Rhodoferax koreense strain DCY-110 plasmid unnamed1.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Rhodoferax.
Submitted (13-JAN-2017) College of Health Science, Korea University, Anamro, Seoul 02841, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP019237.1.\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 Date :: 21-DEC-2016\nAssembly Method :: PacBio SMRT Analysis v. v2.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 146.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/12/2023 01:38:27\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) :: 5,519\nCDSs (total) :: 5,460\nGenes (coding) :: 5,385\nCDSs (with protein) :: 5,385\nGenes (RNA) :: 59\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 75\nCDSs (without protein) :: 75\nPseudo Genes (ambiguous residues) :: 0 of 75\nPseudo Genes (frameshifted) :: 40 of 75\nPseudo Genes (incomplete) :: 54 of 75\nPseudo Genes (internal stop) :: 6 of 75\nPseudo Genes (multiple problems) :: 21 of 75\n##Genome-Annotation-Data-END##
COORDINATES: similar to AA sequence:RefSeq:WP_013689236.1
GO:0016787 - hydrolase activity [Evidence IEA]
frameshifted; incomplete; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012367108.1
GO:0008838 - diaminopropionate ammonia-lyase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019701382.1
COORDINATES: similar to AA sequence:RefSeq:WP_012631089.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012631090.1
COORDINATES: similar to AA sequence:RefSeq:WP_015687573.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015837 - amine transport [Evidence IEA]
The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc.; The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012707.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
transporter substrate-binding domain-containing protein
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_014616174.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018006582.1
GO:0006750 - glutathione biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012206186.1
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_016446384.1
COORDINATES: similar to AA sequence:RefSeq:WP_003274149.1
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_076612070.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011800699.1
TetR/AcrR family transcriptional regulator
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008964415.1
COORDINATES: similar to AA sequence:RefSeq:WP_018609948.1
COORDINATES: similar to AA sequence:RefSeq:WP_007248553.1
COORDINATES: similar to AA sequence:RefSeq:WP_011659691.1
COORDINATES: similar to AA sequence:RefSeq:WP_007381849.1
COORDINATES: similar to AA sequence:RefSeq:WP_018421926.1
COORDINATES: similar to AA sequence:RefSeq:WP_018905524.1
GO:0003824 - catalytic activity [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: similar to AA sequence:RefSeq:WP_008305096.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011797809.1
acetaldehyde dehydrogenase (acetylating)
COORDINATES: protein motif:HMM:NF024934.2
COORDINATES: protein motif:HMM:NF012257.2
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010162363.1
frameshifted; incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.