Allochromatium tepidum strain NZ plasmid pAt1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales; Chromatiaceae; Allochromatium.
Complete genome sequencing of Allochromatium tepidum strain NZ
Submitted (13-APR-2021) Contact:Yusuke Tsukatani JAMSTEC; 2-15, Natsushimacho, Yokosuka 237-0061, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP024564.1.\nAnnotated at DFAST https://dfast.nig.ac.jp/\n\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\nGenome Coverage :: 55x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/10/2023 23:52:11\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) :: 3,293\nCDSs (total) :: 3,232\nGenes (coding) :: 3,117\nCDSs (with protein) :: 3,117\nGenes (RNA) :: 61\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 4\nPseudo Genes (total) :: 115\nCDSs (without protein) :: 115\nPseudo Genes (ambiguous residues) :: 0 of 115\nPseudo Genes (frameshifted) :: 35 of 115\nPseudo Genes (incomplete) :: 97 of 115\nPseudo Genes (internal stop) :: 8 of 115\nPseudo Genes (multiple problems) :: 22 of 115\nCRISPR Arrays :: 4\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:NF018933.2
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:NF018122.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018949013.1
TraM recognition domain-containing protein
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008016379.1
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_012970788.1
COORDINATES: similar to AA sequence:RefSeq:WP_016916442.1
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: protein motif:HMM:NF017973.2
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:TIGR01056.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: similar to AA sequence:RefSeq:WP_012969954.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972309.1
COORDINATES: protein motif:HMM:NF040570.1
COORDINATES: similar to AA sequence:RefSeq:WP_018947738.1
COORDINATES: protein motif:HMM:NF007297.0
type II toxin-antitoxin system HipA family toxin YjjJ
COORDINATES: similar to AA sequence:RefSeq:WP_012972385.1
COORDINATES: similar to AA sequence:RefSeq:WP_004364652.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012972386.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017301931.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018234413.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012970211.1
ADP-ribosylglycohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012970893.1
COORDINATES: similar to AA sequence:RefSeq:WP_012970208.1
COORDINATES: similar to AA sequence:RefSeq:WP_009147041.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972314.1
COORDINATES: similar to AA sequence:RefSeq:WP_004356341.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972330.1
COORDINATES: similar to AA sequence:RefSeq:WP_007041119.1
COORDINATES: similar to AA sequence:RefSeq:WP_011237709.1
COORDINATES: protein motif:HMM:NF014533.2
GO:0009294 - DNA-mediated transformation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012972403.1
COORDINATES: similar to AA sequence:RefSeq:WP_012969346.1
COORDINATES: similar to AA sequence:RefSeq:WP_012969347.1
COORDINATES: protein motif:HMM:NF021551.2
CRISPR system precrRNA processing endoribonuclease RAMP protein Cas6
COORDINATES: similar to AA sequence:RefSeq:WP_012972290.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012972291.1
type III-B CRISPR module RAMP protein Cmr1
COORDINATES: similar to AA sequence:RefSeq:WP_012972292.1
type III-B CRISPR-associated protein Cas10/Cmr2
COORDINATES: similar to AA sequence:RefSeq:WP_012972293.1
type III-B CRISPR module-associated Cmr3 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012972294.1
type III-B CRISPR module RAMP protein Cmr4
COORDINATES: similar to AA sequence:RefSeq:WP_006786731.1
type III-B CRISPR module-associated protein Cmr5
COORDINATES: similar to AA sequence:RefSeq:WP_012972296.1
RAMP superfamily CRISPR-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_012972298.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972299.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972300.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012769581.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972302.1
COORDINATES: similar to AA sequence:RefSeq:WP_015098839.1
COORDINATES: similar to AA sequence:RefSeq:WP_009782918.1
COORDINATES: protein motif:HMM:NF025642.2
COORDINATES: similar to AA sequence:RefSeq:WP_019570942.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972305.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972308.1
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012703253.1
excalibur calcium-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012970080.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972313.1
COORDINATES: similar to AA sequence:RefSeq:WP_010970089.1
COORDINATES: protein motif:HMM:NF036800.2
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_015986425.1
COORDINATES: similar to AA sequence:RefSeq:WP_016857444.1
COORDINATES: protein motif:HMM:NF023742.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011313335.1
COORDINATES: similar to AA sequence:RefSeq:WP_009301768.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: similar to AA sequence:RefSeq:WP_019607111.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516240.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_013516241.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:TIGR02747.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_019576697.1
TraA family conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_019576696.1
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: similar to AA sequence:RefSeq:WP_019576694.1
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:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_019576692.1
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: similar to AA sequence:RefSeq:WP_018207804.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516254.1
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF019843.2
COORDINATES: protein motif:HMM:NF020070.2
COORDINATES: similar to AA sequence:RefSeq:WP_014776674.1
COORDINATES: protein motif:HMM:NF015648.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: similar to AA sequence:RefSeq:WP_005223883.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF013618.2
COORDINATES: protein motif:HMM:TIGR03033.1
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012845362.1
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
Dam family site-specific DNA-(adenine-N6)-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_015281956.1
COORDINATES: similar to AA sequence:RefSeq:WP_009151466.1
COORDINATES: similar to AA sequence:RefSeq:WP_011391317.1
COORDINATES: protein motif:HMM:NF025599.2
COORDINATES: similar to AA sequence:RefSeq:WP_006786734.1
COORDINATES: protein motif:HMM:NF021154.2
COORDINATES: similar to AA sequence:RefSeq:WP_004279690.1
COORDINATES: protein motif:HMM:NF021157.2
GO:0004519 - endonuclease activity [Evidence IEA]
type I-F CRISPR-associated endoribonuclease Cas6/Csy4
COORDINATES: similar to AA sequence:RefSeq:WP_008869721.1
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]
type I-F CRISPR-associated endonuclease Cas1f
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_018949095.1
COORDINATES: similar to AA sequence:RefSeq:WP_006475610.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0008998 - ribonucleoside-triphosphate reductase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
anaerobic ribonucleoside-triphosphate reductase
COORDINATES: protein motif:HMM:NF023101.2
COORDINATES: similar to AA sequence:RefSeq:WP_007637348.1