Jeotgalibacillus malaysiensis strain malaysiensis plasmid unnamed, complete sequence.
Bacteria; Bacillota; Bacilli; Bacillales; Planococcaceae; Jeotgalibacillus.
Complete genome of a marine bacteria Jeotgalibacillus malaysiensis
Submitted (29-AUG-2014) Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Block T02, Skudai, Johor 81310, Malaysia
REFSEQ INFORMATION: The reference sequence is identical to\nCP009417.1.\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 Method :: HGAP SMRT Portal v. 2.1.1\nGenome Coverage :: 314.27x\nSequencing Technology :: PacBio RS II\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/05/2023 19:06:52\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) :: 4,467\nCDSs (total) :: 4,314\nGenes (coding) :: 4,262\nCDSs (with protein) :: 4,262\nGenes (RNA) :: 153\nrRNAs :: 9, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 9, 9 (5S, 16S, 23S)\ntRNAs :: 121\nncRNAs :: 5\nPseudo Genes (total) :: 52\nCDSs (without protein) :: 52\nPseudo Genes (ambiguous residues) :: 0 of 52\nPseudo Genes (frameshifted) :: 15 of 52\nPseudo Genes (incomplete) :: 33 of 52\nPseudo Genes (internal stop) :: 12 of 52\nPseudo Genes (multiple problems) :: 6 of 52\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF039330.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017435496.1
GO:0004812 - aminoacyl-tRNA ligase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]; GO:0004832 - valine-tRNA ligase activity [Evidence IEA]
GO:0006438 - valyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF00230
T-box leader; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:TIGR01550.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: protein motif:HMM:NF014643.2
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_000163757.1
COORDINATES: similar to AA sequence:RefSeq:WP_019241533.1
COORDINATES: protein motif:HMM:NF014698.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018884784.1
COORDINATES: similar to AA sequence:RefSeq:WP_016084993.1
COORDINATES: similar to AA sequence:RefSeq:WP_000673905.1
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010651517.1
COORDINATES: similar to AA sequence:RefSeq:WP_000871791.1
COORDINATES: protein motif:HMM:NF012948.2
GO:0009986 - cell surface [Evidence IEA]
LPXTG cell wall anchor domain-containing protein
COORDINATES: protein motif:HMM:TIGR01076.1
COORDINATES: similar to AA sequence:RefSeq:WP_017428219.1
tRNA(His) guanylyltransferase Thg1 family protein
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: protein motif:HMM:NF040368.1
COORDINATES: similar to AA sequence:RefSeq:WP_003272964.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004176 - ATP-dependent peptidase activity [Evidence IEA]; GO:0004222 - metalloendopeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
FtsH/Yme1/Tma family ATP-dependent metallopeptidase
COORDINATES: similar to AA sequence:RefSeq:WP_016053487.1
COORDINATES: similar to AA sequence:RefSeq:WP_000015694.1
COORDINATES: protein motif:HMM:NF024258.2
COORDINATES: similar to AA sequence:RefSeq:WP_016279649.1
COORDINATES: protein motif:HMM:NF012304.2
COORDINATES: protein motif:HMM:NF025637.2
COORDINATES: similar to AA sequence:RefSeq:WP_016075185.1
COORDINATES: protein motif:HMM:NF025881.2
GO:0004519 - endonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002056875.1
COORDINATES: similar to AA sequence:RefSeq:WP_005340289.1
COORDINATES: similar to AA sequence:RefSeq:WP_005885735.1
COORDINATES: protein motif:HMM:NF014763.2
COORDINATES: similar to AA sequence:RefSeq:WP_004037151.1
COORDINATES: similar to AA sequence:RefSeq:WP_000582858.1
COORDINATES: protein motif:HMM:NF013700.2
COORDINATES: protein motif:HMM:NF021479.2
COORDINATES: protein motif:HMM:NF025005.2
COORDINATES: protein motif:HMM:NF037897.2
COORDINATES: similar to AA sequence:RefSeq:WP_006320570.1
RNA-guided endonuclease TnpB family protein
COORDINATES: protein motif:HMM:NF024102.2
BsuPI-related putative proteinase inhibitor
COORDINATES: similar to AA sequence:RefSeq:WP_010497753.1
COORDINATES: protein motif:HMM:NF024671.2
COORDINATES: protein motif:HMM:NF027249.2
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: protein motif:HMM:NF019976.2
nuclease-related domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013386164.1
COORDINATES: similar to AA sequence:RefSeq:WP_018673131.1
COORDINATES: similar to AA sequence:RefSeq:WP_013311041.1
3-oxoacyl-ACP synthase III family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012958703.1
