Caulobacter rhizosphaerae strain KCTC 52515 plasmid unnamed.
Bacteria; Pseudomonadota; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Caulobacter.
Submitted (11-FEB-2020) College of Biology and the Environment, Nanjing Forestry University, Longpan 59, Nanjing, Jiangsu 210000, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP048816.1.\nBacteria and source DNA available from KCTC 52515.\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 :: DEC-2019\nAssembly Method :: unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 174.0x\nSequencing Technology :: Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/24/2023 04:20:11\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) :: 5,456\nCDSs (total) :: 5,396\nGenes (coding) :: 5,310\nCDSs (with protein) :: 5,310\nGenes (RNA) :: 60\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 3\nPseudo Genes (total) :: 86\nCDSs (without protein) :: 86\nPseudo Genes (ambiguous residues) :: 0 of 86\nPseudo Genes (frameshifted) :: 46 of 86\nPseudo Genes (incomplete) :: 67 of 86\nPseudo Genes (internal stop) :: 3 of 86\nPseudo Genes (multiple problems) :: 29 of 86\n##Genome-Annotation-Data-END##
type strain of Caulobacter rhizosphaerae
COORDINATES: similar to AA sequence:RefSeq:WP_012279485.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012520558.1
COORDINATES: similar to AA sequence:RefSeq:WP_007664962.1
COORDINATES: similar to AA sequence:RefSeq:WP_007664956.1
COORDINATES: similar to AA sequence:RefSeq:WP_007662795.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF033522.2
COORDINATES: protein motif:HMM:NF033537.1
COORDINATES: protein motif:HMM:NF012936.2
COORDINATES: protein motif:HMM:NF033523.0
COORDINATES: similar to AA sequence:RefSeq:WP_007662809.1
GO:0015267 - channel activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF016648.2
COORDINATES: similar to AA sequence:RefSeq:WP_007662812.1
GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
nucleoside triphosphate pyrophosphohydrolase
COORDINATES: protein motif:HMM:NF012792.2
COORDINATES: similar to AA sequence:RefSeq:WP_013845228.1
COORDINATES: protein motif:HMM:NF013964.2
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF019157.2
tannase/feruloyl esterase family alpha/beta hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_009337819.1
COORDINATES: similar to AA sequence:RefSeq:WP_012522936.1
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012279450.1
COORDINATES: protein motif:HMM:NF019370.2
COORDINATES: similar to AA sequence:RefSeq:WP_012522737.1
COORDINATES: similar to AA sequence:RefSeq:WP_012275016.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF019376.2
COORDINATES: similar to AA sequence:RefSeq:WP_007661437.1
COORDINATES: similar to AA sequence:RefSeq:WP_012279444.1
COORDINATES: similar to AA sequence:RefSeq:WP_012279443.1
COORDINATES: similar to AA sequence:RefSeq:WP_012279442.1
COORDINATES: similar to AA sequence:RefSeq:WP_007661420.1
COORDINATES: similar to AA sequence:RefSeq:WP_012279438.1
COORDINATES: similar to AA sequence:RefSeq:WP_012279436.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007661395.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818531.1
COORDINATES: protein motif:HMM:NF014567.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_014260086.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017979715.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_019515550.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010215456.1
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_004212085.1
COORDINATES: protein motif:HMM:NF014850.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
glycoside hydrolase family 2 TIM barrel-domain containing protein
COORDINATES: protein motif:HMM:NF040071.1
COORDINATES: similar to AA sequence:RefSeq:WP_011522912.1
glycoside hydrolase family 3 C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008830707.1
COORDINATES: protein motif:HMM:NF024589.2
COORDINATES: similar to AA sequence:RefSeq:YP_002518137.2
COORDINATES: similar to AA sequence:RefSeq:YP_002518510.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: protein motif:HMM:NF024758.2
trypsin-like peptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_002515958.1
COORDINATES: similar to AA sequence:RefSeq:YP_002515956.4
