Paenibacillus rhizovicinus strain 14171R-81 plasmid unnamed2.
Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus.
Paenibacillus sp. nov., isolated from rhizosphere soil of tomato
Submitted (02-FEB-2020) Agricultural Microbiology Division, National Institute of Agricultural Sciences, 166, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP048288.1.\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 v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 122.36x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/24/2022 03:27:40\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 6,801\nCDSs (total) :: 6,632\nGenes (coding) :: 6,561\nCDSs (with protein) :: 6,561\nGenes (RNA) :: 169\nrRNAs :: 13, 13, 13 (5S, 16S, 23S)\ncomplete rRNAs :: 13, 13, 13 (5S, 16S, 23S)\ntRNAs :: 125\nncRNAs :: 5\nPseudo Genes (total) :: 71\nCDSs (without protein) :: 71\nPseudo Genes (ambiguous residues) :: 0 of 71\nPseudo Genes (frameshifted) :: 19 of 71\nPseudo Genes (incomplete) :: 51 of 71\nPseudo Genes (internal stop) :: 5 of 71\nPseudo Genes (multiple problems) :: 4 of 71\n##Genome-Annotation-Data-END##
type strain of Paenibacillus rhizovicinus
COORDINATES: similar to AA sequence:RefSeq:WP_016084802.1
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: similar to AA sequence:RefSeq:WP_016084804.1
COORDINATES: protein motif:HMM:NF019311.2
low copy number virion structural protein
COORDINATES: similar to AA sequence:RefSeq:WP_012614845.1
COORDINATES: similar to AA sequence:RefSeq:WP_000090426.1
COORDINATES: protein motif:HMM:NF024777.2
COORDINATES: protein motif:HMM:NF012956.2
COORDINATES: similar to AA sequence:RefSeq:WP_000925104.1
COORDINATES: similar to AA sequence:RefSeq:WP_016084824.1
COORDINATES: protein motif:HMM:NF013954.2
GO:0004040 - amidase activity [Evidence IEA]
glucosaminidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016084831.1
COORDINATES: similar to AA sequence:RefSeq:WP_016084834.1
COORDINATES: similar to AA sequence:RefSeq:WP_016084838.1
COORDINATES: protein motif:HMM:NF024603.2
COORDINATES: similar to AA sequence:RefSeq:WP_000246817.1
COORDINATES: similar to AA sequence:RefSeq:WP_015986052.1
COORDINATES: protein motif:HMM:NF015211.2
COORDINATES: protein motif:HMM:NF037161.2
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF019481.2
COORDINATES: protein motif:HMM:NF025554.2
COORDINATES: protein motif:HMM:NF022151.2
COORDINATES: protein motif:HMM:NF012304.2
COORDINATES: protein motif:HMM:NF024803.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: similar to AA sequence:RefSeq:WP_016084643.1
COORDINATES: protein motif:HMM:NF018437.2
GO:0019867 - outer membrane [Evidence IEA]
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0009254 - peptidoglycan turnover [Evidence IEA]
COORDINATES: protein motif:HMM:NF012381.2
COORDINATES: similar to AA sequence:RefSeq:WP_001094255.1
MerR family DNA-binding transcriptional regulator
COORDINATES: protein motif:HMM:NF016526.2
accessory gene regulator B family protein
COORDINATES: protein motif:HMM:TIGR04223.1
COORDINATES: protein motif:HMM:NF024747.2
4Fe-4S cluster-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF018565.2
COORDINATES: protein motif:HMM:NF022657.2
COORDINATES: protein motif:HMM:NF014560.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0050797 - thymidylate synthase (FAD) activity [Evidence IEA]
GO:0006231 - dTMP biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005542715.1
COORDINATES: protein motif:HMM:NF024754.2
COORDINATES: protein motif:HMM:NF013209.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF023101.2
COORDINATES: protein motif:HMM:NF024554.2
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: protein motif:HMM:NF039653.1
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000061604.1
COORDINATES: similar to AA sequence:RefSeq:WP_000453747.1
COORDINATES: similar to AA sequence:RefSeq:WP_013386322.1
COORDINATES: similar to AA sequence:RefSeq:WP_002188062.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256766.1
COORDINATES: protein motif:HMM:NF016381.2
COORDINATES: similar to AA sequence:RefSeq:WP_006318452.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF020438.2
COORDINATES: protein motif:HMM:NF018627.2
COORDINATES: similar to AA sequence:RefSeq:WP_000583728.1
COORDINATES: protein motif:HMM:NF013661.2
GO:0008745 - N-acetylmuramoyl-L-alanine amidase activity [Evidence IEA]
GO:0009253 - peptidoglycan catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000336775.1
COORDINATES: protein motif:HMM:NF003315.0
COORDINATES: protein motif:HMM:NF017663.2
RusA family crossover junction endodeoxyribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_000394584.1
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: similar to AA sequence:RefSeq:WP_002199091.1
COORDINATES: similar to AA sequence:RefSeq:WP_014280924.1
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: similar to AA sequence:RefSeq:WP_015891427.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
class 1b ribonucleoside-diphosphate reductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_015845582.1
GO:0009263 - deoxyribonucleotide biosynthetic process [Evidence IEA]
class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI
COORDINATES: protein motif:HMM:NF015736.2
COORDINATES: similar to AA sequence:RefSeq:WP_001174230.1
primase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016084796.1
COORDINATES: protein motif:HMM:NF016961.2
COORDINATES: similar to AA sequence:RefSeq:WP_016084800.1