Novosphingobium pentaromativorans US6-1 plasmid pLA5, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Novosphingobium.
Complete genome sequence of Novosphingobium pentaromativorans US6-1(T)
Submitted (28-AUG-2014) Marine Biotechnology, KIOST, 787, Haeanro, Ansan, Gyeonggi-do 426-744, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP009295.1.\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 Date :: 26-MAY-2014\nAssembly Method :: Roche gs Assembler v. 2.6; PAC Bio SMRT\n Analysis v. 2.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 128.0x\nSequencing Technology :: Illumina MiSeq; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/08/2023 00:17:37\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) :: 5,173\nCDSs (total) :: 5,106\nGenes (coding) :: 5,011\nCDSs (with protein) :: 5,011\nGenes (RNA) :: 67\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 3\nPseudo Genes (total) :: 95\nCDSs (without protein) :: 95\nPseudo Genes (ambiguous residues) :: 0 of 95\nPseudo Genes (frameshifted) :: 38 of 95\nPseudo Genes (incomplete) :: 69 of 95\nPseudo Genes (internal stop) :: 15 of 95\nPseudo Genes (multiple problems) :: 22 of 95\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Novosphingobium pentaromativorans
COORDINATES: similar to AA sequence:RefSeq:WP_007015708.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013831354.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015706.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831356.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007015704.1
type II toxin-antitoxin system Y4mF family antitoxin
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008603659.1
COORDINATES: protein motif:HMM:NF021255.2
COORDINATES: similar to AA sequence:RefSeq:WP_007015951.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013831421.1
COORDINATES: similar to AA sequence:RefSeq:WP_018270162.1
COORDINATES: similar to AA sequence:RefSeq:WP_013837159.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015811.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0008610 - lipid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015773.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007015775.1
COORDINATES: similar to AA sequence:RefSeq:WP_007166210.1
COORDINATES: similar to AA sequence:RefSeq:WP_014762451.1
COORDINATES: protein motif:HMM:NF024832.2
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: similar to AA sequence:RefSeq:WP_010183206.1
COORDINATES: similar to AA sequence:RefSeq:WP_013837187.1
COORDINATES: similar to AA sequence:RefSeq:WP_006833004.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006833006.1
COORDINATES: similar to AA sequence:RefSeq:WP_006833007.1
COORDINATES: similar to AA sequence:RefSeq:WP_013837189.1
phytanoyl-CoA dioxygenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015793.1
aspartyl/asparaginyl beta-hydroxylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013837191.1
GO:0008676 - 3-deoxy-8-phosphooctulonate synthase activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013837192.1
GO:0016853 - isomerase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
KpsF/GutQ family sugar-phosphate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_013837193.1
3-deoxy-manno-octulosonate cytidylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_013837194.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015797.1
COORDINATES: similar to AA sequence:RefSeq:WP_013837196.1
COORDINATES: similar to AA sequence:RefSeq:WP_013837197.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015800.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013831409.1
fimbria/pilus outer membrane usher protein
COORDINATES: protein motif:HMM:NF012565.2
GO:0071555 - cell wall organization [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013831456.1
PepSY-associated TM helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013831457.1
COORDINATES: protein motif:HMM:NF021873.2
COORDINATES: similar to AA sequence:RefSeq:WP_007792578.1
internal stop; 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_076612098.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011541357.1
COORDINATES: similar to AA sequence:RefSeq:WP_010122993.1
COORDINATES: similar to AA sequence:RefSeq:WP_006967645.1
COORDINATES: similar to AA sequence:RefSeq:WP_006967643.1
COORDINATES: similar to AA sequence:RefSeq:WP_007166231.1
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
Wzz/FepE/Etk N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010122987.1
COORDINATES: similar to AA sequence:RefSeq:WP_010515579.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950672.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011950671.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683476.1
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: similar to AA sequence:RefSeq:WP_010504998.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012048640.1
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_011536541.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
hydrogenase nickel incorporation protein HypB
COORDINATES: protein motif:HMM:NF013334.2
hydrogenase maturation nickel metallochaperone HypA
COORDINATES: similar to AA sequence:RefSeq:WP_011536539.1
high frequency lysogenization protein HflD
COORDINATES: similar to AA sequence:RefSeq:WP_007015758.1
hydrogenase expression/formation protein HypE
COORDINATES: similar to AA sequence:RefSeq:WP_007015757.1
GO:0016530 - metallochaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011536536.1
COORDINATES: similar to AA sequence:RefSeq:WP_011910301.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0051082 - unfolded protein binding [Evidence IEA]
GO:0065003 - protein-containing complex assembly [Evidence IEA]
HypC/HybG/HupF family hydrogenase formation chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_007015754.1
GO:0003998 - acylphosphatase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011536533.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536532.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
GO:0016226 - iron-sulfur cluster assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020176868.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015749.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536529.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015747.1
GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012040800.1
COORDINATES: similar to AA sequence:RefSeq:WP_013896579.1
COORDINATES: similar to AA sequence:RefSeq:WP_020176873.1
nickel-dependent hydrogenase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_015126474.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536522.1
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008068220.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849887.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501669.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015734.1
COORDINATES: protein motif:HMM:NF013530.2
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: protein motif:HMM:NF016903.2
COORDINATES: similar to AA sequence:RefSeq:WP_007166222.1
GO:0015159 - polysaccharide transmembrane transporter activity [Evidence IEA]
GO:0015774 - polysaccharide transport [Evidence IEA]
polysaccharide biosynthesis/export family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007016060.1
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_007016061.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007016062.1
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_013039223.1
COORDINATES: protein motif:HMM:NF017532.2
COORDINATES: similar to AA sequence:RefSeq:WP_017183626.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016068.1
COORDINATES: similar to AA sequence:RefSeq:WP_027033250.1
frameshifted; internal stop; 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_010337543.1
COORDINATES: similar to AA sequence:RefSeq:WP_012890094.1
COORDINATES: protein motif:HMM:NF020893.2
COORDINATES: similar to AA sequence:RefSeq:WP_020710832.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831350.1
COORDINATES: similar to AA sequence:RefSeq:WP_014631478.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831352.1