Rhizobium gallicum bv. gallicum R602sp strain R602 voucher MSDJ1109 plasmid pRgalR602a, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
Complete genome sequence of Rhizobium gallicum bv. gallicum R602
Submitted (08-NOV-2013) Programa de Genomica Evolutiva, Centro de Ciencias Genomicas U.N.A.M., Av. Universidad s/n, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
REFSEQ INFORMATION: The reference sequence is identical to\nCP006878.1.\nBacterial strain is available under request to Dr. Esperanza\nMartinez (emartine@ccg.unam.mx).\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 :: Velvet v. 1.1.06; Newbler v. 5.3;\n phred_Phrap/Consed23; Sspace_Bassic v. 2.0\nGenome Coverage :: 150x\nSequencing Technology :: 454 GS; Titanium; Illumina GAII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/30/2022 05:18:50\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 7,102\nCDSs (total) :: 7,038\nGenes (coding) :: 6,660\nCDSs (with protein) :: 6,660\nGenes (RNA) :: 64\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 4\nPseudo Genes (total) :: 378\nCDSs (without protein) :: 378\nPseudo Genes (ambiguous residues) :: 0 of 378\nPseudo Genes (frameshifted) :: 225 of 378\nPseudo Genes (incomplete) :: 275 of 378\nPseudo Genes (internal stop) :: 55 of 378\nPseudo Genes (multiple problems) :: 155 of 378\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Agricultural field (no beans grown in the 5 previous years)
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007539569.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003518564.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007706586.1
COORDINATES: protein motif:HMM:NF025448.2
COORDINATES: similar to AA sequence:RefSeq:WP_018903831.1
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: similar to AA sequence:RefSeq:WP_011251461.1
COORDINATES: similar to AA sequence:RefSeq:WP_007605812.1
COORDINATES: similar to AA sequence:RefSeq:WP_007605811.1
COORDINATES: similar to AA sequence:RefSeq:WP_007605809.1
COORDINATES: similar to AA sequence:RefSeq:WP_010141875.1
COORDINATES: protein motif:HMM:NF022019.2
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_018245375.1
COORDINATES: similar to AA sequence:RefSeq:WP_018517447.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489415.1
COORDINATES: similar to AA sequence:RefSeq:WP_018329045.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328754.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013637032.1
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_018142663.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328796.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_004129840.1
COORDINATES: similar to AA sequence:RefSeq:WP_011648863.1
GO:0007165 - signal transduction [Evidence IEA]
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_018328798.1
COORDINATES: similar to AA sequence:RefSeq:WP_003586078.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328800.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004674371.1
N-acyl homoserine lactonase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002715008.1
COORDINATES: similar to AA sequence:RefSeq:WP_003586069.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328804.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328805.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_012707178.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328807.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328808.1
COORDINATES: similar to AA sequence:RefSeq:WP_003586055.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003586052.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328811.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328812.1
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328813.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328814.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328815.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_003586045.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019205 - nucleobase-containing compound kinase activity [Evidence IEA]
GO:0006139 - nucleobase-containing compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328817.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018328819.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328820.1
COORDINATES: similar to AA sequence:RefSeq:WP_012760411.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129830.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328823.1
four-carbon acid sugar kinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328824.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328825.1
GO:0018784 - (S)-2-haloacid dehalogenase activity [Evidence IEA]
GO:0006805 - xenobiotic metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328826.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129804.1
isocitrate/isopropylmalate dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004129802.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328829.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129795.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129793.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328832.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004129789.1
GO:0004802 - transketolase activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004129787.1
GO:0042132 - fructose 1,6-bisphosphate 1-phosphatase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328835.1
GO:0004332 - fructose-bisphosphate aldolase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis, and/or gluconeogenesis; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018444789.1
GO:0004807 - triose-phosphate isomerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007817073.1
RpiB/LacA/LacB family sugar-phosphate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_018328838.1
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_004129782.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328840.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129780.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328842.1
COORDINATES: similar to AA sequence:RefSeq:WP_007636546.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129775.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328845.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328846.1
ribulose-bisphosphate carboxylase large subunit family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004129768.1
COORDINATES: similar to AA sequence:RefSeq:WP_007636554.1
GO:0061710 - L-threonylcarbamoyladenylate synthase [Evidence IEA]
GO:0006400 - tRNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328849.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328850.1
