Sphingobium xenophagum strain C1 plasmid p5, 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\nCP022751.1.\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:NF025665.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
glycoside hydrolase family 99-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611221.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR01549.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF016903.2
COORDINATES: protein motif:HMM:NF013530.2
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: protein motif:HMM:NF025072.2
COORDINATES: protein motif:HMM:NF028304.2
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:NF019846.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017183632.1
polysaccharide biosynthesis/export family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054744.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019054745.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019054746.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006967582.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_017183637.1
COORDINATES: similar to AA sequence:RefSeq:WP_018719112.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502306.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183640.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010337543.1
COORDINATES: similar to AA sequence:RefSeq:WP_018076126.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165277.1
COORDINATES: similar to AA sequence:RefSeq:WP_020326821.1
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:NF024880.2
COORDINATES: protein motif:HMM:NF015737.2
autotransporter outer membrane beta-barrel domain-containing protein
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_017183611.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_018251338.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017183615.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183617.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015815.1
COORDINATES: similar to AA sequence:RefSeq:WP_014076558.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183620.1
phytanoyl-CoA dioxygenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017183631.1
Wzz/FepE/Etk N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015820.1
COORDINATES: similar to AA sequence:RefSeq:WP_010515579.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF025025.2