Paracoccus sanguinis strain OM2164 plasmid pPspOM44, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
Genome-Wide Identification of 5-Methylcytosine Sites in Bacterial Genomes By High-Throughput Sequencing of MspJI Restriction Fragments
Submitted (13-APR-2020) Genome Biology, NEB, 240 County Rd, Ipswich, MA 01938, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP051544.1.\nBacteria and source DNA available from NEB microbial collection\n1783.\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 Date :: MAR-2017\nAssembly Method :: HGAP v. 2.3.0\nAssembly Name :: PspOM_new_HGAP3_2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 164.22x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 10:59:31\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) :: 3,248\nCDSs (total) :: 3,190\nGenes (coding) :: 3,116\nCDSs (with protein) :: 3,116\nGenes (RNA) :: 58\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 4\nPseudo Genes (total) :: 74\nCDSs (without protein) :: 74\nPseudo Genes (ambiguous residues) :: 0 of 74\nPseudo Genes (frameshifted) :: 21 of 74\nPseudo Genes (incomplete) :: 60 of 74\nPseudo Genes (internal stop) :: 2 of 74\nPseudo Genes (multiple problems) :: 9 of 74\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
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]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
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]
Derived by automated computational analysis using gene prediction method: Protein Homology.
dihydrolipoyllysine-residue acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_009828024.1
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
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749199.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
GO:0019516 - lactate oxidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820493.1
COORDINATES: similar to AA sequence:RefSeq:WP_009811393.1
GO:0005215 - transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009602860.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
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_003601302.1
COORDINATES: similar to AA sequence:RefSeq:WP_012643726.1
GO:0003904 - deoxyribodipyrimidine photo-lyase activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005864146.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011908442.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011655531.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331387.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:TIGR01552.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_017930026.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008554852.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
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; 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_008033221.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF013258.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611724.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013500677.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011750834.1
GO:0042834 - peptidoglycan binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016849151.1
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: protein motif:HMM:NF018684.2
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_008876096.1
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017318631.1
GO:0030554 - adenyl nucleotide binding [Evidence IEA]; GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611908.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503034.1
COORDINATES: similar to AA sequence:RefSeq:WP_020050886.1
COORDINATES: similar to AA sequence:RefSeq:WP_016920429.1
COORDINATES: similar to AA sequence:RefSeq:WP_018324378.1
class I SAM-dependent DNA methyltransferase
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_008327498.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
FadR/GntR family transcriptional regulator