Sphingobium xenophagum strain C1 plasmid p4, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingobium.
Whole Genome Sequence of Sphingobium hydrophobicum C1: Insights into Adaption to the Electronic-waste Contaminated Sediment
Submitted (11-AUG-2017) Environmental Microbiology Research and Development Center, Guangdong Institute of Microbiology, Xianlie Middle Road, Guangzhou, Guangdong 510070, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP022750.1.\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 :: RS_HGAP_Assembly v. 3\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 175.7x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/24/2023 15:35:59\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) :: 4,548\nCDSs (total) :: 4,482\nGenes (coding) :: 4,326\nCDSs (with protein) :: 4,326\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) :: 156\nCDSs (without protein) :: 156\nPseudo Genes (ambiguous residues) :: 0 of 156\nPseudo Genes (frameshifted) :: 98 of 156\nPseudo Genes (incomplete) :: 63 of 156\nPseudo Genes (internal stop) :: 4 of 156\nPseudo Genes (multiple problems) :: 9 of 156\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Sphingobium hydrophobicum
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013676.2
GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013039089.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]
GO:0006825 - copper ion transport [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
copper resistance system multicopper oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_007407015.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219223.1
COORDINATES: similar to AA sequence:RefSeq:WP_020486670.1
COORDINATES: similar to AA sequence:RefSeq:WP_007407009.1
GO:0042597 - periplasmic space [Evidence IEA]
GO:0005507 - copper ion binding [Evidence IEA]
copper homeostasis periplasmic binding protein CopC
COORDINATES: similar to AA sequence:RefSeq:WP_010219219.1
copper homeostasis membrane protein CopD
COORDINATES: similar to AA sequence:RefSeq:WP_010124876.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_019368253.1
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_011157811.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368255.1
GO:0003674 - molecular_function [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008828909.1
helix-hairpin-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017500344.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368259.1
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_010661783.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953933.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409045.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: similar to AA sequence:RefSeq:WP_017980819.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980820.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954973.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368261.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503418.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188930.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503420.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368264.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010337663.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368266.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010127314.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_013039111.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004212877.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018251219.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_020820506.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406844.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368193.1
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0001539 - cilium or flagellum-dependent cell motility [Evidence IEA]
flagellar hook-basal body complex protein FliE
COORDINATES: similar to AA sequence:RefSeq:WP_007406841.1
COORDINATES: similar to AA sequence:RefSeq:WP_020486675.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212882.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212885.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004212886.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368198.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018251228.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368200.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406854.1
COORDINATES: similar to AA sequence:RefSeq:WP_016916437.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368205.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017503469.1
COORDINATES: similar to AA sequence:RefSeq:WP_013833376.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017503471.1
COORDINATES: similar to AA sequence:RefSeq:WP_013032220.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019368208.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165133.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503475.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054163.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054162.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213195.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503479.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: similar to AA sequence:RefSeq:WP_006949650.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_019368217.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_010339492.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054154.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339495.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339496.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_019368222.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339498.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010339499.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054148.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339755.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368226.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368227.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010339507.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010339509.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339510.1
COORDINATES: protein motif:HMM:NF041551.1
COORDINATES: similar to AA sequence:RefSeq:WP_013836224.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368234.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368235.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339514.1
COORDINATES: similar to AA sequence:RefSeq:WP_018329321.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980773.1
COORDINATES: similar to AA sequence:RefSeq:WP_010163443.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683347.1
COORDINATES: similar to AA sequence:RefSeq:WP_007407018.1
COORDINATES: similar to AA sequence:RefSeq:WP_015314946.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980780.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683363.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368246.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039098.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013039114.1