Paracoccus aminophilus JCM 7686 plasmid pAMI6, 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\nCP006654.1.\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_002723340.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008558591.1
COORDINATES: similar to AA sequence:RefSeq:WP_009566083.1
ParB/RepB/Spo0J family partition protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013039409.1
COORDINATES: similar to AA sequence:RefSeq:WP_010660453.1
type II toxin-antitoxin system CcdA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007510246.1
GO:0004616 - phosphogluconate dehydrogenase (decarboxylating) activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
decarboxylating 6-phosphogluconate dehydrogenase
COORDINATES: protein motif:HMM:NF018299.2
COORDINATES: protein motif:HMM:NF017747.2
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008185828.1
GO:0008777 - acetylornithine deacetylase activity [Evidence IEA]
GO:0006592 - ornithine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012320170.1
COORDINATES: similar to AA sequence:RefSeq:WP_014199765.1
COORDINATES: similar to AA sequence:RefSeq:WP_020673214.1
4-hydroxyphenylacetate 3-hydroxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013802993.1
branched-chain amino acid ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013167424.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_016452302.1
COORDINATES: similar to AA sequence:RefSeq:WP_013167426.1
COORDINATES: similar to AA sequence:RefSeq:WP_013802990.1
COORDINATES: similar to AA sequence:RefSeq:WP_010455275.1
GO:0015444 - P-type magnesium transporter activity [Evidence IEA]
GO:0015693 - magnesium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005416969.1
COORDINATES: similar to AA sequence:RefSeq:WP_006022574.1
COORDINATES: similar to AA sequence:RefSeq:WP_015914715.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014210890.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637534.1
COORDINATES: similar to AA sequence:RefSeq:WP_020808242.1
COORDINATES: protein motif:HMM:NF024795.2
COORDINATES: similar to AA sequence:RefSeq:WP_013893279.1
COORDINATES: similar to AA sequence:RefSeq:WP_019955040.1
COORDINATES: similar to AA sequence:RefSeq:WP_018390411.1
COORDINATES: similar to AA sequence:RefSeq:WP_018115738.1
COORDINATES: protein motif:HMM:NF024376.2
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012738.2
COORDINATES: similar to AA sequence:RefSeq:WP_013421129.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030129.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138796.1
GO:0004781 - sulfate adenylyltransferase (ATP) activity [Evidence IEA]
GO:0019419 - sulfate reduction [Evidence IEA]
sulfate adenylyltransferase subunit CysD
COORDINATES: similar to AA sequence:RefSeq:WP_010335685.1
GO:0005525 - GTP binding [Evidence IEA]; GO:0003924 - GTPase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
sulfate adenylyltransferase subunit CysN
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: similar to AA sequence:RefSeq:WP_010398382.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004329 - formate-tetrahydrofolate ligase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010391897.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_002724926.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011339141.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007796556.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
iron chelate uptake ABC transporter family permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011443267.1
COORDINATES: similar to AA sequence:RefSeq:WP_013065855.1
siderophore ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014198098.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747053.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017999500.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011747055.1
GO:0050480 - imidazolonepropionase activity [Evidence IEA]
GO:0006548 - histidine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010393761.1
GO:0004397 - histidine ammonia-lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010659503.1
GO:0050129 - N-formylglutamate deformylase activity [Evidence IEA]
GO:0019557 - histidine catabolic process to glutamate and formate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019170277.1
COORDINATES: similar to AA sequence:RefSeq:WP_017999505.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007088761.1
GO:0016153 - urocanate hydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006473203.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017999508.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747063.1
COORDINATES: similar to AA sequence:RefSeq:WP_011389053.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_015340969.1
lysophospholipid acyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007753151.1
COORDINATES: similar to AA sequence:RefSeq:WP_007007180.1
COORDINATES: similar to AA sequence:RefSeq:WP_016556799.1
CDP-alcohol phosphatidyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012763934.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019170788.1
COORDINATES: similar to AA sequence:RefSeq:WP_010437772.1
COORDINATES: similar to AA sequence:RefSeq:WP_030003205.1
COORDINATES: similar to AA sequence:RefSeq:WP_013532893.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019294529.1
COORDINATES: similar to AA sequence:RefSeq:WP_010437795.1
COORDINATES: similar to AA sequence:RefSeq:WP_011566366.1
dimethylamine monooxygenase subunit DmmA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019856865.1
COORDINATES: similar to AA sequence:RefSeq:WP_007788185.1
COORDINATES: similar to AA sequence:RefSeq:WP_008280779.1
COORDINATES: similar to AA sequence:RefSeq:WP_007205659.1
GO:0004488 - methylenetetrahydrofolate dehydrogenase (NADP+) activity [Evidence IEA]
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD
COORDINATES: similar to AA sequence:RefSeq:WP_002721207.1
GO:0008864 - formyltetrahydrofolate deformylase activity [Evidence IEA]
GO:0009152 - purine ribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008758701.1
COORDINATES: similar to AA sequence:RefSeq:WP_011751288.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011751289.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: similar to AA sequence:RefSeq:WP_006700618.1
COORDINATES: similar to AA sequence:RefSeq:WP_010397752.1
