Alicycliphilus denitrificans BC plasmid pALIDE01, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Alicycliphilus.
Genome sequences of Alicycliphilus denitrificans strains BC and K601T
Complete sequence of plasmid1 of Alicycliphilus denitrificans BC
Submitted (03-JAN-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002450.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4086861\nSource DNA and organism available from Alfons J.M. Stams\n(Fons.Stams@wur.nl)\nContacts: Alfons J.M. Stams (Fons.Stams@wur.nl)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. it is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Alicycliphilus denitrificans BC\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Missing\nnum_replicons :: 3\nref_biomaterial :: JCM 14587\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Facultative\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.2 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi03280\nGreengenes ID :: 39244\nTemperature Range :: Mesophile\nGram Staining :: Gram-\nDiseases :: None\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: Newbler v. 2.3\nGenome Coverage :: 30x\nSequencing Technology :: WGS\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/22/2023 14:43:30\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) :: 4,718\nCDSs (total) :: 4,652\nGenes (coding) :: 4,576\nCDSs (with protein) :: 4,576\nGenes (RNA) :: 66\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 54\nncRNAs :: 3\nPseudo Genes (total) :: 76\nCDSs (without protein) :: 76\nPseudo Genes (ambiguous residues) :: 0 of 76\nPseudo Genes (frameshifted) :: 21 of 76\nPseudo Genes (incomplete) :: 59 of 76\nPseudo Genes (internal stop) :: 3 of 76\nPseudo Genes (multiple problems) :: 7 of 76\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011486347.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019574726.1
COORDINATES: protein motif:HMM:NF013014.2
COORDINATES: similar to AA sequence:RefSeq:WP_013292847.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: similar to AA sequence:RefSeq:WP_011831742.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019576702.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_019576701.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_019576700.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_019576699.1
COORDINATES: protein motif:HMM:TIGR02747.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_019576697.1
TraA family conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_019576696.1
COORDINATES: similar to AA sequence:RefSeq:WP_019576694.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_019576692.1
COORDINATES: similar to AA sequence:RefSeq:WP_019576691.1
COORDINATES: similar to AA sequence:RefSeq:WP_018207804.1
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF019843.2
fibronectin type III domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011829064.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722479.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_032491591.1
COORDINATES: similar to AA sequence:RefSeq:WP_013104582.1
IS21-like element ISThsp10 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_005792643.1
COORDINATES: similar to AA sequence:RefSeq:WP_013123461.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013721483.1
COORDINATES: similar to AA sequence:RefSeq:WP_013699954.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011798058.1
COORDINATES: similar to AA sequence:RefSeq:WP_004630404.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013722606.1
COORDINATES: similar to AA sequence:RefSeq:WP_014237641.1
COORDINATES: protein motif:HMM:NF023239.2
COORDINATES: similar to AA sequence:RefSeq:WP_013516299.1
COORDINATES: protein motif:HMM:NF017528.2
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_011799846.1
COORDINATES: protein motif:HMM:NF024491.2
COORDINATES: protein motif:HMM:NF013506.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558120.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
Tn3-like element IS1071 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
COORDINATES: similar to AA sequence:RefSeq:WP_012435588.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011342941.1
COORDINATES: similar to AA sequence:RefSeq:WP_011342942.1
type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
COORDINATES: similar to AA sequence:RefSeq:WP_011514928.1
GO:0020037 - heme binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003465043.1
COORDINATES: similar to AA sequence:RefSeq:WP_012732794.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239590.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0005525 - GTP binding [Evidence IEA]
GO:0006777 - Mo-molybdopterin cofactor biosynthetic process [Evidence IEA]
molybdopterin-guanine dinucleotide biosynthesis protein B
COORDINATES: similar to AA sequence:RefSeq:WP_017507802.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013516312.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516313.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516314.1
respiratory nitrate reductase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_013516315.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014235269.1
COORDINATES: similar to AA sequence:RefSeq:WP_008162258.1
COORDINATES: similar to AA sequence:RefSeq:WP_007194476.1
GO:0033743 - peptide-methionine (R)-S-oxide reductase activity [Evidence IEA]
GO:0030091 - protein repair [Evidence IEA]; GO:0006979 - response to oxidative stress [Evidence IEA]
peptide-methionine (R)-S-oxide reductase MsrB
COORDINATES: similar to AA sequence:RefSeq:WP_018079675.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013516320.1
IS21-like element ISIde2 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_013516321.1
IS21-like element ISIde2 family transposase
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_018079567.1
COORDINATES: similar to AA sequence:RefSeq:WP_020424931.1
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_017699145.1
COORDINATES: similar to AA sequence:RefSeq:WP_017159824.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017159823.1
COORDINATES: similar to AA sequence:RefSeq:WP_007857195.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005792921.1
COORDINATES: similar to AA sequence:RefSeq:WP_020723045.1
COORDINATES: protein motif:HMM:NF023101.2
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: protein motif:HMM:NF033527.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF013235.2