Rhizobium etli strain NXC12 plasmid pRetNXC12a, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
Complete genome sequences of Rhizobium genomic linages associated to common bean (phaseolus vulgaris)
Submitted (21-APR-2017) Programa de Genomica Evolutiva, Centro de Ciencias Genomicas / UNAM, Av. Universidad s/n, Cuernavaca, Morelos 62210, Mexico
REFSEQ INFORMATION: The reference sequence is identical to\nCP020907.1.\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 :: Newbler v. 2.5.3; SPAdes v. 2.5.1;\n Velvet v. 1.1.06; Consed v. 23\nReference-guided Assembly :: GCA_000092045.1\nGenome Coverage :: 400x\nSequencing Technology :: 454 and Illumina Hiseq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/24/2023 17:46:44\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) :: 6,540\nCDSs (total) :: 6,477\nGenes (coding) :: 6,201\nCDSs (with protein) :: 6,201\nGenes (RNA) :: 63\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 4\nPseudo Genes (total) :: 276\nCDSs (without protein) :: 276\nPseudo Genes (ambiguous residues) :: 0 of 276\nPseudo Genes (frameshifted) :: 168 of 276\nPseudo Genes (incomplete) :: 175 of 276\nPseudo Genes (internal stop) :: 35 of 276\nPseudo Genes (multiple problems) :: 89 of 276\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_017992440.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003571855.1
nucleoside-diphosphate sugar epimerase/dehydratase
COORDINATES: similar to AA sequence:RefSeq:WP_017997061.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549579.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489884.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427471.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427472.1
GO:0008927 - mannonate dehydratase activity [Evidence IEA]
GO:0006064 - glucuronate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017969330.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007637220.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549565.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003576647.1
COORDINATES: similar to AA sequence:RefSeq:WP_007637215.1
COORDINATES: similar to AA sequence:RefSeq:WP_003511539.1
ABC-F family ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012560092.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549551.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649602.1
COORDINATES: similar to AA sequence:RefSeq:WP_003576661.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016735694.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020047587.1
COORDINATES: similar to AA sequence:RefSeq:WP_007637186.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007637185.1
GO:0009331 - glycerol-3-phosphate dehydrogenase complex [Evidence IEA]
GO:0004368 - glycerol-3-phosphate dehydrogenase (quinone) activity [Evidence IEA]
GO:0006072 - glycerol-3-phosphate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007788441.1
COORDINATES: similar to AA sequence:RefSeq:WP_018246651.1
COORDINATES: similar to AA sequence:RefSeq:WP_017957585.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649611.1
COORDINATES: similar to AA sequence:RefSeq:WP_007788434.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649612.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_016735686.1
GO:0004370 - glycerol kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003549512.1
GO:0004813 - alanine-tRNA ligase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0006419 - alanyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004673581.1
GO:0050570 - 4-hydroxythreonine-4-phosphate dehydrogenase activity [Evidence IEA]
GO:0008615 - pyridoxine biosynthetic process [Evidence IEA]
4-hydroxythreonine-4-phosphate dehydrogenase PdxA
COORDINATES: similar to AA sequence:RefSeq:WP_018484100.1
COORDINATES: similar to AA sequence:RefSeq:WP_016735683.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549488.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018246672.1
COORDINATES: similar to AA sequence:RefSeq:WP_020665211.1
COORDINATES: similar to AA sequence:RefSeq:WP_003571772.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549484.1
COORDINATES: similar to AA sequence:RefSeq:WP_003595851.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012760159.1
four-carbon acid sugar kinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018484110.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011427505.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489858.1
COORDINATES: similar to AA sequence:RefSeq:WP_015928729.1
GO:0004719 - protein-L-isoaspartate (D-aspartate) O-methyltransferase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
protein-L-isoaspartate(D-aspartate) O-methyltransferase
COORDINATES: protein motif:HMM:NF025013.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012489854.1
COORDINATES: similar to AA sequence:RefSeq:WP_003571757.1
COORDINATES: similar to AA sequence:RefSeq:WP_004673154.1
COORDINATES: similar to AA sequence:RefSeq:WP_016735668.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_011427511.1
COORDINATES: similar to AA sequence:RefSeq:WP_003534936.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489849.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011427514.1
COORDINATES: similar to AA sequence:RefSeq:WP_004673166.1
COORDINATES: similar to AA sequence:RefSeq:WP_004673168.1
COORDINATES: similar to AA sequence:RefSeq:WP_004673170.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427517.1
COORDINATES: similar to AA sequence:RefSeq:WP_016735660.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489844.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016735658.1
COORDINATES: similar to AA sequence:RefSeq:WP_017957120.1
COORDINATES: similar to AA sequence:RefSeq:WP_003551488.1
COORDINATES: similar to AA sequence:RefSeq:WP_016735655.1
COORDINATES: similar to AA sequence:RefSeq:WP_016735654.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427525.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012489837.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427527.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004673190.1
COORDINATES: similar to AA sequence:RefSeq:WP_003576750.1
COORDINATES: similar to AA sequence:RefSeq:WP_012556099.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003591049.1
COORDINATES: similar to AA sequence:RefSeq:WP_003591051.1
COORDINATES: similar to AA sequence:RefSeq:WP_003576758.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010007187.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427422.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014857614.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018445057.1
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_014077526.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427534.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649514.1
