Agarilytica rhodophyticola strain 017 plasmid pSU1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Cellvibrionales; Cellvibrionaceae; Agarilytica.
Agarilytica rhodophyticola complete plasmid sequencing and assembly
Submitted (30-MAY-2017) College of Marine Science, Shandong University at Weihai, 180 Wen Hua Xi Lu, Weihai, Shandong Province 264209, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP021745.1.\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##Assembly-Data-START##\nAssembly Method :: SOAPdenovo v. v2.04; GapCloser v. v1.12\nSequencing Technology :: Illumina; PacBio\n##Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/04/2023 04:11:02\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) :: 5,860\nCDSs (total) :: 5,773\nGenes (coding) :: 5,753\nCDSs (with protein) :: 5,753\nGenes (RNA) :: 87\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 74\nncRNAs :: 4\nPseudo Genes (total) :: 20\nCDSs (without protein) :: 20\nPseudo Genes (ambiguous residues) :: 0 of 20\nPseudo Genes (frameshifted) :: 6 of 20\nPseudo Genes (incomplete) :: 18 of 20\nPseudo Genes (internal stop) :: 3 of 20\nPseudo Genes (multiple problems) :: 5 of 20\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Agarilytica rhodophyticola
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF017719.2
GO:0030254 - protein secretion by the type III secretion system [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
CesT family type III secretion system chaperone
COORDINATES: protein motif:HMM:NF018431.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF012339.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: protein motif:HMM:NF012699.2
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013307101.1
COORDINATES: protein motif:HMM:NF025769.2
COORDINATES: protein motif:HMM:NF023802.2
papain-like cysteine protease family protein
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: protein motif:HMM:NF024758.2
trypsin-like peptidase domain-containing protein
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF038122.1
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0052621 - diguanylate cyclase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_076612253.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF014862.2
Clp protease N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007076043.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008264579.1
COORDINATES: protein motif:HMM:NF025168.2
COORDINATES: protein motif:HMM:NF014566.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0071586 - CAAX-box protein processing [Evidence IEA]
CPBP family intramembrane metalloprotease
COORDINATES: protein motif:HMM:NF015585.2
COORDINATES: similar to AA sequence:RefSeq:WP_018414727.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF041278.1
COORDINATES: protein motif:HMM:NF012296.2
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: protein motif:HMM:NF023329.2
COORDINATES: similar to AA sequence:RefSeq:WP_011494896.1
COORDINATES: similar to AA sequence:RefSeq:WP_010362561.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF012859.2
COORDINATES: similar to AA sequence:RefSeq:WP_018275139.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008251014.1
COORDINATES: similar to AA sequence:RefSeq:WP_017876018.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015412 - ABC-type molybdate transporter activity [Evidence IEA]; GO:0030973 - molybdate ion binding [Evidence IEA]
GO:0015689 - molybdate ion transport [Evidence IEA]
molybdate ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF024765.2
COORDINATES: similar to AA sequence:RefSeq:WP_006758655.1
COORDINATES: similar to AA sequence:RefSeq:WP_010558247.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0004601 - peroxidase activity [Evidence IEA]
GO:0006979 - response to oxidative stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018014685.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018276036.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: protein motif:HMM:NF013793.2
ParB/RepB/Spo0J family partition protein
ligand-binding sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_020592547.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione-dependent disulfide-bond oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013648389.1
COORDINATES: protein motif:HMM:NF024854.2
COORDINATES: protein motif:HMM:NF021778.2
beta-propeller fold lactonase family protein
COORDINATES: protein motif:HMM:NF012235.2
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF012873.2
COORDINATES: similar to AA sequence:RefSeq:WP_017930749.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF020771.2
CerR family C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013069.2
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: protein motif:HMM:TIGR01845.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: protein motif:HMM:NF012632.2
COORDINATES: protein motif:HMM:NF024242.2
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019030083.1
COORDINATES: protein motif:HMM:NF021584.2
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_009830841.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013777.2
COORDINATES: protein motif:HMM:NF012546.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: similar to AA sequence:RefSeq:WP_014949203.1
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_002685560.1
COORDINATES: protein motif:HMM:NF015387.2
GO:0030246 - carbohydrate binding [Evidence IEA]