (incomplete) :: 49 of 64\nPseudo Genes (internal stop) :: 18 of 64\nPseudo Genes (multiple problems) :: 21 of 64\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_018001703.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887893.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_003288384.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003550915.1
COORDINATES: similar to AA sequence:RefSeq:WP_017991611.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003550919.1
COORDINATES: similar to AA sequence:RefSeq:WP_012760392.1
COORDINATES: similar to AA sequence:RefSeq:WP_017991609.1
COORDINATES: similar to AA sequence:RefSeq:WP_019856632.1
COORDINATES: similar to AA sequence:RefSeq:WP_017997317.1
GO:0004157 - dihydropyrimidinase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003550924.1
COORDINATES: similar to AA sequence:RefSeq:WP_020628787.1
COORDINATES: similar to AA sequence:RefSeq:WP_012760386.1
COORDINATES: similar to AA sequence:RefSeq:WP_011648914.1
thiamine pyrophosphate-requiring protein
COORDINATES: similar to AA sequence:RefSeq:WP_003550929.1
COORDINATES: similar to AA sequence:RefSeq:WP_012760383.1
COORDINATES: similar to AA sequence:RefSeq:WP_017957495.1
COORDINATES: similar to AA sequence:RefSeq:WP_003815496.1
COORDINATES: protein motif:HMM:NF012967.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_018387990.1
GO:0008863 - formate dehydrogenase (NAD+) activity [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001202.1
COORDINATES: protein motif:HMM:NF012693.2
bifunctional serine/threonine-protein kinase/phosphatase
COORDINATES: nucleotide motif:Rfam:14.4:RF00177
Derived by automated computational analysis using gene prediction method: cmsearch.
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: nucleotide motif:Rfam:14.4:RF02541
COORDINATES: nucleotide motif:Rfam:14.4:RF00001
COORDINATES: similar to AA sequence:RefSeq:WP_013530269.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF012544.2
COORDINATES: protein motif:HMM:NF012993.2
nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase
COORDINATES: protein motif:HMM:NF012422.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018185348.1
COORDINATES: similar to AA sequence:RefSeq:WP_007007383.1
COORDINATES: similar to AA sequence:RefSeq:WP_007007384.1
COORDINATES: similar to AA sequence:RefSeq:WP_018185345.1
NAD(P)H-dependent oxidoreductase subunit E
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_011581942.1
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: similar to AA sequence:RefSeq:WP_012975530.1
COORDINATES: similar to AA sequence:RefSeq:WP_012975529.1
COORDINATES: protein motif:HMM:NF012706.2
COORDINATES: protein motif:HMM:NF012766.2
COORDINATES: similar to AA sequence:RefSeq:WP_013530546.1
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006204043.1
COORDINATES: similar to AA sequence:RefSeq:WP_019646733.1
spermidine/putrescine ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_008878338.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612398.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003099537.1
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_018236789.1
COORDINATES: similar to AA sequence:RefSeq:WP_018236791.1
COORDINATES: similar to AA sequence:RefSeq:WP_013761919.1
bifunctional helix-turn-helix transcriptional regulator/GNAT family N-acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_010392889.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006090185.1
COORDINATES: similar to AA sequence:RefSeq:WP_002964979.1
COORDINATES: similar to AA sequence:RefSeq:WP_009763920.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019401524.1
COORDINATES: similar to AA sequence:RefSeq:WP_011004515.1
GO:0047443 - 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity [Evidence IEA]
4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase
COORDINATES: protein motif:HMM:NF005460.0
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: similar to AA sequence:RefSeq:WP_011909069.1
COORDINATES: similar to AA sequence:RefSeq:WP_013529745.1
pyridoxal phosphate-dependent aminotransferase
COORDINATES: protein motif:HMM:NF013584.2
COORDINATES: similar to AA sequence:RefSeq:WP_011399517.1
amino acid ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012738.2
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_008546717.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_020808834.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF016648.2
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:NF012382.2
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019956757.1
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
COORDINATES: similar to AA sequence:RefSeq:WP_006225750.1
GO:0018826 - methionine gamma-lyase activity [Evidence IEA]
GO:0009093 - cysteine catabolic process [Evidence IEA]; GO:0009087 - methionine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011490819.1
COORDINATES: protein motif:HMM:NF013757.2
COORDINATES: similar to AA sequence:RefSeq:WP_017927749.1
COORDINATES: similar to AA sequence:RefSeq:WP_011909791.1
COORDINATES: similar to AA sequence:RefSeq:WP_011751292.1
COORDINATES: protein motif:HMM:NF012935.2
COORDINATES: protein motif:HMM:NF005559.1
COORDINATES: protein motif:HMM:NF013720.2
COORDINATES: protein motif:HMM:NF015729.2
COORDINATES: protein motif:HMM:NF016088.2
COORDINATES: protein motif:HMM:NF008425.0
GO:0050131 - N-methyl-L-amino-acid oxidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014071.2
hydantoinase/oxoprolinase family protein
COORDINATES: protein motif:HMM:NF014585.2
hydantoinase B/oxoprolinase family protein
COORDINATES: protein motif:HMM:NF012790.2
COORDINATES: similar to AA sequence:RefSeq:WP_019460346.1
COORDINATES: similar to AA sequence:RefSeq:WP_010141373.1
methylenetetrahydrofolate reductase (NAD(P)H)
COORDINATES: similar to AA sequence:RefSeq:WP_013066162.1
COORDINATES: similar to AA sequence:RefSeq:WP_010912545.1
COORDINATES: protein motif:HMM:NF013777.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019844991.1
COORDINATES: similar to AA sequence:RefSeq:WP_018307865.1
NADH:flavin oxidoreductase/NADH oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015094786.1