Rhodanobacter denitrificans strain FW104-R5 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales; Rhodanobacteraceae; Rhodanobacter.
Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer
Submitted (30-NOV-2021) Institute for Environmental Genomics, University of Oklahoma, 101 David L Boren Blvd, Norman, OK 73072, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP088981.1.\nBacteria and source DNA available from Institute for Environmental\nGenomics, Department of Microbiology and Plant Biology, University\nof Oklahoma, Norman, OK, USA.\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 :: Unicycler v. March-2021\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 168.0x\nSequencing Technology :: Illumina; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/08/2023 22:18:18\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) :: 3,823\nCDSs (total) :: 3,763\nGenes (coding) :: 3,725\nCDSs (with protein) :: 3,725\nGenes (RNA) :: 60\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 4\nPseudo Genes (total) :: 38\nCDSs (without protein) :: 38\nPseudo Genes (ambiguous residues) :: 0 of 38\nPseudo Genes (frameshifted) :: 10 of 38\nPseudo Genes (incomplete) :: 26 of 38\nPseudo Genes (internal stop) :: 7 of 38\nPseudo Genes (multiple problems) :: 4 of 38\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_008209282.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_000586559.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354471.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015447718.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
nucleotidyltransferase/DNA polymerase involved in DNA repair
COORDINATES: protein motif:HMM:NF033429.2
GO:0051782 - negative regulation of cell division [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
translesion DNA synthesis-associated protein ImuA
COORDINATES: protein motif:HMM:NF012920.2
COORDINATES: similar to AA sequence:RefSeq:WP_019182763.1
COORDINATES: protein motif:HMM:NF021759.2
COORDINATES: protein motif:HMM:NF024371.2
COORDINATES: similar to AA sequence:RefSeq:WP_014029916.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256896.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400043.1
COORDINATES: protein motif:HMM:NF024755.2
GO:0003896 - DNA primase activity [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
primase-helicase zinc-binding domain-containing protein
COORDINATES: protein motif:HMM:NF017973.2
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: similar to AA sequence:RefSeq:WP_020751064.1
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_007809238.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013506.2
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: protein motif:HMM:NF024117.2
COORDINATES: similar to AA sequence:RefSeq:WP_013723316.1
COORDINATES: protein motif:HMM:NF014342.2
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03734.1
COORDINATES: protein motif:HMM:TIGR03737.1
COORDINATES: protein motif:HMM:TIGR03735.1
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: protein motif:HMM:NF022728.2
COORDINATES: protein motif:HMM:NF039746.1
COORDINATES: similar to AA sequence:RefSeq:WP_014402433.1
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: similar to AA sequence:RefSeq:WP_007081300.1
COORDINATES: similar to AA sequence:RefSeq:WP_006488822.1
COORDINATES: similar to AA sequence:RefSeq:WP_006657722.1
GO:0006402 - mRNA catabolic process [Evidence IEA]; GO:0006109 - regulation of carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF014336.2
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF036894.2
COORDINATES: protein motif:HMM:NF013704.2
COORDINATES: similar to AA sequence:RefSeq:WP_011345727.1
COORDINATES: protein motif:HMM:NF015210.2
COORDINATES: protein motif:HMM:NF028096.2
Ref family recombination enhancement nuclease
COORDINATES: protein motif:HMM:NF008729.0
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
GO:0006139 - nucleobase-containing compound metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF025105.2
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:NF018836.2
GO:0019867 - outer membrane [Evidence IEA]
COORDINATES: protein motif:HMM:NF017152.2
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:TIGR02747.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: protein motif:HMM:NF016820.2
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:TIGR02746.1
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF014638.2
COORDINATES: protein motif:HMM:NF018536.2
COORDINATES: protein motif:HMM:NF041494.1
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:NF025706.2
COORDINATES: protein motif:HMM:NF012651.2
COORDINATES: protein motif:HMM:NF022136.2
COORDINATES: protein motif:HMM:TIGR02520.1
GO:0009297 - pilus assembly [Evidence IEA]; GO:0009306 - protein secretion [Evidence IEA]
PilN family type IVB pilus formation outer membrane protein
COORDINATES: protein motif:HMM:TIGR03021.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF020384.2
COORDINATES: protein motif:HMM:NF016785.2
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019064.2
COORDINATES: similar to AA sequence:RefSeq:WP_007508486.1
COORDINATES: similar to AA sequence:RefSeq:WP_007082531.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007509002.1
COORDINATES: similar to AA sequence:RefSeq:WP_007509096.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447885.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447886.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015447887.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447888.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015447889.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447890.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_015447891.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447892.1
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007509076.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447894.1
COORDINATES: similar to AA sequence:RefSeq:WP_007080830.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447592.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447915.1
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_012511035.1
COORDINATES: similar to AA sequence:RefSeq:WP_008214512.1
COORDINATES: similar to AA sequence:RefSeq:WP_008214509.1
COORDINATES: similar to AA sequence:RefSeq:WP_008214506.1
COORDINATES: similar to AA sequence:RefSeq:WP_008214504.1
COORDINATES: similar to AA sequence:RefSeq:WP_008214502.1
mercuric resistance transcriptional repressor protein MerD
COORDINATES: similar to AA sequence:RefSeq:WP_015447910.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008434956.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447707.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:WP_008208836.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447709.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449104.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449103.1
COORDINATES: similar to AA sequence:RefSeq:WP_015447712.1
COORDINATES: similar to AA sequence:RefSeq:WP_008209286.1
GO:0001228 - DNA-binding transcription activator activity, RNA polymerase II-specific [Evidence IEA]
Hg(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008209284.1