Alicycliphilus denitrificans BC plasmid pALIDE02, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Alicycliphilus.
Genome sequences of Alicycliphilus denitrificans strains BC and K601T
Complete sequence of plasmid2 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\nCP002451.1.\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: similar to AA sequence:RefSeq:WP_006122509.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006122510.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114056.1
COORDINATES: similar to AA sequence:RefSeq:WP_000086826.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_011655356.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011137971.1
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_000426567.1
conjugal transfer transcriptional regulator TraJ
COORDINATES: similar to AA sequence:RefSeq:WP_001127128.1
COORDINATES: similar to AA sequence:RefSeq:WP_011304098.1
COORDINATES: similar to AA sequence:RefSeq:WP_000718516.1
COORDINATES: similar to AA sequence:RefSeq:WP_000826922.1
COORDINATES: similar to AA sequence:RefSeq:WP_000664557.1
DNA binding protein involved in transcriptional regulation
COORDINATES: similar to AA sequence:RefSeq:WP_011342948.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890108.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011114061.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890110.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890112.1
COORDINATES: similar to AA sequence:RefSeq:WP_012478184.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890114.1
COORDINATES: similar to AA sequence:RefSeq:WP_015913627.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890115.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114068.1
COORDINATES: similar to AA sequence:RefSeq:WP_011137973.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558246.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_086558120.1
GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008697511.1
COORDINATES: similar to AA sequence:RefSeq:WP_012584370.1
COORDINATES: similar to AA sequence:RefSeq:WP_004303614.1
COORDINATES: similar to AA sequence:RefSeq:WP_004359146.1
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_011342941.1
COORDINATES: similar to AA sequence:RefSeq:WP_012435588.1
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
incomplete; partial in the middle of a contig; missing C-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_076611932.1
GO:0015074 - DNA integration [Evidence IEA]
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.
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_076611206.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020820181.1
COORDINATES: similar to AA sequence:RefSeq:WP_013521170.1
COORDINATES: similar to AA sequence:RefSeq:WP_013521171.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013521172.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013521173.1
glutathione S-transferase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013521174.1
COORDINATES: similar to AA sequence:RefSeq:WP_013521175.1
COORDINATES: similar to AA sequence:RefSeq:WP_013521176.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014003226.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011114072.1
COORDINATES: similar to AA sequence:RefSeq:WP_000019167.1
COORDINATES: similar to AA sequence:RefSeq:WP_000283041.1
COORDINATES: similar to AA sequence:RefSeq:WP_000132020.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114046.1
COORDINATES: similar to AA sequence:RefSeq:WP_010676131.1
COORDINATES: similar to AA sequence:RefSeq:WP_011013264.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_006122481.1
COORDINATES: similar to AA sequence:RefSeq:WP_000753228.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_011798704.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114050.1
mating pair formation and entry exclusion
COORDINATES: similar to AA sequence:RefSeq:WP_000802794.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_000644148.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011114051.1
P-type conjugative transfer protein TrbL
probable role in the formation of the mating lock (cell-cell contact between donor and recipient) during conjugation on the basis that TrbM shows homology to Haemophilus influenzae adhesin and has an export signal sequence
COORDINATES: similar to AA sequence:RefSeq:WP_010890138.1
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_011798698.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011798697.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798696.1
COORDINATES: similar to AA sequence:RefSeq:WP_001665065.1
COORDINATES: similar to AA sequence:RefSeq:WP_003159185.1
COORDINATES: similar to AA sequence:RefSeq:WP_012585400.1
COORDINATES: similar to AA sequence:RefSeq:WP_014834018.1
COORDINATES: similar to AA sequence:RefSeq:WP_013124600.1
COORDINATES: similar to AA sequence:RefSeq:WP_003155746.1
COORDINATES: similar to AA sequence:RefSeq:WP_011517528.1
COORDINATES: similar to AA sequence:RefSeq:WP_000904941.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229645.1
COORDINATES: similar to AA sequence:RefSeq:WP_001277466.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016240396.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000654684.1
mercury resistance system transport protein MerF
COORDINATES: similar to AA sequence:RefSeq:WP_011633167.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:YP_005229639.1
COORDINATES: similar to AA sequence:RefSeq:WP_000414383.1
GO:0001228 - DNA-binding transcription activator activity, RNA polymerase II-specific [Evidence IEA]
Hg(II)-responsive transcriptional regulator
COORDINATES: protein motif:HMM:NF028004.2
COORDINATES: similar to AA sequence:RefSeq:WP_013521184.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003830784.1
COORDINATES: similar to AA sequence:RefSeq:WP_001247892.1
COORDINATES: similar to AA sequence:RefSeq:WP_008932165.1
Uncharacterized conserved protein, contains double-stranded beta-helix domain
COORDINATES: similar to AA sequence:RefSeq:WP_003465043.1
COORDINATES: similar to AA sequence:RefSeq:WP_011809177.1
COORDINATES: similar to AA sequence:RefSeq:WP_003100856.1
COORDINATES: similar to AA sequence:RefSeq:WP_003100853.1
COORDINATES: similar to AA sequence:RefSeq:WP_019897068.1