GO:0008233 - peptidase activity [Evidence IEA]; GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_002515955.3
COORDINATES: protein motif:HMM:NF039499.1
COORDINATES: similar to AA sequence:RefSeq:WP_013300227.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014880291.1
GO:0015891 - siderophore transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF019474.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020655595.1
COORDINATES: protein motif:HMM:NF014066.2
COORDINATES: protein motif:HMM:NF013429.2
GO:0016853 - isomerase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014026.2
COORDINATES: protein motif:HMM:NF024803.2
COORDINATES: similar to AA sequence:RefSeq:WP_011655266.1
COORDINATES: protein motif:HMM:NF017479.2
COORDINATES: similar to AA sequence:RefSeq:WP_012284674.1
serine hydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006726155.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_012709484.1
COORDINATES: similar to AA sequence:RefSeq:WP_019926710.1
COORDINATES: protein motif:HMM:NF024141.2
COORDINATES: similar to AA sequence:RefSeq:WP_019848378.1
COORDINATES: protein motif:HMM:NF012655.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008264149.1
COORDINATES: similar to AA sequence:RefSeq:WP_013837084.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503156.1
COORDINATES: similar to AA sequence:RefSeq:WP_004615669.1
COORDINATES: similar to AA sequence:RefSeq:WP_013715785.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007675814.1
GO:0003985 - acetyl-CoA C-acetyltransferase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020205071.1
COORDINATES: similar to AA sequence:RefSeq:WP_018062032.1
COORDINATES: protein motif:HMM:NF005714.0
COORDINATES: protein motif:HMM:NF013567.2
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: protein motif:HMM:NF012363.2
COORDINATES: similar to AA sequence:RefSeq:WP_019848377.1
COORDINATES: protein motif:HMM:TIGR00792.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF028442.2
COORDINATES: protein motif:HMM:NF012371.2
COORDINATES: protein motif:HMM:NF013866.2
COORDINATES: similar to AA sequence:RefSeq:WP_017500967.1
COORDINATES: similar to AA sequence:RefSeq:WP_013078906.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953469.1
COORDINATES: similar to AA sequence:RefSeq:WP_013079844.1
GO:0003824 - catalytic activity [Evidence IEA]
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008019871.1
GO:0050032 - L-rhamnonate dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019368872.1
COORDINATES: similar to AA sequence:RefSeq:WP_013079841.1
COORDINATES: similar to AA sequence:RefSeq:WP_019847833.1
COORDINATES: similar to AA sequence:RefSeq:WP_013079840.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0004457 - lactate dehydrogenase activity [Evidence IEA]
GO:0006089 - lactate metabolic process [Evidence IEA]
FMN-dependent L-lactate dehydrogenase LldD
COORDINATES: protein motif:HMM:NF012457.2
COORDINATES: protein motif:HMM:NF036578.2
COORDINATES: protein motif:HMM:TIGR00976.1
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008069082.1
GO:0016901 - oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor [Evidence IEA]
GO:0006089 - lactate metabolic process [Evidence IEA]; GO:0019516 - lactate oxidation [Evidence IEA]
COORDINATES: protein motif:HMM:NF019349.2
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007558009.1
GO:0016836 - hydro-lyase activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013640150.1
COORDINATES: protein motif:HMM:NF012422.2
COORDINATES: similar to AA sequence:RefSeq:WP_012279499.1
COORDINATES: similar to AA sequence:RefSeq:WP_012279498.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_007662413.1
COORDINATES: similar to AA sequence:RefSeq:WP_007662417.1
COORDINATES: similar to AA sequence:RefSeq:WP_012279494.1
COORDINATES: similar to AA sequence:RefSeq:WP_012279493.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_012279492.1
COORDINATES: similar to AA sequence:RefSeq:WP_010123967.1
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_007665661.1
COORDINATES: similar to AA sequence:RefSeq:WP_007665662.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007665663.1
COORDINATES: similar to AA sequence:RefSeq:WP_007664977.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018871325.1
helix-turn-helix domain-containing protein