Allorhizobium ampelinum S4 plasmid pAtS4b, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Allorhizobium; Allorhizobium ampelinum.
Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria
Submitted (14-MAR-2007) Virginia Bioinformatics Institute, Virginia Tech, Washington Street, Box 0477, Blacksburg, VA 24061, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000635.1.\nStrain/DNA available from Tom Burr, Cornell University,\ntjb1@cornell.edu. A. vitis S4 was isolated by Dr. Erno Szegedi in\n1981 from aerial gall that developed on a two-year-old woody\ngrapevine cane.\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 :: 02/05/2023 19:47:51\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) :: 5,800\nCDSs (total) :: 5,729\nGenes (coding) :: 5,554\nCDSs (with protein) :: 5,554\nGenes (RNA) :: 71\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 4\nPseudo Genes (total) :: 175\nCDSs (without protein) :: 175\nPseudo Genes (ambiguous residues) :: 0 of 175\nPseudo Genes (frameshifted) :: 82 of 175\nPseudo Genes (incomplete) :: 122 of 175\nPseudo Genes (internal stop) :: 28 of 175\nPseudo Genes (multiple problems) :: 52 of 175\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_009109568.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009109570.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653007.1
COORDINATES: similar to AA sequence:RefSeq:WP_003498570.1
COORDINATES: similar to AA sequence:RefSeq:WP_007763662.1
COORDINATES: similar to AA sequence:RefSeq:WP_008872104.1
COORDINATES: similar to AA sequence:RefSeq:WP_013525336.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993085.1
COORDINATES: similar to AA sequence:RefSeq:WP_017271252.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332783.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013845224.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_020809218.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007693406.1
GO:0022627 - cytosolic small ribosomal subunit [Evidence IEA]; GO:0000314 - organellar small ribosomal subunit [Evidence IEA]
GO:0003735 - structural constituent of ribosome [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: protein motif:HMM:NF025388.2
COORDINATES: similar to AA sequence:RefSeq:WP_004212819.1
COORDINATES: similar to AA sequence:RefSeq:WP_001138082.1
GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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:NF024685.2
COORDINATES: similar to AA sequence:RefSeq:WP_017245160.1
COORDINATES: similar to AA sequence:RefSeq:WP_018517359.1
COORDINATES: similar to AA sequence:RefSeq:WP_006022639.1
COORDINATES: similar to AA sequence:RefSeq:WP_003529140.1
COORDINATES: similar to AA sequence:RefSeq:WP_007812123.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024252.2
COORDINATES: similar to AA sequence:RefSeq:WP_018097546.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003508774.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501412.1
COORDINATES: similar to AA sequence:RefSeq:WP_003508776.1
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_007199847.1
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501408.1
COORDINATES: similar to AA sequence:RefSeq:WP_003526135.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913785.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655055.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341931.1
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_018240815.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654731.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654887.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982960.1
COORDINATES: protein motif:HMM:NF015354.2
COORDINATES: similar to AA sequence:RefSeq:WP_018516741.1
COORDINATES: similar to AA sequence:RefSeq:WP_006472572.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578771.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341926.1
COORDINATES: protein motif:HMM:NF024098.2
COORDINATES: similar to AA sequence:RefSeq:WP_011654735.1
COORDINATES: similar to AA sequence:RefSeq:WP_006470229.1
COORDINATES: protein motif:HMM:NF037136.2
COORDINATES: similar to AA sequence:RefSeq:WP_012477327.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018482046.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048120.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048121.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892380.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_003501745.1
COORDINATES: similar to AA sequence:RefSeq:WP_006470240.1
COORDINATES: similar to AA sequence:RefSeq:WP_010875410.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_006470242.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_006470243.1
COORDINATES: similar to AA sequence:RefSeq:WP_006470244.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006470245.1
COORDINATES: similar to AA sequence:RefSeq:WP_018237450.1
GO:0004068 - aspartate 1-decarboxylase activity [Evidence IEA]
GO:0006523 - alanine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011376889.1
GO:0008146 - sulfotransferase activity [Evidence IEA]
sulfotransferase family 2 domain-containing protein
COORDINATES: protein motif:HMM:TIGR01141.1
GO:0004400 - histidinol-phosphate transaminase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012885.2
isopropylmalate/homocitrate/citramalate synthase
COORDINATES: protein motif:HMM:NF015411.2
COORDINATES: protein motif:HMM:NF012869.2
COORDINATES: protein motif:HMM:NF015527.2
COORDINATES: protein motif:HMM:NF012610.2
COORDINATES: similar to AA sequence:RefSeq:WP_015886710.1
COORDINATES: similar to AA sequence:RefSeq:WP_071831742.1
IS21-like element ISRel3 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_012976703.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611156.1
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_014531097.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017528.2
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_076612018.1
COORDINATES: similar to AA sequence:RefSeq:WP_006473471.1
COORDINATES: protein motif:HMM:NF012427.2
COORDINATES: protein motif:HMM:NF004035.0
GO:0004020 - adenylylsulfate kinase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006206275.1
GO:0004781 - sulfate adenylyltransferase (ATP) activity [Evidence IEA]
GO:0019419 - sulfate reduction [Evidence IEA]
sulfate adenylyltransferase subunit CysD
COORDINATES: protein motif:HMM:NF014698.2
COORDINATES: protein motif:HMM:NF002458.0
GO:0009316 - 3-isopropylmalate dehydratase complex [Evidence IEA]
GO:0003861 - 3-isopropylmalate dehydratase activity [Evidence IEA]
GO:0009098 - leucine biosynthetic process [Evidence IEA]
3-isopropylmalate dehydratase small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_014199181.1
3-isopropylmalate dehydratase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018546573.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF003417.0
COORDINATES: protein motif:HMM:NF013786.2
GO:0008897 - holo-[acyl-carrier-protein] synthase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
4'-phosphopantetheinyl transferase superfamily protein
COORDINATES: similar to AA sequence:RefSeq:WP_004125932.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974832.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_006473165.1
COORDINATES: protein motif:HMM:NF010413.0
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_018482029.1
COORDINATES: protein motif:HMM:NF010415.0
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_011505220.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_013913818.1
COORDINATES: similar to AA sequence:RefSeq:WP_013984785.1
COORDINATES: similar to AA sequence:RefSeq:WP_006473157.1
COORDINATES: similar to AA sequence:RefSeq:WP_007767702.1
COORDINATES: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: protein motif:HMM:NF012967.2
GO:0016740 - transferase activity [Evidence IEA]