Sinorhizobium americanum strain CFNEI 73 plasmid A, complete sequence.
Sinorhizobium americanum (Ensifer americanus)
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
Genomic differences between typical nodule nitrogen-fixing rhizobial strains and those coming from bean seeds
Submitted (29-OCT-2015) Program of Functional Genomic of Prokaryotes, Center for Genomic Sciences, Av. Universidad s/n Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
REFSEQ INFORMATION: The reference sequence is identical to\nCP013108.1.\nBacteria available from Jaime Mora (jmora@ccg.unam.mx), Centro de\nCiencias Genomicas-UNAM, PO Box 565-A, Cuernavaca, Morelos, Mexico\nCP62210.\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 :: SMRT Analysis v. 2.3.0.140936.p4.150482;\n SPAdes genome assembler v. 3.5.0\nGenome Coverage :: 71X\nSequencing Technology :: Illumina MiSeq; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/12/2023 07:27:59\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) :: 6,308\nCDSs (total) :: 6,242\nGenes (coding) :: 6,040\nCDSs (with protein) :: 6,040\nGenes (RNA) :: 66\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 4\nPseudo Genes (total) :: 202\nCDSs (without protein) :: 202\nPseudo Genes (ambiguous residues) :: 0 of 202\nPseudo Genes (frameshifted) :: 144 of 202\nPseudo Genes (incomplete) :: 98 of 202\nPseudo Genes (internal stop) :: 18 of 202\nPseudo Genes (multiple problems) :: 52 of 202\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_020487493.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016557667.1
COORDINATES: similar to AA sequence:RefSeq:WP_017265750.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241547.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017271873.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210723.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970612.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_003533691.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017270337.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_003535456.1
COORDINATES: similar to AA sequence:RefSeq:WP_014526740.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012652511.1
COORDINATES: similar to AA sequence:RefSeq:WP_011053350.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014188732.1
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: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_012706529.1
COORDINATES: similar to AA sequence:RefSeq:WP_013850466.1
COORDINATES: similar to AA sequence:RefSeq:WP_012707505.1
ISNCY-like element ISRsp17 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_014327452.1
COORDINATES: similar to AA sequence:RefSeq:WP_014763620.1
COORDINATES: similar to AA sequence:RefSeq:WP_017265258.1
COORDINATES: similar to AA sequence:RefSeq:WP_010967898.1
COORDINATES: similar to AA sequence:RefSeq:WP_017269570.1
COORDINATES: similar to AA sequence:RefSeq:WP_014761056.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008837405.1
COORDINATES: similar to AA sequence:RefSeq:WP_020479911.1
COORDINATES: similar to AA sequence:RefSeq:WP_014526767.1
COORDINATES: similar to AA sequence:RefSeq:WP_015007718.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003910 - DNA ligase (ATP) activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014528153.1
COORDINATES: similar to AA sequence:RefSeq:WP_014530255.1
COORDINATES: similar to AA sequence:RefSeq:WP_014763603.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003537129.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210760.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845295.1
COORDINATES: similar to AA sequence:RefSeq:WP_017268596.1
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: similar to AA sequence:RefSeq:WP_013845298.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_014330857.1
COORDINATES: similar to AA sequence:RefSeq:WP_017273444.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808071.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183759.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980713.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015495979.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018238875.1
COORDINATES: protein motif:HMM:NF013431.2
COORDINATES: protein motif:HMM:NF013757.2
IclR family transcriptional regulator C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024771.2
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: protein motif:HMM:NF013530.2
COORDINATES: similar to AA sequence:RefSeq:WP_008958899.1
COORDINATES: similar to AA sequence:RefSeq:WP_020798276.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020810040.1
COORDINATES: similar to AA sequence:RefSeq:WP_002965457.1
COORDINATES: protein motif:HMM:NF020090.2
COORDINATES: similar to AA sequence:RefSeq:WP_019042768.1
