Hydrocarboniclastica marina strain soil36-7 plasmid psoil36-7, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales; Alteromonadaceae; Hydrocarboniclastica.
Marsedoiliclastica nanhaica gen. nov. sp. nov., a novel marine hydrocarbonoclastic bacterium isolated from an in-situ enriched hydrocarbon-degrading consortium in deep-sea sediment
Submitted (17-JUL-2018) State Oceanic Administration, The Third Institute, Room 329, Daxue Road 184, Xiamen, Fujian 361005, P.R. China
REFSEQ INFORMATION: The reference sequence is identical to\nCP031094.1.\nBacteria and source DNA available from Dr. Zongze Shao; The Third\nInstitute of State Oceanic Administration, Daxue Road 184#, Xiamen,\nFujian, 3610015, China.\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 :: SMRT Analysis v. 2.3\nGenome Coverage :: 313\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/05/2023 03:09:40\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) :: 3,764\nCDSs (total) :: 3,702\nGenes (coding) :: 3,679\nCDSs (with protein) :: 3,679\nGenes (RNA) :: 62\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 4\nPseudo Genes (total) :: 23\nCDSs (without protein) :: 23\nPseudo Genes (ambiguous residues) :: 0 of 23\nPseudo Genes (frameshifted) :: 1 of 23\nPseudo Genes (incomplete) :: 22 of 23\nPseudo Genes (internal stop) :: 3 of 23\nPseudo Genes (multiple problems) :: 3 of 23\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+.
COORDINATES: protein motif:HMM:NF020442.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013519429.1
GO:0052699 - ergothioneine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF021530.2
GO:0030745 - dimethylhistidine N-methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004582982.1
COORDINATES: similar to AA sequence:RefSeq:WP_011783704.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004578671.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]
plastocyanin/azurin family copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008169964.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]
GO:0006825 - copper ion transport [Evidence IEA]
copper resistance system multicopper oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_004582978.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612015.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007349961.1
COORDINATES: similar to AA sequence:RefSeq:WP_010793081.1
COORDINATES: similar to AA sequence:RefSeq:WP_011783979.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014422288.1
GO:0047617 - acyl-CoA hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006912365.1
GO:0016790 - thiolester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007152435.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024039.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011354828.1
2Fe-2S iron-sulfur cluster binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015487771.1
COORDINATES: protein motif:HMM:NF013695.2
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
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:NF017124.2
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF037161.2
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_011786688.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849768.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002650501.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020562288.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_007985615.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]; GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0006006 - glucose metabolic process [Evidence IEA]
ArsJ-associated glyceraldehyde-3-phosphate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_017245099.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
organoarsenical effux MFS transporter ArsJ
COORDINATES: similar to AA sequence:RefSeq:WP_012218051.1
ArsO family NAD(P)H-dependent flavin-containing monooxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_011787046.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018717964.1
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: similar to AA sequence:RefSeq:WP_004748794.1
COORDINATES: protein motif:HMM:NF016214.2
COORDINATES: protein motif:HMM:NF013618.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612095.1
COORDINATES: protein motif:HMM:NF013793.2
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:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF013506.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019237.2
GO:0007154 - cell communication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017085213.1
COORDINATES: protein motif:HMM:NF041494.1
COORDINATES: similar to AA sequence:RefSeq:WP_000661886.1
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_001910864.1
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
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: similar to AA sequence:RefSeq:WP_013141547.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: similar to AA sequence:RefSeq:WP_017085231.1
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_000983283.1
COORDINATES: protein motif:HMM:NF011458.0
conjugal transfer mating pair stabilization protein TraN