Pseudovibrio brasiliensis strain Ab134 plasmid pAb134-03.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Stappiaceae; Pseudovibrio.
A novel family of nonribosomal peptides modulate collective behavior in Pseudovibrio bacteria isolated from marine sponges
Submitted (03-MAY-2021) Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP074129.1.\nBacteria and source DNA available from Alessandra S. Eustaquio,\nUniversity of Illinois at Chicago.\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 Method :: SPAdes v. SEP-2017\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 400.0x\nSequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 11:08:44\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) :: 5,418\nCDSs (total) :: 5,324\nGenes (coding) :: 5,296\nCDSs (with protein) :: 5,296\nGenes (RNA) :: 94\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 72\nncRNAs :: 4\nPseudo Genes (total) :: 28\nCDSs (without protein) :: 28\nPseudo Genes (ambiguous residues) :: 0 of 28\nPseudo Genes (frameshifted) :: 5 of 28\nPseudo Genes (incomplete) :: 24 of 28\nPseudo Genes (internal stop) :: 8 of 28\nPseudo Genes (multiple problems) :: 6 of 28\n##Genome-Annotation-Data-END##
type strain of Pseudovibrio brasiliensis
Brazil: Joao Fernandinho Beach, Buzios, state of Rio de Janeiro
COORDINATES: protein motif:HMM:NF040974.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010375789.1
COORDINATES: similar to AA sequence:RefSeq:WP_010375788.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831382.1
COORDINATES: similar to AA sequence:RefSeq:WP_006021198.1
COORDINATES: protein motif:HMM:NF024242.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009488601.1
COORDINATES: similar to AA sequence:RefSeq:WP_018659883.1
COORDINATES: similar to AA sequence:RefSeq:WP_008759252.1
COORDINATES: protein motif:HMM:NF017832.2
COORDINATES: similar to AA sequence:RefSeq:WP_011287949.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
Qat anti-phage system TatD family nuclease QatD
COORDINATES: similar to AA sequence:RefSeq:WP_020179958.1
Qat anti-phage system QueC-like protein QatC
COORDINATES: similar to AA sequence:RefSeq:WP_009822949.1
Qat anti-phage system associated protein QatB
COORDINATES: similar to AA sequence:RefSeq:WP_005413104.1
COORDINATES: similar to AA sequence:RefSeq:WP_017085251.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF013311.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008549198.1
GO:0033103 - protein secretion by the type VI secretion system [Evidence IEA]
Hcp family type VI secretion system effector
COORDINATES: similar to AA sequence:RefSeq:WP_014290239.1
COORDINATES: similar to AA sequence:RefSeq:WP_014284002.1
GO:0003674 - molecular_function [Evidence IEA]
type VI secretion system tip protein TssI/VgrG
COORDINATES: similar to AA sequence:RefSeq:WP_013760980.1
COORDINATES: protein motif:HMM:NF024894.2
COORDINATES: protein motif:HMM:NF013658.2
COORDINATES: similar to AA sequence:RefSeq:WP_004745284.1
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012925.2
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006314261.1
COORDINATES: similar to AA sequence:RefSeq:WP_004211497.1
COORDINATES: protein motif:HMM:NF014273.2
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_019053929.1
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF015118.2
VirB4 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: similar to AA sequence:RefSeq:WP_006939197.1
COORDINATES: similar to AA sequence:RefSeq:WP_020592872.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF015397.2
TraI/MobA(P) family conjugative relaxase
COORDINATES: protein motif:HMM:NF013594.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019295126.1
GO:0008379 - thioredoxin peroxidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR04393.1
incomplete; too short partial abutting assembly gap; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007538470.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011251550.1
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_014290260.1
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: similar to AA sequence:RefSeq:WP_014290262.1
COORDINATES: similar to AA sequence:RefSeq:WP_014284086.1
COORDINATES: similar to AA sequence:RefSeq:WP_008552711.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014285556.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009605777.1
sugar phosphate isomerase/epimerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015494980.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF018513.2
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: protein motif:HMM:NF015445.2
TRAP transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF024799.2
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008552743.1
COORDINATES: similar to AA sequence:RefSeq:WP_015918564.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612398.1
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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:NF015431.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_032072965.1
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019013.2
GO:0030638 - polyketide metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_054784145.1
GO:0004601 - peroxidase activity [Evidence IEA]
GO:0006979 - response to oxidative stress [Evidence IEA]
COORDINATES: protein motif:HMM:NF025217.2
methyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF017206.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558204.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009803438.1
COORDINATES: similar to AA sequence:RefSeq:WP_003602196.1
COORDINATES: protein motif:HMM:NF013777.2
COORDINATES: similar to AA sequence:RefSeq:WP_007689582.1
COORDINATES: similar to AA sequence:RefSeq:WP_019297955.1
urea carboxylase-associated family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013962002.1
COORDINATES: protein motif:HMM:NF013584.2
COORDINATES: similar to AA sequence:RefSeq:WP_019297960.1
COORDINATES: similar to AA sequence:RefSeq:WP_019297934.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF012863.2
GDSL-type esterase/lipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019297937.1
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_019297938.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019297939.1
COORDINATES: similar to AA sequence:RefSeq:WP_008279304.1
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]; GO:0019808 - polyamine binding [Evidence IEA]
GO:0015846 - polyamine transport [Evidence IEA]
spermidine/putrescine ABC transporter substrate-binding protein
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012354.2
COORDINATES: similar to AA sequence:RefSeq:WP_012477429.1
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: similar to AA sequence:RefSeq:WP_018240671.1
COORDINATES: protein motif:HMM:TIGR03454.1