Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
Genome sequence of Paracoccus contaminans isolated from a water microcosm
Submitted (27-MAR-2017) Division of Enteropathogenic Bacteria and Legionella, Robert Koch-Institut, Burgstr. 37, Wernigerode 38855, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP020613.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP3 v. Nov-2015\nGenome Coverage :: 278\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/22/2023 03:06:48\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) :: 2,933\nCDSs (total) :: 2,876\nGenes (coding) :: 2,804\nCDSs (with protein) :: 2,804\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 72\nCDSs (without protein) :: 72\nPseudo Genes (ambiguous residues) :: 0 of 72\nPseudo Genes (frameshifted) :: 38 of 72\nPseudo Genes (incomplete) :: 33 of 72\nPseudo Genes (internal stop) :: 6 of 72\nPseudo Genes (multiple problems) :: 4 of 72\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_020811856.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011808695.1
COORDINATES: protein motif:HMM:NF012678.2
COORDINATES: similar to AA sequence:RefSeq:WP_002710888.1
COORDINATES: similar to AA sequence:RefSeq:WP_002710887.1
COORDINATES: similar to AA sequence:RefSeq:WP_002710886.1
COORDINATES: similar to AA sequence:RefSeq:WP_011809637.1
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_006019442.1
GO:0016773 - phosphotransferase activity, alcohol group as acceptor [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002710883.1
COORDINATES: protein motif:HMM:NF012742.2
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007602971.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725365.1
GO:0008927 - mannonate dehydratase activity [Evidence IEA]
GO:0006064 - glucuronate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006725364.1
COORDINATES: similar to AA sequence:RefSeq:WP_014331408.1
COORDINATES: similar to AA sequence:RefSeq:WP_010972884.1
COORDINATES: similar to AA sequence:RefSeq:WP_016735410.1
sialic acid TRAP transporter substrate-binding protein SiaP
COORDINATES: similar to AA sequence:RefSeq:WP_006725360.1
COORDINATES: similar to AA sequence:RefSeq:WP_007826895.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011909337.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008886912.1
GO:0009331 - glycerol-3-phosphate dehydrogenase complex [Evidence IEA]
GO:0004368 - glycerol-3-phosphate dehydrogenase (quinone) activity [Evidence IEA]
GO:0006072 - glycerol-3-phosphate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015920434.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807258.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018001366.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573169.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001364.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649612.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001362.1
GO:0004370 - glycerol kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF016999.2
COORDINATES: similar to AA sequence:RefSeq:WP_014293576.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_007804085.1
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012072093.1
tripartite tricarboxylate transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018067364.1
COORDINATES: similar to AA sequence:RefSeq:WP_018067365.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011331263.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804006.1
COORDINATES: similar to AA sequence:RefSeq:WP_002724985.1
COORDINATES: protein motif:HMM:NF012669.2
COORDINATES: similar to AA sequence:RefSeq:WP_009565119.1
autoinducer 2 ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007005375.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003517007.1
COORDINATES: similar to AA sequence:RefSeq:WP_011389954.1
COORDINATES: similar to AA sequence:RefSeq:WP_007090237.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982587.1
GO:0004747 - ribokinase activity [Evidence IEA]
GO:0019303 - D-ribose catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011579661.1
GO:0004139 - deoxyribose-phosphate aldolase activity [Evidence IEA]
GO:0009264 - deoxyribonucleotide catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009565110.1
COORDINATES: similar to AA sequence:RefSeq:WP_006560453.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_006560454.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011747498.1
COORDINATES: similar to AA sequence:RefSeq:WP_017991245.1
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_018245111.1
GO:0016159 - muconolactone delta-isomerase activity [Evidence IEA]
GO:0042952 - beta-ketoadipate pathway [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003521926.1
GO:0018576 - catechol 1,2-dioxygenase activity [Evidence IEA]
GO:0019615 - catechol catabolic process, ortho-cleavage [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018245109.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011695017.1
GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004626840.1
benzoate 1,2-dioxygenase electron transfer component BenC
COORDINATES: similar to AA sequence:RefSeq:WP_003550361.1
COORDINATES: similar to AA sequence:RefSeq:WP_003550362.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007794727.1
GO:0047570 - 3-oxoadipate enol-lactonase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018301942.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: similar to AA sequence:RefSeq:WP_010967605.1
COORDINATES: similar to AA sequence:RefSeq:WP_011660855.1
GO:0003985 - acetyl-CoA C-acetyltransferase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_006133765.1
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_010395468.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024242.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012235.2
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011748002.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008952607.1
quinohemoprotein amine dehydrogenase subunit gamma
COORDINATES: similar to AA sequence:RefSeq:WP_009542142.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0043687 - post-translational protein modification [Evidence IEA]
quinohemoprotein amine dehydrogenase maturation protein
COORDINATES: protein motif:HMM:TIGR03908.1
GO:0042597 - periplasmic space [Evidence IEA]
GO:0030058 - amine dehydrogenase activity [Evidence IEA]
GO:0009310 - amine catabolic process [Evidence IEA]
quinohemoprotein amine dehydrogenase subunit alpha
COORDINATES: protein motif:HMM:NF020663.2
COORDINATES: protein motif:HMM:NF013434.2
COORDINATES: similar to AA sequence:RefSeq:WP_019463205.1
COORDINATES: protein motif:HMM:NF016291.2
COORDINATES: similar to AA sequence:RefSeq:WP_019995913.1
COORDINATES: similar to AA sequence:RefSeq:WP_019903732.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018260181.1
COORDINATES: similar to AA sequence:RefSeq:WP_009490714.1
COORDINATES: protein motif:HMM:NF027340.2