transporter substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF014653.2
COORDINATES: similar to AA sequence:RefSeq:WP_006387170.1
COORDINATES: similar to AA sequence:RefSeq:WP_017451850.1
COORDINATES: similar to AA sequence:RefSeq:WP_013232290.1
COORDINATES: similar to AA sequence:RefSeq:WP_007825624.1
amino acid ABC transporter ATP-binding protein
COORDINATES: protein motif:HMM:NF012707.2
COORDINATES: similar to AA sequence:RefSeq:WP_012735299.1
COORDINATES: similar to AA sequence:RefSeq:WP_012735298.1
GO:0030638 - polyketide metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003564910.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003592644.1
COORDINATES: similar to AA sequence:RefSeq:WP_003592645.1
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_012555908.1
COORDINATES: similar to AA sequence:RefSeq:WP_003592647.1
COORDINATES: similar to AA sequence:RefSeq:WP_020566197.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012555911.1
GO:0016773 - phosphotransferase activity, alcohol group as acceptor [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
ADP-dependent glucokinase/phosphofructokinase
COORDINATES: similar to AA sequence:RefSeq:WP_003564927.1
COORDINATES: similar to AA sequence:RefSeq:WP_006201707.1
COORDINATES: similar to AA sequence:RefSeq:WP_014762751.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326514.1
COORDINATES: similar to AA sequence:RefSeq:WP_003581607.1
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014762748.1
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_014762747.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006201703.1
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017266189.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015241453.1
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_017268591.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210779.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_013845309.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210781.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845311.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531074.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531075.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011971088.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_014531077.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_011971086.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531079.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845318.1
COORDINATES: similar to AA sequence:RefSeq:WP_017268587.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241466.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210792.1
COORDINATES: similar to AA sequence:RefSeq:WP_018327241.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328349.1
COORDINATES: similar to AA sequence:RefSeq:WP_009465831.1
COORDINATES: similar to AA sequence:RefSeq:WP_018240710.1
COORDINATES: similar to AA sequence:RefSeq:WP_018327668.1
COORDINATES: similar to AA sequence:RefSeq:WP_017275279.1
COORDINATES: similar to AA sequence:RefSeq:WP_014330893.1
COORDINATES: similar to AA sequence:RefSeq:WP_003537746.1
COORDINATES: similar to AA sequence:RefSeq:WP_017271937.1
COORDINATES: similar to AA sequence:RefSeq:WP_011971072.1
COORDINATES: similar to AA sequence:RefSeq:WP_017267339.1
COORDINATES: similar to AA sequence:RefSeq:WP_041684032.1
COORDINATES: similar to AA sequence:RefSeq:WP_012077401.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_002717997.1
COORDINATES: similar to AA sequence:RefSeq:WP_004541851.1
COORDINATES: similar to AA sequence:RefSeq:WP_010516487.1
COORDINATES: similar to AA sequence:RefSeq:WP_018075340.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241482.1
COORDINATES: similar to AA sequence:RefSeq:WP_017266548.1
COORDINATES: similar to AA sequence:RefSeq:WP_006021192.1
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018076396.1
COORDINATES: similar to AA sequence:RefSeq:WP_018235621.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970807.1
COORDINATES: similar to AA sequence:RefSeq:WP_014529576.1
COORDINATES: similar to AA sequence:RefSeq:WP_017276878.1
COORDINATES: similar to AA sequence:RefSeq:WP_012490282.1
COORDINATES: similar to AA sequence:RefSeq:WP_015633385.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241488.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241489.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241490.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241491.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241493.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241495.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241496.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469541.1
