Polymorphum gilvum SL003B-26A1 plasmid pSL003B, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Polymorphum.
Complete genome sequence of Polymorphum gilvum SL003B-26A1T, a crude oil-degrading bacterium from oil-polluted saline soil
Submitted (02-MAR-2011) Department of Energy and Resources Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, P. R. China
REFSEQ INFORMATION: The reference sequence is identical to\nCP002569.1.\nSource DNA is available from Dr Xiao-Lei Wu\n(xiaolei_wu@pku.edu.cn).\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/07/2023 01:22:51\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) :: 4,498\nCDSs (total) :: 4,438\nGenes (coding) :: 4,394\nCDSs (with protein) :: 4,394\nGenes (RNA) :: 60\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 4\nPseudo Genes (total) :: 44\nCDSs (without protein) :: 44\nPseudo Genes (ambiguous residues) :: 0 of 44\nPseudo Genes (frameshifted) :: 8 of 44\nPseudo Genes (incomplete) :: 38 of 44\nPseudo Genes (internal stop) :: 2 of 44\nPseudo Genes (multiple problems) :: 3 of 44\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_003501433.1
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_003501432.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018240830.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501430.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003501428.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501426.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501424.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501420.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501418.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003525125.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501412.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650718.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501408.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974797.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974883.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501402.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501400.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501398.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524944.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517406.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501391.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003501388.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018431454.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003501379.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654900.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523830.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501373.1
COORDINATES: similar to AA sequence:RefSeq:WP_003495445.1
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009505782.1
GO:0003824 - catalytic activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013654839.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008491906.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_011510447.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF024212.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013845944.1
frameshifted; internal stop; 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:NF039997.1
COORDINATES: similar to AA sequence:RefSeq:WP_007708767.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009507327.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007092483.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013394937.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007092485.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010322184.1
GO:0008774 - acetaldehyde dehydrogenase (acetylating) activity [Evidence IEA]
acetaldehyde dehydrogenase (acetylating)
COORDINATES: similar to AA sequence:RefSeq:WP_010325238.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010339849.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046771.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_018325663.1
COORDINATES: similar to AA sequence:RefSeq:WP_008120548.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_020046774.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974835.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_012649097.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003523577.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_012649099.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892446.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654970.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649103.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501263.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650747.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650748.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501258.1
COORDINATES: similar to AA sequence:RefSeq:WP_006472551.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501469.1
type IV toxin-antitoxin system AbiEi family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_017685527.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.