COORDINATES: similar to AA sequence:RefSeq:WP_015886875.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649512.1
glycerol-3-phosphate dehydrogenase/oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_010661040.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649510.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427540.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427541.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011969240.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011427543.1
GO:0004789 - thiamine-phosphate diphosphorylase activity [Evidence IEA]
GO:0009228 - thiamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014527713.1
COORDINATES: similar to AA sequence:RefSeq:WP_017958428.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427545.1
GO:0016647 - oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013850280.1
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF00059
TPP riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_003576418.1
COORDINATES: similar to AA sequence:RefSeq:WP_003576420.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427549.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004677292.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_016735563.1
GO:0016811 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017969166.1
GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004677295.1
COORDINATES: similar to AA sequence:RefSeq:WP_016735560.1
COORDINATES: similar to AA sequence:RefSeq:WP_003572011.1
COORDINATES: similar to AA sequence:RefSeq:WP_020047725.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427557.1
COORDINATES: similar to AA sequence:RefSeq:WP_003576433.1
COORDINATES: similar to AA sequence:RefSeq:WP_018246945.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione-dependent disulfide-bond oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_003549337.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549335.1
COORDINATES: similar to AA sequence:RefSeq:WP_018246950.1
COORDINATES: similar to AA sequence:RefSeq:WP_017957505.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649720.1
lysophospholipid acyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012559990.1
CDP-alcohol phosphatidyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020047714.1
COORDINATES: similar to AA sequence:RefSeq:WP_018484136.1
COORDINATES: similar to AA sequence:RefSeq:WP_018496189.1
COORDINATES: similar to AA sequence:RefSeq:WP_018246957.1
COORDINATES: similar to AA sequence:RefSeq:WP_017997178.1
COORDINATES: similar to AA sequence:RefSeq:WP_007637397.1
COORDINATES: similar to AA sequence:RefSeq:WP_003525270.1
frameshifted; 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: similar to AA sequence:RefSeq:WP_011427573.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549301.1
GO:0033744 - L-methionine:thioredoxin-disulfide S-oxidoreductase activity [Evidence IEA]; GO:0008113 - peptide-methionine (S)-S-oxide reductase activity [Evidence IEA]
GO:0030091 - protein repair [Evidence IEA]; GO:0006979 - response to oxidative stress [Evidence IEA]
peptide-methionine (S)-S-oxide reductase MsrA
COORDINATES: similar to AA sequence:RefSeq:WP_018484151.1
COORDINATES: similar to AA sequence:RefSeq:WP_004680244.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: similar to AA sequence:RefSeq:WP_017969209.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427578.1
COORDINATES: similar to AA sequence:RefSeq:WP_004680247.1
COORDINATES: similar to AA sequence:RefSeq:WP_018496161.1
COORDINATES: similar to AA sequence:RefSeq:WP_003595646.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427582.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427583.1
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_018448971.1
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
SfnB family sulfur acquisition oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007637355.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003595657.1
COORDINATES: similar to AA sequence:RefSeq:WP_012560163.1
COORDINATES: similar to AA sequence:RefSeq:WP_018484172.1
COORDINATES: similar to AA sequence:RefSeq:WP_018448966.1
COORDINATES: similar to AA sequence:RefSeq:WP_017957455.1
COORDINATES: similar to AA sequence:RefSeq:WP_003595665.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549253.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549251.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427594.1
dipeptide/oligopeptide/nickel ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017969227.1
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_011427596.1
GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA]
GO:0006629 - lipid metabolic process [Evidence IEA]
glycerophosphodiester phosphodiesterase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012489756.1
COORDINATES: similar to AA sequence:RefSeq:WP_018247001.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011427599.1
COORDINATES: similar to AA sequence:RefSeq:WP_003571910.1
COORDINATES: similar to AA sequence:RefSeq:WP_012560147.1
COORDINATES: similar to AA sequence:RefSeq:WP_012760031.1
COORDINATES: similar to AA sequence:RefSeq:WP_007637331.1
COORDINATES: similar to AA sequence:RefSeq:WP_018448955.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649788.1
COORDINATES: similar to AA sequence:RefSeq:WP_016735528.1
COORDINATES: similar to AA sequence:RefSeq:WP_018448952.1
COORDINATES: similar to AA sequence:RefSeq:WP_020047641.1
COORDINATES: similar to AA sequence:RefSeq:WP_017969248.1
COORDINATES: similar to AA sequence:RefSeq:WP_012760015.1
COORDINATES: similar to AA sequence:RefSeq:WP_003595714.1
COORDINATES: similar to AA sequence:RefSeq:WP_011649802.1
COORDINATES: similar to AA sequence:RefSeq:WP_003549191.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012489737.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489736.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011427616.1
COORDINATES: similar to AA sequence:RefSeq:WP_008529912.1
COORDINATES: similar to AA sequence:RefSeq:WP_017957630.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012560117.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0004494 - methylmalonyl-CoA mutase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003571872.1
COORDINATES: similar to AA sequence:RefSeq:WP_018496119.1
methionine ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012759995.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427623.1
COORDINATES: similar to AA sequence:RefSeq:WP_007637243.1
COORDINATES: similar to AA sequence:RefSeq:WP_003571859.1
COORDINATES: similar to AA sequence:RefSeq:WP_003595755.1
COORDINATES: similar to AA sequence:RefSeq:WP_012560106.1