Herbaspirillum seropedicae strain AU13965 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Oxalobacteraceae; Herbaspirillum.
Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals adaptions to survive in human hosts
Submitted (07-DEC-2018) Bioinformatics Department, UFPR - Universidade Federal do Parana, R. Dr. Alcides Vieira Arcoverde, 1225 - Jardim das Americas, Curitiba, Parana 81520260, Brazil
REFSEQ INFORMATION: The reference sequence is identical to\nCP034394.1.\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 Date :: 2017\nAssembly Method :: SPAdes v. 3.10.0; MIRA v. 4.0.2; CLC NGS\n Cell v. 9\nAssembly Name :: UFPR_HseroL2_1.1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 160.0x\nSequencing Technology :: IonTorrent; Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 00:53:34\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) :: 4,818\nCDSs (total) :: 4,748\nGenes (coding) :: 4,719\nCDSs (with protein) :: 4,719\nGenes (RNA) :: 70\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 57\nncRNAs :: 4\nPseudo Genes (total) :: 29\nCDSs (without protein) :: 29\nPseudo Genes (ambiguous residues) :: 0 of 29\nPseudo Genes (frameshifted) :: 6 of 29\nPseudo Genes (incomplete) :: 23 of 29\nPseudo Genes (internal stop) :: 2 of 29\nPseudo Genes (multiple problems) :: 2 of 29\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Division of Infectious Diseases, Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013092495.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005875714.1
COORDINATES: protein motif:HMM:NF024939.2
COORDINATES: similar to AA sequence:RefSeq:WP_009658639.1
COORDINATES: protein motif:HMM:TIGR02218.1
COORDINATES: protein motif:HMM:NF020901.2
COORDINATES: similar to AA sequence:RefSeq:WP_002238694.1
COORDINATES: similar to AA sequence:RefSeq:WP_004935630.1
COORDINATES: protein motif:HMM:NF016990.2
GO:0016032 - viral process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014235318.1
COORDINATES: similar to AA sequence:RefSeq:WP_010951062.1
COORDINATES: protein motif:HMM:NF016732.2
COORDINATES: similar to AA sequence:RefSeq:WP_014235315.1
COORDINATES: protein motif:HMM:NF015550.2
COORDINATES: similar to AA sequence:RefSeq:WP_012436136.1
RusA family crossover junction endodeoxyribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_004152449.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019025346.1
COORDINATES: similar to AA sequence:RefSeq:WP_016452840.1
COORDINATES: similar to AA sequence:RefSeq:WP_016981987.1
COORDINATES: protein motif:HMM:NF017113.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF027273.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011875792.1
GO:0019867 - outer membrane [Evidence IEA]
outer membrane protein assembly factor BamE
COORDINATES: similar to AA sequence:RefSeq:WP_004349421.1
COORDINATES: protein motif:HMM:TIGR00616.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_004532285.1
COORDINATES: similar to AA sequence:RefSeq:WP_013813829.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020803811.1
COORDINATES: protein motif:HMM:NF025352.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]