COORDINATES: protein motif:HMM:NF013691.2
COORDINATES: protein motif:HMM:NF013964.2
COORDINATES: protein motif:HMM:TIGR02937.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF019096.2
NUMOD1 domain-containing DNA-binding protein
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF022883.2
COORDINATES: protein motif:HMM:NF001754.0
COORDINATES: protein motif:HMM:NF025703.2
COORDINATES: protein motif:HMM:NF021446.2
COORDINATES: similar to AA sequence:RefSeq:WP_010773311.1
COORDINATES: protein motif:HMM:NF012774.2
S1 RNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF036614.2
COORDINATES: similar to AA sequence:RefSeq:WP_018355561.1
GO:0004514 - nicotinate-nucleotide diphosphorylase (carboxylating) activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF017496.2
COORDINATES: similar to AA sequence:RefSeq:WP_000587831.1
COORDINATES: protein motif:HMM:NF016364.2
transglutaminase-like domain-containing protein
COORDINATES: protein motif:HMM:NF014083.2
COORDINATES: similar to AA sequence:RefSeq:WP_010349133.1
COORDINATES: protein motif:HMM:NF024139.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF025602.2
COORDINATES: protein motif:HMM:NF024220.2
COORDINATES: similar to AA sequence:RefSeq:WP_013386217.1
COORDINATES: protein motif:HMM:NF024359.2
COORDINATES: protein motif:HMM:NF019844.2
COORDINATES: protein motif:HMM:NF013632.2
COORDINATES: similar to AA sequence:RefSeq:WP_001066995.1
COORDINATES: protein motif:HMM:NF020250.2
LysM peptidoglycan-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010170315.1
COORDINATES: protein motif:HMM:NF013871.2
COORDINATES: protein motif:HMM:NF014048.2
COORDINATES: similar to AA sequence:RefSeq:WP_000149417.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF020123.2
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001240562.1
COORDINATES: similar to AA sequence:RefSeq:WP_001045297.1
COORDINATES: similar to AA sequence:RefSeq:WP_000851043.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_000453488.1
COORDINATES: similar to AA sequence:RefSeq:WP_000804991.1
COORDINATES: protein motif:HMM:NF003296.0
GO:0005524 - ATP binding [Evidence IEA]; GO:0004797 - thymidine kinase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019450.2
copper amine oxidase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001032840.1
GO:0008297 - single-stranded DNA exodeoxyribonuclease activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
single-stranded-DNA-specific exonuclease RecJ
COORDINATES: protein motif:HMM:NF016214.2
COORDINATES: protein motif:HMM:NF024835.2
COORDINATES: similar to AA sequence:RefSeq:WP_019244533.1
GO:0004798 - thymidylate kinase activity [Evidence IEA]
GO:0015949 - nucleobase-containing small molecule interconversion [Evidence IEA]
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012784.2
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: similar to AA sequence:RefSeq:WP_005213795.1
COORDINATES: similar to AA sequence:RefSeq:WP_003272757.1
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_000527010.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF014534.2
HPF/RaiA family ribosome-associated protein
COORDINATES: protein motif:HMM:NF024573.2
COORDINATES: protein motif:HMM:NF019128.2
COORDINATES: similar to AA sequence:RefSeq:WP_016131386.1
GO:0004799 - thymidylate synthase activity [Evidence IEA]
GO:0006231 - dTMP biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024533.2
COORDINATES: protein motif:HMM:NF015683.2
glutathionylspermidine synthase family protein
COORDINATES: protein motif:HMM:NF022571.2
COORDINATES: similar to AA sequence:RefSeq:WP_000572529.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003911 - DNA ligase (NAD+) activity [Evidence IEA]
GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013386111.1
COORDINATES: similar to AA sequence:RefSeq:WP_008408559.1
COORDINATES: protein motif:HMM:NF015637.2
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF017007.2
COORDINATES: protein motif:HMM:NF027263.2
type II toxin-antitoxin system RnlB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_000410166.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: similar to AA sequence:RefSeq:WP_005611835.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003918 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017655.2
COORDINATES: similar to AA sequence:RefSeq:WP_000508999.1