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: similar to AA sequence:RefSeq:WP_016150210.1
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_002965778.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004129756.1
COORDINATES: similar to AA sequence:RefSeq:WP_008534165.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489432.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_018328855.1
COORDINATES: similar to AA sequence:RefSeq:WP_004674388.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328857.1
COORDINATES: similar to AA sequence:RefSeq:WP_012707203.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129732.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328858.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328859.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328860.1
functions to transport ribose at high affinity; forms a complex with RbsA2C2B; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018328861.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129717.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008741 - ribulokinase activity [Evidence IEA]
GO:0019569 - L-arabinose catabolic process to xylulose 5-phosphate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328863.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015341888.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328865.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129705.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007636580.1
COORDINATES: similar to AA sequence:RefSeq:WP_004668623.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129694.1
COORDINATES: similar to AA sequence:RefSeq:WP_004668627.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341892.1
COORDINATES: similar to AA sequence:RefSeq:WP_004668632.1
COORDINATES: similar to AA sequence:RefSeq:WP_004668634.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341894.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489473.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328889.1
COORDINATES: similar to AA sequence:RefSeq:WP_016737438.1
COORDINATES: similar to AA sequence:RefSeq:WP_004671512.1
COORDINATES: similar to AA sequence:RefSeq:WP_004671509.1
COORDINATES: similar to AA sequence:RefSeq:WP_004671507.1
COORDINATES: similar to AA sequence:RefSeq:WP_004671505.1
COORDINATES: similar to AA sequence:RefSeq:WP_004671504.1
COORDINATES: similar to AA sequence:RefSeq:WP_016737426.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328898.1
HAMP domain-containing methyl-accepting chemotaxis protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328899.1
COORDINATES: similar to AA sequence:RefSeq:WP_011084489.1
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.
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_007636478.1
bifunctional diguanylate cyclase/phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_007636476.1
COORDINATES: similar to AA sequence:RefSeq:WP_007636470.1
COORDINATES: similar to AA sequence:RefSeq:WP_052642687.1
frameshifted; 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_018328905.1
GO:0008686 - 3,4-dihydroxy-2-butanone-4-phosphate synthase activity [Evidence IEA]
3,4-dihydroxy-2-butanone-4-phosphate synthase
COORDINATES: similar to AA sequence:RefSeq:WP_018328906.1
COORDINATES: similar to AA sequence:RefSeq:WP_007636460.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328908.1
COORDINATES: similar to AA sequence:RefSeq:WP_007636455.1
COORDINATES: similar to AA sequence:RefSeq:WP_009987854.1
COORDINATES: similar to AA sequence:RefSeq:WP_004130101.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013984725.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328913.1
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_004130093.1
COORDINATES: similar to AA sequence:RefSeq:WP_004130091.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341910.1
COORDINATES: similar to AA sequence:RefSeq:WP_007636442.1
COORDINATES: similar to AA sequence:RefSeq:WP_007636440.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341912.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341913.1
zinc-dependent alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328920.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328921.1
COORDINATES: similar to AA sequence:RefSeq:WP_012489435.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
glycoside hydrolase family 3 C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014529321.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328926.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341919.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015341920.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328930.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328931.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328932.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341923.1
COORDINATES: similar to AA sequence:RefSeq:WP_002969174.1
COORDINATES: similar to AA sequence:RefSeq:WP_002971374.1
GO:0004371 - glycerone kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015341926.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516748.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003525125.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048108.1
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_011427427.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011427428.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427429.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427430.1
COORDINATES: similar to AA sequence:RefSeq:WP_007539642.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427433.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007636626.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477327.1
COORDINATES: similar to AA sequence:RefSeq:WP_003506626.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328954.1
COORDINATES: similar to AA sequence:RefSeq:WP_007636623.1
COORDINATES: similar to AA sequence:RefSeq:WP_004119812.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341944.1
COORDINATES: similar to AA sequence:RefSeq:WP_007536732.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_018516734.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_007637593.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048127.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_011427444.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129936.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341958.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007538730.1
COORDINATES: similar to AA sequence:RefSeq:WP_018009669.1
COORDINATES: similar to AA sequence:RefSeq:WP_004672730.1