COORDINATES: similar to AA sequence:RefSeq:WP_014763460.1
GO:0009190 - cyclic nucleotide biosynthetic process [Evidence IEA]; GO:0035556 - intracellular signal transduction [Evidence IEA]
adenylate/guanylate cyclase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015887770.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332708.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332709.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0015220 - choline transmembrane transporter activity [Evidence IEA]
GO:0015871 - choline transport [Evidence IEA]
choline ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018238872.1
GO:0019285 - glycine betaine biosynthetic process from choline [Evidence IEA]; GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010017895.1
COORDINATES: similar to AA sequence:RefSeq:WP_012490208.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010875274.1
COORDINATES: similar to AA sequence:RefSeq:WP_010875273.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008120589.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326360.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326359.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010875270.1
COORDINATES: similar to AA sequence:RefSeq:WP_017961877.1
COORDINATES: similar to AA sequence:RefSeq:WP_011084957.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_010875267.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011424279.1
COORDINATES: similar to AA sequence:RefSeq:WP_011424280.1
COORDINATES: similar to AA sequence:RefSeq:WP_004371109.1
COORDINATES: similar to AA sequence:RefSeq:WP_018236702.1
COORDINATES: protein motif:HMM:NF017934.2
COORDINATES: similar to AA sequence:RefSeq:WP_014527850.1
COORDINATES: similar to AA sequence:RefSeq:WP_003532145.1
COORDINATES: similar to AA sequence:RefSeq:WP_018237760.1
COORDINATES: similar to AA sequence:RefSeq:WP_017997371.1
COORDINATES: similar to AA sequence:RefSeq:WP_012828143.1
COORDINATES: similar to AA sequence:RefSeq:WP_012143940.1
COORDINATES: similar to AA sequence:RefSeq:WP_018045411.1
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_002714884.1
COORDINATES: similar to AA sequence:RefSeq:WP_003596727.1
COORDINATES: similar to AA sequence:RefSeq:WP_017436379.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845881.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007690479.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014331692.1
COORDINATES: similar to AA sequence:RefSeq:WP_014331691.1
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
putative FMN-dependent luciferase-like monooxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_015342440.1
COORDINATES: similar to AA sequence:RefSeq:WP_014331689.1
COORDINATES: similar to AA sequence:RefSeq:WP_009764445.1
COORDINATES: similar to AA sequence:RefSeq:WP_014331688.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
TIGR04028 family ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_015929302.1
COORDINATES: similar to AA sequence:RefSeq:WP_014763126.1
COORDINATES: similar to AA sequence:RefSeq:WP_014764407.1
COORDINATES: protein motif:HMM:NF024880.2
COORDINATES: similar to AA sequence:RefSeq:WP_018238461.1
sugar phosphate isomerase/epimerase and 4-hydroxyphenylpyruvate domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018238460.1
COORDINATES: similar to AA sequence:RefSeq:WP_018238459.1
COORDINATES: similar to AA sequence:RefSeq:WP_018238458.1
COORDINATES: similar to AA sequence:RefSeq:WP_014762888.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_018456032.1
COORDINATES: similar to AA sequence:RefSeq:WP_014762886.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_015888326.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612156.1
COORDINATES: similar to AA sequence:RefSeq:WP_018238416.1
COORDINATES: similar to AA sequence:RefSeq:WP_012482712.1
COORDINATES: similar to AA sequence:RefSeq:WP_014762823.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970882.1
COORDINATES: similar to AA sequence:RefSeq:WP_012706293.1
COORDINATES: protein motif:HMM:NF014667.2
COORDINATES: protein motif:HMM:NF024583.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015745129.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003929716.1
COORDINATES: similar to AA sequence:RefSeq:WP_007675032.1
frameshifted; 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_014332645.1
COORDINATES: protein motif:HMM:NF037660.2
COORDINATES: similar to AA sequence:RefSeq:WP_015241539.1
COORDINATES: similar to AA sequence:RefSeq:WP_013851074.1
COORDINATES: similar to AA sequence:RefSeq:WP_012881324.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241542.1
COORDINATES: similar to AA sequence:RefSeq:WP_018010470.1
zincin-like metallopeptidase domain-containing protein