COORDINATES: similar to AA sequence:RefSeq:WP_020393917.1
COORDINATES: similar to AA sequence:RefSeq:WP_011751293.1
COORDINATES: similar to AA sequence:RefSeq:WP_010397760.1
COORDINATES: similar to AA sequence:RefSeq:WP_006700607.1
COORDINATES: protein motif:HMM:NF023398.2
COORDINATES: similar to AA sequence:RefSeq:WP_012178795.1
GO:0047869 - dimethylpropiothetin dethiomethylase activity [Evidence IEA]
dimethylsulfonioproprionate lyase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011750902.1
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011647869.1
COORDINATES: similar to AA sequence:RefSeq:WP_010393922.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001669.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001668.1
COORDINATES: similar to AA sequence:RefSeq:WP_002720841.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887997.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001666.1
GO:0008115 - sarcosine oxidase activity [Evidence IEA]
sarcosine oxidase subunit alpha family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001665.1
COORDINATES: similar to AA sequence:RefSeq:WP_008559410.1
GO:0046653 - tetrahydrofolate metabolic process [Evidence IEA]
sarcosine oxidase subunit beta family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001663.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001658.1
COORDINATES: similar to AA sequence:RefSeq:WP_019294533.1
COORDINATES: similar to AA sequence:RefSeq:WP_009818594.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001654.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011047310.1
GO:0004356 - glutamate-ammonia ligase activity [Evidence IEA]
GO:0006542 - glutamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001652.1
FMN-binding glutamate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008759548.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503501.1
glutamine amidotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012067503.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001334.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001335.1
COORDINATES: similar to AA sequence:RefSeq:WP_013947137.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006204484.1
COORDINATES: similar to AA sequence:RefSeq:WP_005628110.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013069274.1
COORDINATES: similar to AA sequence:RefSeq:WP_007879635.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396927.1
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_010141169.1
short-chain fatty acyl-CoA regulator family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011747683.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_002517214.1
GO:0004451 - isocitrate lyase activity [Evidence IEA]
GO:0019752 - carboxylic acid metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012521.2
COORDINATES: similar to AA sequence:RefSeq:WP_016974482.1
COORDINATES: similar to AA sequence:RefSeq:WP_013214533.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747672.1
COORDINATES: similar to AA sequence:RefSeq:WP_013419465.1
COORDINATES: similar to AA sequence:RefSeq:WP_009176279.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747669.1
GO:0050440 - 2-methylcitrate synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013069045.1
GO:0046421 - methylisocitrate lyase activity [Evidence IEA]
GO:0019629 - propionate catabolic process, 2-methylcitrate cycle [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011750611.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750610.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747686.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747687.1
COORDINATES: similar to AA sequence:RefSeq:WP_013383469.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749388.1
COORDINATES: similar to AA sequence:RefSeq:WP_007599628.1
COORDINATES: protein motif:HMM:NF024212.2
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012298.2
COORDINATES: similar to AA sequence:RefSeq:WP_019404036.1
protein phosphatase 2C domain-containing protein
COORDINATES: protein motif:HMM:NF021393.2
type VI secretion system-associated protein TagF
COORDINATES: protein motif:HMM:TIGR03348.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0033103 - protein secretion by the type VI secretion system [Evidence IEA]
type VI secretion system membrane subunit TssM
COORDINATES: protein motif:HMM:TIGR03349.1
GO:0033104 - type VI protein secretion system complex [Evidence IEA]
type VI secretion system protein TssL, long form
COORDINATES: similar to AA sequence:RefSeq:WP_018001518.1
type VI secretion system baseplate subunit TssK
COORDINATES: protein motif:HMM:NF013700.2
COORDINATES: similar to AA sequence:RefSeq:WP_005623018.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001523.1
MotA/TolQ/ExbB proton channel family protein
COORDINATES: protein motif:HMM:NF014525.2
COORDINATES: similar to AA sequence:RefSeq:WP_005863882.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03347.1
type VI secretion system baseplate subunit TssG
COORDINATES: similar to AA sequence:RefSeq:WP_005614124.1
type VI secretion system baseplate subunit TssF
COORDINATES: protein motif:HMM:TIGR03357.1
type VI secretion system baseplate subunit TssE
COORDINATES: similar to AA sequence:RefSeq:WP_018001531.1
type VI secretion system tube protein Hcp
COORDINATES: similar to AA sequence:RefSeq:WP_005614120.1
type VI secretion system contractile sheath large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_005614119.1
type VI secretion system contractile sheath small subunit
COORDINATES: protein motif:HMM:NF018516.2
type VI secretion system ImpA family N-terminal domain-containing protein
COORDINATES: protein motif:HMM:TIGR03354.1
type VI secretion system-associated FHA domain protein TagH
COORDINATES: similar to AA sequence:RefSeq:WP_009177598.1
COORDINATES: protein motif:HMM:NF037679.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018896886.1
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_011749216.1
GO:0055085 - transmembrane transport [Evidence IEA]; GO:0042908 - xenobiotic transport [Evidence IEA]
multidrug efflux RND transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_014875595.1
COORDINATES: similar to AA sequence:RefSeq:WP_011841360.1
COORDINATES: similar to AA sequence:RefSeq:WP_009817034.1
COORDINATES: similar to AA sequence:RefSeq:WP_012178617.1
COORDINATES: similar to AA sequence:RefSeq:WP_019965549.1