Rhodoferax ferrireducens T118 plasmid unnamed1, complete sequence.
Rhodoferax ferrireducens T118 (Albidiferax ferrireducens T118)
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Rhodoferax.
Complete sequence of Plasmid1 of Rhodoferax ferrireducens DSM 15236
Submitted (27-FEB-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000268.1.\nURL -- http://www.jgi.doe.gov\nSource DNA available from Derek Lovley (dlovley@microbio.umass.edu)\nBacteria available from DSMZ: DSM 15236\nContacts: Derek Lovley (dlovley@microbio.umass.edu)\n Paul Richardson (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\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##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/20/2023 01:22:40\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,646\nCDSs (total) :: 4,592\nGenes (coding) :: 4,533\nCDSs (with protein) :: 4,533\nGenes (RNA) :: 54\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 3\nPseudo Genes (total) :: 59\nCDSs (without protein) :: 59\nPseudo Genes (ambiguous residues) :: 0 of 59\nPseudo Genes (frameshifted) :: 12 of 59\nPseudo Genes (incomplete) :: 52 of 59\nPseudo Genes (internal stop) :: 7 of 59\nPseudo Genes (multiple problems) :: 12 of 59\nCRISPR Arrays :: 2\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+.
COORDINATES: protein motif:HMM:NF012652.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: protein motif:HMM:NF022136.2
COORDINATES: protein motif:HMM:NF015487.2
COORDINATES: protein motif:HMM:NF015688.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: protein motif:HMM:TIGR03743.1
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:NF019153.2
COORDINATES: protein motif:HMM:NF017094.2
GO:0044780 - bacterial-type flagellum assembly [Evidence IEA]; GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
flagellar transcriptional regulator FlhD
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:TIGR00621.2
COORDINATES: protein motif:HMM:NF019348.2
COORDINATES: protein motif:HMM:NF024642.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF036878.2
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: protein motif:HMM:NF018381.2
COORDINATES: similar to AA sequence:RefSeq:WP_003056658.1
GO:0007165 - signal transduction [Evidence IEA]
internal stop; 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: protein motif:HMM:NF024565.2
COORDINATES: protein motif:HMM:NF016724.2
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_011462959.1
COORDINATES: similar to AA sequence:RefSeq:WP_012836620.1
COORDINATES: protein motif:HMM:NF024977.2
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF024096.2
PD-(D/E)XK nuclease-like domain-containing protein
COORDINATES: protein motif:HMM:NF039495.1
COORDINATES: protein motif:HMM:NF016408.2
COORDINATES: protein motif:HMM:NF013395.2
COORDINATES: protein motif:HMM:NF013658.2
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007805129.1
class I SAM-dependent DNA methyltransferase
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF018644.2
COORDINATES: similar to AA sequence:RefSeq:WP_018079297.1
COORDINATES: protein motif:HMM:NF024880.2
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF015639.2
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011485838.1
COORDINATES: similar to AA sequence:RefSeq:WP_019577807.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011801061.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03638.1
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
GO:0051607 - defense response to virus [Evidence IEA]; GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
type I-E CRISPR-associated endonuclease Cas1e
COORDINATES: protein motif:HMM:NF020377.2
type I-E CRISPR-associated protein Cas6/Cse3/CasE
COORDINATES: protein motif:HMM:TIGR03116.1
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03115.1
COORDINATES: protein motif:HMM:TIGR03114.1
COORDINATES: protein motif:HMM:TIGR03117.1
type IV CRISPR-associated DEAD/DEAH-box helicase Csf4
COORDINATES: similar to AA sequence:RefSeq:WP_011485853.1
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF013252.2
COORDINATES: protein motif:HMM:NF025339.2
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF014752.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024206.2
ankyrin repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011458668.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004797 - thymidine kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006156674.1
COORDINATES: protein motif:HMM:NF012772.2
bifunctional diguanylate cyclase/phosphodiesterase
COORDINATES: protein motif:HMM:NF013730.2
COORDINATES: protein motif:HMM:NF024860.2
COORDINATES: protein motif:HMM:NF028088.2
COORDINATES: similar to AA sequence:RefSeq:WP_011458658.1
COORDINATES: protein motif:HMM:NF024545.2
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF012485.2
type II and III secretion system protein
Type II secretory pathway component PulD-like protein
GO:0000156 - phosphorelay response regulator activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011254879.1
COORDINATES: protein motif:HMM:TIGR03735.1
COORDINATES: protein motif:HMM:TIGR03737.1
COORDINATES: protein motif:HMM:TIGR03742.1
COORDINATES: protein motif:HMM:TIGR03738.1
COORDINATES: protein motif:HMM:TIGR03741.1
COORDINATES: protein motif:HMM:TIGR03734.1
COORDINATES: protein motif:HMM:NF023277.2
COORDINATES: protein motif:HMM:NF014567.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012211005.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798059.1
COORDINATES: similar to AA sequence:RefSeq:WP_017449699.1
COORDINATES: similar to AA sequence:RefSeq:WP_004085174.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011486216.1
COORDINATES: protein motif:HMM:NF023101.2
COORDINATES: similar to AA sequence:RefSeq:WP_011485825.1
COORDINATES: similar to AA sequence:RefSeq:WP_019486767.1
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015876068.1
COORDINATES: protein motif:HMM:NF016214.2
COORDINATES: similar to AA sequence:RefSeq:WP_011485841.1
COORDINATES: similar to AA sequence:RefSeq:WP_011485842.1
COORDINATES: similar to AA sequence:RefSeq:WP_011485843.1
COORDINATES: similar to AA sequence:RefSeq:WP_011485844.1
COORDINATES: protein motif:HMM:NF013704.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005670241.1
COORDINATES: similar to AA sequence:RefSeq:WP_015765878.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798051.1
COORDINATES: protein motif:HMM:NF024244.2
COORDINATES: protein motif:HMM:NF018148.2
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011486073.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF010401.0
COORDINATES: similar to AA sequence:RefSeq:WP_011797991.1
COORDINATES: protein motif:HMM:TIGR02532.1
COORDINATES: protein motif:HMM:NF020384.2