Paracoccus pantotrophus strain DSM 2944 plasmid pPAN1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
Complete Genome Sequence and Annotation of the Paracoccus pantotrophus type strain DSM 2944
Submitted (23-JAN-2019) Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, Aachen 52074, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP044424.1.\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 :: HGAP v. V.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 162.0x\nSequencing Technology :: PacBio RS\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 02:25:28\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) :: 4,373\nCDSs (total) :: 4,310\nGenes (coding) :: 4,166\nCDSs (with protein) :: 4,166\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) :: 144\nCDSs (without protein) :: 144\nPseudo Genes (ambiguous residues) :: 0 of 144\nPseudo Genes (frameshifted) :: 68 of 144\nPseudo Genes (incomplete) :: 101 of 144\nPseudo Genes (internal stop) :: 19 of 144\nPseudo Genes (multiple problems) :: 41 of 144\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
denitrifying, sulfide-oxidizing effluent-treatment plant
COORDINATES: similar to AA sequence:RefSeq:WP_010394424.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
PQQ-dependent methanol/ethanol family dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_010394422.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_010394418.1
COORDINATES: similar to AA sequence:RefSeq:WP_010394417.1
FIST N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014332540.1
COORDINATES: similar to AA sequence:RefSeq:WP_015695988.1
COORDINATES: protein motif:HMM:NF024573.2
COORDINATES: protein motif:HMM:NF015210.2
COORDINATES: protein motif:HMM:NF012492.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011509689.1
COORDINATES: similar to AA sequence:RefSeq:WP_010137645.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF013298.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
saccharopine dehydrogenase NADP-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611562.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010399234.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type I restriction endonuclease subunit R
COORDINATES: similar to AA sequence:RefSeq:WP_017960149.1
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: 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_008554852.1
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_009827215.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001791.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001792.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819726.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065894.1
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_011331447.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503864.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335981.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815557.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_076611844.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611977.1
COORDINATES: similar to AA sequence:RefSeq:WP_003528599.1
COORDINATES: similar to AA sequence:RefSeq:WP_010399496.1
COORDINATES: similar to AA sequence:RefSeq:WP_004721507.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_016598704.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010399501.1
GO:0004751 - ribose-5-phosphate isomerase activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016972999.1
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010399504.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004820486.1
GO:0005515 - protein binding [Evidence IEA]; GO:0004856 - xylulokinase activity [Evidence IEA]
GO:0042732 - D-xylose metabolic process [Evidence IEA]; GO:0005997 - xylulose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010399509.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_002208808.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002230767.1
COORDINATES: similar to AA sequence:RefSeq:WP_004820478.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_014538264.1
COORDINATES: protein motif:HMM:NF016430.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007815851.1
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: similar to AA sequence:RefSeq:WP_003551146.1
COORDINATES: protein motif:HMM:NF012532.2
GO:0008964 - phosphoenolpyruvate carboxylase activity [Evidence IEA]
GO:0015977 - carbon fixation [Evidence IEA]; GO:0006099 - tricarboxylic acid cycle [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006481819.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010037407.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008758966.1
COORDINATES: protein motif:HMM:NF014684.2
COORDINATES: similar to AA sequence:RefSeq:WP_018185040.1
COORDINATES: similar to AA sequence:RefSeq:WP_018114294.1
COORDINATES: protein motif:HMM:NF024799.2
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018700836.1
COORDINATES: similar to AA sequence:RefSeq:WP_008944546.1
COORDINATES: similar to AA sequence:RefSeq:WP_018700835.1
COORDINATES: similar to AA sequence:RefSeq:WP_018238388.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018700833.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: similar to AA sequence:RefSeq:WP_008560879.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: similar to AA sequence:RefSeq:WP_006953897.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611309.1
COORDINATES: similar to AA sequence:RefSeq:WP_017429933.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017827075.1
COORDINATES: similar to AA sequence:RefSeq:WP_012072567.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
DUF262 domain-containing HNH endonuclease family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009653620.1
class I SAM-dependent DNA methyltransferase
COORDINATES: protein motif:HMM:NF019324.2
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: protein motif:HMM:NF013970.2
COORDINATES: similar to AA sequence:RefSeq:WP_010400642.1
COORDINATES: similar to AA sequence:RefSeq:WP_008261032.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017710114.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_005980118.1
COORDINATES: protein motif:HMM:TIGR03865.1
COORDINATES: similar to AA sequence:RefSeq:WP_011047252.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010394429.1
quinoprotein dehydrogenase-associated SoxYZ-like carrier
COORDINATES: similar to AA sequence:RefSeq:WP_010394426.1
quinoprotein relay system zinc metallohydrolase 1