Sphingobium xenophagum strain C1 plasmid p3, 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\nCP022749.1.\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:NF017088.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019516736.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013040832.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
glutathione-dependent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_010545583.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008994492.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832007.1
COORDINATES: similar to AA sequence:RefSeq:WP_007687207.1
GO:0055085 - transmembrane transport [Evidence IEA]
low affinity iron permease family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950610.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832012.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0051082 - unfolded protein binding [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011950612.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950613.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950614.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832016.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832017.1
hybrid sensor histidine kinase/response regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011950617.1
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
GO:0004803 - transposase activity [Evidence IEA]
IS6-like element IS6100 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_010408975.1
COORDINATES: similar to AA sequence:RefSeq:WP_013503495.1
enoyl-CoA hydratase/isomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006949676.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014954.2
COORDINATES: similar to AA sequence:RefSeq:WP_006949672.1
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: similar to AA sequence:RefSeq:WP_006949666.1
COORDINATES: similar to AA sequence:RefSeq:WP_032488953.1
COORDINATES: protein motif:HMM:NF033527.1
COORDINATES: similar to AA sequence:RefSeq:WP_012975307.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039114.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039098.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_006953926.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213229.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213228.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819805.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011627746.1
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_004213224.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949660.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213217.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819808.1
COORDINATES: similar to AA sequence:RefSeq:WP_011627750.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949657.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949655.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213205.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_006949650.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213202.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213200.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015449336.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213195.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819815.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016055.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819817.1
COORDINATES: similar to AA sequence:RefSeq:WP_020326821.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165277.1
COORDINATES: similar to AA sequence:RefSeq:WP_018076126.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212800.1
reverse transcriptase/maturase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006949645.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213405.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006968047.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054017.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213313.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953883.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213311.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213310.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054019.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953889.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953891.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953897.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054023.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831892.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819825.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213291.1
COORDINATES: similar to AA sequence:RefSeq:WP_008827849.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213289.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054029.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006953917.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma factor-like helix-turn-helix DNA-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213279.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004213277.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213276.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213275.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953923.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213273.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_004213271.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017503729.1
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_006953933.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950543.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829210.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950544.1
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011950545.1
GO:0008853 - exodeoxyribonuclease III activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011950546.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950547.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950553.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831218.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950555.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950556.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831954.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831955.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831956.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831957.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950560.1
GO:0020037 - heme binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012791.2
COORDINATES: similar to AA sequence:RefSeq:WP_012977244.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
GO:0098662 - inorganic cation transmembrane transport [Evidence IEA]
monovalent cation/H+ antiporter subunit A
COORDINATES: similar to AA sequence:RefSeq:WP_007508800.1
COORDINATES: similar to AA sequence:RefSeq:WP_003528838.1
monovalent cation/H+ antiporter subunit D
COORDINATES: similar to AA sequence:RefSeq:WP_011339550.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007683813.1
GO:0015075 - monoatomic ion transmembrane transporter activity [Evidence IEA]
GO:0034220 - monoatomic ion transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009492424.1
GO:0098662 - inorganic cation transmembrane transport [Evidence IEA]; GO:1902600 - proton transmembrane transport [Evidence IEA]
monovalent cation/H(+) antiporter subunit G
COORDINATES: similar to AA sequence:RefSeq:WP_008831959.1
bifunctional diguanylate cyclase/phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_014530399.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018250698.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823877.1
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011413215.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823879.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823880.1
L-dopachrome tautomerase-related protein
COORDINATES: similar to AA sequence:RefSeq:WP_017503035.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503034.1
COORDINATES: similar to AA sequence:RefSeq:WP_014132970.1
glutathione-independent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_014132971.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823887.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954973.1
COORDINATES: similar to AA sequence:RefSeq:NP_308438.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_012783831.1
metal/formaldehyde-sensitive transcriptional repressor
COORDINATES: similar to AA sequence:RefSeq:WP_007406876.1
zinc-dependent alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017503026.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011252867.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612267.1
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:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_008831960.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950563.1
COORDINATES: protein motif:HMM:NF012698.2
COORDINATES: similar to AA sequence:RefSeq:WP_012048970.1
COORDINATES: similar to AA sequence:RefSeq:WP_015459999.1
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_008831965.1
DnaJ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950568.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950570.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831969.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831970.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950573.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950574.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950575.1
xanthine dehydrogenase family protein subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_011950576.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011950577.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831976.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831977.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409817.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950581.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517228.1
GO:0016639 - oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011950583.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831986.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0070063 - RNA polymerase binding [Evidence IEA]
GO:0032784 - regulation of DNA-templated transcription elongation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008831987.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950600.1
COORDINATES: similar to AA sequence:RefSeq:WP_007706479.1
COORDINATES: similar to AA sequence:RefSeq:WP_014194372.1
COORDINATES: similar to AA sequence:RefSeq:WP_003630695.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831992.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831993.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008831994.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013481234.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831996.1
COORDINATES: protein motif:HMM:NF012488.2
COORDINATES: protein motif:HMM:NF015210.2
COORDINATES: similar to AA sequence:RefSeq:WP_008831999.1