COORDINATES: protein motif:HMM:NF014166.2
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
crossover junction endodeoxyribonuclease RuvC
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024367.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003896 - DNA primase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
CHC2 zinc finger domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000133475.1
COORDINATES: protein motif:HMM:NF024078.2
COORDINATES: similar to AA sequence:RefSeq:WP_009899063.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: protein motif:HMM:NF006630.0
GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0015450 - protein-transporting ATPase activity [Evidence IEA]
GO:0043952 - protein transport by the Sec complex [Evidence IEA]
COORDINATES: protein motif:HMM:NF012413.2
COORDINATES: protein motif:HMM:NF019584.2
GO:0036211 - protein modification process [Evidence IEA]
class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI
COORDINATES: similar to AA sequence:RefSeq:WP_014721256.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
ribonucleotide reductase N-terminal alpha domain-containing protein
COORDINATES: protein motif:HMM:NF014868.2
ribonucleoside-diphosphate reductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_018580097.1
GO:0005971 - ribonucleoside-diphosphate reductase complex [Evidence IEA]
GO:0030145 - manganese ion binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
GO:0009265 - 2'-deoxyribonucleotide biosynthetic process [Evidence IEA]
class 1b ribonucleoside-diphosphate reductase subunit beta
COORDINATES: protein motif:HMM:NF012675.2
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF021631.2
nucleotidyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF018627.2
COORDINATES: protein motif:HMM:NF012832.2
COORDINATES: similar to AA sequence:RefSeq:WP_000013366.1
COORDINATES: similar to AA sequence:RefSeq:WP_018978588.1
COORDINATES: protein motif:HMM:TIGR00350.1
COORDINATES: protein motif:HMM:NF013122.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: protein motif:HMM:TIGR00594.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025930.2
COORDINATES: protein motif:HMM:NF014505.2
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: protein motif:HMM:TIGR00573.1
COORDINATES: protein motif:HMM:NF013100.2
transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF020130.2
COORDINATES: protein motif:HMM:NF040112.1
COORDINATES: protein motif:HMM:NF013382.2
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001242608.1
COORDINATES: protein motif:HMM:NF014605.2
COORDINATES: protein motif:HMM:NF013078.2
zinc dependent phospholipase C family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012371117.1
COORDINATES: protein motif:HMM:NF024252.2
COORDINATES: protein motif:HMM:NF013954.2
COORDINATES: similar to AA sequence:RefSeq:WP_016509800.1
COORDINATES: protein motif:HMM:TIGR02104.1
GO:0051060 - pullulanase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015210.2
COORDINATES: protein motif:HMM:NF021384.2
COORDINATES: protein motif:HMM:NF033832.1
COORDINATES: similar to AA sequence:RefSeq:WP_012370621.1
COORDINATES: similar to AA sequence:RefSeq:WP_016053482.1
COORDINATES: protein motif:HMM:NF018095.2
COORDINATES: protein motif:HMM:NF012730.2
COORDINATES: similar to AA sequence:RefSeq:WP_015892756.1
COORDINATES: protein motif:HMM:NF021059.2
COORDINATES: similar to AA sequence:RefSeq:WP_000819335.1
COORDINATES: similar to AA sequence:RefSeq:NP_389875.1
COORDINATES: protein motif:HMM:NF021593.2
COORDINATES: protein motif:HMM:NF024812.2
COORDINATES: similar to AA sequence:RefSeq:WP_020474483.1
COORDINATES: similar to AA sequence:RefSeq:WP_019769881.1
COORDINATES: protein motif:HMM:TIGR01453.1
COORDINATES: protein motif:HMM:NF017808.2
COORDINATES: protein motif:HMM:NF024724.2
COORDINATES: protein motif:HMM:NF022681.2
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_013386301.1
COORDINATES: similar to AA sequence:RefSeq:WP_000790565.1
COORDINATES: protein motif:HMM:NF024898.2
COORDINATES: similar to AA sequence:RefSeq:WP_019003769.1
COORDINATES: protein motif:HMM:NF025535.2
type II toxin-antitoxin system SpoIISA family toxin
COORDINATES: protein motif:HMM:NF024221.2
COORDINATES: similar to AA sequence:RefSeq:WP_013402990.1
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0071973 - bacterial-type flagellum-dependent cell motility [Evidence IEA]
COORDINATES: protein motif:HMM:NF012874.2