Pseudoalteromonas nigrifaciens strain KMM 661 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales; Pseudoalteromonadaceae; Pseudoalteromonas.
Submitted (11-MAR-2015) State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, P. R. China
REFSEQ INFORMATION: The reference sequence is identical to\nCP011038.1.\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 :: SOAPdenovo v. 1.05\nGenome Coverage :: 175x\nSequencing Technology :: Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/23/2023 02:55:17\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,964\nCDSs (total) :: 3,825\nGenes (coding) :: 3,766\nCDSs (with protein) :: 3,766\nGenes (RNA) :: 139\nrRNAs :: 10, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 10, 9, 9 (5S, 16S, 23S)\ntRNAs :: 107\nncRNAs :: 4\nPseudo Genes (total) :: 59\nCDSs (without protein) :: 59\nPseudo Genes (ambiguous residues) :: 0 of 59\nPseudo Genes (frameshifted) :: 16 of 59\nPseudo Genes (incomplete) :: 41 of 59\nPseudo Genes (internal stop) :: 15 of 59\nPseudo Genes (multiple problems) :: 11 of 59\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Pseudoalteromonas nigrifaciens
COORDINATES: similar to AA sequence:RefSeq:WP_010554746.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010554745.1
COORDINATES: protein motif:HMM:NF024242.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF017528.2
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase.; TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_013465794.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF033563.0
COORDINATES: similar to AA sequence:RefSeq:WP_076612036.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010554728.1
DNA replication terminus site-binding protein
COORDINATES: protein motif:HMM:NF022337.2
COORDINATES: similar to AA sequence:RefSeq:WP_010555478.1
COORDINATES: similar to AA sequence:RefSeq:WP_010555477.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006791293.1
GO:0003978 - UDP-glucose 4-epimerase activity [Evidence IEA]
GO:0006012 - galactose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006791294.1
GO:0008108 - UDP-glucose:hexose-1-phosphate uridylyltransferase activity [Evidence IEA]
UDP-glucose--hexose-1-phosphate uridylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_002958851.1
GO:0004335 - galactokinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010555023.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010555024.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010392067.1
GO:0004370 - glycerol kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007580052.1
GO:0009331 - glycerol-3-phosphate dehydrogenase complex [Evidence IEA]
GO:0004368 - glycerol-3-phosphate dehydrogenase (quinone) activity [Evidence IEA]
GO:0006072 - glycerol-3-phosphate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010555027.1
COORDINATES: similar to AA sequence:RefSeq:WP_010557676.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002958844.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014977990.1
COORDINATES: similar to AA sequence:RefSeq:WP_002958818.1
COORDINATES: similar to AA sequence:RefSeq:WP_010554817.1
COORDINATES: similar to AA sequence:RefSeq:WP_010554816.1
COORDINATES: similar to AA sequence:RefSeq:WP_008133378.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004588167.1
GO:0030246 - carbohydrate binding [Evidence IEA]; GO:0016857 - racemase and epimerase activity, acting on carbohydrates and derivatives [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_024604797.1
COORDINATES: similar to AA sequence:RefSeq:WP_012516792.1
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010552919.1
COORDINATES: similar to AA sequence:RefSeq:WP_007583926.1
COORDINATES: similar to AA sequence:RefSeq:WP_007583928.1
GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016788562.1
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025819.2
COORDINATES: protein motif:HMM:NF033611.0
COORDINATES: similar to AA sequence:RefSeq:WP_010554754.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
type I restriction endonuclease subunit R
COORDINATES: similar to AA sequence:RefSeq:WP_010554753.1
putative DNA binding domain-containing protein
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010554751.1
GO:0015666 - restriction endodeoxyribonuclease activity [Evidence IEA]; GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]; GO:0009307 - DNA restriction-modification system [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010555430.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010554747.1