Mesorhizobium amorphae CCNWGS0123 plasmid pM0123a.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Phyllobacteriaceae; Mesorhizobium.
Resequencineg of Mesorhizobium amorphae CCNWGS0123 and comparative plasmidome of 23 symbiotic plasmids from Rhizobia
Submitted (20-APR-2016) College of Life Science, Northwest A&F University, State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, 22 Xinong Road, Yangling 712100, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP015319.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: Celera Assembler v. 8.1\nGenome Coverage :: 134.86X\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/27/2023 03:22:01\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) :: 6,961\nCDSs (total) :: 6,899\nGenes (coding) :: 6,671\nCDSs (with protein) :: 6,671\nGenes (RNA) :: 62\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 4\nPseudo Genes (total) :: 228\nCDSs (without protein) :: 228\nPseudo Genes (ambiguous residues) :: 0 of 228\nPseudo Genes (frameshifted) :: 146 of 228\nPseudo Genes (incomplete) :: 159 of 228\nPseudo Genes (internal stop) :: 39 of 228\nPseudo Genes (multiple problems) :: 96 of 228\n##Genome-Annotation-Data-END##
COORDINATES: similar to AA sequence:RefSeq:WP_019963493.1
incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024771.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: protein motif:HMM:NF020039.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
SMP-30/gluconolactonase/LRE family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_018486334.1
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_011085983.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016654992.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008173413.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006205520.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006205519.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006201736.1
COORDINATES: similar to AA sequence:RefSeq:WP_006201737.1
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_006205516.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006205515.1
class II aldolase/adducin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006205514.1
COORDINATES: protein motif:HMM:NF014068.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019965754.1
COORDINATES: similar to AA sequence:RefSeq:WP_006339618.1
GO:0051304 - chromosome separation [Evidence IEA]
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: similar to AA sequence:RefSeq:WP_020737909.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_007673600.1
COORDINATES: similar to AA sequence:RefSeq:WP_015008551.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004830523.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649795.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015497310.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003588438.1
GO:0070403 - NAD+ binding [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009812749.1
COORDINATES: similar to AA sequence:RefSeq:WP_011350386.1
GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016907292.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: similar to AA sequence:RefSeq:WP_019294449.1
COORDINATES: similar to AA sequence:RefSeq:WP_003588447.1
ring-hydroxylating oxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_009812755.1
COORDINATES: similar to AA sequence:RefSeq:WP_015497316.1
COORDINATES: similar to AA sequence:RefSeq:WP_013949885.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0015837 - amine transport [Evidence IEA]
Members of the family are the ATP-binding subunit of ABC transporters for substrates such as betaine, L-proline or other amino acids, choline, carnitine, etc. The substrate specificity is best determined from the substrate-binding subunit, rather than this subunit, as it interacts with the permease subunit and not with substrate directly.; Members of the family are the ATP-binding subunit of ABC transporters for substrates such as betaine, L-proline or other amino acids, choline, carnitine, etc. The substrate specificity is best determined from the substrate-binding subunit, rather than this subunit, as it interacts with the permease subunit and not with substrate directly; Derived by automated computational analysis using gene prediction method: Protein Homology.
betaine/proline/choline family ABC transporter ATP-binding protein
COORDINATES: protein motif:HMM:NF012738.2
COORDINATES: similar to AA sequence:RefSeq:WP_012507531.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014893.2
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019859987.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006201719.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017183759.1
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_012275061.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019171639.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013649046.1
phosphoenolpyruvate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010875242.1
Tm-1-like ATP-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007917251.1
COORDINATES: similar to AA sequence:RefSeq:WP_004677318.1
COORDINATES: protein motif:HMM:NF013567.2
COORDINATES: similar to AA sequence:RefSeq:WP_006325405.1
COORDINATES: similar to AA sequence:RefSeq:WP_019862711.1
COORDINATES: similar to AA sequence:RefSeq:WP_006325409.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004434108.1
COORDINATES: similar to AA sequence:RefSeq:WP_007826120.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_017264686.1
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_015445642.1
COORDINATES: similar to AA sequence:RefSeq:WP_010970005.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011975103.1
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018327356.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
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_004127721.1
COORDINATES: similar to AA sequence:RefSeq:WP_010153417.1
phytanoyl-CoA dioxygenase family protein
COORDINATES: protein motif:HMM:NF037679.2
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF015995.2
COORDINATES: similar to AA sequence:RefSeq:WP_013896766.1
COORDINATES: similar to AA sequence:RefSeq:WP_011087473.1
COORDINATES: similar to AA sequence:RefSeq:WP_020047865.1
COORDINATES: similar to AA sequence:RefSeq:WP_013525333.1
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_019200234.1
COORDINATES: similar to AA sequence:RefSeq:WP_006205756.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048164.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650748.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578805.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007636254.1
COORDINATES: similar to AA sequence:RefSeq:WP_007283928.1
COORDINATES: similar to AA sequence:RefSeq:WP_015677268.1
COORDINATES: similar to AA sequence:RefSeq:WP_015472924.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
Eco57I restriction-modification methylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015472923.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015472922.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009238709.1
COORDINATES: similar to AA sequence:RefSeq:WP_010915768.1
COORDINATES: similar to AA sequence:RefSeq:WP_010915943.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010915944.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564797.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023699.1
COORDINATES: similar to AA sequence:RefSeq:WP_013533298.1
COORDINATES: similar to AA sequence:RefSeq:WP_010915955.1