Advenella kashmirensis WT001 plasmid pWTk445, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Alcaligenaceae.
Genome implosion elicits host-confinement in Alcaligenaceae: evidence from the comparative genomics of Tetrathiobacter kashmirensis, a pathogen in the making
Whole-genome shotgun sequencing of the sulfur-oxidizing chemoautotroph Tetrathiobacter kashmirensis
Submitted (18-MAY-2012) Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, West Bengal 700054, India
REFSEQ INFORMATION: The reference sequence is identical to\nCP003556.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/12/2023 12:05:17\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) :: 4,448\nCDSs (total) :: 4,397\nGenes (coding) :: 3,572\nCDSs (with protein) :: 3,572\nGenes (RNA) :: 51\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 41\nncRNAs :: 4\nPseudo Genes (total) :: 825\nCDSs (without protein) :: 825\nPseudo Genes (ambiguous residues) :: 0 of 825\nPseudo Genes (frameshifted) :: 771 of 825\nPseudo Genes (incomplete) :: 71 of 825\nPseudo Genes (internal stop) :: 15 of 825\nPseudo Genes (multiple problems) :: 31 of 825\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: similar to AA sequence:RefSeq:WP_006221534.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008161277.1
COORDINATES: protein motif:HMM:NF012607.2
COORDINATES: similar to AA sequence:RefSeq:WP_013394788.1
COORDINATES: similar to AA sequence:RefSeq:WP_006395010.1
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013519135.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906671.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_011493491.1
GO:0004399 - histidinol dehydrogenase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002244211.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
ribbon-helix-helix domain-containing protein
COORDINATES: protein motif:HMM:NF037521.2
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: protein motif:HMM:NF024755.2
GO:0016817 - hydrolase activity, acting on acid anhydrides [Evidence IEA]
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002244205.1
COORDINATES: protein motif:HMM:NF038091.1
COORDINATES: similar to AA sequence:RefSeq:WP_013521333.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_002244202.1
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: similar to AA sequence:RefSeq:WP_002244198.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_002244197.1
COORDINATES: similar to AA sequence:RefSeq:WP_014726312.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF019069.2
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_018025803.1
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004197463.1
COORDINATES: similar to AA sequence:RefSeq:WP_013706315.1
COORDINATES: similar to AA sequence:RefSeq:WP_008642084.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010465839.1
COORDINATES: similar to AA sequence:RefSeq:WP_008855174.1
COORDINATES: protein motif:HMM:NF041546.1
COORDINATES: protein motif:HMM:NF014626.2
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: protein motif:HMM:NF019844.2
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_011840471.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019655850.1
COORDINATES: similar to AA sequence:RefSeq:WP_006683700.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0009263 - deoxyribonucleotide biosynthetic process [Evidence IEA]
ribonucleotide-diphosphate reductase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_012748367.1
COORDINATES: similar to AA sequence:RefSeq:WP_013518747.1
COORDINATES: protein motif:HMM:NF014997.2
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_004285216.1
GO:0019867 - outer membrane [Evidence IEA]
outer membrane protein assembly factor BamE